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Sample records for c100-3 hcr43 ns5

  1. Brazilian Flavivirus phylogeny based on NS5.

    Science.gov (United States)

    Baleotti, Flúvia Graciela; Moreli, Marcos Lázaro; Figueiredo, Luiz Tadeu Moraes

    2003-04-01

    In this work, a comprehensive phylogenetic study based on 600 base pair nucleotide and on putative 200 amino acid sequences of NS5 was carried out in order to establish genetic relationships among 15 strains of 10 Brazilian flaviviruses: Bussuquara, Cacipacore, dengue type 1, 2 and 4, Iguape, Ilheus, Rocio, Saint Louis encephalitis (SLE), and yellow fever. Phylogenetic trees were created by neighbor-joining and maximum parsimony methods. These trees showed Brazilian flaviviruses grouped into three main branches: yellow fever branch, dengue branch subdivided in types 1, 2 and 4 branches, and Japanese encephalitis virus (JEV) complex branch including SLE virus strains, Cacipacore, Iguape, Rocio, Ilheus and Bussuquara. Viruses transmitted by Aedes mosquitoes, such as dengue and urban yellow fever, that are also the only Flavivirus causing hemorrhagic fevers in Brazil, were grouped in the same cluster. Encephalitis associated viruses, transmitted by Culex mosquitoes such as JEV complex branch including SLE virus strains, Cacipacore, Iguape, Rocio, Ilheus and Bussuquara were also grouped in the same clade.

  2. Thermodynamics of the near-extremal NS5-brane

    International Nuclear Information System (INIS)

    We consider the thermodynamics of the near-extremal NS5-brane in type IIA string theory. The central tool we use is to map phases of six-dimensional Kaluza-Klein black holes to phases of near-extremal M5-branes with a transverse circle in eleven-dimensional supergravity. By S-duality these phases correspond to phases of the near-extremal type IIA NS5-brane. One of our main results is that in the canonical ensemble the usual near-extremal NS5-brane background, dual to a uniformly smeared near-extremal M5-brane, is subdominant to a new background of near-extremal M5-branes localized on the transverse circle. This new stable phase has a limiting temperature, which lies above the Hagedorn temperature of the usual NS5-brane phase. We discuss the limiting temperature and compare the different behavior of the NS5-brane in the canonical and microcanonical ensembles. We also briefly comment on the thermodynamics of near-extremal Dp-branes on a transverse circle

  3. Structures of NS5 Methyltransferase from Zika Virus.

    Science.gov (United States)

    Coloma, Javier; Jain, Rinku; Rajashankar, Kanagalaghatta R; García-Sastre, Adolfo; Aggarwal, Aneel K

    2016-09-20

    The Zika virus (ZIKV) poses a major public health emergency. To aid in the development of antivirals, we present two high-resolution crystal structures of the ZIKV NS5 methyltransferase: one bound to S-adenosylmethionine (SAM) and the other bound to SAM and 7-methyl guanosine diphosphate (7-MeGpp). We identify features of ZIKV NS5 methyltransferase that lend to structure-based antiviral drug discovery. Specifically, SAM analogs with functionalities on the Cβ atom of the methionine portion of the molecules that occupy the RNA binding tunnel may provide better specificity relative to human RNA methyltransferases.

  4. Structures of NS5 Methyltransferase from Zika Virus

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    Javier Coloma

    2016-09-01

    Full Text Available The Zika virus (ZIKV poses a major public health emergency. To aid in the development of antivirals, we present two high-resolution crystal structures of the ZIKV NS5 methyltransferase: one bound to S-adenosylmethionine (SAM and the other bound to SAM and 7-methyl guanosine diphosphate (7-MeGpp. We identify features of ZIKV NS5 methyltransferase that lend to structure-based antiviral drug discovery. Specifically, SAM analogs with functionalities on the Cβ atom of the methionine portion of the molecules that occupy the RNA binding tunnel may provide better specificity relative to human RNA methyltransferases.

  5. Structures of NS5 Methyltransferase from Zika Virus.

    Science.gov (United States)

    Coloma, Javier; Jain, Rinku; Rajashankar, Kanagalaghatta R; García-Sastre, Adolfo; Aggarwal, Aneel K

    2016-09-20

    The Zika virus (ZIKV) poses a major public health emergency. To aid in the development of antivirals, we present two high-resolution crystal structures of the ZIKV NS5 methyltransferase: one bound to S-adenosylmethionine (SAM) and the other bound to SAM and 7-methyl guanosine diphosphate (7-MeGpp). We identify features of ZIKV NS5 methyltransferase that lend to structure-based antiviral drug discovery. Specifically, SAM analogs with functionalities on the Cβ atom of the methionine portion of the molecules that occupy the RNA binding tunnel may provide better specificity relative to human RNA methyltransferases. PMID:27633330

  6. On NS5-brane instantons and volume stabilization

    NARCIS (Netherlands)

    Looyestijn, H.T.; Vandoren, S.

    2008-01-01

    We study general aspects of NS5-brane instantons in relation to the stabilization of the volume modulus in Calabi-Yau compactifications of type II strings with fluxes, and their orientifold versions. These instantons correct the Kahler potential and generically yield significant contributions to the

  7. Phylogenetic analysis of the NS5 gene of Zika virus.

    Science.gov (United States)

    Adiga, Rama

    2016-10-01

    ZIKV infection has become a global threat spreading across 31 countries in Central America, South America, and the Caribbean. However, little information is available about the molecular epidemiology of ZIKV. Shared mutation of a threonine residue to alanine at the same position in the C terminal of NS5 sequences was observed in sequences from Colombia, Mexico, Panama, and Martinique. The sequences in the phylogenetic tree fell within the same cluster. Based on shared mutation the presence of a Latin American genotype was proposed. Comparison of African and Asian lineages yielded R29N, N273S, H383Q, and P391S mutation. The study highlights that mutation of amino acids at NS5 may contribute to neutropism of ZIKV. J. Med. Virol. 88:1821-1826, 2016. © 2016 Wiley Periodicals, Inc. PMID:27335310

  8. Heterotic NS5-branes from closed string tachyon condensation

    Science.gov (United States)

    Garcia-Etxebarria, Iñaki; Montero, Miguel; Uranga, Angel

    2014-12-01

    We show how to construct the familiar heterotic NS5 brane as a topological soliton in a supercritical version of heterotic string theory. Closed string tachyon condensation removes the extra dimensions, leaving the NS5 in ten dimensions, in a process highly reminiscent of the K-theoretical description of type II D-branes, but linking nontrivial gauge bundles and geometry. This establishes a new kind of equivalence between gravitational and gauge configurations, reminiscent of the gauge/geometry correspondence. We also use the K-theory description to build other heterotic branes as solitons of closed string tachyons. The construction requires a modification of the anomalous Bianchi identity for H3 in supercritical heterotic string theory. We give various proofs for the existence of this modification.

  9. Phylogenetic analysis of the NS5 gene of Zika virus.

    Science.gov (United States)

    Adiga, Rama

    2016-10-01

    ZIKV infection has become a global threat spreading across 31 countries in Central America, South America, and the Caribbean. However, little information is available about the molecular epidemiology of ZIKV. Shared mutation of a threonine residue to alanine at the same position in the C terminal of NS5 sequences was observed in sequences from Colombia, Mexico, Panama, and Martinique. The sequences in the phylogenetic tree fell within the same cluster. Based on shared mutation the presence of a Latin American genotype was proposed. Comparison of African and Asian lineages yielded R29N, N273S, H383Q, and P391S mutation. The study highlights that mutation of amino acids at NS5 may contribute to neutropism of ZIKV. J. Med. Virol. 88:1821-1826, 2016. © 2016 Wiley Periodicals, Inc.

  10. Discovery of an irreversible HCV NS5B polymerase inhibitor.

    Science.gov (United States)

    Zeng, Qingbei; Nair, Anilkumar G; Rosenblum, Stuart B; Huang, Hsueh-Cheng; Lesburg, Charles A; Jiang, Yueheng; Selyutin, Oleg; Chan, Tin-Yau; Bennett, Frank; Chen, Kevin X; Venkatraman, Srikanth; Sannigrahi, Mousumi; Velazquez, Francisco; Duca, Jose S; Gavalas, Stephen; Huang, Yuhua; Pu, Haiyan; Wang, Li; Pinto, Patrick; Vibulbhan, Bancha; Agrawal, Sony; Ferrari, Eric; Jiang, Chuan-kui; Li, Cheng; Hesk, David; Gesell, Jennifer; Sorota, Steve; Shih, Neng-Yang; Njoroge, F George; Kozlowski, Joseph A

    2013-12-15

    The discovery of lead compound 2e was described. Its covalent binding to HCV NS5B polymerase enzyme was investigated by X-ray analysis. The results of distribution, metabolism and pharmacokinetics were reported. Compound 2e was demonstrated to be potent (replicon GT-1b EC50 = 0.003 μM), highly selective, and safe in in vitro and in vivo assays.

  11. Recombinant HCV variants with NS5A from genotypes 1-7 have different sensitivities to an NS5A inhibitor but not interferon-a

    DEFF Research Database (Denmark)

    Scheel, Troels K H; Gottwein, Judith M; Mikkelsen, Lotte S;

    2011-01-01

    Heterogeneity in the hepatitis C virus (HCV) protein NS5A influences its sensitivity to interferon-based therapy. Furthermore, NS5A is an important target for development of HCV-specific inhibitors. We aimed to develop recombinant infectious cell culture systems that express NS5A from isolates...... of the 7 major HCV genotypes, and determining their sensitivity to a specific NS5A inhibitor and to interferon-a....

  12. Hepatitis C virus expressing reporter tagged NS5A protein

    DEFF Research Database (Denmark)

    2014-01-01

    Hepatitis C reporter viruses containing Core through NS2 of prototype isolates of all major HCV genotypes and the remaining genes of isolate JFH1, by insertion of reporter genes in domain III of HCV NS5A were developed. A deletion upstream of the inserted reporter gene sequence conferred favorabl......77) or of genotype 3a (strain S52)) were also developed. The present inventors additionally developed J6/JFH1 recombinants with the 5'UTR of genotypes 1-6. These recombinants with different 5'UTRs are a useful to study the function of the 5'UTR in a genotype specific manner...

  13. Structure and Function of Flavivirus NS5 Methyltransferase

    Energy Technology Data Exchange (ETDEWEB)

    Zhou,Y.; Ray, D.; Zhao, Y.; Dong, H.; Ren, S.; Li, Z.; Guo, Y.; Bernard, K.; Shi, P.; Li, H.

    2007-01-01

    The plus-strand RNA genome of flavivirus contains a 5' terminal cap 1 structure (m{sup 7}GpppAmG). The flaviviruses encode one methyltransferase, located at the N-terminal portion of the NS5 protein, to catalyze both guanine N-7 and ribose 2'-OH methylations during viral cap formation. Representative flavivirus methyltransferases from dengue, yellow fever, and West Nile virus (WNV) sequentially generate GpppA {yields} m{sup 7}GpppA {yields} m{sup 7}GpppAm. The 2'-O methylation can be uncoupled from the N-7 methylation, since m{sup 7}GpppA-RNA can be readily methylated to m{sup 7}GpppAm-RNA. Despite exhibiting two distinct methylation activities, the crystal structure of WNV methyltransferase at 2.8 {angstrom} resolution showed a single binding site for S-adenosyl-L-methionine (SAM), the methyl donor. Therefore, substrate GpppA-RNA should be repositioned to accept the N-7 and 2'-O methyl groups from SAM during the sequential reactions. Electrostatic analysis of the WNV methyltransferase structure showed that, adjacent to the SAM-binding pocket, is a highly positively charged surface that could serve as an RNA binding site during cap methylations. Biochemical and mutagenesis analyses show that the N-7 and 2'-O cap methylations require distinct buffer conditions and different side chains within the K{sub 61}-D{sub 146}-K{sub 182}-E{sub 218} motif, suggesting that the two reactions use different mechanisms. In the context of complete virus, defects in both methylations are lethal to WNV; however, viruses defective solely in 2'-O methylation are attenuated and can protect mice from later wild-type WNV challenge. The results demonstrate that the N-7 methylation activity is essential for the WNV life cycle and, thus, methyltransferase represents a novel target for flavivirus therapy.

  14. Phosphoproteomics Identified an NS5A Phosphorylation Site Involved in Hepatitis C Virus Replication.

    Science.gov (United States)

    Chong, Weng Man; Hsu, Shih-Chin; Kao, Wei-Ting; Lo, Chieh-Wen; Lee, Kuan-Ying; Shao, Jheng-Syuan; Chen, Yi-Hung; Chang, Justin; Chen, Steve S-L; Yu, Ming-Jiun

    2016-02-19

    The non-structural protein 5A (NS5A) is a hepatitis C virus (HCV) protein indispensable for the viral life cycle. Many prior papers have pinpointed several serine residues in the low complexity sequence I region of NS5A responsible for NS5A phosphorylation; however, the functions of specific phosphorylation sites remained obscure. Using phosphoproteomics, we identified three phosphorylation sites (serines 222, 235, and 238) in the NS5A low complexity sequence I region. Reporter virus and replicon assays using phosphorylation-ablated alanine mutants of these sites showed that Ser-235 dominated over Ser-222 and Ser-238 in HCV replication. Immunoblotting using an Ser-235 phosphorylation-specific antibody showed a time-dependent increase in Ser-235 phosphorylation that correlated with the viral replication activity. Ser-235 phosphorylated NS5A co-localized with double-stranded RNA, consistent with its role in HCV replication. Mechanistically, Ser-235 phosphorylation probably promotes the replication complex formation via increasing NS5A interaction with the human homologue of the 33-kDa vesicle-associated membrane protein-associated protein. Casein kinase Iα (CKIα) directly phosphorylated Ser-235 in vitro. Inhibition of CKIα reduced Ser-235 phosphorylation and the HCV RNA levels in the infected cells. We concluded that NS5A Ser-235 phosphorylated by CKIα probably promotes HCV replication via increasing NS5A interaction with the 33-kDa vesicle-associated membrane protein-associated protein. PMID:26702051

  15. The Dengue Virus NS5 Protein Intrudes in the Cellular Spliceosome and Modulates Splicing

    Science.gov (United States)

    Shah, Priya; Pozzi, Berta; Gebhard, Leopoldo G.; Mammi, Pablo; Yanovsky, Marcelo J.; Andino, Raul; Krogan, Nevan; Srebrow, Anabella; Gamarnik, Andrea V.

    2016-01-01

    Dengue virus NS5 protein plays multiple functions in the cytoplasm of infected cells, enabling viral RNA replication and counteracting host antiviral responses. Here, we demonstrate a novel function of NS5 in the nucleus where it interferes with cellular splicing. Using global proteomic analysis of infected cells together with functional studies, we found that NS5 binds spliceosome complexes and modulates endogenous splicing as well as minigene-derived alternative splicing patterns. In particular, we show that NS5 alone, or in the context of viral infection, interacts with core components of the U5 snRNP particle, CD2BP2 and DDX23, alters the inclusion/exclusion ratio of alternative splicing events, and changes mRNA isoform abundance of known antiviral factors. Interestingly, a genome wide transcriptome analysis, using recently developed bioinformatics tools, revealed an increase of intron retention upon dengue virus infection, and viral replication was improved by silencing specific U5 components. Different mechanistic studies indicate that binding of NS5 to the spliceosome reduces the efficiency of pre-mRNA processing, independently of NS5 enzymatic activities. We propose that NS5 binding to U5 snRNP proteins hijacks the splicing machinery resulting in a less restrictive environment for viral replication. PMID:27575636

  16. The Dengue Virus NS5 Protein Intrudes in the Cellular Spliceosome and Modulates Splicing.

    Science.gov (United States)

    De Maio, Federico A; Risso, Guillermo; Iglesias, Nestor G; Shah, Priya; Pozzi, Berta; Gebhard, Leopoldo G; Mammi, Pablo; Mancini, Estefania; Yanovsky, Marcelo J; Andino, Raul; Krogan, Nevan; Srebrow, Anabella; Gamarnik, Andrea V

    2016-08-01

    Dengue virus NS5 protein plays multiple functions in the cytoplasm of infected cells, enabling viral RNA replication and counteracting host antiviral responses. Here, we demonstrate a novel function of NS5 in the nucleus where it interferes with cellular splicing. Using global proteomic analysis of infected cells together with functional studies, we found that NS5 binds spliceosome complexes and modulates endogenous splicing as well as minigene-derived alternative splicing patterns. In particular, we show that NS5 alone, or in the context of viral infection, interacts with core components of the U5 snRNP particle, CD2BP2 and DDX23, alters the inclusion/exclusion ratio of alternative splicing events, and changes mRNA isoform abundance of known antiviral factors. Interestingly, a genome wide transcriptome analysis, using recently developed bioinformatics tools, revealed an increase of intron retention upon dengue virus infection, and viral replication was improved by silencing specific U5 components. Different mechanistic studies indicate that binding of NS5 to the spliceosome reduces the efficiency of pre-mRNA processing, independently of NS5 enzymatic activities. We propose that NS5 binding to U5 snRNP proteins hijacks the splicing machinery resulting in a less restrictive environment for viral replication. PMID:27575636

  17. HCV NS5A abrogates p53 protein function by interfering with p53-DNA binding

    Institute of Scientific and Technical Information of China (English)

    Guo-Zhong Gong; Yong-Fang Jiang; Yan He; Li-Ying Lai; Ying-Hua Zhu; Xian-Shi Su

    2004-01-01

    AIM: To evaluate the inhibition effect of HCV NS5A on p53 transactivation on p21 promoter and explore its possible mechanism for influencing p53 function.METHODS: p53 function of transactivation on p21 promoter was studied with a luciferase reporter system in which the luciferase gene is driven by p21 promoter, and the p53-DNA binding ability was observed with the use of electrophoretic mobility-shift assay (EMSA). Lipofectin mediated p53 or HCV NS5A expression vectors were used to transfect hepatoma cell lines to observe whether HCV NS5A could abrogate the binding ability of p53 to its specific DNA sequence and p53 transactivation on p21 promoter.Western blot experiment was used for detection of HCV NS5A and p53 proteins expression.RESULTS: Relative luciferase activity driven by p21 promoter increased significantly in the presence of endogenous p53 protein. Compared to the control group, exogenous p53 protein also stimulated p21 promoter driven luciferase gene expression in a dose-dependent way. HCV NS5A protein gradually inhibited both endogenous and exogenous p53 transactivation on p21 promoter with increase of the dose of HCV NS5A expression plasmid. By the experiment of EMSA, we could find p53 binding to its specific DNA sequence and, when co-transfected with increased dose of HCV NS5A expression vector, the p53 binding affinity to its DNA gradually decreased and finally disappeared. Between the Huh 7 cells transfected with p53 expression vector alone or co-transfected with HCV NS5A expression vector, there was no difference in the p53 protein expression.CONCLUSION: HCV NS5A inhibits p53 transactivation on p21 promoter through abrogating p53 binding affinity to its specific DNA sequence. It does not affect p53 protein expression.

  18. Differential sensitivity of 5'UTR-NS5A recombinants of hepatitis C virus genotypes 1-6 to protease and NS5A inhibitors

    DEFF Research Database (Denmark)

    Li, Yi-Ping; Ramirez, Santseharay; Humes, Daryl;

    2014-01-01

    BACKGROUND & AIMS: Hepatitis C virus (HCV) therapy will benefit from the preclinical evaluation of direct-acting antiviral (DAA) agents in infectious culture systems that test the effects on different virus genotypes. We developed HCV recombinants comprising the 5' untranslated region-NS5A (5-5A)...

  19. NS5ATP9 Contributes to Inhibition of Cell Proliferation by Hepatitis C Virus (HCV Nonstructural Protein 5A (NS5A via MEK/Extracellular Signal Regulated Kinase (ERK Pathway

    Directory of Open Access Journals (Sweden)

    Xuesong Gao

    2013-05-01

    Full Text Available Hepatitis C virus (HCV nonstructural protein 5A (NS5A is a remarkable protein as it clearly plays multiple roles in mediating viral replication, host-cell interactions and viral pathogenesis. However, on the impact of cell growth, there have been different study results. NS5ATP9, also known as KIAA0101, p15PAF, L5, and OEACT-1, was first identified as a proliferating cell nuclear antigen-binding protein. Earlier studies have shown that NS5ATP9 might play an important role in HCV infection. The aim of this study is to investigate the function of NS5ATP9 on hepatocellular carcinoma (HCC cell lines proliferation under HCV NS5A expression. The results showed that overexpression of NS5ATP9 inhibited the proliferation of Bel7402 cells, whereas knockdown of NS5ATP9 by interfering RNA promoted the growth of HepG2 cells. Under HCV NS5A expression, RNA interference (RNAi targeting of NS5ATP9 could reverse the inhibition of HepG2 cell proliferation, suggesting that NS5ATP9 might be an anti-proliferation gene that plays an important role in the suppression of cell growth mediated by HCV NS5A via MEK/ERK signaling pathway. These findings might provide new insights into HCV NS5A and NS5ATP9.

  20. Approaches to hepatitis C treatment and cure using NS5A inhibitors

    Directory of Open Access Journals (Sweden)

    Kohler JJ

    2014-03-01

    Full Text Available James J Kohler,1,2 James H Nettles,1,2 Franck Amblard,1,2 Selwyn J Hurwitz,1,2 Leda Bassit,1,2 Richard A Stanton,1 Maryam Ehteshami,1 Raymond F Schinazi1,2 1Center for AIDS Research and Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA; 2Atlanta Veterans Affairs Medical Center, Decatur, GA, USA Abstract: Recent progress in the understanding of hepatitis C virus (HCV biology and the availability of in vitro models to study its replication have facilitated the development of direct-acting antiviral agents (DAAs that target specific steps in the viral replication cycle. Currently, there are three major classes of DAA in clinical development: NS3/4A protease inhibitors, NS5B polymerase inhibitors, and NS5A directed inhibitors. Several compounds thought to bind directly with NS5A are now in various clinical trial phases, including the most advanced, daclatasvir (BMS-790052, ledipasvir (GS-5885, and ABT-267. While many NS5A-targeted compounds demonstrate picomolar potency, the exact mechanism(s of their action is still unclear. In the clinic, NS5A HCV inhibitors show promise as important components in DAA regimens and have multifunctionality. In addition to inhibiting viral replication, they may synergize with other DAAs, possibly by modulating different viral proteins, to help suppress the emergence of resistant viruses. Structure-based models have identified target interaction domains and spatial interactions that explain drug resistance for mutations at specific positions (eg, residues 93 and 31 within NS5A and potential binding partners. This review provides, insights into the unique complexity of NS5A as a central platform for multiple viral/host protein interactions, and possible mechanism(s for the NS5A inhibitors currently undergoing clinical trials that target this nonstructural viral protein. Keywords: HCV replication complex, direct acting antivirals (DAAs, clinical trials

  1. Point mutations in E2, NS3 and NS5A of hepatitis G virus

    Institute of Scientific and Technical Information of China (English)

    Wei Dong Liu; Toshikazu Hada; Ji Dong Cheng; Kazuya Higashino

    2000-01-01

    AIM To compare the point mutation deviations of HGV among E2, NS3 and NSSA.METHODS Seven patients with hepatic diseases from Japan and China were selected for this study. RNAwas extracted and amplified by semi-nested RT-PCR; and the PCR products were sequenced directly.RESULTS The point mutation deviations of HGV ia E2, NS3 and NS5A were 10% - 17%, 11% -23%,and 0% - 5%, in nuclcotide sequences and 4% - 12%, 0%, and 0% - 6% in amino acid sequencesrespectively.CONCLUSION The frequency of variation at the nucleotide level was in the order NS3>E2>NS5A, whileat the amino acid level the order was E2 >NS5A>NS3. The detected sequences from the N-terminus of E2may be the poorly conserved region of HGV.

  2. Direct binding of ledipasvir to HCV NS5A: mechanism of resistance to an HCV antiviral agent.

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    Hyock Joo Kwon

    Full Text Available Ledipasvir, a direct acting antiviral agent (DAA targeting the Hepatitis C Virus NS5A protein, exhibits picomolar activity in replicon cells. While its mechanism of action is unclear, mutations that confer resistance to ledipasvir in HCV replicon cells are located in NS5A, suggesting that NS5A is the direct target of ledipasvir. To date co-precipitation and cross-linking experiments in replicon or NS5A transfected cells have not conclusively shown a direct, specific interaction between NS5A and ledipasvir. Using recombinant, full length NS5A, we show that ledipasvir binds directly, with high affinity and specificity, to NS5A. Ledipasvir binding to recombinant NS5A is saturable with a dissociation constant in the low nanomolar range. A mutant form of NS5A (Y93H that confers resistance to ledipasvir shows diminished binding to ledipasvir. The current study shows that ledipasvir inhibits NS5A through direct binding and that resistance to ledipasvir is the result of a reduction in binding affinity to NS5A mutants.

  3. Fragment-based discovery of hepatitis C virus NS5b RNA polymerase inhibitors

    Energy Technology Data Exchange (ETDEWEB)

    Antonysamy, Stephen S.; Aubol, Brandon; Blaney, Jeff; Browner, Michelle F.; Giannetti, Anthony M.; Harris, Seth F.; Hébert, Normand; Hendle, Jörg; Hopkins, Stephanie; Jefferson, Elizabeth; Kissinger, Charles; Leveque, Vincent; Marciano, David; McGee, Ethel; Nájera, Isabel; Nolan, Brian; Tomimoto, Masaki; Torres, Eduardo; Wright, Tobi (SGX); (Roche)

    2009-07-22

    Non-nucleoside inhibitors of HCV NS5b RNA polymerase were discovered by a fragment-based lead discovery approach, beginning with crystallographic fragment screening. The NS5b binding affinity and biochemical activity of fragment hits and inhibitors was determined by surface plasmon resonance (Biacore) and an enzyme inhibition assay, respectively. Crystallographic fragment screening hits with {approx}1-10 mM binding affinity (K{sub D}) were iteratively optimized to give leads with {approx}200 nM biochemical activity and low {micro}M cellular activity in a Replicon assay.

  4. NS5 Brane and Little String Duality in the pp-wave Limit

    CERN Document Server

    Matlock, P; Viswanathan, K S; Yang, Y

    2003-01-01

    We study NSR strings in the Nappi-Witten background, which is the Penrose limit of a certain NS5-brane supergravity solution. We solve the theory in the light-cone gauge, obtaining the spectrum, which is space-time supersymmetric. In light of the LST/NS5-brane duality, this spectrum should be in correspondence with the states of little string theory in the appropriate limit. A semiclassical analysis verifies that the relationship between energy and angular momentum, after a field redefinition, matches that found for a flat background.

  5. Hagedorn Behavior of Little String Theories from string corrections to NS5-branes

    DEFF Research Database (Denmark)

    Harmark, Troels; Obers, N. A.

    2000-01-01

    We examine the Hagedorn behavior of little string theory using its conjectured duality with near-horizon NS5-branes. In particular, by studying the string-corrected NS5-brane supergravity solution, it is shown that tree-level corrections to the temperature vanish, while the leading one-loop string...... correction generates the correct temperature dependence of the entropy near the Hagedorn temperature. Finally, the Hagedorn behavior of ODp-brane theories, which are deformed versions of little string theory, is considered via their supergravity duals....

  6. Induction of intrahepatic HCV NS4B, NS5A and NS5B-specific cellular immune responses following peripheral immunization.

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    Krystle A Lang Kuhs

    Full Text Available Numerous studies have suggested that an effective Hepatitis C Virus (HCV vaccine must induce strong cytotoxic and IFN-γ+ T cell responses targeting the non-structural region of the virus. Most importantly, these responses must be able to migrate into and remain functional within the liver, an organ known to cause T cell tolerance. Using three novel HCV DNA vaccines encoding non-structural proteins NS4B, NS5A and NS5B, we assessed the ability of peripheral immunization to induce functional intrahepatic immunity both in the presence and absence of cognate HCV antigen expression within the liver. We have shown that these constructs induced potent HCV-specific CD4+ and CD8+ T cell responses in the spleen of C57BL/6 mice and that these responses were detected within the liver following peripheral immunization. Additionally, using a transfection method to express HCV antigen within the liver, we showed that intrahepatic HCV-specific T cells remained highly functional within the liver and retained the ability to become highly activated as evidenced by upregulation of IFN-γ and clearance of HCV protein expressing hepatocytes. Taken together, these findings suggest that peripheral immunization can induce potent HCV-specific T cell responses able to traffic to and function within the tolerant environment of the liver.

  7. Hepatitis C virus NS5A protein modulates template selection by the RNA polymerase in in vitro system.

    Science.gov (United States)

    Ivanov, Alexander V; Tunitskaya, Vera L; Ivanova, Olga N; Mitkevich, Vladimir A; Prassolov, Vladimir S; Makarov, Alexander A; Kukhanova, Marina K; Kochetkov, Sergey N

    2009-01-22

    Hepatitis C virus (HCV) NS5A phosphoprotein is a component of virus replicase. Here we demonstrate that in vitro unphosphorylated NS5A protein inhibits HCV RNA-dependent RNA polymerase (RdRp) activity in polyA-oligoU system but has little effect on synthesis of viral RNA. The phosphorylated casein kinase (CK) II NS5A protein causes the opposite effect on RdRp in each of these systems. The phosphorylation of NS5A protein with CKII does not affect its affinity to the HCV RdRp and RNA. The NS5A phosphorylation with CKI does not change the RdRp activity. Herein we report evidence that the NS5A prevents template binding to the RdRp.

  8. Screening of hepatocyte proteins binding to NS5ABP37 protein by yeast-two hybrid system

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Objective To investigate the biological function of NS5ABP37 and to look for proteins interacting with NS5ABP37 protein in hepatocytes.Methods We constructed bait plasmid expressing NS5ABP37 protein of hepatitis C virus(HCV)by cloning the gene of NS5ABP37 protein into pGBKT7,then the recombinant plasmid DNA was transformed into yeast AH109(α type).The transformed yeast AH109 was mated with yeast Y187(α type)containing liver cDNA library plasmid in 2×YPDA medium.Diploid yeast was plated on synthetic dropout ...

  9. Comparative Investigation of Normal Modes and Molecular Dynamics of Hepatitis C NS5B Protein

    Science.gov (United States)

    Asafi, M. S.; Yildirim, A.; Tekpinar, M.

    2016-04-01

    Understanding dynamics of proteins has many practical implications in terms of finding a cure for many protein related diseases. Normal mode analysis and molecular dynamics methods are widely used physics-based computational methods for investigating dynamics of proteins. In this work, we studied dynamics of Hepatitis C NS5B protein with molecular dynamics and normal mode analysis. Principal components obtained from a 100 nanoseconds molecular dynamics simulation show good overlaps with normal modes calculated with a coarse-grained elastic network model. Coarse-grained normal mode analysis takes at least an order of magnitude shorter time. Encouraged by this good overlaps and short computation times, we analyzed further low frequency normal modes of Hepatitis C NS5B. Motion directions and average spatial fluctuations have been analyzed in detail. Finally, biological implications of these motions in drug design efforts against Hepatitis C infections have been elaborated.

  10. 2'-O methylation of internal adenosine by flavivirus NS5 methyltransferase.

    Directory of Open Access Journals (Sweden)

    Hongping Dong

    Full Text Available RNA modification plays an important role in modulating host-pathogen interaction. Flavivirus NS5 protein encodes N-7 and 2'-O methyltransferase activities that are required for the formation of 5' type I cap (m(7GpppAm of viral RNA genome. Here we reported, for the first time, that flavivirus NS5 has a novel internal RNA methylation activity. Recombinant NS5 proteins of West Nile virus and Dengue virus (serotype 4; DENV-4 specifically methylates polyA, but not polyG, polyC, or polyU, indicating that the methylation occurs at adenosine residue. RNAs with internal adenosines substituted with 2'-O-methyladenosines are not active substrates for internal methylation, whereas RNAs with adenosines substituted with N⁶-methyladenosines can be efficiently methylated, suggesting that the internal methylation occurs at the 2'-OH position of adenosine. Mass spectroscopic analysis further demonstrated that the internal methylation product is 2'-O-methyladenosine. Importantly, genomic RNA purified from DENV virion contains 2'-O-methyladenosine. The 2'-O methylation of internal adenosine does not require specific RNA sequence since recombinant methyltransferase of DENV-4 can efficiently methylate RNAs spanning different regions of viral genome, host ribosomal RNAs, and polyA. Structure-based mutagenesis results indicate that K61-D146-K181-E217 tetrad of DENV-4 methyltransferase forms the active site of internal methylation activity; in addition, distinct residues within the methyl donor (S-adenosyl-L-methionine pocket, GTP pocket, and RNA-binding site are critical for the internal methylation activity. Functional analysis using flavivirus replicon and genome-length RNAs showed that internal methylation attenuated viral RNA translation and replication. Polymerase assay revealed that internal 2'-O-methyladenosine reduces the efficiency of RNA elongation. Collectively, our results demonstrate that flavivirus NS5 performs 2'-O methylation of internal adenosine of

  11. Discovery of ravidasvir (PPI-668) as a potent pan-genotypic HCV NS5A inhibitor.

    Science.gov (United States)

    Zhong, Min; Peng, Eric; Huang, Ningwu; Huang, Qi; Huq, Anja; Lau, Meiyen; Colonno, Richard; Li, Leping

    2016-09-15

    This Letter describes the synthesis, representative structure activity relationship (SAR), activity and PK profiles of a series of functionalized benzimidazole-naphthylene-imidazole derivatives as HCV NS5A inhibitors. This effort successfully led to the discovery of ravidasvir (PPI-668), which has been well tolerated and shown high sustained viral response rates as a key component in all-oral combination regimens in multiple human clinical trials.

  12. Analysis of mutant NS5B proteins encoded by isolates from chimpanzees chronically infected following clonal HCV RNA inoculation

    International Nuclear Information System (INIS)

    We hypothesized that mutations in the HCV NS5B polymerase, which occur during infection, may affect RNA-dependent RNA polymerase (RdRp) activity. NS5B proteins corresponding to a genotype 1a infectious clone and mutants identified in chimpanzees following inoculation with the clone were expressed and purified and their in vitro RdRp activity was compared to a NS5B genotype 1b control. A Gln-65-to-His mutation increased RdRp activity by 1.8-fold as compared to the infectious clone. Moreover, this NS5B1a protein had RdRp activity similar to the NS5B1b control. Three NS5B proteins representing mutations found in another animal had no in vitro RdRp activity. All mutations were maintained in the majority circulating virus for at least 216 weeks. The results demonstrate that some in vivo mutations of NS5B directly enhance in vitro RdRp activity. In addition, they suggest that the in vitro RdRp activity of NS5B may not always reflect in vivo activity within replication complexes

  13. Hepatitis C virus (HCV) NS5A inhibitor- Daclatasvir%丙型肝炎病毒NS5A抑制剂--达卡他韦

    Institute of Scientific and Technical Information of China (English)

    张晓; 钟武

    2016-01-01

    Daclatasvir is an oral tablet for the treatment of hepatitis C virus (HCV) NS5A inhibitor developed by Bristol-Myers Squibb. After Daclatasvir was approved to combine with other antiviral drugs by EU in Augst 2014 for treating adults with genotype 1-4 of HCV, it was also approved for combined use with sofosbuvir for the treatment of patients with chronic hepatitis C virus (HCV) genotype 3 infection by the FDA in July 2015. It is the first drug that has indicated safety and efficiency of chronic hepatitis C virus (HCV) genotype 3 infection without interferon or ribavirin. This provids a new choice for patients who are infected with HCV genotype 3, including individuals who can not tolerate ribavirin. The properties, mechanism, pharmacodynamics, pharmacokinetics, clinical trials, and development process of Daclatasvir were reviewed in this article, which could provide reference to the doctors and researchers.%达卡他韦(Daklinza)是由美国百时美-施贵宝公司(BMS)研制的口服丙型肝炎病毒(HCV)NS5A抑制剂。继2014年欧盟批准其与联合其他抗病毒药用于基因型1-4慢性丙型肝炎成人患者的治疗后,2015年7月美国FDA批准其与索非布韦[sofosbuvir]联合用于慢性HCV基因型3感染的治疗。达卡他韦是第一个无需同时给予干扰素或利巴韦林即可有效治疗基因型3 HCV感染的药物,为该类患者提供了一个新选择,包括那些不能耐受利巴韦林患者。笔者就达卡他韦的基本信息、作用机制、药代动力学、药物相互作用、临床试验及应用等研发动态作一概述,以期能为医院临床用药及药物研究开发提供参考。

  14. Screening of hepatocyte proteins binding to NS5ABP37 protein by yeast-two hybrid system

    Institute of Scientific and Technical Information of China (English)

    Lei Zhang; Qing-yong Ma; Xian-kui Meng; Kang Li; Jun Cheng

    2009-01-01

    Objective To investigate the biological function of NS5ABP37 and to look for proteins interacting with NS5ABP37 protein in hepatocytes. Methods We constructed bait plasmid expressing NS5ABP37 protein of hepatitis C virus (HCV) by cloning the gene of NS5ABP37 protein into pGBKT7, then the recombinant plasmid DNA was transformed into yeast AH109 (α type). The transformed yeast AH109 was mated with yeast Y187 (α type) containing liver cDNA library plasmid in 2×YPDA medium. Diploid yeast was plated on synthetic dropout nutrient medium (SD/-Trp-Leu-His-Ade) containing X-α-gal for selection and screening. After extracting and sequencing of plasmids from positive (blue) colonies, we made a sequence analysis by bioinformatics. Results We screened twenty-five proteins binding to NS5ABP37, including Homo sapiens cyclin Ⅰ (CCNI) gene, Homo sapiens matrix metallopeptidase 25 (MMP25) and Homo sapiens talin 1. Conclusion The yeast-two hybrid system is an effective method for identifying hepatocyte proteins interacting with NS5ABP37 of HCV. And the biological function of NS5ABP37 may be associated with glycometabolism, lipid metabolism and apoptosis.

  15. Crystal Structure of a Novel Dimeric Form of NS5A Domain I Protein from Hepatitis C Virus

    Energy Technology Data Exchange (ETDEWEB)

    Love, Robert A.; Brodsky, Oleg; Hickey, Michael J.; Wells, Peter A.; Cronin, Ciarán N.; Pfizer

    2009-07-10

    A new protein expression vector design utilizing an N-terminal six-histidine tag and tobacco etch virus protease cleavage site upstream of the hepatitis C virus NS5A sequence has resulted in a more straightforward purification method and improved yields of purified NS5A domain I protein. High-resolution diffracting crystals of NS5A domain I (amino acids 33 to 202) [NS5A(33-202)] were obtained by using detergent additive crystallization screens, leading to the structure of a homodimer which is organized differently from that published previously (T. L. Tellinghuisen, J. Marcotrigiano, and C. M. Rice, Nature 435:374-379, 2005) yet is consistent with a membrane association model for NS5A. The monomer-monomer interface of NS5A(33-202) features an extensive buried surface area involving the most-highly conserved face of each monomer. The two alternate structural forms of domain I now available may be indicative of the multiple roles emerging for NS5A in viral RNA replication and viral particle assembly.

  16. Production of a Recombinant Dengue Virus 2 NS5 Protein and Potential Use as a Vaccine Antigen.

    Science.gov (United States)

    Alves, Rúbens Prince Dos Santos; Pereira, Lennon Ramos; Fabris, Denicar Lina Nascimento; Salvador, Felipe Scassi; Santos, Robert Andreata; Zanotto, Paolo Marinho de Andrade; Romano, Camila Malta; Amorim, Jaime Henrique; Ferreira, Luís Carlos de Souza

    2016-06-01

    Dengue fever is caused by any of the four known dengue virus serotypes (DENV1 to DENV4) that affect millions of people worldwide, causing a significant number of deaths. There are vaccines based on chimeric viruses, but they still are not in clinical use. Anti-DENV vaccine strategies based on nonstructural proteins are promising alternatives to those based on whole virus or structural proteins. The DENV nonstructural protein 5 (NS5) is the main target of anti-DENV T cell-based immune responses in humans. In this study, we purified a soluble recombinant form of DENV2 NS5 expressed in Escherichia coli at large amounts and high purity after optimization of expression conditions and purification steps. The purified DENV2 NS5 was recognized by serum from DENV1-, DENV2-, DENV3-, or DENV4-infected patients in an epitope-conformation-dependent manner. In addition, immunization of BALB/c mice with NS5 induced high levels of NS5-specific antibodies and expansion of gamma interferon- and tumor necrosis factor alpha-producing T cells. Moreover, mice immunized with purified NS5 were partially protected from lethal challenges with the DENV2 NGC strain and with a clinical isolate (JHA1). These results indicate that the recombinant NS5 protein preserves immunological determinants of the native protein and is a promising vaccine antigen capable of inducing protective immune responses. PMID:27030586

  17. NS5ATP6 modulates intracellular triglyceride content through FGF21 and independently of SIRT1 and SREBP1.

    Science.gov (United States)

    Li, Zhongshu; Feng, Shenghu; Zhou, Li; Liu, Shunai; Cheng, Jun

    2016-06-17

    The prevalence of nonalcoholic fatty liver disease (NAFLD) is rising strikingly in Western countries and China. The molecular biological mechanism of NAFLD remains unclear, with no effective therapies developed so far. Fibroblast growth factor 21 (FGF21) is a recently discovered hormone, with safe lipid lowering effects. FGF21 analogs are being developed for clinical application. Here we demonstrated that a novel gene, NS5ATP6, modulated intracellular triglyceride (TG) content independently of sirtuin1 (SIRT1) and sterol regulatory element binding protein 1 (SREBP1) in HepG2 cells. Interestingly, NS5ATP6 regulated FGF21 expression both at the mRNA and protein levels. The modulatory effects of NS5ATP6 on intracellular TG content depended upon FGF21. Further studies revealed that NS5ATP6 decreased the promoter activity of FGF21. In addition, NS5ATP6 regulated the expression of miR-577, which directly targeted and regulated FGF21. Therefore, miR-577 might be involved in NS5ATP6 regulation of FGF21 at the post-transcriptional level. In conclusion, NS5ATP6 regulates the intracellular TG level via FGF21, and independently of SIRT1 and SREBP1. PMID:27179781

  18. The HCV non-nucleoside inhibitor Tegobuvir utilizes a novel mechanism of action to inhibit NS5B polymerase function.

    Directory of Open Access Journals (Sweden)

    Christy M Hebner

    Full Text Available Tegobuvir (TGV is a novel non-nucleoside inhibitor (NNI of HCV RNA replication with demonstrated antiviral activity in patients with genotype 1 chronic HCV infection. The mechanism of action of TGV has not been clearly defined despite the identification of resistance mutations mapping to the NS5B polymerase region. TGV does not inhibit NS5B enzymatic activity in biochemical assays in vitro, suggesting a more complex antiviral mechanism with cellular components. Here, we demonstrate that TGV exerts anti-HCV activity utilizing a unique chemical activation and subsequent direct interaction with the NS5B protein. Treatment of HCV subgenomic replicon cells with TGV results in a modified form of NS5B with a distinctly altered mobility on a SDS-PAGE gel. Further analysis reveals that the aberrantly migrating NS5B species contains the inhibitor molecule. Formation of this complex does not require the presence of any other HCV proteins. The intensity of the aberrantly migrating NS5B species is strongly dependent on cellular glutathione levels as well as CYP 1A activity. Furthermore analysis of NS5B protein purified from a heterologous expression system treated with TGV by mass spectrometry suggests that TGV undergoes a CYP- mediated intracellular activation step and the resulting metabolite, after forming a glutathione conjugate, directly and specifically interacts with NS5B. Taken together, these data demonstrate that upon metabolic activation TGV is a specific, covalent inhibitor of the HCV NS5B polymerase and is mechanistically distinct from other classes of the non-nucleoside inhibitors (NNI of the viral polymerase.

  19. The lipid kinase phosphatidylinositol-4 kinase III alpha regulates the phosphorylation status of hepatitis C virus NS5A.

    Directory of Open Access Journals (Sweden)

    Simon Reiss

    2013-05-01

    Full Text Available The lipid kinase phosphatidylinositol 4-kinase III alpha (PI4KIIIα is an essential host factor of hepatitis C virus (HCV replication. PI4KIIIα catalyzes the synthesis of phosphatidylinositol 4-phosphate (PI4P accumulating in HCV replicating cells due to enzyme activation resulting from its interaction with nonstructural protein 5A (NS5A. This study describes the interaction between PI4KIIIα and NS5A and its mechanistic role in viral RNA replication. We mapped the NS5A sequence involved in PI4KIIIα interaction to the carboxyterminal end of domain 1 and identified a highly conserved PI4KIIIα functional interaction site (PFIS encompassing seven amino acids, which are essential for viral RNA replication. Mutations within this region were also impaired in NS5A-PI4KIIIα binding, reduced PI4P levels and altered the morphology of viral replication sites, reminiscent to the phenotype observed by silencing of PI4KIIIα. Interestingly, abrogation of RNA replication caused by mutations in the PFIS correlated with increased levels of hyperphosphorylated NS5A (p58, indicating that PI4KIIIα affects the phosphorylation status of NS5A. RNAi-mediated knockdown of PI4KIIIα or pharmacological ablation of kinase activity led to a relative increase of p58. In contrast, overexpression of enzymatically active PI4KIIIα increased relative abundance of basally phosphorylated NS5A (p56. PI4KIIIα therefore regulates the phosphorylation status of NS5A and viral RNA replication by favoring p56 or repressing p58 synthesis. Replication deficiencies of PFIS mutants in NS5A could not be rescued by increasing PI4P levels, but by supplying functional NS5A, supporting an essential role of PI4KIIIα in HCV replication regulating NS5A phosphorylation, thereby modulating the morphology of viral replication sites. In conclusion, we demonstrate that PI4KIIIα activity affects the NS5A phosphorylation status. Our results highlight the importance of PI4KIIIα in the morphogenesis

  20. Classification of HCV NS5B Polymerase Inhibitors Using Support Vector Machine

    Directory of Open Access Journals (Sweden)

    Changyuan Yu

    2012-03-01

    Full Text Available Using a support vector machine (SVM, three classification models were built to predict whether a compound is an active or weakly active inhibitor based on a dataset of 386 hepatitis C virus (HCV NS5B polymerase NNIs (non-nucleoside analogue inhibitors fitting into the pocket of the NNI III binding site. For each molecule, global descriptors, 2D and 3D property autocorrelation descriptors were calculated from the program ADRIANA.Code. Three models were developed with the combination of different types of descriptors. Model 2 based on 16 global and 2D autocorrelation descriptors gave the highest prediction accuracy of 88.24% and MCC (Matthews correlation coefficient of 0.789 on test set. Model 1 based on 13 global descriptors showed the highest prediction accuracy of 86.25% and MCC of 0.732 on external test set (including 80 compounds. Some molecular properties such as molecular shape descriptors (InertiaZ, InertiaX and Span, number of rotatable bonds (NRotBond, water solubility (LogS, and hydrogen bonding related descriptors performed important roles in the interactions between the ligand and NS5B polymerase.

  1. I. Novel HCV NS5B polymerase inhibitors: Discovery of indole 2-carboxylic acids with C3-heterocycles

    Energy Technology Data Exchange (ETDEWEB)

    Anilkumar, Gopinadhan N.; Lesburg, Charles A.; Selyutin, Oleg; Rosenblum, Stuart B.; Zeng, Qingbei; Jiang, Yueheng; Chan, Tin-Yau; Pu, Haiyan; Vaccaro, Henry; Wang, Li; Bennett, Frank; Chen, Kevin X.; Duca, Jose; Gavalas, Stephen; Huang, Yuhua; Pinto, Patrick; Sannigrahi, Mousumi; Velazquez, Francisco; Venkatraman, Srikanth; Vibulbhan, Bancha; Agrawal, Sony; Butkiewicz, Nancy; Feld, Boris; Ferrari, Eric; He, Zhiqing; Jiang, Chuan-kui; Palermo, Robert E.; Mcmonagle, Patricia; Huang, H.-C.; Shih, Neng-Yang; Njoroge, George; Kozlowski, Joseph A. (Merck)

    2012-05-03

    SAR development of indole-based palm site inhibitors of HCV NS5B polymerase exemplified by initial indole lead 1 (NS5B IC{sub 50} = 0.9 {micro}M, replicon EC{sub 50} > 100 {micro}M) is described. Structure-based drug design led to the incorporation of novel heterocyclic moieties at the indole C3-position which formed a bidentate interaction with the protein backbone. SAR development resulted in leads 7q (NS5B IC{sub 50} = 0.032 {micro}M, replicon EC{sub 50} = 1.4 {micro}M) and 7r (NS5B IC{sub 50} = 0.017 {micro}M, replicon EC{sub 50} = 0.3 {micro}M) with improved enzyme and replicon activity.

  2. Analysis of RNA binding by the dengue virus NS5 RNA capping enzyme.

    Directory of Open Access Journals (Sweden)

    Brittney R Henderson

    Full Text Available Flaviviruses are small, capped positive sense RNA viruses that replicate in the cytoplasm of infected cells. Dengue virus and other related flaviviruses have evolved RNA capping enzymes to form the viral RNA cap structure that protects the viral genome and directs efficient viral polyprotein translation. The N-terminal domain of NS5 possesses the methyltransferase and guanylyltransferase activities necessary for forming mature RNA cap structures. The mechanism for flavivirus guanylyltransferase activity is currently unknown, and how the capping enzyme binds its diphosphorylated RNA substrate is important for deciphering how the flavivirus guanylyltransferase functions. In this report we examine how flavivirus NS5 N-terminal capping enzymes bind to the 5' end of the viral RNA using a fluorescence polarization-based RNA binding assay. We observed that the K(D for RNA binding is approximately 200 nM Dengue, Yellow Fever, and West Nile virus capping enzymes. Removal of one or both of the 5' phosphates reduces binding affinity, indicating that the terminal phosphates contribute significantly to binding. RNA binding affinity is negatively affected by the presence of GTP or ATP and positively affected by S-adensyl methoninine (SAM. Structural superpositioning of the dengue virus capping enzyme with the Vaccinia virus VP39 protein bound to RNA suggests how the flavivirus capping enzyme may bind RNA, and mutagenesis analysis of residues in the putative RNA binding site demonstrate that several basic residues are critical for RNA binding. Several mutants show differential binding to 5' di-, mono-, and un-phosphorylated RNAs. The mode of RNA binding appears similar to that found with other methyltransferase enzymes, and a discussion of diphosphorylated RNA binding is presented.

  3. Confirm the HCV NS5A protein interaction with aconitase 1%HCV NS5A结合蛋白顺乌头酸酶1的验证研究

    Institute of Scientific and Technical Information of China (English)

    王晓杰; 相久全; 韩乐强; 张锦前; 成军

    2011-01-01

    Objective To screen proteins of human liver cDNA library interacting with HCV NS5A and confirm the interaction between HCV N55A protein and aconitate 1 protein.Methods Yeast two hybrid was performed by mating AH109 ( HCV NS5A) with Y187 ( liver cDNA lihrary of human) .The interacted proteins with HCV NS5A were screened from the library.The aconitate 1 gene was amplified at first.The expression vectors of aconitate 1 were constructed.Then the interaction between HCV N55A protein and Homo sapiens aconitate 1 protein was confirmed using co-imruunoprecipitation and mammalian two hybrid experiment.Results The eukaryotic expression vectors of aconitate 1 were constructed.These results showed that Homo sapiens aconitate 1 protein interacted with HCV NS5A protein by co-immunoprecipitation and mammalian two hybrids experiment Conclusion HCV NS5A and Homo sapiens aconitate 1 protein can interact in HepCJ2 cells.%目的 筛选人肝脏cDNA文库中与HCV NS5A的结合蛋白基因,验证其中顺乌头酸酶1与HCV NS5A的相互作用.方法 应用酵母双杂交系统3筛选人肝脏cDNA文库中的HCV NS5A结合蛋白基因,应用哺乳动物双杂交及免疫共沉淀技术验证其中顺乌头酸酶1蛋白与HCV NS5A之间的相瓦作用.结果 成功筛选出人肝脏cD-NA文库中与HCV NS5A存在相瓦作用的蛋白基因,哺乳动物双杂交及免疫共沉淀实验结果 证实HCV NS5A与顺乌头酸酶1蛋白在HepG2细胞内存在相互作用.结论 本实验成功筛选人肝脏cDNA文库中的HCV NS5A结合蛋白基因,并且在体外水平即细胞内证实HCV NS5A与其中的顺乌头酸酶1蛋白之间的相互作用,为进一步细胞内及体内的糖、脂类代谢等功能研究奠定基础.

  4. Potent Allosteric Dengue Virus NS5 Polymerase Inhibitors: Mechanism of Action and Resistance Profiling.

    Science.gov (United States)

    Lim, Siew Pheng; Noble, Christian Guy; Seh, Cheah Chen; Soh, Tingjin Sherryl; El Sahili, Abbas; Chan, Grace Kar Yarn; Lescar, Julien; Arora, Rishi; Benson, Timothy; Nilar, Shahul; Manjunatha, Ujjini; Wan, Kah Fei; Dong, Hongping; Xie, Xuping; Shi, Pei-Yong; Yokokawa, Fumiaki

    2016-08-01

    Flaviviruses comprise major emerging pathogens such as dengue virus (DENV) or Zika virus (ZIKV). The flavivirus RNA genome is replicated by the RNA-dependent-RNA polymerase (RdRp) domain of non-structural protein 5 (NS5). This essential enzymatic activity renders the RdRp attractive for antiviral therapy. NS5 synthesizes viral RNA via a "de novo" initiation mechanism. Crystal structures of the flavivirus RdRp revealed a "closed" conformation reminiscent of a pre-initiation state, with a well ordered priming loop that extrudes from the thumb subdomain into the dsRNA exit tunnel, close to the "GDD" active site. To-date, no allosteric pockets have been identified for the RdRp, and compound screening campaigns did not yield suitable drug candidates. Using fragment-based screening via X-ray crystallography, we found a fragment that bound to a pocket of the apo-DENV RdRp close to its active site (termed "N pocket"). Structure-guided improvements yielded DENV pan-serotype inhibitors of the RdRp de novo initiation activity with nano-molar potency that also impeded elongation activity at micro-molar concentrations. Inhibitors exhibited mixed inhibition kinetics with respect to competition with the RNA or GTP substrate. The best compounds have EC50 values of 1-2 μM against all four DENV serotypes in cell culture assays. Genome-sequencing of compound-resistant DENV replicons, identified amino acid changes that mapped to the N pocket. Since inhibitors bind at the thumb/palm interface of the RdRp, this class of compounds is proposed to hinder RdRp conformational changes during its transition from initiation to elongation. This is the first report of a class of pan-serotype and cell-active DENV RdRp inhibitors. Given the evolutionary conservation of residues lining the N pocket, these molecules offer insights to treat other serious conditions caused by flaviviruses. PMID:27500641

  5. Potent Allosteric Dengue Virus NS5 Polymerase Inhibitors: Mechanism of Action and Resistance Profiling

    Science.gov (United States)

    Lim, Siew Pheng; Noble, Christian Guy; Seh, Cheah Chen; Soh, Tingjin Sherryl; El Sahili, Abbas; Chan, Grace Kar Yarn; Lescar, Julien; Arora, Rishi; Benson, Timothy; Nilar, Shahul; Manjunatha, Ujjini; Wan, Kah Fei; Dong, Hongping; Xie, Xuping; Yokokawa, Fumiaki

    2016-01-01

    Flaviviruses comprise major emerging pathogens such as dengue virus (DENV) or Zika virus (ZIKV). The flavivirus RNA genome is replicated by the RNA-dependent-RNA polymerase (RdRp) domain of non-structural protein 5 (NS5). This essential enzymatic activity renders the RdRp attractive for antiviral therapy. NS5 synthesizes viral RNA via a “de novo” initiation mechanism. Crystal structures of the flavivirus RdRp revealed a “closed” conformation reminiscent of a pre-initiation state, with a well ordered priming loop that extrudes from the thumb subdomain into the dsRNA exit tunnel, close to the “GDD” active site. To-date, no allosteric pockets have been identified for the RdRp, and compound screening campaigns did not yield suitable drug candidates. Using fragment-based screening via X-ray crystallography, we found a fragment that bound to a pocket of the apo-DENV RdRp close to its active site (termed “N pocket”). Structure-guided improvements yielded DENV pan-serotype inhibitors of the RdRp de novo initiation activity with nano-molar potency that also impeded elongation activity at micro-molar concentrations. Inhibitors exhibited mixed inhibition kinetics with respect to competition with the RNA or GTP substrate. The best compounds have EC50 values of 1–2 μM against all four DENV serotypes in cell culture assays. Genome-sequencing of compound-resistant DENV replicons, identified amino acid changes that mapped to the N pocket. Since inhibitors bind at the thumb/palm interface of the RdRp, this class of compounds is proposed to hinder RdRp conformational changes during its transition from initiation to elongation. This is the first report of a class of pan-serotype and cell-active DENV RdRp inhibitors. Given the evolutionary conservation of residues lining the N pocket, these molecules offer insights to treat other serious conditions caused by flaviviruses. PMID:27500641

  6. Episodic adaptive diversification of classical swine fever virus RNA-dependent RNA polymerase NS5B.

    Science.gov (United States)

    Li, Yan; Yang, Zexiao

    2015-12-01

    Classical swine fever virus (CSFV) is the pathogen that causes a highly infectious disease of pigs and has led to disastrous losses to pig farms and related industries. The RNA-dependent RNA polymerase (RdRp) NS5B is a central component of the replicase complex (RC) in some single-stranded RNA viruses, including CSFV. On the basis of genetic variation, the CSFV RdRps could be clearly divided into 2 major groups and a minor group, which is consistent with the phylogenetic relationships and virulence diversification of the CSFV isolates. However, the adaptive signature underlying such an evolutionary profile of the polymerase and the virus is still an interesting open question. We analyzed the evolutionary trajectory of the CSFV RdRps over different timescales to evaluate the potential adaptation. We found that adaptive selection has driven the diversification of the RdRps between, but not within, CSFV major groups. Further, the major adaptive divergence-related sites are located in the surfaces relevant to the interaction with other component(s) of RC and the entrance and exit of the template-binding channel. These results might shed some light on the nature of the RdRp in virulence diversification of CSFV groups.

  7. Episodic adaptive diversification of classical swine fever virus RNA-dependent RNA polymerase NS5B.

    Science.gov (United States)

    Li, Yan; Yang, Zexiao

    2015-12-01

    Classical swine fever virus (CSFV) is the pathogen that causes a highly infectious disease of pigs and has led to disastrous losses to pig farms and related industries. The RNA-dependent RNA polymerase (RdRp) NS5B is a central component of the replicase complex (RC) in some single-stranded RNA viruses, including CSFV. On the basis of genetic variation, the CSFV RdRps could be clearly divided into 2 major groups and a minor group, which is consistent with the phylogenetic relationships and virulence diversification of the CSFV isolates. However, the adaptive signature underlying such an evolutionary profile of the polymerase and the virus is still an interesting open question. We analyzed the evolutionary trajectory of the CSFV RdRps over different timescales to evaluate the potential adaptation. We found that adaptive selection has driven the diversification of the RdRps between, but not within, CSFV major groups. Further, the major adaptive divergence-related sites are located in the surfaces relevant to the interaction with other component(s) of RC and the entrance and exit of the template-binding channel. These results might shed some light on the nature of the RdRp in virulence diversification of CSFV groups. PMID:26485449

  8. Characterisation of divergent flavivirus NS3 and NS5 protein sequences detected in Rhipicephalus microplus ticks from Brazil

    Directory of Open Access Journals (Sweden)

    Sandra Regina Maruyama

    2014-02-01

    Full Text Available Transcripts similar to those that encode the nonstructural (NS proteins NS3 and NS5 from flaviviruses were found in a salivary gland (SG complementary DNA (cDNA library from the cattle tick Rhipicephalus microplus. Tick extracts were cultured with cells to enable the isolation of viruses capable of replicating in cultured invertebrate and vertebrate cells. Deep sequencing of the viral RNA isolated from culture supernatants provided the complete coding sequences for the NS3 and NS5 proteins and their molecular characterisation confirmed similarity with the NS3 and NS5 sequences from other flaviviruses. Despite this similarity, phylogenetic analyses revealed that this potentially novel virus may be a highly divergent member of the genus Flavivirus. Interestingly, we detected the divergent NS3 and NS5 sequences in ticks collected from several dairy farms widely distributed throughout three regions of Brazil. This is the first report of flavivirus-like transcripts in R. microplus ticks. This novel virus is a potential arbovirus because it replicated in arthropod and mammalian cells; furthermore, it was detected in a cDNA library from tick SGs and therefore may be present in tick saliva. It is important to determine whether and by what means this potential virus is transmissible and to monitor the virus as a potential emerging tick-borne zoonotic pathogen.

  9. Legalon-SIL downregulates HCV core and NS5A in human hepatocytes expressing full-length HCV

    Institute of Scientific and Technical Information of China (English)

    Marjan Mehrab-Mohseni; Hossein Sendi; Nury Steuerwald; Sriparna Ghosh; Laura W Schrum; Herbert L Bonkovsky

    2011-01-01

    AIM: To determine the effect of Legalon-SIL (LS) on hepatitis C virus (HCV) core and NS5A expression and on heme oxygenase-1 (HMOX-1) and its transcriptionalregulators in human hepatoma cells expressing full length HCV genotype 1b.METHODS: CON1 cells were treated with 50 μmol/or 200 μmol/L LS. Cells were harvested after 2, 6 and 24 h. HCV RNA and protein levels were determined byquantitative real-time polymerase chain reaction and Western blotting, respectively.RESULTS: HCV RNA (core and NS5A regions) was decreased after 6 h with LS 200 μmol/L (P < 0.05).Both 50 and 200 μmol/L LS decreased HCV RNA levels[core region (by 55% and 88%, respectively) and NS5A region (by 62% and 87%, respectively) after 24 h compared with vehicle (dimethyl sulphoxide) control (P< 0.01). Similarly HCV core and NS5A protein were decreased(by 85%, P < 0.01 and by 65%, P < 0.05, respectively)by LS 200 μmol/L. Bach1 and HMOX-1 RNAwere also downregulated by LS treatment (P < 0.01),while Nrf2 protein was increased (P < 0.05).CONCLUSION: Our results demonstrate that treatment with LS downregulates HCV core and NS5A expression in CON1 cells which express full length HCVgenotype 1b, and suggests that LS may prove to be a valuable alternative or adjunctive therapy for the treatment of HCV infection.

  10. Flavivirus NS3 and NS5 proteins interaction network: a high-throughput yeast two-hybrid screen

    Directory of Open Access Journals (Sweden)

    Canard Bruno

    2011-10-01

    Full Text Available Abstract Background The genus Flavivirus encompasses more than 50 distinct species of arthropod-borne viruses, including several major human pathogens, such as West Nile virus, yellow fever virus, Japanese encephalitis virus and the four serotypes of dengue viruses (DENV type 1-4. Each year, flaviviruses cause more than 100 million infections worldwide, some of which lead to life-threatening conditions such as encephalitis or haemorrhagic fever. Among the viral proteins, NS3 and NS5 proteins constitute the major enzymatic components of the viral replication complex and are essential to the flavivirus life cycle. Results We report here the results of a high-throughput yeast two-hybrid screen to identify the interactions between human host proteins and the flavivirus NS3 and NS5 proteins. Using our screen results and literature curation, we performed a global analysis of the NS3 and NS5 cellular targets based on functional annotation with the Gene Ontology features. We finally created the first flavivirus NS3 and NS5 proteins interaction network and analysed the topological features of this network. Our proteome mapping screen identified 108 human proteins interacting with NS3 or NS5 proteins or both. The global analysis of the cellular targets revealed the enrichment of host proteins involved in RNA binding, transcription regulation, vesicular transport or innate immune response regulation. Conclusions We proposed that the selective disruption of these newly identified host/virus interactions could represent a novel and attractive therapeutic strategy in treating flavivirus infections. Our virus-host interaction map provides a basis to unravel fundamental processes about flavivirus subversion of the host replication machinery and/or immune defence strategy.

  11. A Rab-GAP TBC Domain Protein Binds Hepatitis C Virus NS5A and Mediates Viral Replication▿

    Science.gov (United States)

    Sklan, Ella H.; Staschke, Kirk; Oakes, Tina M.; Elazar, Menashe; Winters, Mark; Aroeti, Benjamin; Danieli, Tsafi; Glenn, Jeffrey S.

    2007-01-01

    Hepatitis C virus (HCV) is an important cause of liver disease worldwide. Current therapies are inadequate for most patients. Using a two-hybrid screen, we isolated a novel cellular binding partner interacting with the N terminus of HCV nonstructural protein NS5A. This partner contains a TBC Rab-GAP (GTPase-activating protein) homology domain found in all known Rab-activating proteins. As the first described interaction between such a Rab-GAP and a viral protein, this finding suggests a new mechanism whereby viruses may subvert host cell machinery for mediating the endocytosis, trafficking, and sorting of their own proteins. Moreover, depleting the expression of this partner severely impairs HCV RNA replication with no obvious effect on cell viability. These results suggest that pharmacologic disruption of this NS5A-interacting partner can be contemplated as a potential new antiviral strategy against a pathogen affecting nearly 3% of the world's population. PMID:17686842

  12. Cell penetrable humanized-VH/V(H)H that inhibit RNA dependent RNA polymerase (NS5B) of HCV.

    Science.gov (United States)

    Thueng-in, Kanyarat; Thanongsaksrikul, Jeeraphong; Srimanote, Potjanee; Bangphoomi, Kunan; Poungpair, Ornnuthchar; Maneewatch, Santi; Choowongkomon, Kiattawee; Chaicumpa, Wanpen

    2012-01-01

    NS5B is pivotal RNA dependent RNA polymerase (RdRp) of HCV and NS5B function interfering halts the virus infective cycle. This work aimed to produce cell penetrable humanized single domain antibodies (SdAb; VH/V(H)H) that interfere with the RdRp activity. Recombinant NS5BΔ55 of genotype 3a HCV with de novo RNA synthetic activity was produced and used in phage biopanning for selecting phage clones that displayed NS5BΔ55 bound VH/V(H)H from a humanized-camel VH/V(H)H display library. VH/V(H)H from E. coli transfected with four selected phage clones inhibited RdRp activity when tested by ELISA inhibition using 3'di-cytidylate 25 nucleotide directed in vitro RNA synthesis. Deduced amino acid sequences of two clones showed V(H)H hallmark and were designated V(H)H6 and V(H)H24; other clones were conventional VH, designated VH9 and VH13. All VH/V(H)H were linked molecularly to a cell penetrating peptide, penetratin. The cell penetrable VH9, VH13, V(H)H6 and V(H)H24 added to culture of Huh7 cells transfected with JHF-1 RNA of genotype 2a HCV reduced the amounts of RNA intracellularly and in culture medium implying that they inhibited the virus replication. VH/V(H)H mimotopes matched with residues scattered on the polymerase fingers, palm and thumb which were likely juxtaposed to form conformational epitopes. Molecular docking revealed that the antibodies covered the RdRp catalytic groove. The transbodies await further studies for in vivo role in inhibiting HCV replication.

  13. Inhibitor candidates's identification of HCV's RNA polymerase NS5B using virtual screening against iPPI-library

    Science.gov (United States)

    Sulistyawati, Indah; Sulistyo Dwi K., P.; Ichsan, Mochammad

    2016-03-01

    Hepatitis C is one of the major causes of chronic liver failure that caused by Hepatitis C Virus (HCV). Preventing the progression of HCV's replication through the inhibition of The RNA polymerase NS5B of Hepatitis C virus (NS5B) can be achieved via 4 binding regions: Site I (Thumb I), Site II (Thumb II), Site III (Palm I), and Site IV (Palm II). The aim of this research is to identify a candidate of NS5B inhibitor as an alternative for Hepatitis C treatment. An NS5B's 3D structure (PDB ID = 3D5M) used in this study has met some criteria of a good model to be used in virtual screening againts iPPI-lib using MTiOpenScreen webserver. The top two natural compounds resulted here then docked using Pyrix 0.8 and discovered trans-6-Benzamido-2-methyldecahydroisoquinoline (-9,1kcal/mol) and 2,4-dichloro-5-[4-(2 methoxyphenyl) piperazine-1-carbonyl]-N-[3-(trifluoromethyl)phenyl] benzenesulfonamide (9,4 kcal/mol) can bind to Tyr448 similar with all three established inhibitors, such as setrobuvir (-11,4 kcal/mol; site 3 inhibitor), CHEMBL379677 (-9,1 kcal/mol; site 1 inhibitor), and nesbuvir (-7,7 kcal/mol; site 4 inhibitor). The results of this study are relatively still needs to be tested, both in vitro and in vivo, in order to obtain more comprehensive knowledges as a follow-up of this predictive study.

  14. 3D-QSAR and molecular docking studies on designing inhibitors of the hepatitis C virus NS5B polymerase

    Science.gov (United States)

    Li, Wenlian; Si, Hongzong; Li, Yang; Ge, Cuizhu; Song, Fucheng; Ma, Xiuting; Duan, Yunbo; Zhai, Honglin

    2016-08-01

    Viral hepatitis C infection is one of the main causes of the hepatitis after blood transfusion and hepatitis C virus (HCV) infection is a global health threat. The HCV NS5B polymerase, an RNA dependent RNA polymerase (RdRp) and an essential role in the replication of the virus, has no functional equivalent in mammalian cells. So the research and development of efficient NS5B polymerase inhibitors provides a great strategy for antiviral therapy against HCV. A combined three-dimensional quantitative structure-activity relationship (QSAR) modeling was accomplished to profoundly understand the structure-activity correlation of a train of indole-based inhibitors of the HCV NS5B polymerase to against HCV. A comparative molecular similarity indices analysis (COMSIA) model as the foundation of the maximum common substructure alignment was developed. The optimum model exhibited statistically significant results: the cross-validated correlation coefficient q2 was 0.627 and non-cross-validated r2 value was 0.943. In addition, the results of internal validations of bootstrapping and Y-randomization confirmed the rationality and good predictive ability of the model, as well as external validation (the external predictive correlation coefficient rext2 = 0.629). The information obtained from the COMSIA contour maps enables the interpretation of their structure-activity relationship. Furthermore, the molecular docking study of the compounds for 3TYV as the protein target revealed important interactions between active compounds and amino acids, and several new potential inhibitors with higher activity predicted were designed basis on our analyses and supported by the simulation of molecular docking. Meanwhile, the OSIRIS Property Explorer was introduced to help select more satisfactory compounds. The satisfactory results from this study may lay a reliable theoretical base for drug development of hepatitis C virus NS5B polymerase inhibitors.

  15. FKBP8 interact with classical swine fever virus NS5A protein and promote virus RNA replication.

    Science.gov (United States)

    Li, Helin; Zhang, Chengcheng; Cui, Hongjie; Guo, Kangkang; Wang, Fang; Zhao, Tianyue; Liang, Wulong; Lv, Qizhuang; Zhang, Yanming

    2016-02-01

    The non-structural 5A (NS5A) protein of classical swine fever virus (CSFV) is proven to be involved in viral replication and can also modulate cellular signaling and host cellular responses via to its ability to interact with various cellular proteins. FKBP8 is also reported to promote virus replication. Here, we show that NS5A specifically interacts with FKBP8 through coimmunoprecipitation and GST-pulldown studies. Additionally, confocal microscopy study showed that NS5A and FKBP8 colocalized in the cytoplasm. Overexpression of FKBP8 via the eukaryotic expression plasmid pDsRED N1 significantly promoted viral RNA synthesis. The cells knockdown of FKBP8 by lentivirus-mediated shRNA markedly decreased the virus replication when infected with CSFV. These data suggest that FKBP8 plays a critical role in the viral life cycle, particularly during the virus RNA replication period. The investigation of FKBP8 protein functions may be beneficial for developing new strategies to treat CSFV infection. PMID:26748656

  16. HCV NS5A protein containing potential ligands for both Src homology 2 and 3 domains enhances autophosphorylation of Src family kinase Fyn in B cells.

    Directory of Open Access Journals (Sweden)

    Kenji Nakashima

    Full Text Available Hepatitis C virus (HCV infects B lymphocytes and induces mixed cryoglobulinemia and B cell non-Hodgkin's lymphoma. The molecular mechanism for the pathogenesis of HCV infection-mediated B cell disorders remains obscure. To identify the possible role for HCV nonstructural 5A (NS5A protein in B cells, we generated the stable B cell lines expressing Myc-His tagged NS5A. Immunoprecipitation study in the presence or absence of pervanadate (PV implied that NS5A was tyrosine phosphorylated by pervanadate (PV treatment of the cells. Therefore we examined pull-down assay by using glutathione S-transferase (GST-fusion proteins of various Src homology 2 (SH2 domains, which associates with phosphotyrosine within a specific amino acid sequence. The results showed that NS5A specifically bound to SH2 domain of Fyn from PV-treated B cells in addition to Src homology 3 (SH3 domain. Substitution of Arg(176 to Lys in the SH2 domain of Fyn abrogated this interaction. Deletion mutational analysis demonstrated that N-terminal region of NS5A was not required for the interaction with the SH2 domain of Fyn. Tyr(334 was identified as a tyrosine phosphorylation site in NS5A. Far-western analysis revealed that SH2 domain of Fyn directly bound to NS5A. Fyn and NS5A were colocalized in the lipid raft. These results suggest that NS5A directly binds to the SH2 domain of Fyn in a tyrosine phosphorylation-dependent manner. Lastly, we showed that the expression of NS5A in B cells increased phosphorylation of activation loop tyrosine in the kinase domain of Fyn. NS5A containing ligand for both SH2 and SH3 domains enhances an aberrant autophosphorylation and kinase activity of Fyn in B cells.

  17. Analysis of functional differences between hepatitis C virus NS5A of genotypes 1-7 in infectious cell culture systems

    DEFF Research Database (Denmark)

    Scheel, Troels K H; Prentoe, Jannick; Carlsen, Thomas H R;

    2012-01-01

    Hepatitis C virus (HCV) is an important cause of chronic liver disease. Several highly diverse HCV genotypes exist with potential key functional differences. The HCV NS5A protein was associated with response to interferon (IFN)-α based therapy, and is a primary target of currently developed...... directly-acting antiviral compounds. NS5A is important for replication and virus production, but has not been studied for most HCV genotypes. We studied the function of NS5A using infectious NS5A genotype 1-7 cell culture systems, and through reverse genetics demonstrated a universal importance......, but ED43(4a) and SA13(5a) also displayed impaired particle assembly. Compared to the original H77C(1a) NS5A recombinant, the changes in LCSII and domain III reduced the amounts of NS5A present. For H77C(1a) and TN(1a) NS5A recombinants, we observed a genetic linkage between NS5A and p7, since introduced...

  18. Analysis of functional differences between hepatitis C virus NS5A of genotypes 1-7 in infectious cell culture systems.

    Directory of Open Access Journals (Sweden)

    Troels K H Scheel

    Full Text Available Hepatitis C virus (HCV is an important cause of chronic liver disease. Several highly diverse HCV genotypes exist with potential key functional differences. The HCV NS5A protein was associated with response to interferon (IFN-α based therapy, and is a primary target of currently developed directly-acting antiviral compounds. NS5A is important for replication and virus production, but has not been studied for most HCV genotypes. We studied the function of NS5A using infectious NS5A genotype 1-7 cell culture systems, and through reverse genetics demonstrated a universal importance of the amphipathic alpha-helix, domain I and II and the low-complexity sequence (LCS I for HCV replication; the replicon-enhancing LCSI mutation S225P attenuated all genotypes. Mutation of conserved prolines in LCSII led to minor reductions in virus production for the JFH1(genotype 2a NS5A recombinant, but had greater effects on other isolates; replication was highly attenuated for ED43(4a and QC69(7a recombinants. Deletion of the conserved residues 414-428 in domain III reduced virus production for most recombinants but not JFH1(2a. Reduced virus production was linked to attenuated replication in all cases, but ED43(4a and SA13(5a also displayed impaired particle assembly. Compared to the original H77C(1a NS5A recombinant, the changes in LCSII and domain III reduced the amounts of NS5A present. For H77C(1a and TN(1a NS5A recombinants, we observed a genetic linkage between NS5A and p7, since introduced changes in NS5A led to changes in p7 and vice versa. Finally, NS5A function depended on genotype-specific residues in domain I, as changing genotype 2a-specific residues to genotype 1a sequence and vice versa led to highly attenuated mutants. In conclusion, this study identified NS5A genetic elements essential for all major HCV genotypes in infectious cell culture systems. Genotype- or isolate- specific NS5A functional differences were identified, which will be important

  19. Discovery of Novel Thiophene-Based, Thumb Pocket 2 Allosteric Inhibitors of the Hepatitis C NS5B Polymerase with Improved Potency and Physicochemical Profiles.

    Science.gov (United States)

    Court, John J; Poisson, Carl; Ardzinski, Andrzej; Bilimoria, Darius; Chan, Laval; Chandupatla, Kishan; Chauret, Nathalie; Collier, Philip N; Das, Sanjoy Kumar; Denis, Francois; Dorsch, Warren; Iyer, Ganesh; Lauffer, David; L'Heureux, Lucille; Li, Pan; Luisi, Brian S; Mani, Nagraj; Nanthakumar, Suganthi; Nicolas, Olivier; Rao, B Govinda; Ronkin, Steven; Selliah, Subajini; Shawgo, Rebecca S; Tang, Qing; Waal, Nathan D; Yannopoulos, Constantin G; Green, Jeremy

    2016-07-14

    The hepatitis C viral proteins NS3/4A protease, NS5B polymerase, and NS5A are clinically validated targets for direct-acting antiviral therapies. The NS5B polymerase may be inhibited directly through the action of nucleosides or nucleotide analogues or allosterically at a number of well-defined sites. Herein we describe the further development of a series of thiophene carboxylate allosteric inhibitors of NS5B polymerase that act at the thumb pocket 2 site. Lomibuvir (1) is an allosteric HCV NS5B inhibitor that has demonstrated excellent antiviral activity and potential clinical utility in combination with other direct acting antiviral agents. Efforts to further explore and develop this series led to compound 23, a compound with comparable potency and improved physicochemical properties.

  20. A crystal structure of the Dengue virus NS5 protein reveals a novel inter-domain interface essential for protein flexibility and virus replication.

    Directory of Open Access Journals (Sweden)

    Yongqian Zhao

    2015-03-01

    Full Text Available Flavivirus RNA replication occurs within a replication complex (RC that assembles on ER membranes and comprises both non-structural (NS viral proteins and host cofactors. As the largest protein component within the flavivirus RC, NS5 plays key enzymatic roles through its N-terminal methyltransferase (MTase and C-terminal RNA-dependent-RNA polymerase (RdRp domains, and constitutes a major target for antivirals. We determined a crystal structure of the full-length NS5 protein from Dengue virus serotype 3 (DENV3 at a resolution of 2.3 Å in the presence of bound SAH and GTP. Although the overall molecular shape of NS5 from DENV3 resembles that of NS5 from Japanese Encephalitis Virus (JEV, the relative orientation between the MTase and RdRp domains differs between the two structures, providing direct evidence for the existence of a set of discrete stable molecular conformations that may be required for its function. While the inter-domain region is mostly disordered in NS5 from JEV, the NS5 structure from DENV3 reveals a well-ordered linker region comprising a short 310 helix that may act as a swivel. Solution Hydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS analysis reveals an increased mobility of the thumb subdomain of RdRp in the context of the full length NS5 protein which correlates well with the analysis of the crystallographic temperature factors. Site-directed mutagenesis targeting the mostly polar interface between the MTase and RdRp domains identified several evolutionarily conserved residues that are important for viral replication, suggesting that inter-domain cross-talk in NS5 regulates virus replication. Collectively, a picture for the molecular origin of NS5 flexibility is emerging with profound implications for flavivirus replication and for the development of therapeutics targeting NS5.

  1. Structural insight and flexible features of NS5 proteins from all four serotypes of Dengue virus in solution

    Energy Technology Data Exchange (ETDEWEB)

    Saw, Wuan Geok; Tria, Giancarlo; Grüber, Ardina; Subramanian Manimekalai, Malathy Sony; Zhao, Yongqian; Chandramohan, Arun; Srinivasan Anand, Ganesh; Matsui, Tsutomu; Weiss, Thomas M.; Vasudevan, Subhash G.; Grüber, Gerhard

    2015-10-31

    Infection by the four serotypes ofDengue virus(DENV-1 to DENV-4) causes an important arthropod-borne viral disease in humans. The multifunctional DENV nonstructural protein 5 (NS5) is essential for capping and replication of the viral RNA and harbours a methyltransferase (MTase) domain and an RNA-dependent RNA polymerase (RdRp) domain. In this study, insights into the overall structure and flexibility of the entire NS5 of all fourDengue virusserotypes in solution are presented for the first time. The solution models derived revealed an arrangement of the full-length NS5 (NS5FL) proteins with the MTase domain positioned at the top of the RdRP domain. The DENV-1 to DENV-4 NS5 forms are elongated and flexible in solution, with DENV-4 NS5 being more compact relative to NS5 from DENV-1, DENV-2 and DENV-3. Solution studies of the individual MTase and RdRp domains show the compactness of the RdRp domain as well as the contribution of the MTase domain and the ten-residue linker region to the flexibility of the entire NS5. Swapping the ten-residue linker between DENV-4 NS5FL and DENV-3 NS5FL demonstrated its importance in MTase–RdRp communication and in concerted interaction with viral and host proteins, as probed by amide hydrogen/deuterium mass spectrometry. Conformational alterations owing to RNA binding are presented.

  2. The C-terminal 18 Amino Acid Region of Dengue Virus NS5 Regulates its Subcellular Localization and Contains a Conserved Arginine Residue Essential for Infectious Virus Production

    Science.gov (United States)

    Ng, Ivan H. W.; Chan, Kitti W. K.; Zhao, Yongqian; Ooi, Eng Eong; Lescar, Julien; Jans, David A.; Forwood, Jade K.

    2016-01-01

    Dengue virus NS5 is the most highly conserved amongst the viral non-structural proteins and is responsible for capping, methylation and replication of the flavivirus RNA genome. Interactions of NS5 with host proteins also modulate host immune responses. Although replication occurs in the cytoplasm, an unusual characteristic of DENV2 NS5 is that it localizes to the nucleus during infection with no clear role in replication or pathogenesis. We examined NS5 of DENV1 and 2, which exhibit the most prominent difference in nuclear localization, employing a combination of functional and structural analyses. Extensive gene swapping between DENV1 and 2 NS5 identified that the C-terminal 18 residues (Cter18) alone was sufficient to direct the protein to the cytoplasm or nucleus, respectively. The low micromolar binding affinity between NS5 Cter18 and the nuclear import receptor importin-alpha (Impα), allowed their molecular complex to be purified, crystallised and visualized at 2.2 Å resolution using x-ray crystallography. Structure-guided mutational analysis of this region in GFP-NS5 clones of DENV1 or 2 and in a DENV2 infectious clone reveal residues important for NS5 subcellular localization. Notably, the trans conformation adopted by Pro-884 allows proper presentation for binding Impα and mutating this proline to Thr, as present in DENV1 NS5, results in mislocalizaion of NS5 to the cytoplasm without compromising virus fitness. In contrast, a single mutation to alanine at NS5 position R888, a residue conserved in all flaviviruses, resulted in a completely non-viable virus, and the R888K mutation led to a severely attenuated phentoype, even though NS5 was located in the nucleus. R888 forms a hydrogen bond with Y838 that is also conserved in all flaviviruses. Our data suggests an evolutionarily conserved function for NS5 Cter18, possibly in RNA interactions that are critical for replication, that is independent of its role in subcellular localization. PMID:27622521

  3. The C-terminal 18 Amino Acid Region of Dengue Virus NS5 Regulates its Subcellular Localization and Contains a Conserved Arginine Residue Essential for Infectious Virus Production.

    Science.gov (United States)

    Tay, Moon Y F; Smith, Kate; Ng, Ivan H W; Chan, Kitti W K; Zhao, Yongqian; Ooi, Eng Eong; Lescar, Julien; Luo, Dahai; Jans, David A; Forwood, Jade K; Vasudevan, Subhash G

    2016-09-01

    Dengue virus NS5 is the most highly conserved amongst the viral non-structural proteins and is responsible for capping, methylation and replication of the flavivirus RNA genome. Interactions of NS5 with host proteins also modulate host immune responses. Although replication occurs in the cytoplasm, an unusual characteristic of DENV2 NS5 is that it localizes to the nucleus during infection with no clear role in replication or pathogenesis. We examined NS5 of DENV1 and 2, which exhibit the most prominent difference in nuclear localization, employing a combination of functional and structural analyses. Extensive gene swapping between DENV1 and 2 NS5 identified that the C-terminal 18 residues (Cter18) alone was sufficient to direct the protein to the cytoplasm or nucleus, respectively. The low micromolar binding affinity between NS5 Cter18 and the nuclear import receptor importin-alpha (Impα), allowed their molecular complex to be purified, crystallised and visualized at 2.2 Å resolution using x-ray crystallography. Structure-guided mutational analysis of this region in GFP-NS5 clones of DENV1 or 2 and in a DENV2 infectious clone reveal residues important for NS5 subcellular localization. Notably, the trans conformation adopted by Pro-884 allows proper presentation for binding Impα and mutating this proline to Thr, as present in DENV1 NS5, results in mislocalizaion of NS5 to the cytoplasm without compromising virus fitness. In contrast, a single mutation to alanine at NS5 position R888, a residue conserved in all flaviviruses, resulted in a completely non-viable virus, and the R888K mutation led to a severely attenuated phentoype, even though NS5 was located in the nucleus. R888 forms a hydrogen bond with Y838 that is also conserved in all flaviviruses. Our data suggests an evolutionarily conserved function for NS5 Cter18, possibly in RNA interactions that are critical for replication, that is independent of its role in subcellular localization. PMID:27622521

  4. In Vitro Antiviral Activity and Resistance Profile Characterization of the Hepatitis C Virus NS5A Inhibitor Ledipasvir

    Science.gov (United States)

    Tian, Yang; Doehle, Brian; Peng, Betty; Corsa, Amoreena; Lee, Yu-Jen; Gong, Ruoyu; Yu, Mei; Han, Bin; Xu, Simin; Dvory-Sobol, Hadas; Perron, Michel; Xu, Yili; Mo, Hongmei; Pagratis, Nikos; Link, John O.; Delaney, William

    2016-01-01

    Ledipasvir (LDV; GS-5885), a component of Harvoni (a fixed-dose combination of LDV with sofosbuvir [SOF]), is approved to treat chronic hepatitis C virus (HCV) infection. Here, we report key preclinical antiviral properties of LDV, including in vitro potency, in vitro resistance profile, and activity in combination with other anti-HCV agents. LDV has picomolar antiviral activity against genotype 1a and genotype 1b replicons with 50% effective concentration (EC50) values of 0.031 nM and 0.004 nM, respectively. LDV is also active against HCV genotypes 4a, 4d, 5a, and 6a with EC50 values of 0.11 to 1.1 nM. LDV has relatively less in vitro antiviral activity against genotypes 2a, 2b, 3a, and 6e, with EC50 values of 16 to 530 nM. In vitro resistance selection with LDV identified the single Y93H and Q30E resistance-associated variants (RAVs) in the NS5A gene; these RAVs were also observed in patients after a 3-day monotherapy treatment. In vitro antiviral combination studies indicate that LDV has additive to moderately synergistic antiviral activity when combined with other classes of HCV direct-acting antiviral (DAA) agents, including NS3/4A protease inhibitors and the nucleotide NS5B polymerase inhibitor SOF. Furthermore, LDV is active against known NS3 protease and NS5B polymerase inhibitor RAVs with EC50 values equivalent to those for the wild type. PMID:26824950

  5. eEF1A Interacts with the NS5A Protein and Inhibits the Growth of Classical Swine Fever Virus

    Directory of Open Access Journals (Sweden)

    Su Li

    2015-08-01

    Full Text Available The NS5A protein of classical swine fever virus (CSFV is involved in the RNA synthesis and viral replication. However, the NS5A-interacting cellular proteins engaged in the CSFV replication are poorly defined. Using yeast two-hybrid screen, the eukaryotic elongation factor 1A (eEF1A was identified to be an NS5A-binding partner. The NS5A–eEF1A interaction was confirmed by coimmunoprecipitation, glutathione S-transferase (GST pulldown and laser confocal microscopy assays. The domain I of eEF1A was shown to be critical for the NS5A–eEF1A interaction. Overexpression of eEF1A suppressed the CSFV growth markedly, and conversely, knockdown of eEF1A enhanced the CSFV replication significantly. Furthermore, eEF1A, as well as NS5A, was found to reduce the translation efficiency of the internal ribosome entry site (IRES of CSFV in a dose-dependent manner, as demonstrated by luciferase reporter assay. Streptavidin pulldown assay revealed that eEF1A could bind to the CSFV IRES. Collectively, our results suggest that eEF1A interacts with NS5A and negatively regulates the growth of CSFV.

  6. eEF1A Interacts with the NS5A Protein and Inhibits the Growth of Classical Swine Fever Virus.

    Science.gov (United States)

    Li, Su; Feng, Shuo; Wang, Jing-Han; He, Wen-Rui; Qin, Hua-Yang; Dong, Hong; Li, Lian-Feng; Yu, Shao-Xiong; Li, Yongfeng; Qiu, Hua-Ji

    2015-08-01

    The NS5A protein of classical swine fever virus (CSFV) is involved in the RNA synthesis and viral replication. However, the NS5A-interacting cellular proteins engaged in the CSFV replication are poorly defined. Using yeast two-hybrid screen, the eukaryotic elongation factor 1A (eEF1A) was identified to be an NS5A-binding partner. The NS5A-eEF1A interaction was confirmed by coimmunoprecipitation, glutathione S-transferase (GST) pulldown and laser confocal microscopy assays. The domain I of eEF1A was shown to be critical for the NS5A-eEF1A interaction. Overexpression of eEF1A suppressed the CSFV growth markedly, and conversely, knockdown of eEF1A enhanced the CSFV replication significantly. Furthermore, eEF1A, as well as NS5A, was found to reduce the translation efficiency of the internal ribosome entry site (IRES) of CSFV in a dose-dependent manner, as demonstrated by luciferase reporter assay. Streptavidin pulldown assay revealed that eEF1A could bind to the CSFV IRES. Collectively, our results suggest that eEF1A interacts with NS5A and negatively regulates the growth of CSFV. PMID:26266418

  7. ADP-ribosylation Factor-related Protein 1 Interacts with NS5A and Regulates Hepatitis C Virus Propagation

    Science.gov (United States)

    Lim, Yun-Sook; Ngo, Huong T. T.; Lee, Jihye; Son, Kidong; Park, Eun-Mee; Hwang, Soon B.

    2016-01-01

    The life cycle of hepatitis C virus (HCV) is tightly coupled to the lipid metabolism of host cells. In order to identify host factors involved in HCV propagation, we have previously screened a small interfering RNA (siRNA) library targeting host genes that control lipid metabolism and lipid droplet (LD) formation using cell culture-grown HCV (HCVcc)-infected cells. In this study, we selected and characterized the gene encoding ADP-ribosylation factor-related protein 1 (ARFRP1). ARFRP1 is essential for LD growth and is involved in the regulation of lipolysis. siRNA-mediated knockdown of ARFRP1 significantly inhibited HCV replication in both subgenomic replicon cells and HCVcc-infected cells. ARFRP1 interacted with NS5A and NS5A partially colocalized with LD. Silencing of ARFRP1 abrogated HCV-induced LD growth and viral protein expressions. Moreover, ARFRP1 recruited synaptosomal-associated protein 23 (SNAP23) to sites in close proximity to LDs in HCV-infected cells. Silencing of ARFRP1 ablated relocalization of SNAP23 to LD. These data indicate that HCV regulates ARFRP1 for LD growth to facilitate viral propagation and thus ARFRP1 may be a potential target for antiviral therapy. PMID:27550144

  8. ADP-ribosylation Factor-related Protein 1 Interacts with NS5A and Regulates Hepatitis C Virus Propagation.

    Science.gov (United States)

    Lim, Yun-Sook; Ngo, Huong T T; Lee, Jihye; Son, Kidong; Park, Eun-Mee; Hwang, Soon B

    2016-01-01

    The life cycle of hepatitis C virus (HCV) is tightly coupled to the lipid metabolism of host cells. In order to identify host factors involved in HCV propagation, we have previously screened a small interfering RNA (siRNA) library targeting host genes that control lipid metabolism and lipid droplet (LD) formation using cell culture-grown HCV (HCVcc)-infected cells. In this study, we selected and characterized the gene encoding ADP-ribosylation factor-related protein 1 (ARFRP1). ARFRP1 is essential for LD growth and is involved in the regulation of lipolysis. siRNA-mediated knockdown of ARFRP1 significantly inhibited HCV replication in both subgenomic replicon cells and HCVcc-infected cells. ARFRP1 interacted with NS5A and NS5A partially colocalized with LD. Silencing of ARFRP1 abrogated HCV-induced LD growth and viral protein expressions. Moreover, ARFRP1 recruited synaptosomal-associated protein 23 (SNAP23) to sites in close proximity to LDs in HCV-infected cells. Silencing of ARFRP1 ablated relocalization of SNAP23 to LD. These data indicate that HCV regulates ARFRP1 for LD growth to facilitate viral propagation and thus ARFRP1 may be a potential target for antiviral therapy. PMID:27550144

  9. Looking for inhibitors of the dengue virus NS5 RNA-dependent RNA-polymerase using a molecular docking approach

    Science.gov (United States)

    Galiano, Vicente; Garcia-Valtanen, Pablo; Micol, Vicente; Encinar, José Antonio

    2016-01-01

    The dengue virus (DENV) nonstructural protein 5 (NS5) contains both an N-terminal methyltransferase domain and a C-terminal RNA-dependent RNA polymerase domain. Polymerase activity is responsible for viral RNA synthesis by a de novo initiation mechanism and represents an attractive target for antiviral therapy. The incidence of DENV has grown rapidly and it is now estimated that half of the human population is at risk of becoming infected with this virus. Despite this, there are no effective drugs to treat DENV infections. The present in silico study aimed at finding new inhibitors of the NS5 RNA-dependent RNA polymerase of the four serotypes of DENV. We used a chemical library comprising 372,792 nonnucleotide compounds (around 325,319 natural compounds) to perform molecular docking experiments against a binding site of the RNA template tunnel of the virus polymerase. Compounds with high negative free energy variation (ΔG <−10.5 kcal/mol) were selected as putative inhibitors. Additional filters for favorable druggability and good absorption, distribution, metabolism, excretion, and toxicity were applied. Finally, after the screening process was completed, we identified 39 compounds as lead DENV polymerase inhibitor candidates. Potentially, these compounds could act as efficient DENV polymerase inhibitors in vitro and in vivo.

  10. Cloning and identification of NS5ATP2 gene and its spliced variant transactivated by hepatitis C virus non-structural protein 5A

    Institute of Scientific and Technical Information of China (English)

    Qian Yang; Jun Cheng; Yan Liu; Yuan Hong; Jian-Jun Wang; Shu-Lin Zhang

    2004-01-01

    AIM: To clone, identify and study new NS5ATP2 gene and its spliced variant transactivated by hepatitis C virus nonstructural protein 5A.METHODS: On the basis of subtractive cDNA library of genes transactivated by NS5A protein of hepatitis C virus, the coding sequence of new gene and its spliced variant were obtained by bioinformatics method. Polymerase chain reaction (PCR)was conducted to amplify NS5ATP2 gene.RESUJLTS: The coding sequence of a new gene and its spliced variant were cloned and identified successfully.CONCLUSION: A new gene has been recognized as the new target transactivated by HCV NS5A protein. These results brought some new clues for studying the biological functions of new genes and pathogenesis of the viral proteins.

  11. Quasispecies evolution in NS5A region of hepatitis C virus genotype 1b during interferon or combined interferon-ribavirin therapy

    Institute of Scientific and Technical Information of China (English)

    Pascal Veillon; Christopher Payan; Hélène Le Guillou-Guillemette; Catherine Gaudy; Fran(c)oise Lunel

    2007-01-01

    AIM: To evaluate the implication of substitutions in the hepatitis C virus (HCV) non-structural 5A (NS5A) protein in the resistance of HCV during mono-interferon (IFN)or combined IFN-ribavirin (IFN-R) therapy. Although NS5A has been reported to interact with the HCV RNA-dependent RNA polymerase, NS5B, as well as with many cellular proteins, the function of NS5A in the life cycle of HCV remains unclear.METHODS: HCV quasispecies were studied by cloning and sequencing of sequential isolates from patients infected by HCV genotype 1b. Patients were treated by IFN-α2b for 3 mo followed by IFN-α2b alone or combined IFN-R therapy for 9 additional months. Patients were categorized intro two groups based on their response to the treatments: 7 with sustained virological response (SVR) (quasispecies = 150) and 3 non-responders (NR) to IFN-R (quasispecies = 106).RESULTS: Prior to treatment, SVR patients displayed a lower complexity of quasispecies than NR patients. Most patients had a decrease in the complexity of quasispecies during therapy. Analysis of amino acids substitutions showed that the degree of the complexity of the interferon sensitivity-determining region (ISDR) and the V3 domain of NS5A protein was able to discriminate the two groups of patients. Moreover, SVR patients displayed more variability in the NS5A region than NR patients.CONCLUSION: These results suggest that detailed molecular analysis of the NS5A region may be important for understanding its function in IFN response during HCV 1b infection.

  12. Resistance Analyses of HCV NS3/4A Protease and NS5B Polymerase from Clinical Studies of Deleobuvir and Faldaprevir

    Science.gov (United States)

    Berger, Kristi L.; Sarrazin, Christoph; Nelson, David R.; Scherer, Joseph; Sha, Nanshi; Marquis, Martin; Côté-Martin, Alexandra; Vinisko, Richard; Stern, Jerry O.; Mensa, Federico J.; Kukolj, George

    2016-01-01

    Background & Aim The resistance profile of anti-hepatitis C virus (HCV) agents used in combination is important to guide optimal treatment regimens. We evaluated baseline and treatment-emergent NS3/4A and NS5B amino-acid variants among HCV genotype (GT)-1a and -1b-infected patients treated with faldaprevir (HCV protease inhibitor), deleobuvir (HCV polymerase non-nucleoside inhibitor), and ribavirin in multiple clinical studies. Methods HCV NS3/4A and NS5B population sequencing (Sanger method) was performed on all baseline plasma samples (n = 1425 NS3; n = 1556 NS5B) and on post-baseline plasma samples from patients with virologic failure (n = 113 GT-1a; n = 221 GT-1b). Persistence and time to loss of resistance-associated variants (RAVs) was estimated using Kaplan–Meier analysis. Results Faldaprevir RAVs (NS3 R155 and D168) and deleobuvir RAVs (NS5B 495 and 496) were rare (90%). Virologic relapse was associated with RAVs in both NS3 and NS5B (53% GT-1b; 52% GT-1b); some virologic relapses had NS3 RAVs only (47% GT-1a; 17% GT-1b). Median time to loss of GT-1b NS5B P495 RAVs post-treatment (5 months) was less than that of GT-1b NS3 D168 (8.5 months) and GT-1a R155 RAVs (11.5 months). Conclusion Faldaprevir and deleobuvir RAVs are more prevalent among virologic failures than at baseline. Treatment response was not compromised by common NS3 polymorphisms; however, alanine at NS5B amino acid 499 at baseline (wild-type in GT-1a, polymorphism in GT-1b) may reduce response to this deleobuvir-based regimen. PMID:27494410

  13. Murine Efficacy and Pharmacokinetic Evaluation of the Flaviviral NS5 Capping Enzyme 2-Thioxothiazolidin-4-One Inhibitor BG-323.

    Directory of Open Access Journals (Sweden)

    Kristen M Bullard

    Full Text Available Arthropod-borne flavivirus infection continues to cause significant morbidity and mortality worldwide. Identification of drug targets and novel antiflaviviral compounds to treat these diseases has become a global health imperative. A previous screen of 235,456 commercially available small molecules identified the 2-thioxothiazolidin-4-one family of compounds as inhibitors of the flaviviral NS5 capping enzyme, a promising target for antiviral drug development. Rational drug design methodologies enabled identification of lead compound BG-323 from this series. We have shown previously that BG-323 potently inhibits NS5 capping enzyme activity, displays antiviral effects in dengue virus replicon assays and inhibits growth of West Nile and yellow fever viruses with low cytotoxicity in vitro. In this study we further characterized BG-323's antiviral activity in vitro and in vivo. We found that BG-323 was able to reduce replication of WNV (NY99 and Powassan viruses in culture, and we were unable to force resistance into WNV (Kunjin in long-term culture experiments. We then evaluated the antiviral activity of BG-323 in a murine model. Mice were challenged with WNV NY99 and administered BG-323 or mock by IP inoculation immediately post challenge and twice daily thereafter. Mice were bled and viremia was quantified on day three. No significant differences in viremia were observed between BG-323-treated and control groups and clinical scores indicated both BG-323-treated and control mice developed signs of illness on approximately the same day post challenge. To determine whether differences in in vitro and in vivo efficacy were due to unfavorable pharmacokinetic properties of BG-323, we conducted a pharmacokinetic evaluation of this small molecule. Insights from pharmacokinetic studies indicate that BG-323 is cell permeable, has a low efflux ratio and does not significantly inhibit two common cytochrome P450 (CYP P450 isoforms thus suggesting this molecule

  14. Label Free Inhibitor Screening of Hepatitis C Virus (HCV) NS5B Viral Protein Using RNA Oligonucleotide

    Science.gov (United States)

    Roh, Changhyun; Kim, Sang Eun; Jo, Sung-Kee

    2011-01-01

    Globally, over 170 million people (ca. 3% of the World’s population) are infected with the hepatitis C virus (HCV), which can cause serious liver diseases such as chronic hepatitis, evolving into subsequent health problems. Driven by the need to detect the presence of HCV, as an essential factor in diagnostic medicine, the monitoring of viral protein has been of great interest in developing simple and reliable HCV detection methods. Despite considerable advances in viral protein detection as an HCV disease marker, the current enzyme linked immunosorbent assay (ELISA) based detection methods using antibody treatment have several drawbacks. To overcome this bottleneck, an RNA aptamer become to be emerged as an antibody substitute in the application of biosensor for detection of viral protein. In this study, we demonstrated a streptavidin-biotin conjugation method, namely, the RNA aptamer sensor system that can quantify viral protein with detection level of 700 pg mL−1 using a biotinylated RNA oligonucleotide on an Octet optical biosensor. Also, we showed this method can be used to screen inhibitors of viral protein rapidly and simply on a biotinylated RNA oligonucleotide biosensor. Among the inhibitors screened, (−)-Epigallocatechin gallate showed high binding inhibition effect on HCV NS5B viral protein. The proposed method can be considered a real-time monitoring method for inhibitor screening of HCV viral protein and is expected to be applicable to other types of diseases. PMID:22163979

  15. How hepatitis C virus counteracts the interferon response: the jury is still out on NS5A.

    Science.gov (United States)

    Tan, S L; Katze, M G

    2001-05-25

    Interferons (IFNs) induce an antiviral state in the cell through complex and indirect mechanisms, which culminate in a direct inhibition of viral replication and stimulation of the host adaptive responses. Viruses often counteract with elaborate strategies to interfere with the induction as well as action of IFN effector molecules. This evolutionary battle between viruses and IFN components is a subject of intense research aimed at understanding the immunopathogenesis of viruses and the molecular basis of IFN signaling and action. In the case with hepatitis C virus (HCV), this may have profound implications for the therapeutic use of recombinant IFN in treating chronic hepatitis C. Depending on the subtype of HCV, current IFN-based treatment regimens are effective for only a small subset of chronic hepatitis C patients. Thus, one of the Holy Grails in HCV research is to understand the mechanisms by which the virus may evade IFN antiviral surveillance and establish persistent infection, which may eventually provide insights into new avenues for better antiviral therapy. Despite the lack of an efficient tissue culture system and an appropriate animal model for HCV infection, several mechanisms have been proposed based on clinical studies and in vitro experiments. This minireview focuses on the HCV NS5A nonstructural protein, which is implicated in playing a role in HCV tolerance to IFN treatment, possibly in part through its ability to inhibit the cellular IFN-induced PKR protein kinase.

  16. Microwave assisted synthesis of some novel Flurbiprofen hydrazide- hydrazones as anti-HCV NS5B and anticancer agents

    Directory of Open Access Journals (Sweden)

    Sevil Aydın

    2013-01-01

    Full Text Available The synthesis of a new series of flurbiprofen hydrazide-hydrazones using microwave assisted reactions is described. Substituted aldehydes were condensed with flurbiprofen hydrazide by microwave irradiation to corresponding hydrazones. Synthesis of N’-[(4-bromothiophen-2-ylmethylidene]-2-(2-fluorobiphenyl-4-yl propanehydrazide (3o employing microwave assisted process resulted in higher yields, in faster time and with less chemical waste compared to traditional techniques. (2-fluorobiphenyl-4-yl-N’-(phenylmethylidenepropanehydrazide (3p andN’-[(2-chloro-6-fluorophenyl methylidene]-2-(2-fluorobiphenyl-4-ylpropanehydrazide (3s inhibited the growth of a leukemia cancercell line HL-60 (TB by 66.37% and an ovarian cancer cell line OVCAR-4 by 77.34% (singledose, 10μM, respectively at the National Cancer Institute (NCI, but had no significant ef-fect on a panel of sixty human tumor cell lines. Flurbiprofen hydrazide-hydrazones were weak inhibitors of hepatitis C virus NS5B polymerase activity with N’-[(5-ethylfuran-2-ylmethylidene]-2-(2-fluorobiphenyl-4-ylpropanehydrazide (3m being the most active of this series. Binding mode investigations of compound 3m suggested that allosteric pocket (AP-B may be the potential binding site for flurbiprofen hydrazones and these results will alsoassist in further derivatization of 3m using the green chemistry approach and improve the potency of S-flurbiprofen hydrazide hydrazones

  17. Label Free Inhibitor Screening of Hepatitis C Virus (HCV NS5B Viral Protein Using RNA Oligonucleotide

    Directory of Open Access Journals (Sweden)

    Sang Eun Kim

    2011-06-01

    Full Text Available Globally, over 170 million people (ca. 3% of the World’s population are infected with the hepatitis C virus (HCV, which can cause serious liver diseases such as chronic hepatitis, evolving into subsequent health problems. Driven by the need to detect the presence of HCV, as an essential factor in diagnostic medicine, the monitoring of viral protein has been of great interest in developing simple and reliable HCV detection methods. Despite considerable advances in viral protein detection as an HCV disease marker, the current enzyme linked immunosorbent assay (ELISA based detection methods using antibody treatment have several drawbacks. To overcome this bottleneck, an RNA aptamer become to be emerged as an antibody substitute in the application of biosensor for detection of viral protein. In this study, we demonstrated a streptavidin-biotin conjugation method, namely, the RNA aptamer sensor system that can quantify viral protein with detection level of 700 pg mL−1 using a biotinylated RNA oligonucleotide on an Octet optical biosensor. Also, we showed this method can be used to screen inhibitors of viral protein rapidly and simply on a biotinylated RNA oligonucleotide biosensor. Among the inhibitors screened, (−-Epigallocatechin gallate showed high binding inhibition effect on HCV NS5B viral protein. The proposed method can be considered a real-time monitoring method for inhibitor screening of HCV viral protein and is expected to be applicable to other types of diseases.

  18. In vitro and in vivo antiviral activity and resistance profile of ombitasvir, an inhibitor of hepatitis C virus NS5A.

    Science.gov (United States)

    Krishnan, Preethi; Beyer, Jill; Mistry, Neeta; Koev, Gennadiy; Reisch, Thomas; DeGoey, David; Kati, Warren; Campbell, Andrew; Williams, Laura; Xie, Wangang; Setze, Carolyn; Molla, Akhteruzzaman; Collins, Christine; Pilot-Matias, Tami

    2015-02-01

    Ombitasvir (ABT-267) is a hepatitis C virus (HCV) NS5A inhibitor with picomolar potency, pan-genotypic activity, and 50% effective concentrations (EC50s) of 0.82 to 19.3 pM against HCV genotypes 1 to 5 and 366 pM against genotype 6a. Ombitasvir retained these levels of potency against a panel of 69 genotype 1 to 6 chimeric replicons containing the NS5A gene derived from HCV-infected patients, despite the existence of natural sequence diversity within NS5A. In vitro resistance selection identified variants that conferred resistance to ombitasvir in the HCV NS5A gene at amino acid positions 28, 30, 31, 58, and 93 in genotypes 1 to 6. Ombitasvir was evaluated in vivo in a 3-day monotherapy study in 12 HCV genotype 1-infected patients at 5, 25, 50, or 200 mg dosed once daily. All patients in the study were HCV genotype 1a infected and were without preexisting resistant variants at baseline as determined by clonal sequencing. Decreases in HCV RNA up to 3.1 log10 IU/ml were observed. Resistance-associated variants at position 28, 30, or 93 in NS5A were detected in patient samples 48 hours after the first dose. Clonal sequencing analysis indicated that wild-type virus was largely suppressed by ombitasvir during 3-day monotherapy, and at doses higher than 5 mg, resistant variant M28V was also suppressed. Ombitasvir was well tolerated at all doses, and there were no serious or severe adverse events. These data support clinical development of ombitasvir in combination with inhibitors targeting HCV NS3/4A protease (ABT-450 with ritonavir) and HCV NS5B polymerase (ABT-333, dasabuvir) for the treatment of chronic HCV genotype 1 infection. (Study M12-116 is registered at ClinicalTrials.gov under registration no. NCT01181427.). PMID:25451055

  19. Screening for proteins interacting with NS5 0f Japanese encephalitis virus by yeast two-hybrid technique%酵母双杂交技术筛选与乙型脑炎病毒NS5相互作用的蛋白

    Institute of Scientific and Technical Information of China (English)

    周希珍; 赵慧; 李晓峰; 邓永强; 秦成峰; 秦鄂德; 高岚

    2011-01-01

    Objective To screen possible human proteins that interact with the non-structural protein 5 (NS5) of Japanese encephalitis virus (JEV) by yeast two-hybrid system. Methods The bait plasmid pSos-NS5 carrying JEV NS5 gene was first constructed and transformed to veast cells, and then validated by the self-activation and toxicity assay. Then, a human umbilical vein endothelial cells cDNA library was used for screening with the bait plasmid pSos-NS5, and positive clones were selected based on nutritional requirements (Leucine and Uracil) and temperature change, and verified by one to one back-hybridization. Finally, the plasmids from the positive clones were sequenced and analyzed by Blast with sequences from GenBank. Results The bait plasmid pSos-NS5 was successfully constructed and confirmed to be no self-activation actiity and toxicity to the host veast cells. Three positive clones (10, 11, and 4'6) were then selected from the human umbilical vein endothelial cells cDNA library with the bait plasmid pSos-NS5. Then, the plasmid from clone 4'6 was sequenced and BLAST analysis within GenBank showed that the sequences were highly homologous to the TC21 gene. Finally, these data indicated TC21 protein might be the putative candidate protein that interacted with the NS5 protein of JEV. Conclusion A candidate host protein has been identified by the veast two-hybrid system, which will be helpful for understanding the biological function of NS5 of JEV,and further research should be warranted in the future.%目的 应用酵母双杂交技术筛选与乙型脑炎病毒NS5蛋白相互作用的宿主蛋白.方法 构建表达乙型脑炎病毒NS5蛋白的诱饵质粒pSos-NS5,经自激活和毒性实验后对人脐静脉内皮细胞cDNA文库进行筛选,挑取37℃条件下在缺失亮氨酸和尿嘧啶培养基上生长的克隆,利用一对一酵母回复性杂交实验进行验证,然后测定阳性克隆插入片段序列,通过Blast分析确定可能与NS5

  20. Resistance-Associated NS5A Variants of Hepatitis C Virus Are Susceptible to Interferon-Based Therapy.

    Directory of Open Access Journals (Sweden)

    Jun Itakura

    Full Text Available The presence of resistance-associated variants (RAVs of hepatitis C virus (HCV attenuates the efficacy of direct acting antivirals (DAAs. The objective of this study was to characterize the susceptibility of RAVs to interferon-based therapy.Direct and deep sequencing were performed to detect Y93H RAV in the NS5A region. Twenty nine genotype 1b patients with detectable RAV at baseline were treated by a combination of simeprevir, pegylated interferon and ribavirin. The longitudinal changes in the proportion of Y93H RAV during therapy and at breakthrough or relapse were determined.By direct sequencing, Y93H RAV became undetectable or decreased in proportion at an early time point during therapy (within 7 days in 57% of patients with both the Y93H variant and wild type virus at baseline when HCV RNA was still detectable. By deep sequencing, the proportion of Y93H RAV against Y93 wild type was 52.7% (5.8%- 97.4% at baseline which significantly decreased to 29.7% (0.16%- 98.3% within 7 days of initiation of treatment (p = 0.023. The proportion of Y93H RAV was reduced in 21 of 29 cases (72.4% and a marked reduction of more than 10% was observed in 14 cases (48.7%. HCV RNA reduction was significantly greater for Y93H RAV (-3.65±1.3 logIU/mL/day than the Y93 wild type (-3.35±1.0 logIU/mL/day (p<0.001.Y93H RAV is more susceptible to interferon-based therapy than the Y93 wild type.

  1. Metabolism and Disposition of Pan-Genotypic Inhibitor of Hepatitis C Virus NS5A Ombitasvir in Humans.

    Science.gov (United States)

    Shen, Jianwei; Serby, Michael; Surber, Bruce; Lee, Anthony J; Ma, Junli; Badri, Prajakta; Menon, Rajeev; Kavetskaia, Olga; de Morais, Sonia M; Sydor, Jens; Fischer, Volker

    2016-08-01

    Ombitasvir (also known as ABT-267) is a potent inhibitor of hepatitis C virus (HCV) nonstructural protein 5A (NS5A), which has been developed in combination with paritaprevir/ritonavir and dasabuvir in a three direct-acting antiviral oral regimens for the treatment of patients infected with HCV genotype 1. This article describes the mass balance, metabolism, and disposition of ombitasvir in humans without coadministration of paritaprevir/ritonavir and dasabuvir. Following the administration of a single 25-mg oral dose of [(14)C]ombitasvir to four healthy male volunteers, the mean total percentage of the administered radioactive dose recovered was 92.1% over the 192-hour sample collection in the study. The recovery from the individual subjects ranged from 91.4 to 93.1%. Ombitasvir and corresponding metabolites were primarily eliminated in feces (90.2% of dose), mainly as unchanged parent drug (87.8% of dose), but minimally through renal excretion (1.9% of dose). Biotransformation of ombitasvir in human involves enzymatic amide hydrolysis to form M23 (dianiline), which is further metabolized through cytochrome P450-mediated oxidative metabolism (primarily by CYP2C8) at the tert-butyl group to generate oxidative and/or C-desmethyl metabolites. [(14)C]Ombitasvir, M23, M29, M36, and M37 are the main components in plasma, representing about 93% of total plasma radioactivity. The steady-state concentration measurement of ombitasvir metabolites by liquid chromatography-mass spectrometry analysis in human plasma following multiple doses of ombitasvir, in combination with paritaprevir/ritonavir and dasabuvir, confirmed that ombitasvir is the main component (51.9% of all measured drug-related components), whereas M29 (19.9%) and M36 (13.1%) are the major circulating metabolites. In summary, the study characterized ombitasvir metabolites in circulation, the metabolic pathways, and the elimination routes of the drug. PMID:27179128

  2. Pharmacokinetic, Pharmacodynamic, and Drug-Interaction Profile of the Hepatitis C Virus NS5B Polymerase Inhibitor Sofosbuvir.

    Science.gov (United States)

    Kirby, Brian J; Symonds, William T; Kearney, Brian P; Mathias, Anita A

    2015-07-01

    Sofosbuvir (SOVALDI(®)), a potent, once-daily, orally administered nucleotide analog prodrug inhibitor of the hepatitis C virus (HCV) NS5B polymerase is approved in the USA, EU, Canada, and other regions for the treatment of HCV infection as a component of an antiviral treatment regimen. Sofosbuvir undergoes intracellular activation to form GS-461203 (active triphosphate, not detected in plasma), and ultimately the inactive, renally eliminated metabolite GS-331007. GS-331007 was identified as the primary analyte of interest for clinical pharmacology studies as it accounted for >90 % of systemic drug-related material exposure, and provided comparable exposure-response relationships for viral kinetics as observed for sofosbuvir. GS-331007 and sofosbuvir exhibit linear pharmacokinetics with minimal accumulation upon multiple dosing. Compared to healthy subjects, HCV-infected patients had modestly lower (39 %) GS-331007 area under the plasma concentration-time curve (AUC) and higher sofosbuvir AUC (60 %). Sofosbuvir can be administered without dose modification in HCV-infected patients with any degree of hepatic impairment or mild to moderate renal impairment. Sofosbuvir has a low propensity for clinically significant drug interactions with common concomitant medications used by HCV-infected patients. Clinically significant alterations in GS-331007 or sofosbuvir exposures are limited to potent inducers of intestinal P-glycoprotein that may lower exposure. In HCV-infected patients, demographic variables do not significantly influence GS-331007 and sofosbuvir exposures and no consistent exposure-response relationships were observed for efficacy or safety. This review focuses on the clinical pharmacokinetics, pharmacodynamics, and pharmacokinetic-pharmacodynamic relationships of sofosbuvir, and summarizes a number of drug interaction studies with important concomitant medications commonly used by HCV-infected patients.

  3. 应用表达谱芯片筛选HCV NS5B基因转染Hun 7.5细胞所致表达差异的糖、脂类代谢基因%Screening of genes differentially expressed in Hun 7.5 cells transfected with HCV NS5B gene

    Institute of Scientific and Technical Information of China (English)

    刘文祥; 汪涛; 侯鹏

    2013-01-01

    目的 构建HCV NS5B的真核表达载体pCDNA3.1(-)HCV NS5B,研究HCV NS5B在Hun 7.5细胞中表达导致的糖、脂类代谢相关基因的差异表达.方法 真核表达载体pCDNA3.1(-)HCV NS5B转染Hun 7.5细胞,培养48h后提取细胞蛋白进行Western blot检测;将pcDNA3.1(-)HCV NS5B和pcDNA3.1(-)载体分别转染Hun 7.5细胞后,提取mRNA并逆转录为cDNA,运用基因表达谱芯片技术分析糖、脂类代谢相关的差异表达基因.结果 成功构建了HCV NS5B的真核表达载体pCDNA3.1(-) HCV NS5B;转染Hun 7.5细胞后HCV NSSB在细胞内可以表达;基因表达谱芯片技术筛选,分别发现了其中5个显著上调和3个显著下调的糖、脂类代谢相关基因.结论 筛选HCVNS5B转染Hun 7.5细胞后的糖、脂类物质代谢相关的差异表达基因,从而为丙型肝炎病毒感染合并糖尿病、脂肪肝等代谢性疾病分子生物学机制的研究提供重要依据.%Objective To detect HCV NS5B expression and screen the differential expression gene in Hun 7.5 cell transfected with HCV NS5B using gene chip technology.Methods The expression vector of pcDNA3.1(-) HCV NS5B was transfected into Hun 7.5 cell line.The expression of HCV NS5B protein was detected by western-blotting method.The differential expression of genes in the Hun 7.5 transfected with pcDNA3.1 (-)HCV NS5B and pcDNA3.1 (-) was detected respectively using cDNA microarray technique.Results The expression vector has been confirmed by restriction enzyme digestion.The expression of HCV NS5B protein has been confirmed by western blotting.High quality mRNA and cDNA had been prepared and successful microarray screening had been conducted.The results showed that 5 genes were up-regulated and 3 genes were down-regulated in Hun 7.5 cell line transfected with HCV NS5B,which was associated with metabolism of glucose and lipid.Conclusions cDNA microarray technology was successfully used to screen the genes differentially expressed in Hun 7.5 cell line

  4. New Inhibitors of the DENV-NS5 RdRp from Carpolepis laurifolia as Potential Antiviral Drugs for Dengue Treatment

    Directory of Open Access Journals (Sweden)

    Paul Coulerie

    2014-05-01

    Full Text Available Since a few decades the dengue virus became a major public health concern and no treatment is available yet. In order to propose potential antidengue compounds for chemotherapy we focused on DENV RNA polymerase (DENV-NS5 RdRp which is specific and essential for the virus replication. Carpolepis laurifolia belongs to the Myrtaceae and is used as febrifuge in traditional kanak medicine. Leaf extract of this plant has been identified as a hit against the DENV-NS5 RdRp. Here we present a bioguided fractionation of the leaf extract of C. laurifolia which is also the first phytochemical evaluation of this plant. Five flavonoids, namely quercetin (1, 6-methyl-7-methoxyapigenin (2, avicularin (3, quercitrin (4 and hyperoside (5, together with betulinic acid (6, were isolated from the leaf extract of C. laurifolia. All isolated compounds were tested individually against the DENV-NS5 RdRp and compared with four other commercial flavonoids: isoquercitrin (7, spiraeoside (8, quercetin-3,4’-di-O-glucoside (9 and rutine (10. Compounds 3, 4, 6, 8 and 10 displayed IC 50 ranging from 1.7 to 2.1 µM, and were the most active against the DENV-NS5 RdRp.

  5. Hepatitis C Virus (HCV) NS5B Nonnucleoside Inhibitors Specifically Block Single-Stranded Viral RNA Synthesis Catalyzed by HCV Replication Complexes In Vitro▿

    OpenAIRE

    Yang, Wengang; Sun, Yongnian; Phadke, Avinash; Deshpande, Milind; Huang, Mingjun

    2006-01-01

    Replication complexes of hepatitis C virus synthesized two major species of viral RNA in vitro, double stranded and single stranded. NS5B nonnucleoside inhibitors inhibited dose dependently the synthesis of single-stranded RNA but not double-stranded RNA. Moreover, replication complexes carrying a mutation resistant to a nonnucleoside inhibitor lost their susceptibilities to the inhibitor.

  6. Effects of Resistance-Associated NS5A Mutations in Hepatitis C Virus on Viral Production and Susceptibility to Antiviral Reagents

    Science.gov (United States)

    Nitta, Sayuri; Asahina, Yasuhiro; Matsuda, Mami; Yamada, Norie; Sugiyama, Ryuichi; Masaki, Takahiro; Suzuki, Ryosuke; Kato, Nobuyuki; Watanabe, Mamoru; Wakita, Takaji; Kato, Takanobu

    2016-01-01

    Direct-acting antivirals (DAAs) for hepatitis C virus (HCV) have potent anti-HCV effects but may provoke resistance-associated variants (RAVs). In this study, we assessed the characteristics of these RAVs and explored efficacious anti-HCV reagents using recombinant HCV with NS5A from a genotype 1b strain. We replaced the NS5A of JFH1 with that of Con1 (JFH1/5ACon1) and introduced known NS5A inhibitor resistance mutations (L31M, L31V, L31I and Y93H) individually or in combination. Susceptibilities against anti-HCV reagents were also investigated. RAVs with Y93H exhibited high extracellular core antigen levels and infectivity titers. Variants with any single mutation showed mild to moderate resistance against NS5A inhibitors, whereas variants with double mutations at both L31 and Y93 showed severe resistance. The variants with mutations exhibited similar levels of susceptibility to interferon (IFN)-α, IFN-λ1, IFN-λ3 and Ribavirin. Variants with the Y93H mutation were more sensitive to protease inhibitors compared with JFH1/5ACon1. In conclusion, the in vitro analysis indicated that the Y93H mutation enhanced infectious virus production, suggesting advantages in the propagation of RAVs with this mutation. However, these RAVs were susceptible to protease inhibitors. Thus, a therapeutic regimen that includes these reagents is a promising means to eradicate these RAVs. PMID:27703205

  7. Accounting for target flexibility and water molecules by docking to ensembles of target structures: the HCV NS5B palm site I inhibitors case study.

    Science.gov (United States)

    Barreca, Maria Letizia; Iraci, Nunzio; Manfroni, Giuseppe; Gaetani, Rosy; Guercini, Chiara; Sabatini, Stefano; Tabarrini, Oriana; Cecchetti, Violetta

    2014-02-24

    The introduction of new anti-HCV drugs in therapy is an imperative need and is necessary with a view to develop an interferon-free therapy. Thus, the discovery and development of novel small molecule inhibitors of the viral NS5B polymerase represent an exciting area of research for many pharmaceutical companies and academic groups. This study represents a contribution to this field and relies on the identification of the best NS5B model(s) to be used in structure-based computational approaches aimed at identifying novel non-nucleoside inhibitors of one of the protein allosteric sites, namely, palm site I. First, the NS5B inhibitors at palm site I were classified as water-mediated or nonwater-mediated ligands depending on their ability to interact with or displace a specific water molecule. Then, we took advantage of the available X-ray structures of the NS5B/ligand complexes to build different models of protein/water combinations, which were used to investigate the influence on docking studies of solvent sites as well as of the influence of the protein conformations. As the overall trend, we observed improved performance in the docking results of the water-mediated inhibitors by inclusion of explicit water molecules, with an opposite behavior generally happening for the nonwater-mediated inhibitors. The best performing target structures for the two ligand sets were then used for virtual screening simulations of a library containing the known NS5B inhibitors along with related decoys to assess the best performing targets ensembles on the basis of their ability to discriminate active and inactive compounds as well as to generate the correct binding modes. The parallel use of different protein structures/water sets outperformed the use of a single target structure, with the two-protein 3H98/2W-2FVC/7W and 3HKY/NoW-3SKE/NoW models resulting in the best performing ensembles for water-mediated inhibitors and nonwater-mediated inhibitors, respectively. The information

  8. TRIM14 inhibits hepatitis C virus infection by SPRY domain-dependent targeted degradation of the viral NS5A protein

    Science.gov (United States)

    Wang, Shanshan; Chen, Yongzhi; Li, Chunfeng; Wu, Yaoxing; Guo, Lei; Peng, Changwei; Huang, Yueping; Cheng, Genhong; Qin, F. Xiao-Feng

    2016-01-01

    Tripartite motif 14 (TRIM14) was reported to function as a mitochondrial signaling adaptor in mediating innate immune responses. However, the involvement of TRIM14 in host defense against viral infection and molecular mechanisms remain unclear. Here, we demonstrated that enforced expression of TRIM14 could potently inhibit the infection and replication of HCV in hepatocytes, whereas TRIM14 knockout cells became more susceptible to HCV infection. Interestingly, further experiments revealed that such anti-HCV activity was independent of activating the NF-κB or interferon pathways but required the C-terminal SPRY domain of no signaling capacity. In searching for mechanisms how TRIM14 exerts its antiviral function we found that TRIM14 interacted with HCV encoded non-structural protein NS5A and could strongly induce its degradation dependent on the NS5A1 subdomain. Interestingly extensive domain mapping analyses revealed that NS5A degradation was mediated by the highly conserved SPRY domain of TRIM14, which might involve the K48 ubiquitination pathway. Collectively, our work uncovered a new mechanism responsible for host defense against HCV infection, and could potentially aid the development of novel anti-HCV therapeutics. PMID:27578425

  9. Structure-based optimization and derivatization of 2-substituted quinolone-based non-nucleoside HCV NS5B inhibitors with submicromolar cellular replicon potency.

    Science.gov (United States)

    Cheng, Yu; Shen, Jian; Peng, Run-Ze; Wang, Gui-Feng; Zuo, Jian-Ping; Long, Ya-Qiu

    2016-06-15

    HCV NS5B polymerase is an attractive and validated target for anti-HCV therapy. Starting from our previously identified 2-aryl quinolones as novel non-nucleoside NS5B polymerase inhibitors, structure-based optimization furnished 2-alkyl-N-benzyl quinolones with improved antiviral potency by employing privileged fragment hybridization strategy. The N-(4-chlorobenzyl)-2-(methoxymethyl)quinolone derivative 5f proved to be the best compound of this series, exhibiting a selective sub-micromolar antiviral effect (EC50=0.4μM, SI=10.8) in Huh7.5.1 cells carrying a HCV genotype 2a. Considering the undesirable pharmacokinetic property of the highly substituted quinolones, a novel chemotype of 1,6-naphthyridine-4,5-diones were evolved via scaffold hopping, affording brand new structure HCV inhibitors with compound 6h (EC50 (gt2a)=2.5μM, SI=7.2) as a promising hit. Molecular modeling studies suggest that both of 2-alkyl quinolones and 1,6-naphthyridine-4,5-diones function as HCV NS5B thumb pocket II inhibitors. PMID:27133482

  10. Inhibition on IFN-βExpression by hCV ns3 and ns5A in HepG2 Cells

    Institute of Scientific and Technical Information of China (English)

    2013-01-01

    Objective To observe the effects of HCV protein, NS3 and NS5A on IFN-βin HepG2 cells and its regulation mechanism. Methods Human liver hepatocellular carcinoma cells HepG2 were transfected with recombinant eukaryotic plasmid pcDNA3.1/myc-His-core, NS3 or NS5A to overexpress these proteins, and the expression of IFN-βwere detected by qRT-PCR, Western blotting and ELISA. Luc2P reporter plasmids pGL4.10-IFNβ-P were constructed and transfected into HepG2 cells, and the activity of IFN-βpromoter were determined through luciferase assay for regulation mechanism study. Results Both mRNA level and protein expression of IFN-β were significantly decreased (P Conclusions HCV protein NS3 and NS5A could inhibit innate IFN-β expression and thus escape immune selection and hinder the host immune responses.

  11. Combinations of siRNAs against La Autoantigen with NS5B or hVAP-A Have Additive Effect on Inhibition of HCV Replication

    Science.gov (United States)

    Mandal, Anirban; Ganta, Krishna Kumar

    2016-01-01

    Hepatitis C virus is major cause of chronic liver diseases such as chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. Presently available direct-acting antiviral drugs have improved success rate; however, high cost limits their utilization, especially in developing countries like India. In the present study, we evaluated anti-HCV potential of several siRNAs targeted against the HCV RNA-dependent RNA polymerase NS5B and cellular factors, La autoantigen, PSMA7, and human VAMP-associated protein to intercept different steps of viral life cycle. The target genes were downregulated individually as well as in combinations and their impact on viral replication was evaluated. Individual downregulation of La autoantigen, PSMA7, hVAP-A, and NS5B resulted in inhibition of HCV replication by about 67.2%, 50.7%, 39%, and 52%, respectively. However, antiviral effect was more pronounced when multiple genes were downregulated simultaneously. Combinations of siRNAs against La autoantigen with NS5B or hVAP-A resulted in greater inhibition in HCV replication. Our findings indicate that siRNA is a potential therapeutic tool for inhibiting HCV replication and simultaneously targeting multiple viral steps with the combination of siRNAs is more effective than silencing a single target. PMID:27446609

  12. A novel immuno-competitive capture mass spectrometry strategy for protein-protein interaction profiling reveals that LATS kinases regulate HCV replication through NS5A phosphorylation.

    Science.gov (United States)

    Meistermann, Hélène; Gao, Junjun; Golling, Sabrina; Lamerz, Jens; Le Pogam, Sophie; Tzouros, Manuel; Sankabathula, Sailaja; Gruenbaum, Lore; Nájera, Isabel; Langen, Hanno; Klumpp, Klaus; Augustin, Angélique

    2014-11-01

    Mapping protein-protein interactions is essential to fully characterize the biological function of a protein and improve our understanding of diseases. Affinity purification coupled to mass spectrometry (AP-MS) using selective antibodies against a target protein has been commonly applied to study protein complexes. However, one major limitation is a lack of specificity as a substantial part of the proposed binders is due to nonspecific interactions. Here, we describe an innovative immuno-competitive capture mass spectrometry (ICC-MS) method to allow systematic investigation of protein-protein interactions. ICC-MS markedly increases the specificity of classical immunoprecipitation (IP) by introducing a competition step between free and capturing antibody prior to IP. Instead of comparing only one experimental sample with a control, the methodology generates a 12-concentration antibody competition profile. Label-free quantitation followed by a robust statistical analysis of the data is then used to extract the cellular interactome of a protein of interest and to filter out background proteins. We applied this new approach to specifically map the interactome of hepatitis C virus (HCV) nonstructural protein 5A (NS5A) in a cellular HCV replication system and uncovered eight new NS5A-interacting protein candidates along with two previously validated binding partners. Follow-up biological validation experiments revealed that large tumor suppressor homolog 1 and 2 (LATS1 and LATS2, respectively), two closely related human protein kinases, are novel host kinases responsible for NS5A phosphorylation at a highly conserved position required for optimal HCV genome replication. These results are the first illustration of the value of ICC-MS for the analysis of endogenous protein complexes to identify biologically relevant protein-protein interactions with high specificity.

  13. Phylogenetic analysis of NS5B gene of classical swine fever virus isolates indicates plausible Chinese origin of Indian subgroup 2.2 viruses.

    Science.gov (United States)

    Patil, S S; Hemadri, D; Veeresh, H; Sreekala, K; Gajendragad, M R; Prabhudas, K

    2012-02-01

    Twenty-three CSFV isolates recovered from field outbreaks in various parts of India during 2006-2009 were used for genetic analysis in the NS5B region (409 nts). Seventeen of these were studied earlier [16] in the 5'UTR region. Phylogenetic analysis indicated the continued dominance of subgroup 1.1 strains in the country. Detailed analysis of a subgroup 2.2 virus indicated the plausible Chinese origin of this subgroup in India and provided indirect evidence of routes of CSFV movement within South East Asia region.

  14. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH interaction with 3' ends of Japanese encephalitis virus RNA and colocalization with the viral NS5 protein

    Directory of Open Access Journals (Sweden)

    Chou Shih-Jie

    2009-04-01

    Full Text Available Abstract Replication of the Japanese encephalitis virus (JEV genome depends on host factors for successfully completing their life cycles; to do this, host factors have been recruited and/or relocated to the site of viral replication. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH, a cellular metabolic protein, was found to colocalize with viral RNA-dependent RNA polymerase (NS5 in JEV-infected cells. Subcellular fractionation further indicated that GAPDH remained relatively constant in the cytosol, while increasing at 12 to 24 hours postinfection (hpi and decreasing at 36 hpi in the nuclear fraction of infected cells. In contrast, the redistribution patterns of GAPDH were not observed in the uninfected cells. Co-immunoprecipitation of GAPDH and JEV NS5 protein revealed no direct protein-protein interaction; instead, GAPDH binds to the 3' termini of plus- and minus-strand RNAs of JEV by electrophoretic mobility shift assays. Accordingly, GAPDH binds to the minus strand more efficiently than to the plus strand of JEV RNAs. This study highlights the findings that infection of JEV changes subcellular localization of GAPDH suggesting that this metabolic enzyme may play a role in JEV replication.

  15. An updated evolutionary study of Flaviviridae NS3 helicase and NS5 RNA-dependent RNA polymerase reveals novel invariable motifs as potential pharmacological targets.

    Science.gov (United States)

    Papageorgiou, Louis; Loukatou, Styliani; Sofia, Kossida; Maroulis, Dimitrios; Vlachakis, Dimitrios

    2016-06-21

    The rate of Flaviviridae family virus infections worldwide has increased dramatically in the last few years. In addition, infections caused by arthropod vector viruses including Hepatitis C, West Nile, Dengue fever, Yellow fever and Japanese encephalitis are emerging throughout the world. Based on a recent taxon update, the Flaviviridae family comprises four main genera; Flavivirus, Hepacivirus, Pestivirus and a recent genus Pegivirus. Although the new scientific classification plays a key role in providing useful information about the relationships between viruses, many new documented viruses remain unclassified. Furthermore, based on the different results of several studies the classification is unclear. In an effort to provide more insights into the classification of viruses, a holistic evolutionary study of the two viral enzymes NS3 helicase and NS5 RNA-dependent RNA polymerase (RdRp) has been conducted in this study. These two viral enzymes are very crucial for the inhibition of viruses due to the fact that they are involved in the survival, proliferation and transmission of viruses. The main goal of this study is the presentation of two novel updated phylogenetic trees of the enzymes NS3 helicase and NS5 RdRp as a reliable phylogeny "map" to correlate the information of the closely related viruses and identify new possible targets for the Flaviviridae family virus inhibition. Despite the earliest trials for drugs against Flaviviridae related viruses, no antiviral drug vaccine has been available to date. Therefore there is an urgent need for research towards the development of efficient antiviral agents. PMID:26864387

  16. Cell-death-inducing DFFA-like Effector B Contributes to the Assembly of Hepatitis C Virus (HCV) Particles and Interacts with HCV NS5A

    Science.gov (United States)

    Cai, Hua; Yao, Wenxia; Li, Leike; Li, Xinlei; Hu, Longbo; Mai, Runming; Peng, Tao

    2016-01-01

    Hepatitis C virus (HCV) uses components of the very-low-density lipoprotein (VLDL) pathway for assembly/release. We previously reported that hepatocyte nuclear factor 4α (HNF4α) participates in HCV assembly/release through downstream factors those participate in VLDL assembly/secretion. Cell-death-inducing DFFA-like effector B (CIDEB) is an important regulator of the VLDL pathway. CIDEB is required for entry of HCV particles from cell culture (HCVcc), but the effects of CIDEB on the post-entry steps of the HCV lifecycle are unclear. In the present study, we determined that CIDEB is required for HCV assembly in addition to HCVcc entry. Furthermore, CIDEB interacts with the HCV NS5A protein, and the N terminus of CIDEB and the domain I of NS5A are involved in this interaction. Moreover, CIDEB silencing impairs the association of apolipoprotein E (ApoE) with HCV particles. Interestingly, CIDEB is also required for the post-entry stages of the dengue virus (DENV) life cycle. Collectively, these results indicate that CIDEB is a new host factor that is involved in HCV assembly, presumably by interacting with viral protein, providing new insight into the exploitation of the VLDL regulator CIDEB by HCV. PMID:27282740

  17. 酵母双杂合系统在丙型肝炎病毒NS5A研究中的应用%IDENTIFICATION OF THE NOVEL HEPATITIS C VIRUS NS5A-INTERACTING PROTEINS IN YEAST TWO-HYBRID SYSTEM

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    酵母双杂合系统是在酵母细胞中研究蛋白-蛋白相互作用的新技术.应用该技术,以丙型肝炎病毒(HCV)非结构蛋白5A(NS5A)为"诱饵",筛检了人肝癌细胞HepG2来源的cDNA文库,获得了7个NS5A结合蛋白的基因克隆.报道了其中两个粜钥寺?#2、#16)的结果,并对"人核小体组装蛋白相关蛋白"(Human nucleosome assembly protein-related protein,hNRP)和"载脂蛋白A-I"(Apolipoprotein A-I)与NS5A结合的生物学意义进行了讨论.

  18. A cooperative interaction between nontranslated RNA sequences and NS5A protein promotes in vivo fitness of a chimeric hepatitis C/GB virus B.

    Directory of Open Access Journals (Sweden)

    Lucile Warter

    Full Text Available GB virus B (GBV-B is closely related to hepatitis C virus (HCV, infects small non-human primates, and is thus a valuable surrogate for studying HCV. Despite significant differences, the 5' nontranslated RNAs (NTRs of these viruses fold into four similar structured domains (I-IV, with domains II-III-IV comprising the viral internal ribosomal entry site (IRES. We previously reported the in vivo rescue of a chimeric GBV-B (vGB/III(HC containing HCV sequence in domain III, an essential segment of the IRES. We show here that three mutations identified within the vGB/III(HC genome (within the 3'NTR, upstream of the poly(U tract, and NS5A coding sequence are necessary and sufficient for production of this chimeric virus following intrahepatic inoculation of synthetic RNA in tamarins, and thus apparently compensate for the presence of HCV sequence in domain III. To assess the mechanism(s underlying these compensatory mutations, and to determine whether 5'NTR subdomains participating in genome replication do so in a virus-specific fashion, we constructed and evaluated a series of chimeric subgenomic GBV-B replicons in which various 5'NTR subdomains were substituted with their HCV homologs. Domains I and II of the GBV-B 5'NTR could not be replaced with HCV sequence, indicating that they contain essential, virus-specific RNA replication elements. In contrast, domain III could be swapped with minimal loss of genome replication capacity in cell culture. The 3'NTR and NS5A mutations required for rescue of the related chimeric virus in vivo had no effect on replication of the subgenomic GBneoD/III(HC RNA in vitro. The data suggest that in vivo fitness of the domain III chimeric virus is dependent on a cooperative interaction between the 5'NTR, 3'NTR and NS5A at a step in the viral life cycle subsequent to genome replication, most likely during particle assembly. Such a mechanism may be common to all hepaciviruses.

  19. A phylogenetic analysis using full-length viral genomes of South American dengue serotype 3 in consecutive Venezuelan outbreaks reveals novel NS5 mutation

    Science.gov (United States)

    Schmidt, DJ; Pickett, BE; Camacho, D; Comach, G; Xhaja, K; Lennon, NJ; Rizzolo, K; de Bosch, N; Becerra, A; Nogueira, ML; Mondini, A; da Silva, EV; Vasconcelos, PF; Muñoz-Jordán, JL; Santiago, GA; Ocazionez, R; Gehrke, L; Lefkowitz, EJ; Birren, BW; Henn, MR; Bosch, I

    2013-01-01

    Dengue virus currently causes 50-100 million infections annually. Comprehensive knowledge about the evolution of Dengue in response to selection pressure is currently unavailable, but would greatly enhance vaccine design efforts. In the current study, we sequenced 187 new dengue virus serotype 3(DENV-3) genotype III whole genomes isolated from Asia and the Americas. We analyzed them together with previously-sequenced isolates to gain a more detailed understanding of the evolutionary adaptations existing in this prevalent American serotype. In order to analyze the phylogenetic dynamics of DENV-3 during outbreak periods; we incorporated datasets of 48 and 11 sequences spanning two major outbreaks in Venezuela during 2001 and 2007-2008 respectively. Our phylogenetic analysis of newly sequenced viruses shows that subsets of genomes cluster primarily by geographic location, and secondarily by time of virus isolation. DENV-3 genotype III sequences from Asia are significantly divergent from those from the Americas due to their geographical separation and subsequent speciation. We measured amino acid variation for the E protein by calculating the Shannon entropy at each position between Asian and American genomes. We found a cluster of 7 amino acid substitutions having high variability within E protein domain III, which has previously been implicated in serotype-specific neutralization escape mutants. No novel mutations were found in the E protein of sequences isolated during either Venezuelan outbreak. Shannon entropy analysis of the NS5 polymerase mature protein revealed that a G374E mutation, in a region that contributes to interferon resistance in other flaviviruses by interfering with JAK-STAT signaling was present in both the Asian and American sequences from the 2007-2008 Venezuelan outbreak, but was absent in the sequences from the 2001 Venezuelan outbreak. In addition to E, several NS5 amino acid changes were unique to the 2007-2008 epidemic in Venezuela and may

  20. Intracellular expression of the proliferative marker Ki-67 and viral proteins (NS3, NS5A and C in chronic, long lasting hepatitis C virus (HCV infection.

    Directory of Open Access Journals (Sweden)

    Karolina Olejniczak

    2008-01-01

    Full Text Available Hepatitis C virus (HCV continues to represent the main causative agent of the hepatitis, which leads to chronic transformation of the process in 60-80% individuals. It remains unclear how far cellular expression of HCV proteins in vivo may represent an index of progression of the disease and of proliferative activity in the liver in chronic hepatitis C. Aim of the studies included detection and subcellular localization of three HCV proteins (NS3, NS5A and C in liver biopsies from adults (n=19 with chronic, long lasting hepatitis C as related to hepatocyte proliferative activity. The immunocytochemical ABC (avidin biotin-peroxidase complex technique was applied, alone or associated with the ImmunoMax technique. Results of the immunocytochemical tests were compared to histological alterations in liver biopsies, proliferation index and with selected clinical data. A significantly higher expression of NS3 protein was noted, as compared to expressions of NS5A and C proteins. In all the patients, cytoplasmic localization of all proteins dominated over nuclear localization (p0.05. At the level of electron microscopy, protein localization in endoplasmic reticulum (ER membranes, mitochondria, perinuclear region and/or in hepatocyte cell nucleus was observed. No direct relationships could be demonstrated between expressions of HCV proteins and of Ki-67 antigen. No correlations could also be demonstrated between cellular expression of any HCV protein on one hand and grading or staging, alanine transaminase (ALT, serum level of HCV RNA or alpha-fetoprotein (AFP on the other. However, positive correlations were disclosed between proliferative activity of hepatocytes on one hand and patient's age, grading and staging on the other. Advanced hepatic fibrosis correlated also with serum levels of AFP. The studies were supplemented with data on subcellular localization of HCV proteins. Moreover, they indicated that in HCV infection grading and staging

  1. Isolation and structural characterization of Coryxin, a novel cyclic lipopeptide from Corynebacterium xerosis NS5 having emulsifying and anti-biofilm activity.

    Science.gov (United States)

    Dalili, Dina; Amini, Mohsen; Faramarzi, Mohammad Ali; Fazeli, Mohammad Reza; Khoshayand, Mohammad Reza; Samadi, Nasrin

    2015-11-01

    Herein we reported the structure and several properties of a new biosurfactants produced by Corynebacterium xerosis strain NS5. This strain was capable of producing a novel lipopeptide biosurfactant that we have named coryxin. The biosurfactant structure was characterized by using Fourier transform infrared spectroscopy (FTIR), Nuclear magnetic resonance spectroscopy (NMR), and Liquid chromatography-mass spectrometry (LC-MS). It contained a hydrophobic moiety of 3-hydroxydecanoic acid and a peptide part predicted as a sequence of seven amino acids including Asn-Arg-Asn-Gln-Pro-Asn-Ser. Coryxin lowered the surface tension of water to 31.4 mN/m, with a critical micelle concentration of 25mg/l. It was a strong emulsifier with an emulsification index of 61% against n-hexane. Coryxin showed antibacterial activity against test organisms belonging to Gram-positive and Gram-negative bacteria and disrupted preformed biofilms of Staphylococcus aureus (82.5%), Streptococcus mutans (80%), Escherichia coli (66%) and Pseudomonas aeruginosa (30%). In conclusion, microbial surfactant from C. xerosis exhibited inhibitory and disruptive activities against biofilm formation that could be of use in biofilm-related menace. PMID:26280817

  2. Mutations in nonstructural 5A gene of hepatitis C virus and its response to interferon alfa%丙型肝炎病毒NS5A基因变异与干扰素疗效的关系

    Institute of Scientific and Technical Information of China (English)

    张琳; 赵桂珍; 石理兰; 曹丽

    2003-01-01

    目的:探讨HCV1b型慢性丙型肝炎患者HCV NS5A基因变异与干扰素(IFN)疗效的关系,NS5A2209-2248片断是否存在干扰素敏感决定区(ISDR).方法:留取慢性丙型肝炎患者干扰素治疗前血清,应用RT-PCR法扩增NS5A基因片段,用直接测序法进行核苷酸及氨基酸序列测定.结果:11例HCV1b型患者中1例为中间型,其余为野生型.2例表现为完全应答,均为野生型,9例为无应答.两组之间核苷酸及氨基酸序列无显著差异.对1例患者的动态观察发现,干扰素治疗后其核苷酸及氨基酸序列均有所变化,改变了其在基因树中的位置.结论:HCVlb型NS5A基因变异与干扰素疗效无关,NS5A2209-2248区高度保守.未证实存在ISDR.干扰素治疗可引起HCV准种改变.

  3. Hepatitis C Genotype Prevalence in Monastir Region, Tunisia: Correlation between 5' Untranslated Region (5'UTR), Non-structural 5B (NS5B), and Core Sequences in HCV Subtyping.

    Science.gov (United States)

    Souii, Amira; Elargoubi, Aida; Fallecker, Catherine; Mastouri, Maha; Drouet, Emmanuel

    2016-09-01

    Hepatitis C virus (HCV) is a causative agent of chronic liver disease, cirrhosis, and hepatocellular carcinoma. It constitutes a major public health around the world. There is no vaccine available against HCV, and current therapies are effective in only small percentage of patients. HCV has wide population-specific genotype variability. Genotype knowledge and viral load assessment are equally important for designing therapeutic strategies. Taking into account that the molecular epidemiology of HCV variants circulating in Tunisia is not yet well elucidated, and that, at present, little is known about the distribution pattern of HCV in Monastir region (Tunisia), we aimed, herein, to evaluate the prevalence of HCV genotypes in Monastir and to identify risk-related factors. For this purpose, 50 anti-HCV antibody-positive cases were diagnosed and subjected to viral RNA extraction, amplification, genotyping, and viral load quantification. Molecular epidemiology was studied by 5' untranslated region (5' UTR) sequencing as compared with the non-structural 5B (NS5B) and core region sequences. Overall concordance between 5' UTR, core, and NS5B sequencing was 100 %. The highest prevalent genotype was 1b (50 %) followed by genotypes 1a (16 %), 4a (12 %), 2a (10 %), 2c (8 %), and 3a (4 %). Interestingly, the subtype 1b had a statistically significant higher viral load than the other genotypes followed by subtype 1a. Based on these data, this study revealed a high prevalence of HCV genotype 1 (subtypes 1b and 1a) compared to other genotypes. A continued monitoring of HCV and knowledge of circulating genotypes could impact on future vaccine formulations. PMID:27189386

  4. The neurovirulence and neuroinvasiveness of chimeric tick-borne encephalitis/dengue virus can be attenuated by introducing defined mutations into the envelope and NS5 protein genes and the 3' non-coding region of the genome

    International Nuclear Information System (INIS)

    Tick-borne encephalitis (TBE) is a severe disease affecting thousands of people throughout Eurasia. Despite the use of formalin-inactivated vaccines in endemic areas, an increasing incidence of TBE emphasizes the need for an alternative vaccine that will induce a more durable immunity against TBE virus (TBEV). The chimeric attenuated virus vaccine candidate containing the structural protein genes of TBEV on a dengue virus genetic background (TBEV/DEN4) retains a high level of neurovirulence in both mice and monkeys. Therefore, attenuating mutations were introduced into the envelope (E315) and NS5 (NS5654,655) proteins, and into the 3' non-coding region (Δ30) of TBEV/DEN4. The variant that contained all three mutations (vΔ30/E315/NS5654,655) was significantly attenuated for neuroinvasiveness and neurovirulence and displayed a reduced level of replication and virus-induced histopathology in the brains of mice. The high level of safety in the central nervous system indicates that vΔ30/E315/NS5654,655 should be further evaluated as a TBEV vaccine.

  5. Multi-parameter optimization of aza-follow-ups to BI 207524, a thumb pocket 1 HCV NS5B polymerase inhibitor. Part 2: Impact of lipophilicity on promiscuity and in vivo toxicity.

    Science.gov (United States)

    Beaulieu, Pierre L; Bolger, Gordon; Deon, Dan; Duplessis, Martin; Fazal, Gulrez; Gagnon, Alexandre; Garneau, Michel; LaPlante, Steven; Stammers, Timothy; Kukolj, George; Duan, Jianmin

    2015-03-01

    We describe our efforts to identify analogs of thumb pocket 1 HCV NS5B inhibitor 1 (aza-analog of BI 207524) with improved plasma to liver partitioning and a predicted human half-life consistent with achieving a strong antiviral effect at a reasonable dose in HCV-infected patients. Compounds 3 and 7 were identified that met these criteria but exhibited off-target promiscuity in an in vitro pharmacology screen and in vivo toxicity in rats. High lipophilicity in this class was found to correlate with increased probability for promiscuous behavior and toxicity. The synthesis of an 8×11 matrix of analogs allowed the identification of C3, an inhibitor that displayed comparable potency to 1, improved partitioning to the liver and reduced lipophilicity. Although C3 displayed reduced propensity for in vitro off-target inhibition and the toxicity profile in rats was improved, the predicted human half-life of this compound was short, resulting in unacceptable dosing requirements to maintain a strong antiviral effect in patients.

  6. Inferring Protective CD8+ T-Cell Epitopes for NS5 Protein of Four Serotypes of Dengue Virus Chinese Isolates Based on HLA-A, -B and -C Allelic Distribution: Implications for Epitope-Based Universal Vaccine Design.

    Directory of Open Access Journals (Sweden)

    Jiandong Shi

    Full Text Available Dengue is one of the most globally serious vector-borne infectious diseases in tropical and subtropical areas for which there are currently no effective vaccines. The most highly conserved flavivirus protein, NS5, is an indispensable target of CD8+ T-cells, making it an ideal vaccine design target. Using the Immune Epitope Database (IEDB, CD8+ T-cell epitopes of the dengue virus (DENV NS5 protein were predicted by genotypic frequency of the HLA-A,-B, and-C alleles in Chinese population. Antigenicity scores of all predicted epitopes were analyzed using VaxiJen v2.0. The IEDB analysis revealed that 116 antigenic epitopes for HLA-A (21,-B (53, and-C (42 had high affinity for HLA molecules. Of them, 14 had 90.97-99.35% conversancy among the four serotypes. Moreover, five candidate epitopes, including 200NS5210 (94.84%, A*11:01, 515NS5525 (98.71%, A*24:02, 225NS5232 (99.35%, A*33:03, 516NS5523 (98.71%, A*33:03, and 284NS5291 (98.06%, A*33:03, were presented by HLA-A. Four candidate epitopes, including 234NS5241 (96.77%, B*13:01, 92NS599 (98.06%, B*15:01, B*15:02, and B*46:01, 262NS5269 (92.90%, B*38:02, and 538NS5547 (90.97%, B*51:01, were presented by HLA-B. Another 9 candidate epitopes, including 514NS5522 (98.71%, C*01:02, 514NS5524 (98.71%, C*01:02 and C*14:02, 92NS599 (98.06%, C*03:02 and C*15:02, 362NS5369 (44.84%, C*03:04 and C*08:01, 225NS5232 (99.35%, C*04:01, 234NS5241(96.77%, C*04:01, 361NS5369 (94.84%, C*04:01, 515NS5522 (98.71%, C*14:02, 515NS5524 (98.71%, C*14:02, were presented by HLA-C. Further data showed that the four-epitope combination of 92NS599 (B*15:01, B*15:02, B*46:01, C*03:02 and C*15:02, 200NS5210 (A*11:01, 362NS5369 (C*03:04, C*08:01, and 514NS5524 (C*01:02, C*14:02 could vaccinate >90% of individuals in China. Further in vivo study of our inferred novel epitopes will be needed for a T-cell epitope-based universal vaccine development that may prevent all four China-endemic DENV serotypes.

  7. Evaluation of Resistance-Associated Substitutions in NS5A Using Direct Sequence and Cycleave Method and Treatment Outcome with Daclatasvir and Asunaprevir for Chronic Hepatitis C Genotype 1

    Science.gov (United States)

    Ishii, Kunihide; Morita, Masaru; Morita, Yasuyo; Sugiyama, Gen; Fukushima, Hirofumi; Yano, Yoichi; Noguchi, Kazunori; Nakamura, Hiroki; Hisatomi, Junjiro; Kumemura, Hiroto; Shirachi, Miki; Iwane, Shinji; Okada, Michiaki; Honma, Yuichi; Arinaga-Hino, Teruko; Miyajima, Ichiro; Ogata, Kei; Kuwahara, Reiichiro; Amano, Keisuke; Kawaguchi, Toshihiro; Kuromatsu, Ryoko; Torimura, Takuji

    2016-01-01

    Background The aim of this study was to evaluate the efficacy of daclatasvir plus asunaprevir therapy in patients infected with hepatitis C virus and determine its relevance to resistant variants. Methods A total of 629 consecutive patients infected with hepatitis C virus genotype 1 were assessed. Daclatasvir (60 mg/day) plus asunaprevir (200 mg/day) was given for 24 weeks. The virological responses and resistance-associated substitutions of hepatitis C virus mutants were examined by the direct sequence and cycleave methods were evaluated. Results Overall, 89.4% (555/621) of patients exhibited a sustained virological response (SVR). The SVR rates in the patients with wild type, mixed, and mutant type Y93 by direct sequencing were 92.5% (520/562), 70.3% (26/37), and 42.9% (9/21), respectively. The SVR rates in the patients with 100%, 90%, 80%-30%, and 20%-0% Y93 wild by the cycleave method were 93.4% (456/488), 88.2%(30/34), 56.0%(14/25), and 36.8%(7/19), respectively. In contrast, the SVR rates for the wild type and mixed/mutant type L31 by direct sequencing were 90.2% (534/592) and 72.4% (21/29), respectively. In the multivariate analyses, the wild type Y93, no history of simeprevir therapy, the wild type L31, and low HCV RNA level were independent factors of SVR. Conclusion NS5A resistance-associated substitutions, especially Y93H, were major factors predicting the SVR. Although direct sequencing can predict the SVR rate, the cycleave method is considered to be more useful for predicting the SVR when used in combination. PMID:27684567

  8. G-Structures and Wrapped NS5-Branes

    CERN Document Server

    Gauntlett, J P; Pakis, S; Waldram, D; Gauntlett, Jerome P.; Martelli, Dario; Pakis, Stathis; Waldram, Daniel

    2002-01-01

    We analyse the geometrical structure of supersymmetric solutions of type II supergravity of the form R^{1,9-n} x M_n with non-trivial NS flux and dilaton. Solutions of this type arise naturally as the near-horizon limits of wrapped NS fivebrane geometries. We concentrate on the case n=7, preserving two or four supersymmetries, corresponding to branes wrapped on associative or SLAG three-cycles. Given the existence of Killing spinors, we show that M_7 admits a G_2-structure or an SU(3)-structure, respectively, of specific type. We also prove the converse result. We use the existence of these geometric structures as a new technique to derive some known and new explicit solutions, as well as a simple theorem implying that we have vanishing NS three-form and constant dilaton whenever M_7 is compact with no boundary. The analysis extends simply to other type II examples and also to type I supergravity.

  9. Immunogenicity of HGV NS5 protein expressed from Sf9 insect cells

    Institute of Scientific and Technical Information of China (English)

    Hao Ren; Fen Lu Zhu; Shi Ying Zhu; Yan Bin Song; Zhong Tian Qi

    2001-01-01

    @@ INTRODUCTIONAlthough reliable assays for the detection ofhepatitis C virus and E virus became available, still10% 20% hepatitis are not caused byhepatitis A-E virus[1-3]. In 1996, two research groups isolatedthis agent independently and almost simultaneouslyand named hepatitis G virus and GB virus C,respectively[4-7].

  10. Characterization of forced degradation products and in silico toxicity prediction of Sofosbuvir: A novel HCV NS5B polymerase inhibitor.

    Science.gov (United States)

    Swain, Debasish; Samanthula, Gananadhamu; Bhagat, Shweta; Bharatam, P V; Akula, Venkatakrishna; Sinha, Barij N

    2016-02-20

    Sofosbuvir is a direct acting antiviral medication used to treat Hepatitis C viral infection. The present study focuses on the degradation behavior of the drug under various stress conditions (hydrolysis, oxidative, thermal and photolytic) as per International Conference on Harmonization (ICH Q1A (R2)) guidelines. A high performance liquid chromatographic system (HPLC) was used to develop a selective, precise and accurate method for separating all the degradation products. The separation was achieved on a Sunfire™ C18 (150mm×4.6mm×5μm) stationary phase with a mobile phase of 10mM ammonium acetate (pH 5.0) buffer and acetonitrile in gradient elution mode. A quadrupole-time of flight mass analyzer equipped with an electrospray ionization technique was used to propose the structural information based on the MS/MS and accurate mass measurements. Seven degradation products were identified and characterised by LC-ESI-QTOF-MS/MS. In silico toxicity of the drug and its degradation products was determined using TOPKAT and DEREK toxicity prediction softwares. The proposed method was validated as per the ICH Q2 guidelines. PMID:26771133

  11. Intra-host variation structure of classical swine fever virus NS5B in relation to antiviral therapy.

    Science.gov (United States)

    Haegeman, Andy; Vrancken, Robert; Neyts, Johan; Koenen, Frank

    2013-05-01

    Classical swine fever (CSF) is one of most important diseases of the Suidea with severe social economic consequences in case of outbreaks. Antivirals have been demonstrated, in recent publications, to be an interesting alternative method of fighting the disease. However, classical swine fever virus is an RNA virus which presents a challenge as intra-host variation and the error prone RNA dependent RNA polymerase (RdRp) could lead to the emergence/selection of resistant variants hampering further treatment. Therefore, it was the purpose of this study to investigate the intra-host variation of the RdRp gene, targeted by antivirals, in respect to antiviral treatment. Using the non-unique nucleotide changes, a limited intra-host variation was found in the wild type virus with 2 silent and 2 non-synonymous sites. This number shifted significantly when an antiviral resistant variant was analyzed. In total 22nt changes were found resulting in 14 amino acid changes whereby each genome copy contained at least 2 amino-acid changes in the RdRp. Interestingly, the frequency of the mutations situated in close proximity to a region involved in antiviral resistance in CSFV and bovine viral diarrhea virus (BVDV) was elevated compared to the other mutations. None of the identified mutations in the resistant variant and which could potentially result in antiviral resistance was present in the wild type virus as a non-unique mutation. In view of the spectrum of mutations identified in the resistance associated region and that none of the resistance associated mutations reported for another strain of classical swine fever for the same antiviral were observed in the study, it can be suggested that multiple mutations confer resistance to some degree. Although the followed classical approach allowed the analysis the RdRp as a whole, the contribution of unique mutations to the intra-host variation could not be completely resolved. There was a significant difference in de number of unique mutations found between: 1/wild type virus and the antiviral resistant variant and 2/between both and the number to be expected from the error rate of the RT-PCR process. This indicates that the some of the unique mutations contributed to the intra-host variation and that the antiviral pressure also shifted this pattern. This is important as one of the non-synonymous mutations found in the resistant variant and which was located in the antiviral resistance associated region, was present in the wild type virus as a unique mutation. The findings presented in this study not only show the importance of intra-host variation analysis but also warrants further research certainly in view of the potential inclusion of antivirals in a control/eradication strategy. PMID:23511203

  12. Combination treatment with hepatitis C virus protease and NS5A inhibitors is effective against recombinant genotype 1a, 2a, and 3a viruses

    DEFF Research Database (Denmark)

    Gottwein, Judith M; Jensen, Sanne B; Li, Yi-Ping;

    2013-01-01

    With the development of directly acting antivirals, hepatitis C virus (HCV) therapy entered a new era. However, rapid selection of resistance mutations necessitates combination therapy. To study combination therapy in infectious culture systems, we aimed at developing HCV semi-full-length (semi...... against previously developed 2a recombinants J6/JFH1 and J6cc. Daclatasvir had intermediate efficacy against J6/JFH1, while low sensitivity was confirmed against J6cc. Using a cross-titration scheme, infected cultures were treated until viral escape or on-treatment virologic suppression occurred. Compared...

  13. Development and application of hepatitis C reporter viruses with genotype 1 to 7 core-nonstructural protein 2 (NS2) expressing fluorescent proteins or luciferase in modified JFH1 NS5A

    DEFF Research Database (Denmark)

    Gottwein, Judith M; Jensen, Tanja B; Mathiesen, Christian K;

    2011-01-01

    to 2a(J6) tagged with EGFP, DsRed-Express2, mCherry, or Renilla luciferase (RLuc), yielding peak supernatant infectivity titers of 4 to 5 log(10) focus-forming units (FFU)/ml. 2a(J6) with ¿40 or ¿25 was fully viable in Huh7.5 cells. In human liver chimeric mice, 2a(J6)-EGFP¿40 acquired various...

  14. Probing Maldacena-Nunez in IR with ${\\bar D3}$ branes

    OpenAIRE

    Pal, Shesansu Sekhar

    2004-01-01

    We probed Maldacena-Nunez solution in IR with p coincident anti D3 branes and found that these probe branes become a fuzzy NS5 brane. Doing the dual analysis i.e. from the NS5 brane point of view with the charge of p anti D3 brane on the world-volume of NS5 brane, we showed that to leading order this potential matches with that of p anti D3 branes and the potential on the NS5 brane has a stable minima and have also calculated the potential, from the NS5 brane point of view, for a small fluctu...

  15. Affinity-Based Screening Technology and HCV Drug Discovery

    Institute of Scientific and Technical Information of China (English)

    LI Bin

    2003-01-01

    @@ NS5A is one of the non-structural gene products encoded by Hepatitis C virus (HCV) and related viruses that are essential for viral replication. The amino acid sequence of NS5A is conserved between different HCV genotypes and the primary amino acid sequence of NS5A is unique to HCV and closely related viruses. Importantly, NS5A is unrelated to any human protein. This indicates that drugs designed to block the actions of NS5A could inhibit the replication of HCV without showing toxic side effects in human host cells, thus making NS5A inhibitors ideal anti-viral drugs. However, there are presently no functional assays for this essential viral protein. Therefore, conventional high throughput screening (HTS) approaches can not be used to discover antiviral drugs against NS5A.

  16. Hepatitis C virus nonstructural protein-5A activates sterol regulatory element-binding protein-1c through transcription factor Sp1

    Energy Technology Data Exchange (ETDEWEB)

    Xiang, Zhonghua; Qiao, Ling; Zhou, Yan [Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5E3 (Canada); Babiuk, Lorne A. [University of Alberta, Edmonton, Alberta (Canada); Liu, Qiang, E-mail: qiang.liu@usask.ca [Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Saskatchewan, Canada S7N 5E3 (Canada)

    2010-11-19

    Research highlights: {yields} A chimeric subgenomic HCV replicon expresses HCV-3a NS5A in an HCV-1b backbone. {yields} HCV-3a NS5A increases mature SREBP-1c protein level. {yields} HCV-3a NS5A activates SREBP-1c transcription. {yields} Domain II of HCV-3a NS5A is more effective in SREBP-1c promoter activation. {yields} Transcription factor Sp1 is required for SREBP-1c activation by HCV-3a NS5A. -- Abstract: Steatosis is an important clinical manifestation of hepatitis C virus (HCV) infection. The molecular mechanisms of HCV-associated steatosis are not well understood. Sterol regulatory element-binding protein-1c (SREBP-1c) is a key transcription factor which activates the transcription of lipogenic genes. Here we showed that the nuclear, mature SREBP-1c level increases in the nucleus of replicon cells expressing HCV-3a nonstructural protein-5A (NS5A). We further showed that HCV-3a NS5A up-regulates SREBP-1c transcription. Additional analysis showed that transcriptional factor Sp1 is involved in SREBP-1c activation by HCV-3a NS5A because inhibition of Sp1 activity by mithramycin A or a dominant-negative Sp1 construct abrogated SREBP-1c promoter activation by HCV-3a NS5A. In addition, chromatin immunoprecipitation (ChIP) assay demonstrated enhanced binding of Sp1 on the SREBP-1c promoter in HCV-3a NS5A replicon cells. These results showed that HCV-3a NS5A activates SREBP-1c transcription through Sp1. Taken together, our results suggest that HCV-3a NS5A is a contributing factor for steatosis caused by HCV-3a infection.

  17. Interaction of dengue virus nonstructural protein 5 with Daxx modulates RANTES production

    International Nuclear Information System (INIS)

    Highlights: ► For the first time how DENV NS5 increases RANTES production. ► DENV NS5 physically interacts with human Daxx. ► Nuclear localization of NS5 is required for Daxx interaction and RANTES production. -- Abstract: Dengue fever (DF), dengue hemorrhagic fever (DHF), and dengue shock syndrome (DSS), caused by dengue virus (DENV) infection, are important public health problems in the tropical and subtropical regions. Abnormal hemostasis and plasma leakage are the main patho-physiological changes in DHF/DSS. A remarkably increased production of cytokines, the so called ‘cytokine storm’, is observed in the patients with DHF/DSS. A complex interaction between DENV proteins and the host immune response contributes to cytokine production. However, the molecular mechanism(s) by which DENV nonstructural protein 5 (NS5) mediates these responses has not been fully elucidated. In the present study, yeast two-hybrid assay was performed to identify host proteins interacting with DENV NS5 and a death-domain-associate protein (Daxx) was identified. The in vivo relevance of this interaction was suggested by co-immunoprecipitation and nuclear co-localization of these two proteins in HEK293 cells expressing DENV NS5. HEK293 cells expressing DENV NS5-K/A, which were mutated at the nuclear localization sequences (NLS), were created to assess its functional roles in nuclear translocation, Daxx interaction, and cytokine production. In the absence of NLS, DENV NS5 could neither translocate into the nucleus nor interact with Daxx to increase the DHF-associated cytokine, RANTES (CCL5) production. This work demonstrates the interaction between DENV NS5 and Daxx and the role of the interaction on the modulation of RANTES production.

  18. Interaction of dengue virus nonstructural protein 5 with Daxx modulates RANTES production

    Energy Technology Data Exchange (ETDEWEB)

    Khunchai, Sasiprapa [Division of Molecular Medicine, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok (Thailand); Graduate Program in Immunology, Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok (Thailand); Junking, Mutita [Division of Molecular Medicine, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok (Thailand); Suttitheptumrong, Aroonroong; Yasamut, Umpa [Division of Molecular Medicine, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok (Thailand); Graduate Program in Immunology, Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok (Thailand); Sawasdee, Nunghathai [Division of Molecular Medicine, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok (Thailand); Netsawang, Janjuree [Faculty of Medical Technology, Rangsit University, Bangkok (Thailand); Morchang, Atthapan [Division of Molecular Medicine, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok (Thailand); Graduate Program in Immunology, Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok (Thailand); Chaowalit, Prapaipit [Division of Molecular Medicine, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok (Thailand); Noisakran, Sansanee [Medical Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Bangkok (Thailand); Yenchitsomanus, Pa-thai, E-mail: grpye@mahidol.ac.th [Division of Molecular Medicine, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok (Thailand); and others

    2012-06-29

    Highlights: Black-Right-Pointing-Pointer For the first time how DENV NS5 increases RANTES production. Black-Right-Pointing-Pointer DENV NS5 physically interacts with human Daxx. Black-Right-Pointing-Pointer Nuclear localization of NS5 is required for Daxx interaction and RANTES production. -- Abstract: Dengue fever (DF), dengue hemorrhagic fever (DHF), and dengue shock syndrome (DSS), caused by dengue virus (DENV) infection, are important public health problems in the tropical and subtropical regions. Abnormal hemostasis and plasma leakage are the main patho-physiological changes in DHF/DSS. A remarkably increased production of cytokines, the so called 'cytokine storm', is observed in the patients with DHF/DSS. A complex interaction between DENV proteins and the host immune response contributes to cytokine production. However, the molecular mechanism(s) by which DENV nonstructural protein 5 (NS5) mediates these responses has not been fully elucidated. In the present study, yeast two-hybrid assay was performed to identify host proteins interacting with DENV NS5 and a death-domain-associate protein (Daxx) was identified. The in vivo relevance of this interaction was suggested by co-immunoprecipitation and nuclear co-localization of these two proteins in HEK293 cells expressing DENV NS5. HEK293 cells expressing DENV NS5-K/A, which were mutated at the nuclear localization sequences (NLS), were created to assess its functional roles in nuclear translocation, Daxx interaction, and cytokine production. In the absence of NLS, DENV NS5 could neither translocate into the nucleus nor interact with Daxx to increase the DHF-associated cytokine, RANTES (CCL5) production. This work demonstrates the interaction between DENV NS5 and Daxx and the role of the interaction on the modulation of RANTES production.

  19. Investigation of the mode of binding of a novel series of N-benzyl-4-heteroaryl-1-(phenylsulfonyl)piperazine-2-carboxamides to the hepatitis C virus polymerase

    Energy Technology Data Exchange (ETDEWEB)

    Gentles, Robert G.; Sheriff, Steven; Beno, Brett R.; Wan, Changhong; Kish, Kevin; Ding, Min; Zheng, Xiaofan; Chupak, Louis; Poss, Michael A.; Witmer, Mark R.; Morin, Paul; Wang, Ying-Kai; Rigat, Karen; Lemm, Julie; Voss, Stacey; Liu, Mengping; Pelosi, Lenore; Roberts, Susan B.; Gao, Min; Kadow, John F. (BMS)

    2013-11-20

    Structure based rationales for the activities of potent N-benzyl-4-heteroaryl-1-(phenylsulfonyl)piperazine-2-carboxamide inhibitors of the hepatitis C viral polymerase are described herein. These compounds bind to the hepatitis C virus non-structural protein 5B (NS5B), and co-crystal structures of select examples from this series with NS5B are reported. Comparison of co-crystal structures of a potent analog with both NS5B genotype 1a and genotype 1b provides a possible explanation for the genotype-selectivity observed with this compound class and suggests opportunities for the further optimization of the series.

  20. Penrose Limits of Branes and Marginal Intersecting Branes

    CERN Document Server

    Ryang, S

    2003-01-01

    We construct the Penrose limit backgrounds in closed forms along the generic null geodesics for the near-horizon geometries of D1, D3, D5, NS1 and NS5 branes. The Penrose limit metrics of D1, D5 and NS1 have non-trivial dependence of the light-cone time coordinate, while those of D3 and NS5 have no its dependence. We study the Penrose limits on the marginal 1/4 supersymmetric configurations of standard intersecting branes, such as the NS-NS intersection of NS1 and NS5, the R-R intersections of Dp and Dq over some spatial dimensions and the mix intersections of NS5 and Dp over (p -1)-dimensional spaces. They are classified into three types that correspond to the Penrose limits of D1, D3 and D5 backgrounds.

  1. Analysis of real time PCR amplification efficiencies from three genomic region of dengue virus.

    Science.gov (United States)

    Odreman-Macchioli, María; Vielma, Silvana; Atchley, Daniel; Comach, Guillermo; Ramirez, Alvaro; Pérez, Saberio; Téllez, Luis; Quintero, Beatriz; Hernández, Erick; Muñoz, Maritza; Mendoza, José

    2013-03-01

    Early diagnosis of dengue virus (DENV) infection represents a key factor in preventing clinical complications attributed to the disease. The aim of this study was to evaluate the amplification efficiencies of an in-house quantitative real time-PCR (qPCR) assay of DENV, using the non-structural conserved genomic region protein-5 (NS5) versus two genomic regions usually employed for virus detection, the capsid/pre-membrane region (C-prM) and the 3'-noncoding region (3'NC). One-hundred sixty seven acute phase serum samples from febrile patients were used for validation purposes. Results showed that the three genomic regions had similar amplification profiles and correlation coefficients (0.987-0.999). When isolated viruses were used, the NS5 region had the highest qPCR efficiencies for the four serotypes (98-100%). Amplification from acute serum samples showed that 41.1% (67/167) were positive for the universal assay by at least two of the selected genomic regions. The agreement rates between NS5/C-prM and NS5/3'NC regions were 56.7% and 97%, respectively. Amplification concordance values between C-prM/NS5 and NS5/3'NC regions showed a weak (kappa = 0.109; CI 95%) and a moderate (kappa = 0.489; CI 95%) efficiencies in amplification, respectively. Serotyping assay using a singleplex NS5-TaqMan format was much more sensitive than the C-prM/SYBR Green I protocol (76%). External evaluation showed a high sensitivity (100%), specificity (78%) and high agreement between the assays. According to the results, the NS5 genomic region provides the best genomic region for optimal detection and typification of DENV in clinical samples. PMID:23781709

  2. Hepatitis C virus non-structural 5B protein interacts with cyclin A2 and regulates viral propagation

    DEFF Research Database (Denmark)

    Pham, Long; Ngo, HT; Lim, YS;

    2012-01-01

    ) specifically interacted with CycA2 in vitro and in vivo. Protein interaction was mediated through the cyclin box of CycA2 and the palm domain of NS5B. We further showed that R/HxL motif in the palm domain of HCV NS5B mediated protein interaction with CycA2 and this interaction was necessary for HCV replication...

  3. Development of viable TAP-tagged dengue virus for investigation of host-virus interactions in viral replication.

    Science.gov (United States)

    Poyomtip, Teera; Hodge, Kenneth; Matangkasombut, Ponpan; Sakuntabhai, Anavaj; Pisitkun, Trairak; Jirawatnotai, Siwanon; Chimnaronk, Sarin

    2016-03-01

    Dengue virus (DENV) is a mosquito-borne flavivirus responsible for life-threatening dengue haemorrhagic fever (DHF) and dengue shock syndrome (DSS). The viral replication machinery containing the core non-structural protein 5 (NS5) is implicated in severe dengue symptoms but molecular details remain obscure. To date, studies seeking to catalogue and characterize interaction networks between viral NS5 and host proteins have been limited to the yeast two-hybrid system, computational prediction and co-immunoprecipitation (IP) of ectopically expressed NS5. However, these traditional approaches do not reproduce a natural course of infection in which a number of DENV NS proteins colocalize and tightly associate during the replication process. Here, we demonstrate the development of a recombinant DENV that harbours a TAP tag in NS5 to study host-virus interactions in vivo. We show that our engineered DENV was infective in several human cell lines and that the tags were stable over multiple viral passages, suggesting negligible structural and functional disturbance of NS5. We further provide proof-of-concept for the use of rationally tagged virus by revealing a high confidence NS5 interaction network in human hepatic cells. Our analysis uncovered previously unrecognized hnRNP complexes and several low-abundance fatty acid metabolism genes, which have been implicated in the viral life cycle. This study sets a new standard for investigation of host-flavivirus interactions.

  4. Biochemical characterization of a recombinant Japanese encephalitis virus RNA-dependent RNA polymerase

    Directory of Open Access Journals (Sweden)

    Kim Chan-Mi

    2007-07-01

    Full Text Available Abstract Background Japanese encephalitis virus (JEV NS5 is a viral nonstructural protein that carries both methyltransferase and RNA-dependent RNA polymerase (RdRp domains. It is a key component of the viral RNA replicase complex that presumably includes other viral nonstructural and cellular proteins. The biochemical properties of JEV NS5 have not been characterized due to the lack of a robust in vitro RdRp assay system, and the molecular mechanisms for the initiation of RNA synthesis by JEV NS5 remain to be elucidated. Results To characterize the biochemical properties of JEV RdRp, we expressed in Escherichia coli and purified an enzymatically active full-length recombinant JEV NS5 protein with a hexahistidine tag at the N-terminus. The purified NS5 protein, but not the mutant NS5 protein with an Ala substitution at the first Asp of the RdRp-conserved GDD motif, exhibited template- and primer-dependent RNA synthesis activity using a poly(A RNA template. The NS5 protein was able to use both plus- and minus-strand 3'-untranslated regions of the JEV genome as templates in the absence of a primer, with the latter RNA being a better template. Analysis of the RNA synthesis initiation site using the 3'-end 83 nucleotides of the JEV genome as a minimal RNA template revealed that the NS5 protein specifically initiates RNA synthesis from an internal site, U81, at the two nucleotides upstream of the 3'-end of the template. Conclusion As a first step toward the understanding of the molecular mechanisms for JEV RNA replication and ultimately for the in vitro reconstitution of viral RNA replicase complex, we for the first time established an in vitro JEV RdRp assay system with a functional full-length recombinant JEV NS5 protein and characterized the mechanisms of RNA synthesis from nonviral and viral RNA templates. The full-length recombinant JEV NS5 will be useful for the elucidation of the structure-function relationship of this enzyme and for the

  5. Complex Pattern of Resistance-Associated Substitutions of Hepatitis C Virus after Daclatasvir/Asunaprevir Treatment Failure

    Science.gov (United States)

    Hasebe, Chitomi; Osaki, Yukio; Joko, Kouji; Yagisawa, Hitoshi; Sakita, Shinya; Okushin, Hiroaki; Satou, Takashi; Hisai, Hiroyuki; Abe, Takehiko; Tsuji, Keiji; Tamada, Takashi; Kobashi, Haruhiko; Mitsuda, Akeri; Ide, Yasushi; Ogawa, Chikara; Tsuruta, Syotaro; Takaguchi, Kouichi; Murakawa, Miyako; Asahina, Yasuhiro; Enomoto, Nobuyuki; Izumi, Namiki

    2016-01-01

    Backgrounds & Aims We aimed to clarify the characteristics of resistance-associated substitutions (RASs) after treatment failure with NS5A inhibitor, daclatasvir (DCV) in combination with NS3/4A inhibitor, asunaprevir (ASV), in patients with chronic hepatitis C virus genotype 1b infection. Methods This is a nationwide multicenter study conducted by the Japanese Red Cross Liver Study Group. The sera were obtained from 68 patients with virological failure after 24 weeks of DCV/ASV treatment. RASs in NS5A and NS3 were determined by population sequencing. Results The frequency of signature RASs at position D168 of NS3 was 68%, and at positions L31 and Y93 of NS5A was 79 and 76%, respectively. The frequency of dual signature RASs in NS5A (L31-RAS and Y93-RAS) was 63%. RASs at L28, R30, P32, Q54, P58, and A92 in addition to dual signature RAS were detected in 5, 5, 1, 22, 2, and 0 patients, respectively. In total, triple, quadruple, and quintuple RASs in combination with dual signature RAS were detected in 35, 10, and 1.5% patients, respectively. These RASs were detected in patients without baseline RASs or who prematurely discontinued therapy. Co-existence of D168 RAS in NS3 and L31 and/or Y93 RAS in NS5A was observed in 62% of patients. Conclusion Treatment-emergent RASs after failure with DCV/ASV combination therapy are highly complex in more than 50% of the patients. The identification of complex RAS patterns, which may indicate high levels of resistance to NS5A inhibitors, highlights the need for RAS sequencing when considering re-treatment with regimens including NS5A inhibitors. PMID:27776192

  6. Flaviviral Replication Complex: Coordination between RNA Synthesis and 5'-RNA Capping.

    Science.gov (United States)

    Klema, Valerie J; Padmanabhan, Radhakrishnan; Choi, Kyung H

    2015-08-13

    Genome replication in flavivirus requires (-) strand RNA synthesis, (+) strand RNA synthesis, and 51-RNA capping and methylation. To carry out viral genome replication, flavivirus assembles a replication complex, consisting of both viral and host proteins, on the cytoplasmic side of the endoplasmic reticulum (ER) membrane. Two major components of the replication complex are the viral non-structural (NS) proteins NS3 and NS5. Together they possess all the enzymatic activities required for genome replication, yet how these activities are coordinated during genome replication is not clear. We provide an overview of the flaviviral genome replication process, the membrane-bound replication complex, and recent crystal structures of full-length NS5. We propose a model of how NS3 and NS5 coordinate their activities in the individual steps of (-) RNA synthesis, (+) RNA synthesis, and 51-RNA capping and methylation.

  7. Rotating and orbiting strings in the near-horizon brane backgrounds

    CERN Document Server

    Ryang, S

    2003-01-01

    Using the Schwarzschild-type coordinates in stead of the global ones we reconstruct the classical rotating closed string solutions in the AdS*5 x S*5 backgrounds. They are explicitly described by the Jacobi elliptic and trigonometrical functions of worldsheet coordinates. We study the orbiting closed string configurations in the near-horizon geometries of Dp, NS1 and NS5 branes, and derive the energy and spin of them, whose relation takes a simple form for short strings. Specially in the D5 and NS5 backgrounds we have a linear relation that the energy of the point-like string is proportional to the spin, which is associated with the spectrum of strings in the pp-wave geometries obtained by taking a special Penrose limit on the D5 and NS5 backgrounds.

  8. Robust full-length hepatitis C virus genotype 2a and 2b infectious cultures using mutations identified by a systematic approach applicable to patient strains

    DEFF Research Database (Denmark)

    Li, Yi-Ping; Ramirez, Santseharay; Gottwein, Judith M;

    2012-01-01

    Hepatitis C virus (HCV) infection is a leading cause of chronic liver diseases worldwide, but treatment options are limited. Basic HCV research required for vaccine and drug development has been hampered by inability to culture patient isolates, and to date only the JFH1 (genotype 2a) recombinant...... in vitro. Through a systematic approach of culturing J6 with minimal JFH1 sequences, we identified three mutations in NS3, NS4A, and NS5B that permitted full-length J6 propagation and adaptation with infectivity titers comparable to JFH1-based systems. The most efficient recombinant, J6cc, had six adaptive...... mutations and did not accumulate additional changes following viral passage. We demonstrated that HCV NS3/NS4A protease-, NS5A- and NS5B polymerase-directed drugs respectively inhibited full-length J6 infection dose dependently. Importantly, the three J6-derived mutations enabled culture adaptation...

  9. Inhibitors for the hepatitis C virus RNA polymerase explored by SAR with advanced machine learning methods.

    Science.gov (United States)

    Weidlich, Iwona E; Filippov, Igor V; Brown, Jodian; Kaushik-Basu, Neerja; Krishnan, Ramalingam; Nicklaus, Marc C; Thorpe, Ian F

    2013-06-01

    Hepatitis C virus (HCV) is a global health challenge, affecting approximately 200 million people worldwide. In this study we developed SAR models with advanced machine learning classifiers Random Forest and k Nearest Neighbor Simulated Annealing for 679 small molecules with measured inhibition activity for NS5B genotype 1b. The activity was expressed as a binary value (active/inactive), where actives were considered molecules with IC50 ≤0.95 μM. We applied our SAR models to various drug-like databases and identified novel chemical scaffolds for NS5B inhibitors. Subsequent in vitro antiviral assays suggested a new activity for an existing prodrug, Candesartan cilexetil, which is currently used to treat hypertension and heart failure but has not been previously tested for anti-HCV activity. We also identified NS5B inhibitors with two novel non-nucleoside chemical motifs. PMID:23608107

  10. Analysis of Hepatitis C Virus Genotype 1b Resistance Variants in Japanese Patients Treated with Paritaprevir-Ritonavir and Ombitasvir.

    Science.gov (United States)

    Krishnan, Preethi; Schnell, Gretja; Tripathi, Rakesh; Beyer, Jill; Reisch, Thomas; Zhang, Xinyan; Setze, Carolyn; Rodrigues, Lino; Burroughs, Margaret; Redman, Rebecca; Chayama, Kazuaki; Kumada, Hiromitsu; Collins, Christine; Pilot-Matias, Tami

    2016-02-01

    Treatment of HCV genotype 1b (GT1b)-infected Japanese patients with paritaprevir (NS3/4A inhibitor boosted with ritonavir) and ombitasvir (NS5A inhibitor) in studies M12-536 and GIFT-I demonstrated high sustained virologic response (SVR) rates. The virologic failure rate was 3% (13/436) across the two studies. Analyses were conducted to evaluate the impact of baseline resistance-associated variants (RAVs) on treatment outcome and the emergence and persistence of RAVs in patients experiencing virologic failure. Baseline paritaprevir resistance-conferring variants in NS3 were infrequent, while Y93H in NS5A was the most prevalent ombitasvir resistance-conferring variant at baseline. A comparison of baseline prevalence of polymorphisms in Japanese and western patients showed that Q80L and S122G in NS3 and L28M, R30Q, and Y93H in NS5A were significantly more prevalent in Japanese patients. In the GIFT-I study, the prevalence of Y93H in NS5A varied between 13% and 21% depending on the deep-sequencing detection threshold. Among patients with Y93H comprising 40% of their preexisting viral population, the 24-week SVR (SVR24) rates were >99% (276/277), 93% (38/41), and 76% (25/33), respectively, indicating that the prevalence of Y93H within a patient's viral population is a good predictor of treatment response. The predominant RAVs at the time of virologic failure were D168A/V in NS3 and Y93H alone or in combination with other variants in NS5A. While levels of NS3 RAVs declined over time, NS5A RAVs persisted through posttreatment week 48. Results from these analyses are informative in understanding the resistance profile of an ombitasvir- plus paritaprevir/ritonavir-based regimen in Japanese GT1b-infected patients. PMID:26643326

  11. Direct-acting Antiviral Agents Resistance-associated Polymorphisms in Chinese Treatment-na(i)ve Patients Infected with Genotype 1b Hepatitis C Virus

    Institute of Scientific and Technical Information of China (English)

    Ye Wang; Hui-Ying Rao; Xing-Wang Xie; Lai Wei

    2015-01-01

    Background:It has been reported that several baseline polymorphisms of direct-acting antivirals (DAAs) agents resistance-associated variants (RAVs) would affect the treatment outcomes of patients chronically infected with hepatitis C virus (CHC).The aim of this study is to investigate the prevalence of DAAs RAVs in treatment-na(i)ve GT1b CHC patients.Methods:Direct sequencing and ultra-deep sequencing of the HCV NS3,NS5A,and NS5B gene were performed in baseline serum samples of treatment-ha(i)ve patients infected with genotype lb hepatitis C virus (HCVs).Results:One hundred and sixty CHC patients were studied.Complete sequence information was obtained for 145 patients (NS3),148 patients (NS5A),and 137 patients (NS5B).Treatment-failure associated variants of DAAs were detected:56.6% (82/145) of the patients presented S122G for simeprevir (NS3 protease inhibitor);10.1% (14/148) of the patients presented Y93H for daclatasvir and ledipasvir (NS5A protein inhibitors);94.2% (129/137) of the patients presented C316N for sofosbuvir (NS5B polymerase inhibitor).Nearly,all of the DAAs RAVs detected by ultra-deep sequencing could be detected by direct sequencing.Conclusions:The majority of genotype lb CHC patients in China present a virus population carrying HCV DAAs RAVs.Pretreatment sequencing of HCV genome might need to be performed when patients infected with GTlb HCV receiving DAAs-containing regimens in China.Population sequencing would be quite quantified for the work.

  12. Stability of the resistance to the thiosemicarbazone derived from 5,6-dimethoxy-1-indanone, a non-nucleoside polymerase inhibitor of bovine viral diarrhea virus.

    Science.gov (United States)

    Castro, Eliana F; Campos, Rodolfo H; Cavallaro, Lucía V

    2014-01-01

    Bovine viral diarrhea virus (BVDV) is the prototype Pestivirus. BVDV infection is distributed worldwide and causes serious problems for the livestock industry. The thiosemicarbazone of 5,6-dimethoxy-1-indanone (TSC) is a non-nucleoside polymerase inhibitor (NNI) of BVDV. All TSC-resistant BVDV variants (BVDV-TSCr T1-5) present an N264D mutation in the NS5B gene (RdRp) whereas the variant BVDV-TSCr T1 also presents an NS5B A392E mutation. In the present study, we carried out twenty passages of BVDV-TSCr T1-5 in MDBK cells in the absence of TSC to evaluate the stability of the resistance. The viral populations obtained (BVDV R1-5) remained resistant to the antiviral compound and conserved the mutations in NS5B associated with this phenotype. Along the passages, BVDV R2, R3 and R5 presented a delay in the production of cytopathic effect that correlated with a decrease in cell apoptosis and intracellular accumulation of viral RNA. The complete genome sequences that encode for NS2 to NS5B, Npro and Erns were analyzed. Additional mutations were detected in the NS5B of BVDV R1, R3 and R4. In both BVDV R2 and R3, most of the mutations found were localized in NS5A, whereas in BVDV R5, the only mutation fixed was NS5A V177A. These results suggest that mutations in NS5A could alter BVDV cytopathogenicity. In conclusion, the stability of the resistance to TSC may be due to the fixation of different compensatory mutations in each BVDV-TSCr. During their replication in a TSC-free medium, some virus populations presented a kind of interaction with the host cell that resembled a persistent infection: decreased cytopathogenicity and viral genome synthesis. This is the first report on the stability of antiviral resistance and on the evolution of NNI-resistant BVDV variants. The results obtained for BVDV-TSCr could also be applied for other NNIs. PMID:24950191

  13. Hagedorn Behavior of Little String Theories

    CERN Document Server

    Harmark, T

    2000-01-01

    We examine the Hagedorn behavior of little string theory using its conjectured duality with near-horizon NS5-branes. In particular, by studying the string-corrected NS5-brane supergravity solution, it is shown that tree-level corrections to the temperature vanish, while the leading one-loop string correction generates the correct temperature dependence of the entropy near the Hagedorn temperature. Finally, the Hagedorn behavior of ODp-brane theories, which are deformed versions of little string theory, is considered via their supergravity duals.

  14. Investigation of the influence of the nonstructural protein 5A of hepatitis C virus on cell proliferation, apoptosis and carcinogenesis in vitro and in vivo

    OpenAIRE

    Kriegs, Malte

    2010-01-01

    The hepatitis C virus (HCV) is an enveloped positive-strand RNA virus which belongs to the family of the Flaviviridea. The genome codes for the structural proteins core, E1 and E2 and the nonstructural proteins p7, NS2, NS3, NS4A, NS4B, NS5A and NS5B. Because the nonstructural protein 5A is able to deregulate important signalling cascades for cell proliferation and differantiation, the protein is thought to play a major role in the development of HCV-associated HCC progression. In the firs...

  15. The Heterotic Enhancon

    CERN Document Server

    Natsuume, M

    2002-01-01

    The enhancon mechanism is studied in the heterotic string theory. We consider the N_L=0 winding strings with momentum (NS1-W*) and the Kaluza-Klein dyons (KK5-NS5*). The NS1-W* and KK5-NS5* systems are dualized to the D4-D0* and D6-D2* systems respectively under the d=6 heterotic/IIA S-duality. The heterotic form has a number of advantages over the type IIA form. We study these backgrounds and obtain the enhancon radii by brane probe analysis. The results are consistent with the S-duality.

  16. D-Brane solutions in a light-like linear dilaton background

    CERN Document Server

    Nayak, R R; Nayak, Rashmi R.; Panigrahi, Kamal L.

    2006-01-01

    The light-like linear dilaton background presents a simple time dependent solution of type II supergravity equations of motion that preserves 1/2 supersymmetry in ten dimensions. We construct supergravity D-brane solutions in a linear dilaton background starting from the known intersecting brane solutions in string theory. By applying a Penrose limit on the intersecting (NS1-NS5-NS5')- brane solution, we find out a D5-brane in a linear dilaton background. We solve the Killing spinor equations for the brane solutions explicitly, and show that they preserve 1/4 supersymmetry. We also find a M5-brane solution in eleven dimensional supergravity.

  17. HLA-B27 Selects for Rare Escape Mutations that Significantly Impair Hepatitis C Virus Replication and Require Compensatory Mutations

    OpenAIRE

    Neumann-Haefelin, Christoph; Oniangue-Ndza, Cesar; Kuntzen, Thomas; Schmidt, Julia; Nitschke, Katja; Sidney, John; Caillet-Saguy, Célia; Binder, Marco; Kersting, Nadine; Kemper, Michael W.; Power, Karen A.; Ingber, Susan; Reyor, Laura L.; Hills-Evans, Kelsey; Kim, Arthur Y.

    2011-01-01

    HLA-B27 is associated with spontaneous viral clearance in hepatitis C virus (HCV) infection. Viral escape within the immunodominant HLA-B27 restricted HCV-specific CD8+ T cell epitope NS5B2841-2849 (ARMILMTHF) has been shown to be limited by viral fitness costs as well as broad T cell cross-recognition, suggesting a potential mechanism of protection by HLA-B27. Here, we studied the subdominant HLA-B27 restricted epitope NS5B2936-2944 (GRAAICGKY) in order to further define the mechanisms of pr...

  18. Stability of the resistance to the thiosemicarbazone derived from 5,6-dimethoxy-1-indanone, a non-nucleoside polymerase inhibitor of bovine viral diarrhea virus.

    Directory of Open Access Journals (Sweden)

    Eliana F Castro

    Full Text Available Bovine viral diarrhea virus (BVDV is the prototype Pestivirus. BVDV infection is distributed worldwide and causes serious problems for the livestock industry. The thiosemicarbazone of 5,6-dimethoxy-1-indanone (TSC is a non-nucleoside polymerase inhibitor (NNI of BVDV. All TSC-resistant BVDV variants (BVDV-TSCr T1-5 present an N264D mutation in the NS5B gene (RdRp whereas the variant BVDV-TSCr T1 also presents an NS5B A392E mutation. In the present study, we carried out twenty passages of BVDV-TSCr T1-5 in MDBK cells in the absence of TSC to evaluate the stability of the resistance. The viral populations obtained (BVDV R1-5 remained resistant to the antiviral compound and conserved the mutations in NS5B associated with this phenotype. Along the passages, BVDV R2, R3 and R5 presented a delay in the production of cytopathic effect that correlated with a decrease in cell apoptosis and intracellular accumulation of viral RNA. The complete genome sequences that encode for NS2 to NS5B, Npro and Erns were analyzed. Additional mutations were detected in the NS5B of BVDV R1, R3 and R4. In both BVDV R2 and R3, most of the mutations found were localized in NS5A, whereas in BVDV R5, the only mutation fixed was NS5A V177A. These results suggest that mutations in NS5A could alter BVDV cytopathogenicity. In conclusion, the stability of the resistance to TSC may be due to the fixation of different compensatory mutations in each BVDV-TSCr. During their replication in a TSC-free medium, some virus populations presented a kind of interaction with the host cell that resembled a persistent infection: decreased cytopathogenicity and viral genome synthesis. This is the first report on the stability of antiviral resistance and on the evolution of NNI-resistant BVDV variants. The results obtained for BVDV-TSCr could also be applied for other NNIs.

  19. Supergravity and Light-Like Non-commutativity

    CERN Document Server

    Alishahiha, M; Russo, Jorge G; Alishahiha, Mohsen; Oz, Yaron; Russo, Jorge G.

    2000-01-01

    We construct dual supergravity descriptions of field theories and little string theories with light-like non-commutativity. The field theories are realized on the world-volume of Dp branes with light-like NS $B$ field and M5 branes with light-like $C$ field. The little string theories are realized on the world-volume of NS5 branes with light-like RR $A$ fields. The supergravity backgrounds are closely related to the $A=0,B=0,C=0$ backgrounds. We discuss the implications of these results. We also construct dual supergravity descriptions of ODp theories realized on the worldvolume of NS5 branes with RR backgrounds.

  20. Daclatasvir plus peginterferon alfa and ribavirin for treatment-naive chronic hepatitis C genotype 1 or 4 infection

    DEFF Research Database (Denmark)

    Hézode, Christophe; Hirschfield, Gideon M; Ghesquiere, Wayne;

    2015-01-01

    OBJECTIVE: To evaluate the safety and efficacy of daclatasvir, an HCV NS5A inhibitor with pangenotypic activity, administered with peginterferon-alfa-2a/ribavirin. DESIGN: In this Phase 2b double-blind, placebo-controlled study, treatment-naive adults with HCV genotype 1 (N=365) or 4 (N=30) infec...

  1. Efficient replication of genotype 3a and 4a hepatitis C virus replicons in human hepatoma cells

    DEFF Research Database (Denmark)

    Saeed, Mohsan; Scheel, Troels K H; Gottwein, Judith M;

    2012-01-01

    to express a chimeric fusion protein of firefly luciferase and neomycin phosphotransferase to yield stable replicon-expressing cells. Using these constructs, the inhibitory effects of beta interferon (IFN-β), an NS3 protease inhibitor, and an NS5B nucleoside polymerase inhibitor were readily detected...

  2. Kaluza-Klein monopole and 5-brane effective actions

    NARCIS (Netherlands)

    Eyras, E; Lozano, Y

    2000-01-01

    We review the construction of the Kaluza-Klein monopole of the Type IIA theory in the most general case of a massive background, as well as its relation via T-duality with the Type IIB NS-5-brane. This last effective action is shown to be related by S-duality to the D5-brane effective action. [GRAPH

  3. Drug: D08951 [KEGG MEDICUS

    Lifescience Database Archive (English)

    Full Text Available Hepatitis C [DS:H00413] nonnucleoside polymerase inhibitor HCV NS5B is RNA-dependent RNA polymerase(RdRP). N...D08951 Drug Nesbuvir (USAN) C22H23FN2O5S 446.1312 446.4918 D08951.gif Treatment of

  4. The juxtamembrane sequence of the Hepatitis C virus polymerase can affect RNA synthesis and inhibition by allosteric polymerase inhibitors.

    Science.gov (United States)

    Wen, Y; Lin, X; Fan, B; Ranjith-Kumar, C T; Kao, C C

    2015-08-01

    The Hepatitis C virus (HCV) RNA-dependent RNA polymerase (RdRp), nonstructural protein 5B (NS5B), is anchored in the membrane through a C-terminal helix. A sequence of ca. 12 residues that connects the catalytically competent portion of the RdRp and the C-terminal helix, the juxtamembrane sequence (JMS), has a poorly defined role in RdRp function in a large part since it is translated from a cis-acting RNA element (CRE) that is essential for HCV replication. Using a HCV replicon that transposed a second copy of CRE to the 3' UTR of the HCV replicon, we demonstrate that amino acid substitutions in the JMS were detrimental for HCV replicon replication. Substitutions in the JMS also resulted in a defect in de novo-initiated RNAs synthesis in vitro and in a cell-based reporter assay. A nonnucleoside inhibitor of the NS5B that binds to the catalytic pocket was less potent in inhibiting NS5B in the presence of JMS mutations. The JMS mutants exhibit reduced stability in thermodenaturation assays, suggesting that the JMS helps confer a more stable conformation to NS5B that could impact RNA synthesis. PMID:25895103

  5. Restricted Isotypic Antibody Reactivity to Hepatitis C Virus Synthetic Peptides in Immunocompromised Patients

    Science.gov (United States)

    Devesa, Marisol; de Saez, Arlette; León, Graciela; Sirit, Firelei; Cosson, Clarisa; Bermúdez, Henry; Liprandi, Ferdinando; Noya, Oscar; Pujol, Flor H.

    1999-01-01

    An enzyme immunoassay based on three synthetic peptides from the core, NS4, and NS5 regions of hepatitis C virus allowed the detection of antibodies in 100% of immunocompetent infected patients and in 91% of immunocompromised patients (hemodialysis and hemophiliac patients). Immune impairment seemed to restrict the spectrum of antibody isotypes reacting to the core peptide. PMID:10066669

  6. Function of nonstructural 5A protein of genotype 2a in replication and infection of HCV with gene substitution

    Institute of Scientific and Technical Information of China (English)

    Yong-Zhi Wang; Wen-Bo Wang; Ming-Mei Cao; Wen Wang; Lan-Juan Zhao; Gang Xu; Hao Ren; Zhong-Tian Qi

    2011-01-01

    AIM: To explore the function of Nonstructural 5A (NS5A) protein of genotype 2a (JFH1) in the replication and infection of hepatitis C virus (HCV).METHODS: Intergenotypic chimera FL-J6JFH/J4NS5A was constructed by inserting NS5A gene from 1b stain HC-J4 by the overlapping polymerase chain reaction (PPCR) method and the restriction enzyme reaction.In vitro RNA transcripts of chimera, prototype J6JFH and negative control J6JFH1 (GNDD) were prepared and transfected into Huh-7.5 cells with liposomes. Immunofluorescence assay (IFA), fluorescence quantitative PCR and infection assay were performed to determine the protein expression and gene replication in Huh-7.5 cells.RESULTS: The HCV RNA levels in FL-J6JFH/J4NS5A chimera RNA transfected cells were significantly lower than the wild type at any indicated time point (2.58± 5.97×106 vs 4.27 ± 1.72×104, PP = 00.0032). The maximal level of HCV RNA in chimera was 5.6±1.8×104 GE/μg RNA at day 34 after transfection, while the wild type reached a peak level at day 13 which was 126 folds higher (70.65 ± 14.11×105 vs 0.56 ± 0.90×105, = 0.028). HCV proteins could also be detected by IFA in chimera-transfected cells with an obviously low level. Infection assay showed that FL-J6JFH/J4NS5A chimera could produce infectious virus particles, ranging from 10 ± 5 ffu/mL to 78.3 ± 23.6 ffu/mL, while that of FL-J6JFH1 ranged from 5.8 ± 1.5×102 ffu/mL to 2.5 ± 1.4×104 ffu/mL.CONCLUSION: JFH1 NS5A might play an important role in the robust replication of J6JFH1. The establishment of FL-J6JFH/J4NS5A provided a useful platform for studying the function of other proteins of HCV.

  7. Resistance analysis of baseline and treatment-emergent variants in hepatitis C virus genotype 1 in the AVIATOR study with paritaprevir-ritonavir, ombitasvir, and dasabuvir.

    Science.gov (United States)

    Krishnan, Preethi; Tripathi, Rakesh; Schnell, Gretja; Reisch, Thomas; Beyer, Jill; Irvin, Michelle; Xie, Wangang; Larsen, Lois; Cohen, Daniel; Podsadecki, Thomas; Pilot-Matias, Tami; Collins, Christine

    2015-09-01

    AVIATOR, a phase 2 clinical trial, evaluated ritonavir-boosted paritaprevir (a protease inhibitor), ombitasvir (an NS5A inhibitor), and dasabuvir (a nonnucleoside polymerase inhibitor) (the three-drug [3D] regimen) with or without ribavirin (RBV) for 8, 12, or 24 weeks in 406 HCV genotype 1 (GT1)-infected patients. The rate of sustained virologic response 24 weeks after treatment ranged from 88% to 100% across the arms of the 3D regimen with or without RBV; 20 GT1a-infected patients and 1 GT1b-infected patient experienced virologic failure (5.2%). Baseline resistance-conferring variants in NS3 were rare. M28V in GT1a and Y93H in GT1b were the most prevalent preexisting variants in NS5A, and C316N in GT1b and S556G in both GT1a and GT1b were the most prevalent variants in NS5B. Interestingly, all the GT1a sequences encoding M28V in NS5A were from the United States, while GT1b sequences encoding C316N and S556G in NS5B were predominant in the European Union. Variants preexisting at baseline had no significant impact on treatment outcome. The most prevalent treatment-emergent resistance-associated variants (RAVs) in GT1a were R155K and D168V in NS3, M28T and Q30R in NS5A, and S556G in NS5B. The single GT1b-infected patient experiencing virologic failure had no RAVs in any target. A paritaprevir-ritonavir dose of 150/100 mg was more efficacious in suppressing R155K in NS3 than a 100/100-mg dose. In patients who failed after receiving 12 or more weeks of treatment, RAVs were selected in all 3 targets, while most patients who relapsed after 8 weeks of treatment did so without any detectable RAVs. Results from this study guided the selection of the optimal treatment regimen, treatment duration, and paritaprevir dose for further development of the 3D regimen. (This study has been registered at ClinicalTrials.gov under registration number NCT01464827.). PMID:26100711

  8. POTENSI PROBIOTIK BAKTERI ASAM LAKTAT ASAL BEKASAM IKAN NILA [Probiotic Potential of Bekasam Lactic Acid Bacteria of Tilapia Fish

    Directory of Open Access Journals (Sweden)

    Astri Nurnaafi

    2015-07-01

    Full Text Available Bekasam is well known in Indonesia as one of fermented fish product. Several fermented products generate lactic acid bacteria (LAB which has probiotic potential with beneficial effects on human health. However, In Indonesia, the research on LAB isolated from fermented fish product, including bekasam, is still rarely conducted. The aim of this study was to evaluate the probiotic potential of LAB isolated from bekasam. Two LAB isolates namely NS(5 and NS(6 were selected based on their resistance to gastric pH (pH 2.0, intestinal pH (pH 7.2 and bile salts (0.5% oxgal. Pathogenic test, antimicrobial activity test, characterization and identification of the isolats were also performed respectively. The result showed that NS(5 isolate survived at pH 2.0, pH 7.2 and bile salts (oxgal. It was obtained that NS(5 isolate was non pathogenic bacteria which exhibited antimicrobial activity against Salmonella Typhimurium ATCC 14028 and Escherichia coli. The characterization result showed that NS(5 isolate was Gram-positive bacteria, rod-shaped, non-endospore producer, negative catalase, homofermentative, non motile, having an amilolitik as well as lipolitik activity and able to grow at 30-37°C, NaCl 2-7% dan pH 4.4-9.6. Isolate NS(5 isolate was then identified as Lactobacillus plantarum 1 strain with 99.9% of similarity. Meanwhile, NS(6 isolate was not able to survive in the medium containing bile salts (oxgal, therefore it was not categorized as a probiotic candidate.

  9. Hepatitis C virus induces E6AP-dependent degradation of the retinoblastoma protein.

    Directory of Open Access Journals (Sweden)

    Tsubasa Munakata

    2007-09-01

    Full Text Available Hepatitis C virus (HCV is a positive-strand RNA virus that frequently causes persistent infections and is uniquely associated with the development of hepatocellular carcinoma. While the mechanism(s by which the virus promotes cancer are poorly defined, previous studies indicate that the HCV RNA-dependent RNA polymerase, nonstructural protein 5B (NS5B, forms a complex with the retinoblastoma tumor suppressor protein (pRb, targeting it for degradation, activating E2F-responsive promoters, and stimulating cellular proliferation. Here, we describe the mechanism underlying pRb regulation by HCV and its relevance to HCV infection. We show that the abundance of pRb is strongly downregulated, and its normal nuclear localization altered to include a major cytoplasmic component, following infection of cultured hepatoma cells with either genotype 1a or 2a HCV. We further demonstrate that this is due to NS5B-dependent ubiquitination of pRb and its subsequent degradation via the proteasome. The NS5B-dependent ubiquitination of pRb requires the ubiquitin ligase activity of E6-associated protein (E6AP, as pRb abundance was restored by siRNA knockdown of E6AP or overexpression of a dominant-negative E6AP mutant in cells containing HCV RNA replicons. E6AP also forms a complex with pRb in an NS5B-dependent manner. These findings suggest a novel mechanism for the regulation of pRb in which the HCV NS5B protein traps pRb in the cytoplasm, and subsequently recruits E6AP to this complex in a process that leads to the ubiquitination of pRb. The disruption of pRb/E2F regulatory pathways in cells infected with HCV is likely to promote hepatocellular proliferation and chromosomal instability, factors important for the development of liver cancer.

  10. Prokaryotical expression of structural and non-structural proteins of hepatitis G virus

    Institute of Scientific and Technical Information of China (English)

    Ning-Shao Xia; Hai-Jie Yang; Jun Zhang; Chang-Qing Lin; Ying-Bin Wang; Juan Wang; Mei-YunZhan; MH Ng

    2001-01-01

    AIM To study the epitope distribution of hepatitis G virus (HGV) and to seek for the potential recombinant antigens for the development of HGV diagnositic reagents.METHODS Fourteen clones encompassing HGV gene fragments from core to NS3 and NS5 were constructed using prokaryotic expression vector pRSET and (or)pGEX. and expressed in E. coli. Western blotting and ELISA were used to detect the immunoreactivity of these recombinant proteins.``RESULTS One clone with HGV fragment from core to El(Gl). one from E2 (G31), three from NS3 (G6, G61, G7),one from NS5B (G821) and one chimeric fragment from NS3and NS5B (G61 821) could be expressed well and showed obvious immunoreactivity by Western blotting.One clone with I-KGV framment from NS5B (G82) was also well expressed, but could not show immunoreactivity by Western blotting. No obvious expression was found in the other six clones. All the expressed recombinant proteins were in inclusion body form, except the protein G61 which could be expressed in soluble form. Further purified recombinant proteins Gl, G,31, G61, G821 and G61 821were detected in indirected ELISA as coating antigen respectively. Only recombinant Gl could still show immunoreactivity, and the other four recombinant proteins failed to react to the HGV antibody positive sera.Western blotting results indicated that the immunoactivity of these four recombinant proteins were lost during purification.``CONCLUSION Core to El, E2. NS3 and NS5 fragment of HGV contain antigenic epitopes, which could be produced in prokaryotically expressed recombinant proteins. A high. yield recombinant protein (Gl) located in HGV core to E1 could remain its epitope after purification, which showed the potential that G1 could be used as a coating antigen to develop an ELISA kit for HGV specific antibody diagnosis.``

  11. Hepatitis C Virus Genotype 4 Resistance and Subtype Demographic Characterization of Patients Treated with Ombitasvir plus Paritaprevir/Ritonavir

    Science.gov (United States)

    Tripathi, Rakesh; Beyer, Jill; Reisch, Thomas; Krishnan, Preethi; Lu, Liangjun; Dekhtyar, Tatyana; Hall, Coleen; Vilchez, Regis A.; Pilot-Matias, Tami; Collins, Christine

    2015-01-01

    Hepatitis C virus (HCV) genotype 4 (GT4) is genetically diverse, with 17 confirmed subtypes, and comprises approximately 13% of infections worldwide. In this study, we identified GT4 subtypes by phylogenetic analysis, assessed differences in patient demographics across GT4 subtypes, examined baseline sequence variability among subtypes and the potential impact on treatment outcome, and analyzed the development of viral resistance in patients who received a regimen of ombitasvir (nonstructural protein 5A [NS5A] inhibitor) plus ritonavir-boosted paritaprevir (NS3/4A inhibitor) with or without ribavirin (RBV) for the treatment of HCV GT4 infection. Phylogenetic analysis of HCV NS3/4A, NS5A, and NS5B nucleotide sequences identified 7 subtypes (4a, 4b, 4c, 4d, 4f, 4g/4k, and 4o) among 132 patient samples. Subtype prevalence varied by country, and the distributions of patient birth cohort and race were significantly different across GT4 subtypes 4a, 4d, and non-4a/4d. Baseline amino acid variability was detected in NS5A across GT4 subtypes but had no impact on treatment outcome. Three patients experienced virologic failure and were infected with subtype 4d, and the predominant resistance-associated variants at the time of failure were D168V in NS3 and L28V in NS5A. Overall, high response rates were observed among patients infected with 7 HCV GT4 subtypes, with no impact of baseline variants on treatment outcome. GT4 subtype distribution in this study differed based on patient demographics and geography. PMID:26282418

  12. Improved serodiagnosis of hepatitis C virus infection with synthetic peptide antigen from capsid protein.

    OpenAIRE

    Hosein, B; Fang, C T; Popovsky, M A; J. Ye; Zhang, M; WANG, C. Y.

    1991-01-01

    Cloning and expression of hepatitis C virus have allowed the development of immunoassays to detect hepatitis C virus infection. However, currently available recombinant fusion protein C100-3 assays, based on a nonstructural protein of the virus, are limited in sensitivity, particularly for detecting acute infection. In this report seroconversion panels showed that an assay based on synthetic peptides, derived from immunodominant regions of both capsid and nonstructural proteins, accelerated h...

  13. Dicty_cDB: Contig-U15693-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available ixed Tissue and... 111 1e-19 1 ( AZ917266 ) 4911.fd64h15.x1 Saccharomyces bayanus MCYC 623-6C... 100 3e-19 2 ( EF650282 ) Diogm...EF650282_1( EF650282 |pid:none) Diogmites grossus alanyl-tRNA synt... 273 1e-71 (B1IJG7) RecName: Full=Alany

  14. Characterization of the Anti-HCV Activities of the New Cyclophilin Inhibitor STG-175

    Science.gov (United States)

    Gallay, Philippe A.; Chatterji, Udayan; Bobardt, Michael D.; Long, Zhengyu; Zhang, Shengli; Su, Zhuang

    2016-01-01

    Shortened current direct-acting antiviral (DAA) therapies while less expensive, have not provided satisfactory efficacy in naïve cirrhotics, treatment experienced non-cirrhotics or even genotype-3 (GT3)-infected patients. Since DAA regimens consist of the same classes of inhibitors—NS5A (NS5Ai) and NS5B (NS5Bi) +/- NS3 (NS3i) inhibitors—it is likely that their costs will be high and will provide similar degrees of protection. Integrating drugs with distinct mechanisms of action (MoA) into DAA regimens could provide the solution for shortening the period of treatment. One such class of agents is the cyclophilin inhibitors (CypI), which has shown efficacy in patients. Resistance-associated variants persist for years post-treatment in patients exposed to NS5Ai or NS5Bi who fail to achieve a sustained virologic response, impairing their chance for cure on retreatment with existing DAA combinations. Because of their high barrier to resistance, CypI may be particularly useful as a rescue therapy for patients who have relapsed with DAA resistance-associated variants. In this study, we analyzed the anti-HCV properties of the novel cyclosporine A (CsA) derivate—STG-175. The non-immunosuppressive STG-175 possesses a high (EC50 11.5–38.9 nM) multi-genotypic (GT1a to 4a) anti-HCV activity. STG-175 clears cells from HCV since no viral replication rebound was observed after cessation of drug treatment. It presents a higher barrier to resistance than other CypI or selected DAAs. HCV variants, which emerged under STG-175 pressure, are only ~2-fold resistant to the drug. No cross-resistance was observed with DAAs STG-175 was efficacious against DAA-resistant HCV variants. Drug combination studies revealed that STG-175 provides additive and synergistic effects against GT1a to 4a. STG-175 inhibits the infection of HCV, HIV-1 and HBV in mono-, dual- and triple-infection settings. Altogether these results suggest that the new CypI STG-175 represents an attractive drug partner

  15. Similar prevalence of low-abundance drug-resistant variants in treatment-naive patients with genotype 1a and 1b hepatitis C virus infections as determined by ultradeep pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Severine Margeridon-Thermet

    Full Text Available Hepatitis C virus (HCV variants that confer resistance to direct-acting-antiviral agents (DAA have been detected by standard sequencing technology in genotype (G 1 viruses from DAA-naive patients. It has recently been shown that virological response rates are higher and breakthrough rates are lower in G1b infected patients than in G1a infected patients treated with certain classes of HCV DAAs. It is not known whether this corresponds to a difference in the composition of G1a and G1b HCV quasispecies in regards to the proportion of naturally occurring DAA-resistant variants before treatment.We used ultradeep pyrosequencing to determine the prevalence of low-abundance (<25% of the sequence reads DAA-resistant variants in 191 NS3 and 116 NS5B isolates from 208 DAA-naive G1-infected patients.A total of 3.5 million high-quality reads of ≥ 200 nucleotides were generated. The median coverage depth was 4150x and 4470x per NS3 and NS5B amplicon, respectively. Both G1a and G1b populations showed Shannon entropy distributions, with no difference between G1a and G1b in NS3 or NS5B region at the nucleotide level. A higher number of substitutions that confer resistance to protease inhibitors were observed in G1a isolates (mainly at amino acid 80 of the NS3 region. The prevalence of amino acid substitutions that confer resistance to NS5B non-nucleoside inhibitors was similar in G1a and G1b isolates. The NS5B S282T variant, which confers resistance to the polymerase inhibitors mericitabine and sofosbuvir, was not detected in any sample.The quasispecies genetic diversity and prevalence of DAA-resistant variants was similar in G1a and G1b isolates and in both NS3 and NS5B regions, suggesting that this is not a determinant for the higher level of DAA resistance observed across G1a HCV infected patients upon treatment.

  16. Evidence of intratypic recombination in natural populations of hepatitis C virus

    International Nuclear Information System (INIS)

    Hepatitis C virus (HCV) has high genomic variability and, since its discovery, at least six different types and an increasing number of subtypes have been reported. Genotype 1 is the most prevalent genotype found in South America. In the present study, three different genomic regions (5 UTR, core and NS5B) of four HCV strains isolated from Peruvian patients were sequenced in order to investigate the congruence of HCV genotyping for these three genomic regions. Phylogenetic analysis using 5 UTR-core sequences found strain PE22 to be related to subtype 1a. To test the possibility of genetic recombination, phylogenetic studies were carried out, revealing that a crossover event had taken place in the NS5B protein. We discuss the consequences of this observation on HCV genotype classification, laboratory diagnosis and treatment of HCV infection

  17. Phytochemical Study of Myrtopsis corymbosa, Perspectives for Anti-dengue Natural Compound Research

    Directory of Open Access Journals (Sweden)

    Paul Coulerie

    2013-05-01

    Full Text Available In order to find new molecules for anti-viral drug design, we screened 102 ethyl acetate extracts obtained from 51 plants native from New-Caledonia for an antiviral activity against the dengue 2 virus RNA dependant RNA polymerase (DENV-NS5 RdRp. Leaf and bark extracts of Myrtopsis corymbosa which strongly inhibited the DENV-NS5 were selected for chemical investigation. We present here the first chemical study of M. corymbosa which led us to isolate three coumarins, namely ramosin (1, myrsellinol (1 and myrsellin (3, and three alkaloids, namely skimmianine (4, γ-fagarin (4 and haplopin (6. These compounds were identified as major compounds from the active extracts of the plant. However, they demonstrated only weak antiviral activity on the dengue virus. Further studies are necessary to know if the antiviral activity is due to a synergy between several compounds or due to the presence of other minor compounds.

  18. Heterotic string plus five-brane systems with asymptotic AdS3

    CERN Document Server

    Gemmer, Karl-Philip; Lechtenfeld, Olaf; Nölle, Christoph; Popov, Alexander D

    2012-01-01

    We present NS1+NS5-brane solutions of heterotic supergravity on curved geometries. They interpolate between a near horizon AdS3 x X^k x T^{7-k} region and R^{1,1} x c(X^k) x T^{7-k}, where X^k (with k = 3,5,6,7) is a k-dimensional geometric Killing spinor manifold, c(X^k) its Ricci-flat cone and T^{7-k} a (7-k)-torus. The solutions require first order alpha'-corrections to the field equations, and special point-like instantons play an important role, whose singular support is a calibrated submanifold wrapped by the NS5-brane. It is also possible to add a gauge anti-5-brane. We determine the super isometries of the near horizon geometry which are supposed to appear as symmetries of the holographically dual two-dimensional conformal field theory.

  19. Divergent antiviral effects of bioflavonoids on the hepatitis C virus life cycle

    Energy Technology Data Exchange (ETDEWEB)

    Khachatoorian, Ronik, E-mail: RnKhch@ucla.edu [Molecular Biology Interdepartmental Ph.D. Program (MBIDP), Molecular Biology Institute, David Geffen School of Medicine at University of California, Los Angeles, California, CA (United States); Molecular Biology Institute, David Geffen School of Medicine at University of California, Los Angeles, California, CA (United States); Arumugaswami, Vaithilingaraja, E-mail: VArumugaswami@mednet.ucla.edu [Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at University of California, Los Angeles, California, CA (United States); Department of Surgery, Regenerative Medicine Institute at Cedars-Sinai Medical Center, Los Angeles, California, CA (United States); Raychaudhuri, Santanu, E-mail: SRaychau@ucla.edu [Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at University of California, Los Angeles, California, CA (United States); Yeh, George K., E-mail: GgYeh@ucla.edu [Molecular Biology Interdepartmental Ph.D. Program (MBIDP), Molecular Biology Institute, David Geffen School of Medicine at University of California, Los Angeles, California, CA (United States); Molecular Biology Institute, David Geffen School of Medicine at University of California, Los Angeles, California, CA (United States); Maloney, Eden M., E-mail: EMaloney@ucla.edu [Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California, CA (United States); Wang, Julie, E-mail: JulieW1521@ucla.edu [Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at University of California, Los Angeles, California, CA (United States); and others

    2012-11-25

    We have previously demonstrated that quercetin, a bioflavonoid, blocks hepatitis C virus (HCV) proliferation by inhibiting NS5A-driven internal ribosomal entry site (IRES)-mediated translation of the viral genome. Here, we investigate the mechanisms of antiviral activity of quercetin and six additional bioflavonoids. We demonstrate that catechin, naringenin, and quercetin possess significant antiviral activity, with no associated cytotoxicity. Infectious virion secretion was not significantly altered by these bioflavonoids. Catechin and naringenin demonstrated stronger inhibition of infectious virion assembly compared to quercetin. Quercetin markedly blocked viral translation whereas catechin and naringenin demonstrated mild activity. Similarly quercetin completely blocked NS5A-augmented IRES-mediated translation in an IRES reporter assay, whereas catechin and naringenin had only a mild effect. Moreover, quercetin differentially inhibited HSP70 induction compared to catechin and naringenin. Thus, the antiviral activity of these bioflavonoids is mediated through different mechanisms. Therefore combination of these bioflavonoids may act synergistically against HCV.

  20. Three-dimensional N=4 Linear Quivers and non-Abelian T-duals

    CERN Document Server

    Lozano, Yolanda; Montero, Jesus; Nunez, Carlos

    2016-01-01

    In this paper we construct a new Type IIB background with an $AdS_4$ factor that preserves ${\\cal N}=4$ Supersymmetry. This solution is obtained using a non-Abelian T-duality transformation on the Type IIA reduction of the $AdS_4\\times S^7$ background. We interpret our configuration as a patch of a more general background with localised sources, dual to the renormalisation fixed point of a $T_{\\rho}^{\\hat{\\rho}} (SU(N))$ quiver field theory. This relates explicitly the $AdS_4$ geometry to a D3-D5-NS5 brane intersection, illuminating what seems to be a more general phenomenon, relating $AdS_{p+1}$ backgrounds generated by non-Abelian T-duality to Dp-D(p+2)-NS5 branes intersections.

  1. Genetic clustering of recent classical swine fever virus isolates from Karnataka, India revealed the emergence of subtype 2.2 replacing subtype 1.1.

    Science.gov (United States)

    Shivaraj, D B; Patil, S S; Rathnamma, D; Hemadri, D; Isloor, S; Geetha, S; Manjunathareddy, G B; Gajendragad, M R; Rahman, H

    2015-09-01

    The phylogenetic analysis of 11 CSFV isolates from Karnataka, India obtained during the year 2012-13 was undertaken to obtain the most reliable genetic typing of the CSFV isolates based on E2, NS5B and 5'UTR genomic regions. The study indicated that all the 11 CSFV isolates belonged to subgroup 2.2. The most reliable classification was obtained with sequence data from the NS5B region which separated all the isolates based on the history of outbreak and geographic origin. Analysis of full length E2 amino acid sequences revealed different genetic makeup of Indian 2.2 isolates compared to 2.2 isolates from different countries. The group 2.2 viruses are gradually spreading as confirmed by frequent detection/ isolation of group 2.2 viruses in the recent years and replacing the subgroup 1.1 viruses, which were hitherto predominantly involved in CSF outbreaks in India. PMID:26396984

  2. ( p, q)-five brane and ( p, q)-string solutions, their bound state and its near horizon limit

    Science.gov (United States)

    Klusoň, Josef

    2016-06-01

    We determine ( p, q)-string and ( p, q)-five brane solutions of type IIB supergravity using SL (2 , ℤ)-symmetry of the full type IIB superstring theory. We also determine SL (2 , ℤ)-transformed solution corresponding to the bound state of NS5-branes and fundamental strings. Then we analyze its near horizon limit and we show that it leads to the AdS3 × S 3 with mixed fluxes.

  3. Meta-Stable Brane Configurations by Quartic Superpotential for Bifundamentals

    Science.gov (United States)

    Ahn, Changhyun

    The type IIA nonsupersymmetric meta-stable brane configuration consisting of three NS5-branes, D4-branes and anti-D4-branes where the electric gauge theory superpotential has a quartic term for the bifundamentals besides a mass term is constructed. By adding the orientifold 4-plane and 6-plane to this brane configuration, we also describe the intersecting brane configurations of type IIA string theory corresponding to the meta-stable nonsupersymmetric vacua of corresponding gauge theories.

  4. A complement-microglial axis drives synapse loss during virus-induced memory impairment.

    Science.gov (United States)

    Vasek, Michael J; Garber, Charise; Dorsey, Denise; Durrant, Douglas M; Bollman, Bryan; Soung, Allison; Yu, Jinsheng; Perez-Torres, Carlos; Frouin, Arnaud; Wilton, Daniel K; Funk, Kristen; DeMasters, Bette K; Jiang, Xiaoping; Bowen, James R; Mennerick, Steven; Robinson, John K; Garbow, Joel R; Tyler, Kenneth L; Suthar, Mehul S; Schmidt, Robert E; Stevens, Beth; Klein, Robyn S

    2016-06-23

    Over 50% of patients who survive neuroinvasive infection with West Nile virus (WNV) exhibit chronic cognitive sequelae. Although thousands of cases of WNV-mediated memory dysfunction accrue annually, the mechanisms responsible for these impairments are unknown. The classical complement cascade, a key component of innate immune pathogen defence, mediates synaptic pruning by microglia during early postnatal development. Here we show that viral infection of adult hippocampal neurons induces complement-mediated elimination of presynaptic terminals in a murine WNV neuroinvasive disease model. Inoculation of WNV-NS5-E218A, a WNV with a mutant NS5(E218A) protein leads to survival rates and cognitive dysfunction that mirror human WNV neuroinvasive disease. WNV-NS5-E218A-recovered mice (recovery defined as survival after acute infection) display impaired spatial learning and persistence of phagocytic microglia without loss of hippocampal neurons or volume. Hippocampi from WNV-NS5-E218A-recovered mice with poor spatial learning show increased expression of genes that drive synaptic remodelling by microglia via complement. C1QA was upregulated and localized to microglia, infected neurons and presynaptic terminals during WNV neuroinvasive disease. Murine and human WNV neuroinvasive disease post-mortem samples exhibit loss of hippocampal CA3 presynaptic terminals, and murine studies revealed microglial engulfment of presynaptic terminals during acute infection and after recovery. Mice with fewer microglia (Il34(-/-) mice with a deficiency in IL-34 production) or deficiency in complement C3 or C3a receptor were protected from WNV-induced synaptic terminal loss. Our study provides a new murine model of WNV-induced spatial memory impairment, and identifies a potential mechanism underlying neurocognitive impairment in patients recovering from WNV neuroinvasive disease. PMID:27337340

  5. Cyclophilin Inhibitors Remodel the Endoplasmic Reticulum of HCV-Infected Cells in a Unique Pattern Rendering Cells Impervious to a Reinfection.

    Directory of Open Access Journals (Sweden)

    Udayan Chatterji

    Full Text Available The mechanisms of action by which cyclophilin inhibitors (CypI interfere with the HCV life cycle remain poorly understood. We reported that CypI and NS5A inhibitors (NS5Ai, but not other classes of anti-HCV agents, prevent assembly of double membrane vesicles (DMVs, which protect replication complexes. We demonstrated that both NS5A and the isomerase cyclophilin A (CypA are required for DMV formation. Here, we examined whether CypI mediate an additional antiviral effect that could further explain the high efficacy of CypI. We identified a unique action of CypI. CypI remodel the organization of the endoplasmic reticulum (ER of HCV-infected cells, but not of uninfected cells. This effect is specific since it was not observed for other classes of anti-HCV agents including NS5Ai, and has no effect on the viability of CypI-treated cells. Since ER serves as platform for the establishment of HCV replication complexes, we asked whether the ER reorganization by CypI would prevent cells from being newly infected. Remarkably, CypI-treated HCV-pre-infected cells remain totally impervious to a reinfection, suggesting that the CypI-mediated ER reorganization prevents a reinfection. This block is not due to residual CypI since CypI-resistant HCV variants also fail to infect these cells. The ER reorganization by CypI is rapid and reversible. This study provides the first evidence that CypI trigger a unique ER reorganization of infected cells, rendering cells transiently impervious to a reinfection. This study further suggests that the HCV-induced ER rearrangement represents a key target for the development of new therapies.

  6. Molecular genotyping of HCV infection in seropositive blood donor

    Science.gov (United States)

    Zarin, Siti Noraziah Abu; Ibrahim, Nazlina

    2013-11-01

    This study is to investigate the prevalence of hepatitis C virus infection in seropositive blood donor. RNA was extracted from 32 positive samples in National Blood Centre and Melaka Hospital. The core and NS5B sequences were obtained from 23 samples. Genotype 3a is most prevalent in this study followed by genotype 1a. Evidence of mixed-genotypes (3a and 1b) infections was found in 5 subjects.

  7. Screening of cellular proteins that interact with the classical swine fever virus non-structural protein 5A by yeast two-hybrid analysis

    Indian Academy of Sciences (India)

    Chengcheng Zhang; Lei He; Kai Kang; Heng Chen; Lei Xu; Yanming Zhang

    2014-03-01

    Classical swine fever virus (CSFV), the pathogen of classical swine fever (CSF), causes severe hemorrhagic fever and vascular necrosis in domestic pigs and wild boar. A large number of evidence has proven that non-structural 5A (NS5A) is not only a very important part of viral replication complex, but also can regulate host cell’s function; however, the underlying mechanisms remain poorly understood. In the current study, aiming to find more clues in understanding the molecular mechanisms of CSFV NS5A’s function, the yeast two-hybrid (Y2H) system was adopted to screen for CSFV NS5A interactive proteins in the cDNA library of the swine umbilical vein endothelial cell (SUVEC). Alignment with the NCBI database revealed 16 interactive proteins: DDX5, PSMC3, NAV1, PHF5A, GNB2L1, CSDE1, HSPA8, BRMS1, PPP2R3C, AIP, TMED10, POLR1C, TMEM70, METAP2, CHORDC1 and COPS6. These proteins are mostly related to gene transcription, protein folding, protein degradation and metabolism. The interactions detected by the Y2H system should be considered as preliminary results. Since identifying novel pathways and host targets, which play essential roles during infection, may provide potential targets for therapeutic development. The finding of proteins obtained from the SUVEC cDNA library that interact with the CSFV NS5A protein provide valuable information for better understanding the interactions between this viral protein and the host target proteins.

  8. Drug: D10165 [KEGG MEDICUS

    Lifescience Database Archive (English)

    Full Text Available D10165 Drug Setrobuvir (USAN) C25H25FN4O6S2 560.12 560.6176 D10165.gif Treatment of...Hepatitis C Antiinfectives [BR:br08307] Antivirals Anti-HCV agent Polymerase inhibitor NS5B polymerase inhibitor Setrobuvir D101...65 Setrobuvir (USAN) CAS: 1071517-39-9 PubChem: 135626883 LigandBox: D101

  9. A complement-microglial axis drives synapse loss during virus-induced memory impairment.

    Science.gov (United States)

    Vasek, Michael J; Garber, Charise; Dorsey, Denise; Durrant, Douglas M; Bollman, Bryan; Soung, Allison; Yu, Jinsheng; Perez-Torres, Carlos; Frouin, Arnaud; Wilton, Daniel K; Funk, Kristen; DeMasters, Bette K; Jiang, Xiaoping; Bowen, James R; Mennerick, Steven; Robinson, John K; Garbow, Joel R; Tyler, Kenneth L; Suthar, Mehul S; Schmidt, Robert E; Stevens, Beth; Klein, Robyn S

    2016-06-22

    Over 50% of patients who survive neuroinvasive infection with West Nile virus (WNV) exhibit chronic cognitive sequelae. Although thousands of cases of WNV-mediated memory dysfunction accrue annually, the mechanisms responsible for these impairments are unknown. The classical complement cascade, a key component of innate immune pathogen defence, mediates synaptic pruning by microglia during early postnatal development. Here we show that viral infection of adult hippocampal neurons induces complement-mediated elimination of presynaptic terminals in a murine WNV neuroinvasive disease model. Inoculation of WNV-NS5-E218A, a WNV with a mutant NS5(E218A) protein leads to survival rates and cognitive dysfunction that mirror human WNV neuroinvasive disease. WNV-NS5-E218A-recovered mice (recovery defined as survival after acute infection) display impaired spatial learning and persistence of phagocytic microglia without loss of hippocampal neurons or volume. Hippocampi from WNV-NS5-E218A-recovered mice with poor spatial learning show increased expression of genes that drive synaptic remodelling by microglia via complement. C1QA was upregulated and localized to microglia, infected neurons and presynaptic terminals during WNV neuroinvasive disease. Murine and human WNV neuroinvasive disease post-mortem samples exhibit loss of hippocampal CA3 presynaptic terminals, and murine studies revealed microglial engulfment of presynaptic terminals during acute infection and after recovery. Mice with fewer microglia (Il34(-/-) mice with a deficiency in IL-34 production) or deficiency in complement C3 or C3a receptor were protected from WNV-induced synaptic terminal loss. Our study provides a new murine model of WNV-induced spatial memory impairment, and identifies a potential mechanism underlying neurocognitive impairment in patients recovering from WNV neuroinvasive disease.

  10. (p,q)-Five Brane and (p,q)-String Solutions, their Bound State and its Near Horizon Limit

    CERN Document Server

    Kluson, J

    2016-01-01

    We determine (p,q)-string and (p,q)-five brane solutions of type IIB supergravity using SL(2,Z)-symmetry of the full type IIB superstring theory. We also determine SL(2,Z)-transformed solution corresponding to the bound state of NS5-branes and fundamental strings. Then we analyze its near horizon limit and we show that it leads to the AdS(3)xS(3) with mixed fluxes.

  11. Cyclophilin Inhibitors Remodel the Endoplasmic Reticulum of HCV-Infected Cells in a Unique Pattern Rendering Cells Impervious to a Reinfection

    Science.gov (United States)

    Chatterji, Udayan; Bobardt, Michael; Schaffer, Lana; Wood, Malcolm; Gallay, Philippe A.

    2016-01-01

    The mechanisms of action by which cyclophilin inhibitors (CypI) interfere with the HCV life cycle remain poorly understood. We reported that CypI and NS5A inhibitors (NS5Ai), but not other classes of anti-HCV agents, prevent assembly of double membrane vesicles (DMVs), which protect replication complexes. We demonstrated that both NS5A and the isomerase cyclophilin A (CypA) are required for DMV formation. Here, we examined whether CypI mediate an additional antiviral effect that could further explain the high efficacy of CypI. We identified a unique action of CypI. CypI remodel the organization of the endoplasmic reticulum (ER) of HCV-infected cells, but not of uninfected cells. This effect is specific since it was not observed for other classes of anti-HCV agents including NS5Ai, and has no effect on the viability of CypI-treated cells. Since ER serves as platform for the establishment of HCV replication complexes, we asked whether the ER reorganization by CypI would prevent cells from being newly infected. Remarkably, CypI-treated HCV-pre-infected cells remain totally impervious to a reinfection, suggesting that the CypI-mediated ER reorganization prevents a reinfection. This block is not due to residual CypI since CypI-resistant HCV variants also fail to infect these cells. The ER reorganization by CypI is rapid and reversible. This study provides the first evidence that CypI trigger a unique ER reorganization of infected cells, rendering cells transiently impervious to a reinfection. This study further suggests that the HCV-induced ER rearrangement represents a key target for the development of new therapies. PMID:27442520

  12. Hepatitis C Drugs: The End of the Pegylated Interferon Era and the Emergence of All-Oral, Interferon-Free Antiviral Regimens: A Concise Review

    Directory of Open Access Journals (Sweden)

    Alan Hoi Lun Yau

    2014-01-01

    Full Text Available Between 2001 and 2011, the standard of care for chronic hepatitis C virus (HCV infection was a combination of pegylated interferon (PEGIFN and ribavirin (RBV. In May 2011, boceprevir and telaprevir, two first-generation NS3/4A protease inhibitors, were approved in combination with PEG-IFN and RBV for 24 to 48 weeks in hepatitis C virus genotype 1 infections. In December 2013, simeprevir, a second-generation NS3/4A protease inhibitor, was approved for use with PEG-IFN and RBV for 12 weeks in genotype 1, while sofosbuvir, a NS5B nucleotide polymerase inhibitor, was approved for use with PEG-IFN and RBV for 12 weeks in genotypes 1 and 4, as well as with RBV alone for 12 weeks in genotype 2 and for 24 weeks in genotype 3. Sofosbuvir combined with simeprevir or an NS5A replication complex inhibitor (ledipasvir or daclatasvir with or without RBV for 12 weeks in genotype 1 resulted in a sustained virological response >90%, irrespective of previous treatment history or presence of cirrhosis. Similarly impressive sustained virological response rates have been shown with ABT-450/r (ritonavir-boosted NS3/4A protease inhibitor-based regimens in combination with other direct-acting antiviral agent(s with or without RBV for 12 weeks in genotype 1. The optimal all-oral interferon-free antiviral regimen likely entails a combination of an NS5B nucleotide polymerase inhibitor with either a second-generation NS3/4A protease inhibitor or an NS5A replication complex inhibitor with or without RBV. Further research is needed to determine the role of resistance testing, clarify the optimal follow-up duration post-treatment, and evaluate the antiviral efficacy and safety in difficult-to-cure patient populations.

  13. Pharmacoinformatics approach for investigation of alternative potential hepatitis C virus nonstructural protein 5B inhibitors

    Directory of Open Access Journals (Sweden)

    Mirza MU

    2015-03-01

    Full Text Available Muhammad Usman Mirza,1 Noor-Ul-Huda Ghori,2 Nazia Ikram,3 Abdur Rehman Adil,4 Sadia Manzoor3 1Centre for Research in Molecular Medicine (CRiMM, The University of Lahore, Lahore, 2Atta-ur-Rehman School of Applied Biosciences (ASAB, National University of Science and Technology, Islamabad, 3Institute of Molecular Biology and Biotechnology (IMBB, The University of Lahore, Lahore, Pakistan; 4Centre for Excellence in Molecular Biology (CEMB, The University of Punjab, Lahore, Pakistan Abstract: Hepatitis C virus (HCV is one of the major viruses affecting the world today. It is a highly variable virus, having a rapid reproduction and evolution rate. The variability of genomes is due to hasty replication catalyzed by nonstructural protein 5B (NS5B which is also a potential target site for the development of anti-HCV agents. Recently, the US Food and Drug Administration approved sofosbuvir as a novel oral NS5B inhibitor for the treatment of HCV. Unfortunately, it is much highlighted for its pricing issues. Hence, there is an urgent need to scrutinize alternate therapies against HCV that are available at affordable price and do not have associated side effects. Such a need is crucial especially in underdeveloped countries. The search for various new bioactive compounds from plants is a key part of pharmaceutical research. In the current study, we applied a pharmacoinformatics-based approach for the identification of active plant-derived compounds against NS5B. The results were compared to docking results of sofosbuvir. The lead compounds with high-binding ligands were further analyzed for pharmacokinetic and pharmacodynamic parameters based on in silico absorption, distribution, metabolism, excretion, and toxicity (ADMET profile. The results showed the potential alternative lead compounds that can be developed into commercial drugs having high binding energy and promising ADMET properties. Keywords: hepatitis C, NS5B inhibitors, molecular docking, Auto

  14. Heads or Tails: Genotyping of Hepatitis C Virus Concerning the 2k/1b Circulating Recombinant Form

    Science.gov (United States)

    Schuermans, Wim; Orlent, Hans; Desombere, Isabelle; Descheemaeker, Patrick; Van Vlierberghe, Hans; Geerts, Anja; Verhelst, Xavier; Reynders, Marijke; Padalko, Elizaveta

    2016-01-01

    As different hepatitis C virus (HCV) genotypes respond differently to initiated therapy, correct HCV genotyping is essential. A potential risk for misclassification of the intergenotypic HCV circulating recombinant form (CRF) 2k/1b strains exists, depending on the genotyping method used. The aim was to investigate the differences in HCV genotyping methods with regard to CRF 2k/1b and to gain insight in the prevalence of the CRF 2k/1b. Genotyping results by Versant HCV Genotype Assay were compared with nonstructural protein 5B (NS5B) sequencing. In total, from November 2001 until March 2015, 3296 serum samples were analyzed by Versant HCV Genotype Assay. As misclassified CRF is harbored among HCV genotype 2, we further focused our search on 142 (4.3%) samples positive for HCV genotype 2. On 116 (81.7%) retrieved samples, the NS5B sequencing was performed. Twelve out of the 116 retrieved samples (10.3%) were classified as CRF 2k/1b by sequencing of the NS5B region. Ten of these 12 samples were originally misclassified as genotype 2a or 2c, while 2 of them were misclassified as genotype 2. Our results show that the current prevalence of CRF 2k/1b is underestimated. The importance of correct HCV genotyping is emphasized, considering the tailored choice of treatment regimen and overall prognosis. PMID:27563879

  15. Efficient infectious cell culture systems of the hepatitis C virus (HCV) prototype strains HCV-1 and H77

    DEFF Research Database (Denmark)

    Li, Yi-Ping; Ramirez, Santseharay; Mikkelsen, Lotte;

    2015-01-01

    . Using CD81-deficient Huh7 cells, we further demonstrated the importance of A970T/I1312V/A2919T or A970T/C2419R/A2919T for virus assembly and that the I1312V/C2419R combination played a major role in virus release. Using a similar approach, we found that NS5B mutation F2994R, identified here from culture...... efficient infectious cell culture systems for these genotype 1a strains by using the HCV-1/SF9_A and H77C in vivo infectious clones. We initially adapted a genome with the HCV-1 5'UTR-NS5A (where UTR stands for untranslated region) and the JFH1 NS5B-3'UTR (5-5A recombinant), including the genotype 2a......-adapted full-length TN viruses and a common NS3 helicase mutation (S1368P) derived from viable H77C and HCV-1 5-5A recombinants, initiated replication and culture adaptation of H77C containing LSG and TNcc(1a)-adaptive mutations. An H77C recombinant harboring 19 mutations (H77Ccc) replicated and spread...

  16. Clinical impact of the hepatitis C virus mutations in the era of directly acting antivirals.

    Science.gov (United States)

    Coppola, Nicola; Minichini, Carmine; Starace, Mario; Sagnelli, Caterina; Sagnelli, Evangelista

    2016-10-01

    Introduced in 2013-2014, the second- and third-wave directly acting antivirals (DAAs) have strongly enhanced the efficacy and tolerability of anti-HCV treatment, with a sustained virological response (SVR) in 90-95% of cases treated. The majority of patients who did not achieve an SVR were found to be infected with HCV strains with a reduced susceptibility to these drugs. Indeed, the high error rate of the viral polymerase and a fast virion production (100-fold higher than the human immunodeficiency virus) result in a mixture of viral genetic populations (quasi-species) pre-existing treatment initiation. These mutants occur frequently in the NS5A region, with a moderate frequency in the NS3/4A region and rarely in the NS5B region. Treatment-induced resistant mutants to NS5A DAAs persist for years after treatment discontinuation, whereas those resistant to the NS3 DAAs have a shorter duration. This review focuses on the type and prevalence of viral strains with a reduced sensitivity to DAAs, their clinical impact and influence on the response to treatment and, consequently, on treatment choice for DAA-experienced patients. J. Med. Virol. 88:1659-1671, 2016. © 2016 Wiley Periodicals, Inc. PMID:26991255

  17. Serendipitous identification of natural intergenotypic recombinants of hepatitis C in Ireland.

    LENUS (Irish Health Repository)

    Moreau, Isabelle

    2006-01-01

    BACKGROUND: Recombination between hepatitis C single stranded RNA viruses is a rare event. Natural viable intragenotypic and intergenotypic recombinants between 1b-1a, 1a-1c and 2k-1b, 2i-6p, respectively, have been reported. Diagnostically recombinants represent an intriguing challenge. Hepatitis C genotype is defined by interrogation of the sequence composition of the 5\\' untranslated region [5\\'UTR]. Occasionally, ambiguous specimens require further investigation of the genome, usually by interrogation of the NS5B region. The original purpose of this study was to confirm the existence of a suspected mixed genotype infection of genotypes 2 and 4 by clonal analysis at the NS5B region of the genome in two specimens from two separate individuals. This initial identification of genotype was based on analysis of the 5\\'UTR of the genome by reverse line probe hybridisation [RLPH]. RESULTS: The original diagnosis of a mixed genotype infection was not confirmed by clonal analysis of the NS5B region of the genome. The phylogenetic analysis indicated that both specimens were natural intergenotypic recombinant forms of HCV. The recombination was between genotypes 2k and 1b for both specimens. The recombination break point was identified as occurring within the NS2 region of the genome. CONCLUSION: The viral recombinants identified here resemble the recombinant form originally identified in Russia. The RLPH pattern observed in this study may be a signature indicative of this particular type of intergenotype recombinant of hepatitis C meriting clonal analysis of NS2.

  18. HCV genotyping using statistical classification approach

    Directory of Open Access Journals (Sweden)

    Norris Ellie D

    2009-07-01

    Full Text Available Abstract The genotype of Hepatitis C Virus (HCV strains is an important determinant of the severity and aggressiveness of liver infection as well as patient response to antiviral therapy. Fast and accurate determination of viral genotype could provide direction in the clinical management of patients with chronic HCV infections. Using publicly available HCV nucleotide sequences, we built a global Position Weight Matrix (PWM for the HCV genome. Based on the PWM, a set of genotype specific nucleotide sequence "signatures" were selected from the 5' NCR, CORE, E1, and NS5B regions of the HCV genome. We evaluated the predictive power of these signatures for predicting the most common HCV genotypes and subtypes. We observed that nucleotide sequence signatures selected from NS5B and E1 regions generally demonstrated stronger discriminant power in differentiating major HCV genotypes and subtypes than that from 5' NCR and CORE regions. Two discriminant methods were used to build predictive models. Through 10 fold cross validation, over 99% prediction accuracy was achieved using both support vector machine (SVM and random forest based classification methods in a dataset of 1134 sequences for NS5B and 947 sequences for E1. Prediction accuracy for each genotype is also reported.

  19. Braneworld localisation in hyperbolic spacetime

    CERN Document Server

    Crampton, B; Stelle, K S

    2014-01-01

    We present a construction employing a type IIA supergravity and 3-form flux background together with an NS5-brane that localises massless gravity near the 5-brane worldvolume. The nonsingular underlying type IIA solution is a lift to 10D of the vacuum solution of the 6D Salam-Sezgin model and has a hyperbolic ${\\cal H}^{(2,2)}\\times S^1$ structure in the lifting dimensions. A fully back-reacted solution including the NS5-brane is constructed by recognising the 10D Salam-Sezgin vacuum solution as a "brane resolved through transgression." The background hyperbolic structure plays a key r\\^ole in generating a mass gap in the spectrum of the transverse-space wave operator, which gives rise to the localisation of gravity on the 6D NS5-brane worldvolume, or, equally, in a further compactification to 4D. Also key to the successful localisation of gravity is the specific form of the corresponding transverse wavefunction Schr\\"odinger problem, which asymptotically involves a $V=-1/(4\\rho^2)$ potential, where $\\rho$ is...

  20. Development of innovative and versatile polythiol probes for use on ELOSA or electrochemical biosensors: application in hepatitis C virus genotyping.

    Science.gov (United States)

    Lereau, Myriam; Fournier-Wirth, Chantal; Mayen, Julie; Farre, Carole; Meyer, Albert; Dugas, Vincent; Cantaloube, Jean-François; Chaix, Carole; Vasseur, Jean-Jacques; Morvan, François

    2013-10-01

    The aim of this study was to develop versatile diagnostic tools based on the use of innovative polythiolated probes for the detection of multiple viruses. This approach is compatible with optical enzyme-linked oligosorbent assay (ELOSA) or electrochemical (biosensors) detection methods. The application targeted here concerns the rapid genotyping of Hepatitis C virus (HCV). HCV genotyping is one of the predictive parameters currently used to define the antiviral treatment strategy and is based on the sequencing of the viral NS5b region. Generic and specific NS5b amplicons were produced by real-time polymease chain reaction (RT-PCR) on HCV(+) human plasma. Original NS5b probes were designed for genotypes 1a/1b, 2a/2b/2c, 3a, and 4a/4d. Robust polythiolated probes were anchored with good efficacy on maleimide-activated microplates (MAM) and gold electrodes. Their grafting on MAM greatly increased the sensitivity of the ELOSA test which was able to detect HCV amplicons with good sensitivity (10 nM) and specificity. Moreover, the direct and real-time electrochemical detection by differential pulse voltammetry enabled a detection limit of 10 fM to be reached with good reproducibility. These innovative polythiolated probes have allowed us to envisage developing flexible, highly sensitive, and easy-to-handle platforms dedicated to the rapid screening and genotyping of a wide range of viral agents. PMID:24050654

  1. Sofosbuvir plus ledipasvir in combination for the treatment of hepatitis C infection.

    Science.gov (United States)

    Bourlière, Marc; Adhoute, Xavier; Ansaldi, Christelle; Oules, Valérie; Benali, Souad; Portal, Isabelle; Castellani, Paul; Halfon, Philippe

    2015-01-01

    Sofsobuvir is the first-in-class NS5B nucleotide inhibitor to be launched as a treatment for the hepatitis C virus (HCV). Its viral potency, pan genotypic activity and high barrier to resistance make it the ideal candidate to become a backbone for several IFN-free regimens. Ledipasvir is a NS5A inhibitor with multi genotypic activity but modest barrier to resistance. The once-daily fixed-dose combination of sofosbuvir plus ledipasvir is the first-in-market single-tablet regimen for the treatment of hepatitis C infection. Recent data demonstrated that this FDC alone, or in combination with ribavirin, is able to achieve HCV cure of at least 90% or more among genotype 1,4, 5 and 6 patients. This combination appears to be suboptimal in genotype 3 patients and other direct acting antiviral combinations with sofosbuvir will help to fulfill this gap in the near future. The safety profile of the fixed dose combination is good. Resistance is not an issue with sofosbuvir but may be a significant issue with regards to ledipasvir for those rare individuals who harbor baseline HCV NS5A resistance-associated variants that conferred a high resistance level. The rational for using FDCs and the available clinical data are reviewed.

  2. Anti-hepatitis C virus drugs:research advances%抗丙型肝炎病毒药物研究进展

    Institute of Scientific and Technical Information of China (English)

    王靖; 何小羊

    2015-01-01

    慢性丙型肝炎病毒(HCV)感染是全球性的公共卫生问题之一,可导致严重的肝病,包括肝硬化及肝癌. 传统的标准治疗方案利巴韦林+聚乙二醇化干扰素对病毒响应率低,副作用大,难以有效治疗HCV感染. 近年来,多种新类型HCV抑制剂得以开发,包括直接抗病毒药物(DAA)以及宿主靶向药物. 这些药物针对病毒生命周期中的必需蛋白,主要包括NS3/4A蛋白酶、NS5B聚合酶、NS5A蛋白或病毒复制相关宿主因子,具有较高的抗病毒活性及良好的安全性和耐受性. 核苷类NS5B聚合酶抑制剂sofosbuvir的成功上市,使HCV的治疗取得了突破性进展.本文综述了近年来抗HCV药物的发展情况,总结了各类抗HCV药物的结构、作用机制及相关抗病毒性质.%Chronic hepatitis C virus (HCV) infection is one of global public health problems, and predominantly results in severe hepatic diseases including hepatic cirrhosis and hepatocellular carcinoma. The traditional standard of care for chronic HCV is the combination of ribavirin and pegylated interferon, which is insufficient to cure the HCV infection due to the suboptimal sustained viral response and severe side effects. Recently new therapeutic approaches have been developed, including direct-acting antiviral agents (DAA) and host-targeting agents, which target essential proteins or host factors in HCV life cycle, such as NS3/4A protease, NS5B polymerase and NS5A protein. These agents exhibit high efficacy, improving safety and tolerability. Thus, the approval of the nucleotide polymerase inhibitor sofosbuvir provides a breakthrough therapy against chronic hepatitis C infection. This review describes the current different classes of HCV inhibitors during the last decades, and their chemical structures, mechanisms and related anti-viral property.

  3. Chronic hepatitis C: future treatment

    Directory of Open Access Journals (Sweden)

    Wendt A

    2014-01-01

    Full Text Available Astrid Wendt, Xavier Adhoute, Paul Castellani, Valerie Oules, Christelle Ansaldi, Souad Benali, Marc BourlièreDepartment of Hepato-Gastroenterology, Hôpital Saint-Joseph, Marseille, FranceAbstract: The launch of first-generation protease inhibitors (PIs is a major step forward in HCV treatment. However, the major advance is up to now restricted to genotype 1 (GT-1 patients. The development of second-wave and second-generation PIs yields higher antiviral potency through plurigenotypic activity, more convenient daily administration, fewer side effects and, for the second-generation PIs, potential activity against resistance-associated variants. NS5B inhibitors include nucleoside/nucleotide inhibitors (NIs and non-nucleotide inhibitors (NNIs. NIs have high efficacy across all genotypes. Sofosbuvir has highly potent antiviral activity across all genotypes in association with pegylated interferon and ribavirin (PR, thus allowing shortened treatment duration. NS5A inhibitors (NS5A.I have highly potent antiviral activity. It has recently been shown for the first time that NS5A.I in combination with protease inhibitors can cure GT-1b null responders in an interferon-free regimen. Besides, several studies demonstrate that interferon (IFN-free regimens with direct-acting antiviral agent combinations are able to cure a large number of either naïve or treatment-experienced GT-1 patients. Moreover, quadruple regimen with PR is able to cure almost all GT-1 null responders. The development of pan-genotypic direct-acting antiviral agents (NIs or NS5A.I allows new combinations with or without PR that increase the rate of sustained virological response for all patients, even for those with cirrhosis and independently of the genotype. Therefore, the near future of HCV treatment looks promising. The purpose of this article is to provide an overview of the clinical results recently reported for HCV treatment.Keywords: SVR, direct antiviral agents, host

  4. Establishment of a simple assay in vitro for hepatitis C virus NS3 serine protease based on recombinant substrate and single-chain protease

    Institute of Scientific and Technical Information of China (English)

    Gui-Xin Du; Li-Hua Hou; Rong-Bin Guan; Yi-Gang Tong; Hai-Tao Wang

    2002-01-01

    AIM: To establish a simple and convenient assay in vitro for the Hepatitis C virus NS3 serine protease based on the recombinant protease and substrate, and to evaluate its feasibility in screening the enzyme inhibitors. METHODS: Based on the crystallographic structure of hepatitis C virus (HCV) serine protease, a novel single-chain serine protease was designed, in which the central sequence of cofactor NS4A was linked to the N-terminus of NS3 serine protease domain via a flexible linker GSGS. The fusion gene was obtained by two-step PCR that was carried out with three primers and then cloned into the prokaryotic expression vector pQE30, and the recombinant clone was verified by DNA sequencing. The single-chain recombinant protease was expressed when the E.coliwas induced with IPTG and the expression conditions were optimized to produce large amount of soluble protease. The recombinant substrate NS5ab that covers the cleavage point NS5A/B was also expressed in E.coli. Both of the protease and substrate were purified by using Ni-NTA agarose metal affinity resin, then they were mixed together in a specific buffer, and the mixture was analyzed by SDS-PAGE. The cleavage system was used to evaluate some compounds for their inhibitory activity on serine protease.RESULTS: The single-chain recombinant protease was overexpressed as soluble protein when the E. coliwas induced at a low dosage of IPTG (0.2 mM) and cultured at a low temperature (15℃). The protease was purified by using Ni-NTA agarose metal affinity resin (the purity is over 95 %).The recombinant substrate NS5ab was expressed in an insoluble form and could refold successfully after purification and dialysis. A simple and convenient assay in vitro was established, in which the purified single-chain serine protease could cleave the recombinant substrate NS5ab into two fragments that were visualized by SDS-PAGE. PMSF had an effect on inhibiting activity of serine protease, while EDTA had not.CONCLUSION: A simple

  5. In Vitro Activity and Resistance Profile of Dasabuvir, a Nonnucleoside Hepatitis C Virus Polymerase Inhibitor

    Science.gov (United States)

    Koev, Gennadiy; Irvin, Michelle; Beyer, Jill; Liu, Yaya; Krishnan, Preethi; Reisch, Thomas; Mondal, Rubina; Wagner, Rolf; Molla, Akhteruzzaman; Maring, Clarence; Collins, Christine

    2014-01-01

    Dasabuvir (ABT-333) is a nonnucleoside inhibitor of the RNA-dependent RNA polymerase encoded by the hepatitis C virus (HCV) NS5B gene. Dasabuvir inhibited recombinant NS5B polymerases derived from HCV genotype 1a and 1b clinical isolates, with 50% inhibitory concentration (IC50) values between 2.2 and 10.7 nM, and was at least 7,000-fold selective for the inhibition of HCV genotype 1 polymerases over human/mammalian polymerases. In the HCV subgenomic replicon system, dasabuvir inhibited genotype 1a (strain H77) and 1b (strain Con1) replicons with 50% effective concentration (EC50) values of 7.7 and 1.8 nM, respectively, with a 13-fold decrease in inhibitory activity in the presence of 40% human plasma. This level of activity was retained against a panel of chimeric subgenomic replicons that contained HCV NS5B genes from 22 genotype 1 clinical isolates from treatment-naive patients, with EC50s ranging between 0.15 and 8.57 nM. Maintenance of replicon-containing cells in medium containing dasabuvir at concentrations 10-fold or 100-fold greater than the EC50 resulted in selection of resistant replicon clones. Sequencing of the NS5B coding regions from these clones revealed the presence of variants, including C316Y, M414T, Y448C, Y448H, and S556G, that are consistent with binding to the palm I site of HCV polymerase. Consequently, dasabuvir retained full activity against replicons known to confer resistance to other polymerase inhibitors, including the S282T variant in the nucleoside binding site and the M423T, P495A, P495S, and V499A single variants in the thumb domain. The use of dasabuvir in combination with inhibitors targeting HCV NS3/NS4A protease (ABT-450 with ritonavir) and NS5A (ombitasvir) is in development for the treatment of HCV genotype 1 infections. PMID:25534735

  6. Cloning and Prokaryotic Expression of α-Gliadin Gene from Psathyrostachys huashanica%华山新麦草α-醇溶蛋白基因的克隆及原核表达

    Institute of Scientific and Technical Information of China (English)

    王玉卿; 赵继新; 庞玉辉; 降彦苗; 陈新宏; 武军; 刘淑会

    2011-01-01

    [Objective] The present study aimed at cloning and analyzing the α-gliadin genes from Psathyrostachys huashanica and expressing it in E. coli. [Method] The α-gliadin genes were amplified from P. huashanica by AS-PCR and then the cloned gene Gli-Ns-5 was inserted into pET-28a(+). The recombinant plasmids pET28a-Gli-Ns were expressed in a prokaryotic expression system after its transformation into BL21(DE3) pLysS host strain. [Result] Four new α-glidain genes, Gli-Ns-2 (FJ713595), Gli-Ns-3 (GQ139525), Gli-Ns-4 (GQ139526) and Gli-Ns-5 (GQ139527), were isolated and characterized from the genomic DNA of Psathyrostachys huashanica. Molecular structure analysis revealed that these four genes had the typical structure of α-gliadin and contained 8 or 9 cysteine residues, respectively. Two internal stop codons were identified in coding region of FJ713595,indicating that it was a pseudogene. The results of SDS-PAGE and Western-blot demonstrated that the fusion protein could express normally in the prokaryotic expression system. [Conclusion] The four α-gliadin genes ofPsathyrostachys huashanica were cloned and the gene Gli-Ns-5 (GQ139527) was successfully expressed in E.coli. This study could provide new candidate genes for wheat quality improvement.%[目的]克隆华山新麦草(Psathyrostachys huashanica)的α-醇溶蛋白基因,并对其进行生物信息学分析,构建该基因的原核表达载体,在大肠杆菌中诱导表达融合蛋白.[方法]采用同源克隆法从华山新麦草基因组DNA中分离克隆出α-醇溶蛋白基因并进行序列分析,将克隆的华山新麦草仅α-醇溶蛋白基因Gli-Ns-5克隆到表达载体pET-28a(+)上,获得重组质粒pET28a-Gli-Ns转化大肠杆菌BL21(DE3)并诱导表达.[结果]从华山新麦草基因组DNA中克隆了4个α-醇溶蛋白基因:Gli-Ns-2(FJ713595)、Gli-Ns-3(GQ139525)、Gli-Ns-4(G0139526)和Gli-Ns-5(GQ139527).序列分析表明,4条序列具有α-醇溶蛋白的典型结构特征,含有8个或9个

  7. Biochemical Characterization of the Active Anti-Hepatitis C Virus Metabolites of 2,6-Diaminopurine Ribonucleoside Prodrug Compared to Sofosbuvir and BMS-986094.

    Science.gov (United States)

    Ehteshami, Maryam; Tao, Sijia; Ozturk, Tugba; Zhou, Longhu; Cho, Jong Hyun; Zhang, Hongwang; Amiralaei, Sheida; Shelton, Jadd R; Lu, Xiao; Khalil, Ahmed; Domaoal, Robert A; Stanton, Richard A; Suesserman, Justin E; Lin, Biing; Lee, Sam S; Amblard, Franck; Whitaker, Tony; Coats, Steven J; Schinazi, Raymond F

    2016-08-01

    Ribonucleoside analog inhibitors (rNAI) target the hepatitis C virus (HCV) RNA-dependent RNA polymerase nonstructural protein 5B (NS5B) and cause RNA chain termination. Here, we expand our studies on β-d-2'-C-methyl-2,6-diaminopurine-ribonucleotide (DAPN) phosphoramidate prodrug 1 (PD1) as a novel investigational inhibitor of HCV. DAPN-PD1 is metabolized intracellularly into two distinct bioactive nucleoside triphosphate (TP) analogs. The first metabolite, 2'-C-methyl-GTP, is a well-characterized inhibitor of NS5B polymerase, whereas the second metabolite, 2'-C-methyl-DAPN-TP, behaves as an adenosine base analog. In vitro assays suggest that both metabolites are inhibitors of NS5B-mediated RNA polymerization. Additional factors, such as rNAI-TP incorporation efficiencies, intracellular rNAI-TP levels, and competition with natural ribonucleotides, were examined in order to further characterize the potential role of each nucleotide metabolite in vivo Finally, we found that although both 2'-C-methyl-GTP and 2'-C-methyl-DAPN-TP were weak substrates for human mitochondrial RNA (mtRNA) polymerase (POLRMT) in vitro, DAPN-PD1 did not cause off-target inhibition of mtRNA transcription in Huh-7 cells. In contrast, administration of BMS-986094, which also generates 2'-C-methyl-GTP and previously has been associated with toxicity in humans, caused detectable inhibition of mtRNA transcription. Metabolism of BMS-986094 in Huh-7 cells leads to 87-fold higher levels of intracellular 2'-C-methyl-GTP than DAPN-PD1. Collectively, our data characterize DAPN-PD1 as a novel and potent antiviral agent that combines the delivery of two active metabolites. PMID:27216050

  8. Systematic analysis of enhancer and critical cis-acting RNA elements in the protein-encoding region of the hepatitis C virus genome.

    Science.gov (United States)

    Chu, Derrick; Ren, Songyang; Hu, Stacy; Wang, Wei Gang; Subramanian, Aparna; Contreras, Deisy; Kanagavel, Vidhya; Chung, Eric; Ko, Justine; Amirtham Jacob Appadorai, Ranjit Singh; Sinha, Sanjeev; Jalali, Ziba; Hardy, David W; French, Samuel W; Arumugaswami, Vaithilingaraja

    2013-05-01

    Hepatitis C virus (HCV) causes chronic hepatitis, cirrhosis, and liver cancer. cis-acting RNA elements of the HCV genome are critical for translation initiation and replication of the viral genome. We hypothesized that the coding regions of nonstructural proteins harbor enhancer and essential cis-acting replication elements (CRE). In order to experimentally identify new cis RNA elements, we utilized an unbiased approach to introduce synonymous substitutions. The HCV genome coding for nonstructural proteins (nucleotide positions 3872 to 9097) was divided into 17 contiguous segments. The wobble nucleotide positions of each codon were replaced, resulting in 33% to 41% nucleotide changes. The HCV genome containing one of each of 17 mutant segments (S1 to S17) was tested for genome replication and infectivity. We observed that silent mutations in segment 13 (S13) (nucleotides [nt] 7457 to 7786), S14 (nt 7787 to 8113), S15 (nt 8114 to 8440), S16 (nt 8441 to 8767), and S17 (nt 8768 to 9097) resulted in impaired genome replication, suggesting CRE structures are enriched in the NS5B region. Subsequent high-resolution mutational analysis of NS5B (nt 7787 to 9289) using approximately 51-nucleotide contiguous subsegment mutant viruses having synonymous mutations revealed that subsegments SS8195-8245, SS8654-8704, and SS9011-9061 were required for efficient viral growth, suggesting that these regions act as enhancer elements. Covariant nucleotide substitution analysis of a stem-loop, JFH-SL9098, revealed the formation of an extended stem structure, which we designated JFH-SL9074. We have identified new enhancer RNA elements and an extended stem-loop in the NS5B coding region. Genetic modification of enhancer RNA elements can be utilized for designing attenuated HCV vaccine candidates.

  9. Phylogeographic characterization of tick-borne encephalitis virus from patients, rodents and ticks in Slovenia.

    Directory of Open Access Journals (Sweden)

    Luka Fajs

    Full Text Available Tick-borne encephalitis virus (TBEV is the most important arboviral agent causing infections of the central nervous system in central Europe. Previous studies have shown that TBEV exhibits pronounced genetic variability, which is often correlated to the geographical origin of TBEV. Genetic variability of TBEV has previously been studied predominantly in rodents and ticks, while information about the variability in patients is scarce. In order to understand the molecular relationships of TBEV between natural hosts, vectors and humans, as well as correlation between phylogenetic and geographical clustering, sequences of TBEV E and NS5 protein genes, were obtained by direct sequencing of RT-PCR products from TBE-confirmed patients as well as from rodents and ticks collected from TBE-endemic regions in Slovenia. A total of 27 partial E protein gene sequences representing 15 human, 4 rodent and 8 tick samples and 30 partial NS5 protein gene sequences representing 17 human, 5 rodent and 8 tick samples were obtained. The complete genome sequence of TBEV strain Ljubljana I was simultaneously obtained. Phylogenetic analysis of the E and NS5 protein gene sequences revealed a high degree of TBEV variability in patients, ticks and rodents. Furthermore, an evident correlation between geographical and phylogenetic clustering was shown that was independent of the TBEV host. Moreover, we show the presence of a possible recombination event in the TBEV genome obtained from a patient sample, which was supported with multiple recombination event detection methods. This is the first study that simultaneously analyzed the genetic relationships of directly sequenced TBEV samples from patients, ticks and rodents and provides the largest set of patient-derived TBEV sequences up to date. In addition, we have confirmed the geographical clustering of TBEV sequences in Slovenia and have provided evidence of a possible recombination event in the TBEV genome, obtained from a

  10. Natural selection of adaptive mutations in non-structural genes increases trans-encapsidation of hepatitis C virus replicons lacking envelope protein genes.

    Science.gov (United States)

    Fournier, Carole; Helle, François; Descamps, Véronique; Morel, Virginie; François, Catherine; Dedeurwaerder, Sarah; Wychowski, Czeslaw; Duverlie, Gilles; Castelain, Sandrine

    2013-05-01

    A trans-packaging system for hepatitis C virus (HCV) replicons lacking envelope glycoproteins was developed. The replicons were efficiently encapsidated into infectious particles after expression in trans of homologous HCV envelope proteins under the control of an adenoviral vector. Interestingly, expression in trans of core or core, p7 and NS2 with envelope proteins did not enhance trans-encapsidation. Expression of heterologous envelope proteins, in the presence or absence of heterologous core, p7 and NS2, did not rescue single-round infectious particle production. To increase the titre of homologous, single-round infectious particles in our system, successive cycles of trans-encapsidation and infection were performed. Four cycles resulted in a 100-fold increase in the yield of particles. Sequence analysis revealed a total of 16 potential adaptive mutations in two independent experiments. Except for a core mutation in one experiment, all the mutations were located in non-structural regions mainly in NS5A (four in domain III and two near the junction with the NS5B gene). Reverse genetics studies suggested that D2437A and S2443T adaptive mutations, which are located at the NS5A-B cleavage site did not affect viral replication, but enhanced the single-round infectious particles assembly only in trans-encapsidation model. In conclusion, our trans-encapsidation system enables the production of HCV single-round infectious particles. This system is adaptable and can positively select variants. The adapted variants promote trans-encapsidation and should constitute a valuable tool in the development of replicon-based HCV vaccines. PMID:23288424

  11. A highly sensitive and selective viral protein detection method based on RNA oligonucleotide nanoparticle

    Science.gov (United States)

    Roh, Changhyun; Lee, Ho-Young; Kim, Sang-Eun; Jo, Sung-Kee

    2010-01-01

    Globally, approximately 170 million people (representing approximately 3% of the population worldwide), are infected with hepatitis C virus (HCV) and at risk of serious liver disease, including chronic hepatitis. We propose a new quantum dots (QDs)-supported RNA oligonucleotide approach for the specific and sensitive detection of viral protein using a biochip. This method was developed by immobilizing a HCV nonstructural protein 5B (NS5B) on the surface of a glass chip via the formation of a covalent bond between an amine protein group and a ProLinker™ glass chip. The QDs-supported RNA oligonucleotide was conjugated via an amide formation reaction from coupling of a 5′-end-amine-modified RNA oligonucleotide on the surface of QDs displaying carboxyl groups via standard EDC coupling. The QDs-conjugated RNA oligonucleotide was interacted to immobilized viral protein NS5B on the biochip. The detection is based on the variation of signal of QDs-supported RNA oligonucleotide bound on an immobilized biochip. It was demonstrated that the value of the signal has a linear relationship with concentrations of the HCV NS5B viral protein in the 1 μg mL−1 to 1 ng mL−1 range with a detection limit of 1 ng mL−1. The major advantages of this RNA-oligonucleotide nanoparticle assay are its good specificity, ease of performance, and ability to perform one-spot monitoring. The proposed method could be used as a general method of HCV detection and is expected to be applicable to other types of diseases as well. PMID:20517476

  12. Genetic vaccination with Flt3-L and GM-CSF as adjuvants:Enhancement of cellular and humoral immune responses that results in protective immunity in a murine model of hepatitis C virus infection

    Institute of Scientific and Technical Information of China (English)

    Jens Encke; Jomo Bernardin; Jasmin Geib; Gocha Barbakadze; Raymond Bujdoso; Wolfgang Stremmel

    2006-01-01

    AIM: To investigate whether transfection of plasmid DNA encoding these cytokines enhances both humoral and cellular immune responses to hepatitis C virus (HCV) in a murine model.METHODS: We established a tumor model of HCV infection using syngenic mouse myeloma cells stably transfected with NS5. Co-vaccination of DNA encoding granulocyte macrophage colony-stimulating factor (GMCSF) and Fit-3 ligand together with a plasmid encoding for the HCV NS5 protein was carried out. Mice were sacrificed 14 d after the last immunization event with collection of spleen cells and serum to determine humoral and cellular immune responses.RESULTS: Co-vaccination of DNA encoding GM-CSF and Flt-3 ligand together with a plasmid encoding for the HCV NS5 protein induced increased antibody responses and CD4+ T cell proliferation to this protein. Vaccination with DNA encoding GM-CSF and Flt-3L promoted protection against tumor formation and/or reduction in mice coimmunized with cytokine-encoding DNA constructs. This suggests this strategy is capable of generating cytotoxic T lymphocyte activity in vivo. Following inoculation with plasmid DNA encoding Flt-3L, no increase in spleen size or in dendritic cell (DC) and natural killer cell numbers was observed. This was in contrast to a dramatic increase of both cell types after administration of recombinant Flt3-L in vivo. This suggests that vaccination with plasmid DNA encoding cytokines that regulate DC generation and mobilization may not promote unwanted side effects, such as autoimmunity, splenic fibrosis or hematopoietic malignancies that may occur with administration of recombinant forms of these proteins.CONCLUSION: Our data support the view that plasmid DNA vaccination is a promising approach for HCV immunization, and may provide a general adjuvant vaccination strategy against malignancies and other pathogens.

  13. Production of infectious genotype 1b virus particles in cell culture and impairment by replication enhancing mutations.

    Directory of Open Access Journals (Sweden)

    Thomas Pietschmann

    2009-06-01

    Full Text Available With the advent of subgenomic hepatitis C virus (HCV replicons, studies of the intracellular steps of the viral replication cycle became possible. These RNAs are capable of self-amplification in cultured human hepatoma cells, but save for the genotype 2a isolate JFH-1, efficient replication of these HCV RNAs requires replication enhancing mutations (REMs, previously also called cell culture adaptive mutations. These mutations cluster primarily in the central region of non-structural protein 5A (NS5A, but may also reside in the NS3 helicase domain or at a distinct position in NS4B. Most efficient replication has been achieved by combining REMs residing in NS3 with distinct REMs located in NS4B or NS5A. However, in spite of efficient replication of HCV genomes containing such mutations, they do not support production of infectious virus particles. By using the genotype 1b isolate Con1, in this study we show that REMs interfere with HCV assembly. Strongest impairment of virus formation was found with REMs located in the NS3 helicase (E1202G and T1280I as well as NS5A (S2204R, whereas a highly adaptive REM in NS4B still allowed virus production although relative levels of core release were also reduced. We also show that cells transfected with the Con1 wild type genome or the genome containing the REM in NS4B release HCV particles that are infectious both in cell culture and in vivo. Our data provide an explanation for the in vitro and in vivo attenuation of cell culture adapted HCV genomes and may open new avenues for the development of fully competent culture systems covering the therapeutically most relevant HCV genotypes.

  14. Evolution of viral RNA in a Chinese patient to interferon/ribavirin therapy for hepatitis C

    Institute of Scientific and Technical Information of China (English)

    Xian-Zi Wen; Zhi-Hai Chen; Ya-Zhi Wei; Jia-Fu Ji

    2012-01-01

    Objective:The combination of interferon (IFN) and ribavirin (RBV) is the standard therapy for hepatitis C virus (HCV) infection.HCV genotype 2a has proved more amenable to the therapy,but its efficacy is yet limited.This study aimed to investigate the mechanism of the poor response in a case of HCV genotype 2a infection.Methods:We analyzed dynamic change of HCV RNA from a patient,infected with HCV genotype 2a,showing a poor virological response to IFN/RBV as judged 12 weeks after initiation of the therapy by HCV clone sequencing.Then we constructed subgenomic Japanese fulminant hepatitis-1 (JFH1) replicon and different chimeric replicons with humanized Gaussia luciferase gene.The chimeric replicons were derived from subgenomic JFH1 replicon,in which the NS5A region was replaced by the patient's sequence from the pre/post-treatment,and the chimeric replicons' susceptibility to IFN were evaluated by relative Gausia Luciferase activity.Results:The pretreatment HCV sequences appeared almost uniform,and the quasispecies variation was further more simplified after 12 weeks of therapy.Besides,the quasispecies variation seemed to be more diversified in the NS5A,relatively,a region crucial for IFN response,and each of chimeric replicons exhibited distinct response to IFN.Conclusions:During the course of the chronic infection,HCV population seems to be adapted to the patient's immunological system,and further to be selected by combination of IFN/RBV therapy,indicating quasispecies may completely eliminated by addition of other drugs with targets different from those of IFN.In addition,each different response of chimeric replicon to IFN is most likely related to amino acid changes in or near the IFN-sensitivity determining region (ISDR) of NS5A during chronic infection and IFN/RBV therapy.

  15. Natural Polymorphisms Conferring Resistance to HCV Protease and Polymerase Inhibitors in Treatment-Naive HIV/HCV Co-Infected Patients in China.

    Directory of Open Access Journals (Sweden)

    Kali Zhou

    Full Text Available The advent of direct-acting agents (DAAs has improved treatment of HCV in HIV co-infection, but may be limited by primary drug resistance. This study reports the prevalence of natural polymorphisms conferring resistance to NS3/4A protease inhibitors and NS5B polymerase inhibitors in treatment-naïve HIV/HCV co-infected individuals in China.Population based NS3/4A sequencing was completed for 778 treatment-naïve HIV/HCV co-infected patients from twelve provinces. NS3 sequences were amplified by nested PCR using in-house primers for genotypes 1-6. NS5B sequencing was completed for genotyping in 350 sequences. Resistance-associated variants (RAVs were identified in positions associated with HCV resistance.Overall, 72.8% (566/778 of all HCV sequences had at least one RAV associated with HCV NS3/4A protease inhibitor resistance. Variants were found in 3.6% (7/193 of genotype 1, 100% (23/23 of genotype 2, 100% (237/237 of genotype 3 and 92% (299/325 of genotype 6 sequences. The Q80K variant was present in 98.4% of genotype 6a sequences. High-level RAVs were rare, occurring in only 0.8% of patients. 93% (64/69 patients with genotype 1b also carried the C316N variant associated with NS5B low-level resistance.The low frequency of high-level RAVs associated with primary HCV DAA resistance among all genotypes in HIV/HCV co-infected patients is encouraging. Further phenotypic studies and clinical research are needed.

  16. Natural Polymorphisms Conferring Resistance to HCV Protease and Polymerase Inhibitors in Treatment-Naïve HIV/HCV Co-Infected Patients in China

    Science.gov (United States)

    Wang, Charles; Hu, Fengyu; Ning, Chuanyi; Lan, Yun; Tang, Xiaoping; Tucker, Joseph D.; Cai, Weiping

    2016-01-01

    Background The advent of direct-acting agents (DAAs) has improved treatment of HCV in HIV co-infection, but may be limited by primary drug resistance. This study reports the prevalence of natural polymorphisms conferring resistance to NS3/4A protease inhibitors and NS5B polymerase inhibitors in treatment-naïve HIV/HCV co-infected individuals in China. Methods Population based NS3/4A sequencing was completed for 778 treatment-naïve HIV/HCV co-infected patients from twelve provinces. NS3 sequences were amplified by nested PCR using in-house primers for genotypes 1–6. NS5B sequencing was completed for genotyping in 350 sequences. Resistance-associated variants (RAVs) were identified in positions associated with HCV resistance. Results Overall, 72.8% (566/778) of all HCV sequences had at least one RAV associated with HCV NS3/4A protease inhibitor resistance. Variants were found in 3.6% (7/193) of genotype 1, 100% (23/23) of genotype 2, 100% (237/237) of genotype 3 and 92% (299/325) of genotype 6 sequences. The Q80K variant was present in 98.4% of genotype 6a sequences. High-level RAVs were rare, occurring in only 0.8% of patients. 93% (64/69) patients with genotype 1b also carried the C316N variant associated with NS5B low-level resistance. Conclusions The low frequency of high-level RAVs associated with primary HCV DAA resistance among all genotypes in HIV/HCV co-infected patients is encouraging. Further phenotypic studies and clinical research are needed. PMID:27341031

  17. Structural and functional studies of nonstructural protein 2 of the hepatitis C virus reveal its key role as organizer of virion assembly.

    Directory of Open Access Journals (Sweden)

    Vlastimil Jirasko

    Full Text Available Non-structural protein 2 (NS2 plays an important role in hepatitis C virus (HCV assembly, but neither the exact contribution of this protein to the assembly process nor its complete structure are known. In this study we used a combination of genetic, biochemical and structural methods to decipher the role of NS2 in infectious virus particle formation. A large panel of NS2 mutations targeting the N-terminal membrane binding region was generated. They were selected based on a membrane topology model that we established by determining the NMR structures of N-terminal NS2 transmembrane segments. Mutants affected in virion assembly, but not RNA replication, were selected for pseudoreversion in cell culture. Rescue mutations restoring virus assembly to various degrees emerged in E2, p7, NS3 and NS2 itself arguing for an interaction between these proteins. To confirm this assumption we developed a fully functional JFH1 genome expressing an N-terminally tagged NS2 demonstrating efficient pull-down of NS2 with p7, E2 and NS3 and, to a lower extent, NS5A. Several of the mutations blocking virus assembly disrupted some of these interactions that were restored to various degrees by those pseudoreversions that also restored assembly. Immunofluorescence analyses revealed a time-dependent NS2 colocalization with E2 at sites close to lipid droplets (LDs together with NS3 and NS5A. Importantly, NS2 of a mutant defective in assembly abrogates NS2 colocalization around LDs with E2 and NS3, which is restored by a pseudoreversion in p7, whereas NS5A is recruited to LDs in an NS2-independent manner. In conclusion, our results suggest that NS2 orchestrates HCV particle formation by participation in multiple protein-protein interactions required for their recruitment to assembly sites in close proximity of LDs.

  18. Daclatasvir-containing all-oral regimens for the treatment of hepatitis C virus infection.

    Science.gov (United States)

    Yang, Sheng-Shun; Kao, Jia-Horng

    2016-03-01

    The treatment of chronic hepatitis C is revolutionizing rapidly. The aim of this study is to review the efficacy and safety of daclatasvir (DCV)-containing all-oral regimens in clinical studies for chronic hepatitis C treatment. Using PubMed and search terms of 'DCV,' 'hepatitis C virus (HCV) treatment,' and 'HCV NS5A inhibitors,' literature on the clinical development of DCV, as well as abstracts presented at the April 2015 annual meeting of the European Association for the Study of the Liver (EASL) and November 2014 annual meeting of the American Association for the Study of Liver Diseases were reviewed. The final search was undertaken on 14 July 2015. With its potent antiviral activity to all HCV genotypes (GT) demonstrated in preclinical, phases 1-3 studies, DCV has been acting as a very competent team player in clinical trials of all-oral regimens. It is generally safe and well tolerated with a low genetic barrier to resistance and low potential for drug-drug interaction. Administered with a non-structural protein 3 (NS3) protease inhibitor (asunaprevir, ASV) with or without a non-nucleoside NS5B polymerase inhibitor (beclabuvir, BCV), or a nucleotide NS5B polymerase inhibitor (sofosbuvir, SOF), DCV is able to achieve greater than a 90-% HCV eradication rate in both treatment-naïve and treatment-experienced patients with GT 1. A triple combination regimen with DCV/ASV/BCV results in 100% sustained virologic response (SVR) rates in HCV GT 4 treatment-naïve subjects. DCV/SOF combination also had demonstrated up to 90-% SVR rates in GT 3-infected non-cirrhotic patients. The efficacy and safety of DCV-containing all-oral regimens highlight a new era of interferon-free therapy for chronic hepatitis C. PMID:26542068

  19. Human Dengue Antibodies against Structural and Nonstructural Proteins

    OpenAIRE

    Valdés, Katia; Alvarez, Mayling; Pupo, Maritza; Vázquez, Susana; Rodríguez, Rayner; Guzmán, María G.

    2000-01-01

    Antibodies against dengue virus type 2 and 4 proteins in acute-phase sera of 10 primary and 10 secondary dengue fever and dengue hemorrhagic fever patients were studied by Western blotting. In the first group the immune response was barely detectable, while in the second group more proteins were detected, with a very strong reaction. Anti-NS1 and -NS3 antibodies were detected mainly in secondary cases. Anti-E, -NS3, and -NS5 antibodies were detected in a high number of cases. The possibility ...

  20. Comparative Amino Acid Sequences of Dengue Viruses

    OpenAIRE

    Haishi, Shozo; TANAKA Mariko; Igarashi, Akira

    1990-01-01

    Amino acid (AA) sequences of 4 serotype of dengue viruses deduced from their nucleotide (nt) sequences of genomic RNA were analyzed for each genome segment and each stretch of 10 AA residues. Precursor of membrane protein (pM), and 4 nonstructural proteins (NS1, NS3, NS4B, NS5) were highly conserved, while another nonstructural protein (NS2A) was least conserved among 5 strains of dengue viruses. When homology was compared among heterotypic viruses, type 1 and type 3 dengue viruses showed clo...

  1. Preheating and Entropy Perturbations in Axion Monodromy Inflation

    CERN Document Server

    ,

    2016-01-01

    We study the preheating of gauge fields in a simple axion monodromy model and compute the induced entropy perturbations and their effect on the curvature fluctuations. We find that the correction to the spectrum of curvature perturbations has a blue spectrum with index $n_s = 5/2$. Hence, these induced modes are harmless for the observed structure of the universe. Since the spectrum is blue, there is the danger of overproduction of primordial black holes. However, we show that the observational constraints are easily satisfied.

  2. Advantages of a single-cycle production assay to study cell culture-adaptive mutations of hepatitis C virus

    DEFF Research Database (Denmark)

    Russell, Rodney S; Meunier, Jean-Christophe; Takikawa, Shingo;

    2008-01-01

    mutations that were selected during serial passage in Huh-7.5 cells were studied. Recombinant genomes containing all five mutations produced 3-4 logs more infectious virions than did wild type. Neither a coding mutation in NS5A nor a silent mutation in E2 was adaptive, whereas coding mutations in E2, p7......, and NS2 all increased virus production. A single-cycle replication assay in CD81-deficient cells was developed to study more precisely the effect of the adaptive mutations. The E2 mutation had minimal effect on the amount of infectious virus released but probably enhanced entry into cells. In contrast...

  3. Core as a Novel Viral Target for Hepatitis C Drugs

    OpenAIRE

    Guillaume Mousseau; Snyder, John K.; Arthur Donny Strosberg; Virginia Takahashi; Smitha Kota

    2010-01-01

    Hepatitis C virus (HCV) infects over 130 million people worldwide and is a major cause of liver disease. No vaccine is available. Novel specific drugs for HCV are urgently required, since the standard-of-care treatment of pegylated interferon combined with ribavirin is poorly tolerated and cures less than half of the treated patients. Promising, effective direct-acting drugs currently in the clinic have been described for three of the ten potential HCV target proteins: NS3/NS4A protease, NS5B...

  4. Twistor approach to string compactifications: A review

    Energy Technology Data Exchange (ETDEWEB)

    Alexandrov, Sergei, E-mail: salexand@univ-montp2.fr

    2013-01-01

    We review a progress in obtaining the complete non-perturbative effective action of type II string theory compactified on a Calabi–Yau manifold. This problem is equivalent to understanding quantum corrections to the metric on the hypermultiplet moduli space. We show how all these corrections, which include D-brane and NS5-brane instantons, are incorporated in the framework of the twistor approach, which provides a powerful mathematical description of hyperkähler and quaternion-Kähler manifolds. We also present new insights on S-duality, quantum mirror symmetry, connections to integrable models and topological strings.

  5. Modularity, quaternion-Kähler spaces, and mirror symmetry

    Energy Technology Data Exchange (ETDEWEB)

    Alexandrov, Sergei; Banerjee, Sibasish [Université Montpellier 2, Laboratoire Charles Coulomb UMR 5221, F-34095 Montpellier (France)

    2013-10-15

    We provide an explicit twistorial construction of quaternion-Kähler manifolds obtained by deformation of c-map spaces and carrying an isometric action of the modular group SL(2,Z). The deformation is not assumed to preserve any continuous isometry and therefore this construction presents a general framework for describing NS5-brane instanton effects in string compactifications with N= 2 supersymmetry. In this context the modular invariant parametrization of twistor lines found in this work yields the complete non-perturbative mirror map between type IIA and type IIB physical fields.

  6. Polyclonal antibody preparation and expression in liver tissues of transactivated protein 5 of hepatitis C virus nonstructural 5A

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Objective To prepare polyclonal antibody of transactivated protein 5 of hepatitis C virus nonstructural 5A (NA5ATP5) and to explore its expression in the liver tissues. Methods In Escherichia coli BL21,the prokaryotic expression vector pET32a(+)-NS5ATP5 was induced by isopropyl-β-D-thiogalactoside (IPTG),and it was analyzed with sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Western blotting. And the purified protein was used to immunize the rabbit to prepare polyclonal antibody,wi...

  7. Twistor approach to string compactifications: A review

    International Nuclear Information System (INIS)

    We review a progress in obtaining the complete non-perturbative effective action of type II string theory compactified on a Calabi–Yau manifold. This problem is equivalent to understanding quantum corrections to the metric on the hypermultiplet moduli space. We show how all these corrections, which include D-brane and NS5-brane instantons, are incorporated in the framework of the twistor approach, which provides a powerful mathematical description of hyperkähler and quaternion-Kähler manifolds. We also present new insights on S-duality, quantum mirror symmetry, connections to integrable models and topological strings.

  8. I,ROBOT

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    《少电》的读者们,大家好。我是来自未来的全能型机器人NS-5——如果大家觉得这十名字太生硬,可以叫我Robot(罗伯特),这是一个对所有机器人适用的名字,嘿嘿。相信大家都知道,个人计算机在上个世纪的八十年代得

  9. Genetic Diversity and Selective Pressure in Hepatitis C Virus Genotypes 1–6: Significance for Direct-Acting Antiviral Treatment and Drug Resistance

    Science.gov (United States)

    Cuypers, Lize; Li, Guangdi; Libin, Pieter; Piampongsant, Supinya; Vandamme, Anne-Mieke; Theys, Kristof

    2015-01-01

    Treatment with pan-genotypic direct-acting antivirals, targeting different viral proteins, is the best option for clearing hepatitis C virus (HCV) infection in chronically infected patients. However, the diversity of the HCV genome is a major obstacle for the development of antiviral drugs, vaccines, and genotyping assays. In this large-scale analysis, genome-wide diversity and selective pressure was mapped, focusing on positions important for treatment, drug resistance, and resistance testing. A dataset of 1415 full-genome sequences, including genotypes 1–6 from the Los Alamos database, was analyzed. In 44% of all full-genome positions, the consensus amino acid was different for at least one genotype. Focusing on positions sharing the same consensus amino acid in all genotypes revealed that only 15% was defined as pan-genotypic highly conserved (≥99% amino acid identity) and an additional 24% as pan-genotypic conserved (≥95%). Despite its large genetic diversity, across all genotypes, codon positions were rarely identified to be positively selected (0.23%–0.46%) and predominantly found to be under negative selective pressure, suggesting mainly neutral evolution. For NS3, NS5A, and NS5B, respectively, 40% (6/15), 33% (3/9), and 14% (2/14) of the resistance-related positions harbored as consensus the amino acid variant related to resistance, potentially impeding treatment. For example, the NS3 variant 80K, conferring resistance to simeprevir used for treatment of HCV1 infected patients, was present in 39.3% of the HCV1a strains and 0.25% of HCV1b strains. Both NS5A variants 28M and 30S, known to be associated with resistance to the pan-genotypic drug daclatasvir, were found in a significant proportion of HCV4 strains (10.7%). NS5B variant 556G, known to confer resistance to non-nucleoside inhibitor dasabuvir, was observed in 8.4% of the HCV1b strains. Given the large HCV genetic diversity, sequencing efforts for resistance testing purposes may need to be

  10. Sofosbuvir treatment and hepatitis C virus infection

    Institute of Scientific and Technical Information of China (English)

    2016-01-01

    Hepatitis C virus (HCV) infection is a serious problemworldwide. The use of interferon-based therapy hasmade HCV eradication challenging. The recent appearanceof direct-acting antiviral agents (DAAs) haschanged HCV therapy. Combining the use of DAAs withpeginterferon and ribavirin has improved treatmentefficacy. Furthermore, the combination of different orallyadministered DAAs has enabled interferon-free therapywith much higher efficacy and safety. In particular,sofosbuvir, a nucleotide-based NS5B inhibitor, preventsHCV RNA synthesis by acting as a "chain terminator".Treatment with sofosbuvir has attained an extremelyhigh rate of sustained virologic response. The currentreview summarizes the efficacy and safety of sofosbuvirtherapy.

  11. 2001 spring school on superstrings and related matters

    International Nuclear Information System (INIS)

    This proceedings contains the lectures given at the 2001 Trieste Spring School on String Theory. Several important and active areas of research in string theory related topics were covered in this school. One of the main topics of the School was the recently conjectured duality between gauge theory living on D-branes and and gravity (or more precisely string theory) living in the near horizon geometry around the D-branes. J. Maldacena gave a set of lectures on the gauge theory/gravity duality in different examples. M. Strassler's lectures dealt with a very interesting generalization of the gauge theory/gravity duality for the case of a confining gauge theory. D. Kutasov's lectures dealt with Little String Theories (LST) that are supposed to describe the physics of the NS5-branes. Using the holographic principle, interesting features of LST were deduced by describing the string theory in the background of NS5-branes. E. Verlinde gave a set of lectures on holographic principle in the context of radiation dominated FRW universe. Other topics included lectures by R. Gopakumar on the solitons in non-commutative gauge theories that are relevant in the context of D-branes in the background on anti-symmetric tensor field, and lectures by M. Douglas on D-branes on Calabi-Yau spaces

  12. A multi-step strategy to obtain crystals of the dengue virus RNA-dependent RNA polymerase that diffract to high resolution

    International Nuclear Information System (INIS)

    Crystals of the RNA-dependent RNA polymerase catalytic domain from the dengue virus NS5 protein have been obtained using a strategy that included expression screening of naturally occurring serotype variants of the protein, the addition of divalent metal ions and crystal dehydration. These crystals diffract to 1.85 Å resolution and are thus suitable for a structure-based drug-design program. Dengue virus, a member of the Flaviviridae genus, causes dengue fever, an important emerging disease with several million infections occurring annually for which no effective therapy exists. The viral RNA-dependent RNA polymerase NS5 plays an important role in virus replication and represents an interesting target for the development of specific antiviral compounds. Crystals that diffract to 1.85 Å resolution that are suitable for three-dimensional structure determination and thus for a structure-based drug-design program have been obtained using a strategy that included expression screening of naturally occurring serotype variants of the protein, the addition of divalent metal ions and crystal dehydration

  13. New hepatitis C therapies in clinical development

    Directory of Open Access Journals (Sweden)

    Vermehren Johannes

    2011-07-01

    Full Text Available Abstract With the current standard of care for the treatment of chronic hepatitis C, a combination of pegylated interferon alfa and ribavirin, sustained virologic response rates can be achieved in approximately 50% of patients only. Improved understanding of the viral life cycle has led to the identification of numerous potential targets for novel, direct-acting antiviral compounds. Inhibitors of the NS3/4A protease are currently the most advanced in clinical development. Recently completed phase 3 studies of the two protease inhibitors telaprevir and boceprevir, each given in combination with standard of care, yielded sustained virologic response rates in the range of 66-75% in treatment-naive patients and 59-66% in treatment-experienced patients with HCV genotype 1 infection. Studies of second-generation protease inhibitors, with the potential advantage of improved potency, drug metabolism and pharmacokinetics profile, are already underway. Inhibitors of the HCV NS5A protein and NS5B polymerase are potentially active across different HCV genotypes and have shown promising antiviral efficacy in early clinical studies. Other emerging mechanisms include silymarin components and inhibitors of cell proteins required for HCV replication. While improved formulations of current HCV therapies are also being developed, future hopes lie on the combination of direct-acting antivirals with the eventual possibility of interferon-free treatment regimens.

  14. Heterotic/Type II Triality and Instantons on $K_{3}$

    CERN Document Server

    Kiritsis, Elias B; Pioline, B

    2000-01-01

    A detailed understanding of instanton effects for half-BPS couplings is pursued in theories with 16 supersymmetries. In particular, we investigate the duality between heterotic string on $T^4$ and type IIA on $K_3$ at the $T^4/Z_2$ orbifold point, as well as their higher and lower dimensional versions. We present a remarkably clean quantitative test of the duality at the level of $F^4$ couplings, by completely matching a purely one-loop heterotic amplitude to a purely tree-level type II result. The triality of $SO(4,4)$ and several other miracles are shown to be crucial for the duality to hold. Exact non-perturbative new results for type I', F on $K_3$, M on $K_3$, and IIB on $K_3$ are found, and the general form of D-instanton contributions in type IIA or B on $T^4/\\Z_2$ is obtained. We also analyze the NS5-brane contributions in type II on $K_3\\times T^2$, and predict the value $\\mu (N)=\\sum_{d|N} (1/d^3)$ for the bulk contribution to the index of the NS5-brane world-volume theory on $K_3 \\times T^2$.

  15. 3d N=2 mirror symmetry, pq-webs and monopole superpotentials

    CERN Document Server

    Benvenuti, Sergio

    2016-01-01

    D3 branes stretching between webs of (p,q) 5branes provide an interesting class of 3d N=2 theories. For generic pq-webs however the low energy field theory is not known. We use 3d mirror symmetry and Type IIB S-duality to construct Abelian gauge theories corresponding to D3 branes ending on both sides of a pq-web made of many coincident NS5's intersecting one D5. These theories contain chiral monopole operators in the superpotential and enjoy a non trivial pattern of global symmetry enhancements. In the special case of the pq-web with one D5 and one NS5, the 3d low energy SCFT admits three dual formulations. This triality can be applied locally inside bigger quiver gauge theories. We prove our statements using partial mirror symmetry \\`a la Kapustin-Strassler, showing the equality of the S^3_b partition functions and studying the quantum chiral rings.

  16. Comparative analysis of hepatitis C virus phylogenies from coding and non-coding regions: the 5' untranslated region (UTR fails to classify subtypes

    Directory of Open Access Journals (Sweden)

    Leitner Thomas

    2006-12-01

    Full Text Available Abstract Background The duration of treatment for HCV infection is partly indicated by the genotype of the virus. For studies of disease transmission, vaccine design, and surveillance for novel variants, subtype-level classification is also needed. This study used the Shimodaira-Hasegawa test and related statistical techniques to compare phylogenetic trees obtained from coding and non-coding regions of a whole-genome alignment for the reliability of subtyping in different regions. Results Different regions of the HCV genome yield inconsistent phylogenies, which can lead to erroneous conclusions about classification of a given infection. In particular, the highly conserved 5' untranslated region (UTR yields phylogenetic trees with topologies that differ from the HCV polyprotein and complete genome phylogenies. Phylogenetic trees from the NS5B gene reliably cluster related subtypes, and yield topologies consistent with those of the whole genome and polyprotein. Conclusion These results extend those from previous studies and indicate that, unlike the NS5B gene, the 5' UTR contains insufficient variation to resolve HCV classifications to the level of viral subtype, and fails to distinguish genotypes reliably. Use of the 5' UTR for clinical tests to characterize HCV infection should be replaced by a subtype-informative test.

  17. Sofosbuvir/velpatasvir: A promising combination.

    Science.gov (United States)

    Bonaventura, Aldo; Montecucco, Fabrizio

    2016-07-01

    Hepatitis C virus (HCV) affects 3% of the world population. It represents the main cause of chronic liver disease and is responsible for extra-hepatic complications, such as type 2 diabetes and cardiovascular diseases. HCV includes 7 genotypes differing in the nucleotide sequence variability, the geographic distribution, the rates of viral clearance, the risk of progression to liver fibrosis and to hepatocellular carcinoma, and the response to therapy. Last years have seen remarkable advances in the field of HCV infection with the approval of direct antiviral agents (DAAs) targeting key viral proteins involved in the HCV replication. Several oral regimens combining DAAs from different families have been developed and these regimens showed increased and sustained virological response rates to above 90% reducing the treatment duration to 12 wk or less. In particular, sofosbuvir, a nucleotide analogue nonstructural (NS)5B polymerase inhibitor, and velpatasvir, a NS5A inhibitor, have been tested in two phase 3 trials, the ASTRAL-2 (against HCV genotype 2) and the ASTRAL-3 (against HCV genotype 3), demonstrating to be effective, safe, and well tolerated in patients who were 18 years of age or older and had at least a 6-mo history of HCV infection with a compensated liver disease. PMID:27429714

  18. A report on the outbreak of Zika virus on Easter Island, South Pacific, 2014.

    Science.gov (United States)

    Tognarelli, J; Ulloa, S; Villagra, E; Lagos, J; Aguayo, C; Fasce, R; Parra, B; Mora, J; Becerra, N; Lagos, N; Vera, L; Olivares, B; Vilches, M; Fernández, J

    2016-03-01

    Zika virus (ZIKV) is an emerging mosquito-borne flavivirus circulating in Asia and Africa. In 2013, a large outbreak was reported on the archipelago of French Polynesia. In this study, we report the detection and molecular characterization of Zika virus for the first time in Chile from an outbreak among the inhabitants of Easter Island. A total of 89 samples from patients suspected of having ZIKV infection were collected between the period from January to May, 2014. Molecular diagnosis of the virus was performed by RT-PCR followed by the sequencing of the region containing the NS5 gene. A comparison of the viral nucleic acid sequence with those of other strains of ZIKA virus was performed using the MEGA software. Fifty-one samples were found positive for ZIKV by RT-PCR analysis. Further analysis of the NS5 gene revealed that the ZIKV strains identified in Easter Island were most closely related to those found in French Polynesia (99.8 to 99.9% nt and 100% aa sequence identity). These results strongly suggest that the transmission pathway leading to the introduction of Zika virus on Easter Island has its origin in French Polynesia.

  19. A multi-step strategy to obtain crystals of the dengue virus RNA-dependent RNA polymerase that diffract to high resolution

    Energy Technology Data Exchange (ETDEWEB)

    Yap, Thai Leong [Novartis Institute for Tropical Diseases, 10 Biopolis Road, Chromos Building, Singapore 138670 (Singapore); School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 (Singapore); Chen, Yen Liang; Xu, Ting; Wen, Daying; Vasudevan, Subhash G. [Novartis Institute for Tropical Diseases, 10 Biopolis Road, Chromos Building, Singapore 138670 (Singapore); Lescar, Julien, E-mail: julien@ntu.edu.sg [Novartis Institute for Tropical Diseases, 10 Biopolis Road, Chromos Building, Singapore 138670 (Singapore); School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 (Singapore)

    2007-02-01

    Crystals of the RNA-dependent RNA polymerase catalytic domain from the dengue virus NS5 protein have been obtained using a strategy that included expression screening of naturally occurring serotype variants of the protein, the addition of divalent metal ions and crystal dehydration. These crystals diffract to 1.85 Å resolution and are thus suitable for a structure-based drug-design program. Dengue virus, a member of the Flaviviridae genus, causes dengue fever, an important emerging disease with several million infections occurring annually for which no effective therapy exists. The viral RNA-dependent RNA polymerase NS5 plays an important role in virus replication and represents an interesting target for the development of specific antiviral compounds. Crystals that diffract to 1.85 Å resolution that are suitable for three-dimensional structure determination and thus for a structure-based drug-design program have been obtained using a strategy that included expression screening of naturally occurring serotype variants of the protein, the addition of divalent metal ions and crystal dehydration.

  20. Identification of mosquito-borne flavivirus sequences using universal primers and reverse transcription/polymerase chain reaction.

    Science.gov (United States)

    Pierre, V; Drouet, M T; Deubel, V

    1994-01-01

    A reverse transcription/polymerase chain reaction (RT/PCR) protocol for the rapid detection and identification of flaviviruses was developed using a set of universal oligonucleotide primers. These primers correspond to sequences in the 3' non-coding region and in the NS5 gene which are highly conserved among the mosquito-borne flaviviruses. The sequences of the resulting amplified products were analysed for dengue 1, dengue 2, dengue 3, dengue 4, Japanese encephalitis, West Nile, yellow fever and Zika viruses, and compared with the published sequences of other flaviviruses. The 291-297 nucleotides corresponding to the C-terminus of NS5 gene showed 56 to 76% similarity, whereas the 3' non-coding region (190 to 421 nucleotides) showed only 20 to 36% similarity. Genetic classification of the Zika virus supported its traditional serological grouping. Recombinant plasmids containing the flavivirus sequences were used in a nucleic acid hybridization test to identify the RT/PCR products derived from viral RNA extracted from experimentally infected mosquitoes. The plasmids were dotted on a strip of nitrocellulose membrane and incubated with the RT/PCR product labelled with digoxigenin during the PCR step. This is a valuable method for the rapid and specific identification of mosquito-borne flaviviruses in biological specimens and for subsequent sequence analysis.

  1. [Cloning alphavirus and flavivirus sequences for use as positive controls in molecular diagnostics].

    Science.gov (United States)

    Camacho, Daría; Reyes, Jesús; Franco, Leticia; Comach, Guillermo; Ferrer, Elizabeth

    2016-06-01

    The purpose of the study was to obtain a positive control to validate molecular techniques (reverse transcription- polymerase chain reaction [RT-PCR]) used in the diagnosis and research of viral infections. From strains of Chikungunya virus (CHIKV), Zika virus, and Dengue virus (DENV-1, DENV-2, DENV- 3, and DENV-4) viral RNAs were extracted to obtain complementary DNA using RT-PCR from the nsP4 (CHIKV), NS5 (Zika virus), C/prM-M, and 5'UTR-C (DENV-1, DENV-2, DENV-3, DENV-4) sequences, which were cloned into pGEM®-T Easy. Cloning was confirmed through colony PCR, from which plasmid DNA was extracted for fragment cloning verification. Cloning of cDNA corresponding to nsP4, NS5, C/prM-M, and 5'UTR-C of the different viral agents was achieved. In conclusion, recombinant plasmids were obtained with each of the sequences specified for further assessment as positive controls in molecular techniques in an effort to avoid the use of cell cultures, which can be costly, time-consuming, and potentially dangerous.

  2. Triterpenoid Saponins Isolated from Platycodon grandiflorum Inhibit Hepatitis C Virus Replication

    Directory of Open Access Journals (Sweden)

    Jong-Woo Kim

    2013-01-01

    Full Text Available Hepatitis C virus (HCV infection is a major cause of liver disease, including cirrhosis and hepatocellular carcinoma. Due to significant adverse effects and emergence of resistant strains of currently developed anti-HCV agents, plant extracts have been considered to be potential sources of new bioactive compounds against HCV. The aim of this study was to evaluate the functional effects of triterpenoid saponins contained in the root extract of Platycodon grandiflorum (PG on viral enzyme activities and replication in both HCV replicon cells and cell culture grown HCV- (HCVcc- infected cells. Inhibitory activities of triterpenoid saponins from PG were verified by NS5B RNA-dependent RNA polymerase assay and were further confirmed in the context of HCV replication. Six triterpenoid saponins (platycodin D, platycodin D2, platycodin D3, deapioplatycodin D, deapioplatycodin D2, and platyconic acid A, PG saponin mixture (PGSM, were identified as active components exerting anti-HCV activity. Importantly, PGSM exerted synergistic anti-HCV activity in combination with either interferon-α or NS5A inhibitors. We demonstrated that combinatorial treatment of PGSM and IFN-α efficiently suppressed colony formation with significant reduction in drug resistant variant of HCV. These data suggest that triterpenoid saponin may represent a novel anti-HCV therapeutic agent.

  3. Genetic diversity of the hepatitis C virus: Impact and issues in the antiviral therapy

    Institute of Scientific and Technical Information of China (English)

    H Le Guillou-Guillemette; S Vallet; C Gaudy-Graffin; C Payan; A Pivert; A Goudeau; F Lunel-Fabiani

    2007-01-01

    The hepatitis C Virus (HCV) presents a high degree of genetic variability which is explained by the combination of a lack of proof reading by the RNA dependant RNA polymerase and a high level of viral replication. The resuiting genetic polymorphism defines a classification in clades, genotypes, subtypes, isolates and quasispecies.This diversity is known to reflect the range of responses to Interferon therapy. The genotype is one of the predictive parameters currently used to define the antiviral treatment strategy and the chance of therapeutic success. Studies have also reported the potential impact of the viral genetic polymorphism in the outcome of antiviral therapy in patients infected by the same HCV genotype. Both structural and non structural genomic regions of HCV have been suggested to be involved in the Interferon pathway and the resistance to antiviral therapy. In this review, we first detail the viral basis of HCV diversity.Then, the HCV genetic regions that may be implicated in resistance to therapy are described, with a focus on the structural region encoded by the E2 gene and the non-structural genes NS3, NS5A and NS5B. Both mechanisms of the Interferon resistance and of the new antiviral drugs are described in this review.

  4. New pseudodimeric aurones as palm pocket inhibitors of Hepatitis C virus RNA-dependent RNA polymerase.

    Science.gov (United States)

    Meguellati, Amel; Ahmed-Belkacem, Abdelhakim; Nurisso, Alessandra; Yi, Wei; Brillet, Rozenn; Berqouch, Nawel; Chavoutier, Laura; Fortuné, Antoine; Pawlotsky, Jean-Michel; Boumendjel, Ahcène; Peuchmaur, Marine

    2016-06-10

    The NS5B RNA-dependent RNA polymerase (RdRp) is a key enzyme for Hepatitis C Virus (HCV) replication. In addition to the catalytic site, this enzyme is characterized by the presence of at least four allosteric pockets making it an interesting target for development of inhibitors as potential anti-HCV drugs. Based on a previous study showing the potential of the naturally occurring aurones as inhibitors of NS5B, we pursued our efforts to focus on pseudodimeric aurones that have never been investigated so far. Hence, 14 original compounds characterized by the presence of a spacer between the benzofuranone moieties were synthesized and investigated as HCV RdRp inhibitors by means of an in vitro assay. The most active inhibitor, pseudodimeric aurone 4, induced high inhibition activity (IC50 = 1.3 μM). Mutagenic and molecular modeling studies reveal that the binding site for the most active derivatives probably is the palm pocket I instead of the thumb pocket I as for the monomeric derivatives. PMID:27017550

  5. Two Distinct Hepatitis C Virus Genotype 1a Clades Have Different Geographical Distribution and Association With Natural Resistance to NS3 Protease Inhibitors.

    Science.gov (United States)

    De Luca, Andrea; Di Giambenedetto, Simona; Lo Presti, Alessandra; Sierra, Saleta; Prosperi, Mattia; Cella, Eleonora; Giovanetti, Marta; Torti, Carlo; Caudai, Cinzia; Vicenti, Ilaria; Saladini, Francesco; Almi, Paolo; Grima, Pierfrancesco; Blanc, Pierluigi; Fabbiani, Massimiliano; Rossetti, Barbara; Gagliardini, Roberta; Kaiser, Rolf; Ciccozzi, Massimo; Zazzi, Maurizio

    2015-04-01

    Background.  Hepatitis C virus (HCV) genotype 1 is the most prevalent worldwide. Subtype 1a, compared with 1b, shows lower response rates and higher propensity to select for drug resistance to NS3 and selected NS5A and nonnucleoside NS5B inhibitors. Two distinct clades of subtype 1a have been described. Methods.  Using Bayesian methodology, we performed a time-scaled phylogeny reconstruction of clade separation and characterized the geographic distribution, phylodynamics, and association with natural resistance variants of NS3 sequences from 362 patients carrying subtype 1a HCV. Results.  All sequences segregated in 2 clearly distinct clades. Clade I showed an earlier origin from the common ancestor compared with clade II. Clade I virus was more prevalent in non-European countries, represented mostly by United States, compared with European (75.7% vs 49.3%; P < .001). The prevalence of the natural NS3 variant Q80K, associated with resistance to the macrocyclic protease inhibitor simeprevir, was detected in 51.6% of clade I and 0% of clade II (P < .001); clade I showed a lower genetic barrier for Q80K, whereas no sign of selective pressure at any protease inhibitor resistance-associated codon was detected. Conclusions.  Hepatitis C virus subtype 1a clades have a clearly different distribution in Europe and the United States, and the natural resistance mutation Q80K is exclusively associated with clade I. PMID:26213689

  6. Approved Antiviral Drugs over the Past 50 Years.

    Science.gov (United States)

    De Clercq, Erik; Li, Guangdi

    2016-07-01

    Since the first antiviral drug, idoxuridine, was approved in 1963, 90 antiviral drugs categorized into 13 functional groups have been formally approved for the treatment of the following 9 human infectious diseases: (i) HIV infections (protease inhibitors, integrase inhibitors, entry inhibitors, nucleoside reverse transcriptase inhibitors, nonnucleoside reverse transcriptase inhibitors, and acyclic nucleoside phosphonate analogues), (ii) hepatitis B virus (HBV) infections (lamivudine, interferons, nucleoside analogues, and acyclic nucleoside phosphonate analogues), (iii) hepatitis C virus (HCV) infections (ribavirin, interferons, NS3/4A protease inhibitors, NS5A inhibitors, and NS5B polymerase inhibitors), (iv) herpesvirus infections (5-substituted 2'-deoxyuridine analogues, entry inhibitors, nucleoside analogues, pyrophosphate analogues, and acyclic guanosine analogues), (v) influenza virus infections (ribavirin, matrix 2 protein inhibitors, RNA polymerase inhibitors, and neuraminidase inhibitors), (vi) human cytomegalovirus infections (acyclic guanosine analogues, acyclic nucleoside phosphonate analogues, pyrophosphate analogues, and oligonucleotides), (vii) varicella-zoster virus infections (acyclic guanosine analogues, nucleoside analogues, 5-substituted 2'-deoxyuridine analogues, and antibodies), (viii) respiratory syncytial virus infections (ribavirin and antibodies), and (ix) external anogenital warts caused by human papillomavirus infections (imiquimod, sinecatechins, and podofilox). Here, we present for the first time a comprehensive overview of antiviral drugs approved over the past 50 years, shedding light on the development of effective antiviral treatments against current and emerging infectious diseases worldwide. PMID:27281742

  7. Daclatasvir: potential role in hepatitis C

    Directory of Open Access Journals (Sweden)

    Lee C

    2013-10-01

    Full Text Available Choongho Lee College of Pharmacy, Dongguk University-Seoul, Goyang, Republic of Korea  Abstract: Chronic hepatitis C virus (HCV infection is responsible for the development of liver cirrhosis and hepatocellular carcinoma. It has been a tremendous burden on global health care systems. With the advent of a number of new direct-acting and host-targeting antiviral agents, current interferon-α- and ribavirin-based HCV therapy has started to move towards an interferon-sparing or even interferon-free strategy. In this regard, a recently identified NS5A inhibitor, daclatasvir, showed a great promise in clinical trials as another new class of direct-acting anti-HCV therapeutics, with a distinct mechanism of action. In this review, a variety of preclinical as well as clinical proof-of-concept studies of daclatasvir, including the studies of its discovery, mechanism of action, viral resistance, and host polymorphism profiles are reviewed. In addition, a role of daclatasvir in the future therapy for HCV patients is discussed briefly. Keywords: hepatitis C virus, nonstructural protein 5A, NS5A inhibitor, hepatitis C treatment

  8. Dengue Virus Control of Type I IFN Responses: A History of Manipulation and Control.

    Science.gov (United States)

    Castillo Ramirez, Jorge Andrés; Urcuqui-Inchima, Silvio

    2015-06-01

    The arthropod-borne diseases caused by dengue virus (DENV) are a major and emerging problem of public health worldwide. Infection with DENV causes a series of clinical manifestations ranging from mild flu syndrome to severe diseases that include hemorrhage and shock. It has been demonstrated that the innate immune response plays a key role in DENV pathogenesis. However, in recent years, it was shown that DENV evades the innate immune response by blocking type I interferon (IFN-I). It has been demonstrated that DENV can inhibit both the production and the signaling of IFN-I. The viral proteins, NS2A and NS3, inhibit IFN-I production by degrading cellular signaling molecules. In addition, the viral proteins, NS2A, NS4A, NS4B, and NS5, can inhibit IFN-I signaling by blocking the phosphorylation of the STAT1 and STAT2 molecules. Finally, NS5 mediates the degradation of STAT2 using the proteasome machinery. In this study, we briefly review the most recent insights regarding the IFN-I response to DENV infection and its implication for pathogenesis. PMID:25629430

  9. Structure of Hepatitis C Virus Polymerase in Complex with Primer-Template RNA

    Energy Technology Data Exchange (ETDEWEB)

    Mosley, Ralph T.; Edwards, Thomas E.; Murakami, Eisuke; Lam, Angela M.; Grice, Rena L.; Du, Jinfa; Sofia, Michael J.; Furman, Philip A.; Otto, Michael J. (Pharmasset); (Emerald)

    2012-08-01

    The replication of the hepatitis C viral (HCV) genome is accomplished by the NS5B RNA-dependent RNA polymerase (RdRp), for which mechanistic understanding and structure-guided drug design efforts have been hampered by its propensity to crystallize in a closed, polymerization-incompetent state. The removal of an autoinhibitory {beta}-hairpin loop from genotype 2a HCV NS5B increases de novo RNA synthesis by >100-fold, promotes RNA binding, and facilitated the determination of the first crystallographic structures of HCV polymerase in complex with RNA primer-template pairs. These crystal structures demonstrate the structural realignment required for primer-template recognition and elongation, provide new insights into HCV RNA synthesis at the molecular level, and may prove useful in the structure-based design of novel antiviral compounds. Additionally, our approach for obtaining the RNA primer-template-bound structure of HCV polymerase may be generally applicable to solving RNA-bound complexes for other viral RdRps that contain similar regulatory {beta}-hairpin loops, including bovine viral diarrhea virus, dengue virus, and West Nile virus.

  10. Cloning of RNA-dependent RNA Polymerase (RdRp Gene from Genotype Dengue Type-2 (New Guinea-C Strain

    Directory of Open Access Journals (Sweden)

    Samian, R.

    2005-01-01

    Full Text Available Dengue virus causes febrile disease in human. Dengue infection causes dengue fever that is not life threatening. However, a severe form of the disease called dengue hemorrhagic fever (DH or dengue shock syndrome (DSS, proven to be fatal. A positive single stranded RNA virus genome encodes for a single polyprotein precursor and is arranged in the order of NH2-C-prM-E-NS1-NS2A-NS2B-NS3-NS4A-NS4B-NS5-COOH. The purpose of this study was to clone NS5 gene that encodes for the RNA-dependent RNA polymerase (RdRp. This enzyme plays an important role in viral RNA replication. The RdRp associated by cofactors produce minus-strand single stranded RNA, which in turn, serves as a template for the production of new plus-strand single stranded genome. The virus RNA was extracted from Aedes albopictus cell line C6/36 that was infected with dengue virus type 2. Then, the extracted virus RNA was used as the template for RT-PCR. A 2.7 kb DNA fragment, representing the RNA-dependent RNA polymerase gene, wassuccessfully amplified using specific primers. The PCR product was then cloned into cloning vector (pGEM-T and transformed into E. coli JM109.

  11. Highly efficient full-length hepatitis C virus genotype 1 (strain TN) infectious culture system

    DEFF Research Database (Denmark)

    Li, Yi-Ping; Ramirez, Santseharay; Jensen, Sanne B;

    2012-01-01

    Chronic infection with hepatitis C virus (HCV) is an important cause of end stage liver disease worldwide. In the United States, most HCV-related disease is associated with genotype 1 infection, which remains difficult to treat. Drug and vaccine development was hampered by inability to culture...... patient isolates representing HCV genotypes 1-7 and subtypes; only a recombinant 2a genome (strain JFH1) spontaneously replicated in vitro. Recently, we identified three mutations F1464L/A1672S/D2979G (LSG) in the nonstructural (NS) proteins, essential for development of full-length HCV 2a (J6) and 2b (J8......) culture systems in Huh7.5 cells. Here, we developed a highly efficient genotype 1a (strain TN) full-length culture system. We initially found that the LSG substitutions conferred viability to an intergenotypic recombinant composed of TN 5' untranslated region (5'UTR)-NS5A and JFH1 NS5B-3'UTR; recovered...

  12. Association of Hepatitis C Virus With Insulin Resistance: Evidences From Animal Studies and Clinical Studie

    Directory of Open Access Journals (Sweden)

    Sadaf Badar

    2012-01-01

    Full Text Available Context: HCV infection is strongly associated with development of insulin resistance and type-2 diabetes, however molecular mechanism of these associations is not known. The aim of this review was to conduct a comprehensive literature search to understand the nature of the association between hepatitis C virus (HCV infection and insulin resistance (IR. We also explored the role of HCV core protein and NS5a in modulating the course of the insulin-signaling pathway.Evidence Acquisitions: We searched Directory of Open Access Journals (DOAJ Google Scholar, Pubmed (NLM, LISTA (EBSCO, Web of Science (TS and PakMediNet.Results: Emerging evidence suggests an association between HCV infection and carotid/coronary vascular disease. IR appears to be a dominant underlying cause of accelerated atherosclerosis in patients with chronic hepatitis C (CHC. HCV can induce IR directly through the stimulation of SOCS3 and PPA2, and both of these molecules have been shown to inhibit interferon-α signaling. Improvement of insulin sensitivity may increase the response rate to antiviral treatment and prevent IR complications, including vascular diseases. The results of several clinical trials that have used insulin sensitizers (metformin and PPAR-γ agonists have been inconclusive.Conclusions: Beside the association between HCV and IR, the published data also have showed the possible association of HCV core and NS5A protein with IR.

  13. [Cloning alphavirus and flavivirus sequences for use as positive controls in molecular diagnostics].

    Science.gov (United States)

    Camacho, Daría; Reyes, Jesús; Franco, Leticia; Comach, Guillermo; Ferrer, Elizabeth

    2016-06-01

    The purpose of the study was to obtain a positive control to validate molecular techniques (reverse transcription- polymerase chain reaction [RT-PCR]) used in the diagnosis and research of viral infections. From strains of Chikungunya virus (CHIKV), Zika virus, and Dengue virus (DENV-1, DENV-2, DENV- 3, and DENV-4) viral RNAs were extracted to obtain complementary DNA using RT-PCR from the nsP4 (CHIKV), NS5 (Zika virus), C/prM-M, and 5'UTR-C (DENV-1, DENV-2, DENV-3, DENV-4) sequences, which were cloned into pGEM®-T Easy. Cloning was confirmed through colony PCR, from which plasmid DNA was extracted for fragment cloning verification. Cloning of cDNA corresponding to nsP4, NS5, C/prM-M, and 5'UTR-C of the different viral agents was achieved. In conclusion, recombinant plasmids were obtained with each of the sequences specified for further assessment as positive controls in molecular techniques in an effort to avoid the use of cell cultures, which can be costly, time-consuming, and potentially dangerous. PMID:27656926

  14. Genome-wide analysis for identification of adaptive diversification between hepatitis C virus subtypes 1a and 1b.

    Science.gov (United States)

    Li, Yan; Wang, Ruirui; Du, Xiaogang; Zhang, Mingwang; Xie, Meng

    2016-07-01

    Hepatitis C virus (HCV) is a major cause of liver disease and has been estimated to infect approximately 2%-3% of the world's population. HCV genotype 1 is the subject of intense research and clinical investigations because of its worldwide prevalence and poor access to treatment for patients in developing countries and marginalized populations. The predominant subtypes 1a and 1b of HCV genotype 1 present considerable differences in epidemiological features. However, the genetic signature underlying such phenotypic functional divergence is still an open question. Here, we performed a genome-wide evolutionary study on HCV subtypes 1a and 1b. The results show that adaptive selection has driven the diversification between these subtypes. Furthermore, the major adaptive divergence-related changes have occurred on proteins E1, NS4B, NS5A, and NS5B. Structurally, a number of adaptively selected sites cluster in functional regions potentially relevant to (i) membrane attachment and (ii) the interactions with viral and host cell factors and the genome template. These results might provide helpful hints about the molecular determinants of epidemiological divergence between HCV 1a and 1b.

  15. Distribution and heterogeneity of hepatitis C genotypes in hepatitis patients in Cameroon.

    Science.gov (United States)

    Pasquier, Christophe; Njouom, Richard; Ayouba, Ahidjo; Dubois, Martine; Sartre, Michèle Tagni; Vessière, Aurelia; Timba, Isabelle; Thonnon, Jocelyn; Izopet, Jacques; Nerrienet, Eric

    2005-11-01

    Hepatitis C virus infects humans world-wide. The virus genome varies greatly and it has several genotypes. HCV infection is highly prevalent in Central Africa and Cameroon. Initial studies on the genetic variability of HCV showed infection with HCV genotypes 1, 2, and 4. We have now sequenced the NS5b and E2 regions of 156 HCV isolates collected from patients presenting for diagnosis in Yaounde and used the data to describe the distribution of HCV genotypes and subtypes in patients with hepatitis in Cameroon. Genotype 1 was more frequent than Genotypes 4 and 2. Genotypes 1 and 4 were highly heterogeneous, containing many subtypes described previously (1b, 1c, 1e, 1h, 1l, 4f, 4t, 4p, 4k) and unsubtyped groups. There was a systematic phylogenetic concordance between NS5b and E2 sequence clustering. The Genotype 2 sequences did not vary. Neither subject age nor gender influenced HCV distribution. HCV Genotypes 1 and 4 are very heterogeneous in Cameroon, perhaps due to ancient infections. The homogeneity of HCV Genotype 2 indicates its more recent introduction from western Africa.

  16. 2015 Philip S. Portoghese Medicinal Chemistry Lectureship. Curing Hepatitis C Virus Infection with Direct-Acting Antiviral Agents: The Arc of a Medicinal Chemistry Triumph.

    Science.gov (United States)

    Meanwell, Nicholas A

    2016-08-25

    The development of direct-acting antiviral agents that can cure a chronic hepatitis C virus (HCV) infection after 8-12 weeks of daily, well-tolerated therapy has revolutionized the treatment of this insidious disease. In this article, three of Bristol-Myers Squibb's HCV programs are summarized, each of which produced a clinical candidate: the NS3 protease inhibitor asunaprevir (64), marketed as Sunvepra, the NS5A replication complex inhibitor daclatasvir (117), marketed as Daklinza, and the allosteric NS5B polymerase inhibitor beclabuvir (142), which is in late stage clinical studies. A clinical study with 64 and 117 established for the first time that a chronic HCV infection could be cured by treatment with direct-acting antiviral agents alone in the absence of interferon. The development of small molecule HCV therapeutics, designed by medicinal chemists, has been hailed as "the arc of a medical triumph" but may equally well be described as "the arc of a medicinal chemistry triumph". PMID:27501244

  17. Structure-Based Discovery of Novel Cyclophilin A Inhibitors for the Treatment of Hepatitis C Virus Infections.

    Science.gov (United States)

    Yang, Suhui; K R, Jyothi; Lim, Sangbin; Choi, Tae Gyu; Kim, Jin-Hwan; Akter, Salima; Jang, Miran; Ahn, Hyun-Jong; Kim, Hee-Young; Windisch, Marc P; Khadka, Daulat B; Zhao, Chao; Jin, Yifeng; Kang, Insug; Ha, Joohun; Oh, Byung-Chul; Kim, Meehyein; Kim, Sung Soo; Cho, Won-Jea

    2015-12-24

    Hepatitis C virus (HCV) is a major cause of end-stage liver disease. Direct-acting antivirals (DAAs), including inhibitors of nonstructural proteins (NS3/4A protease, NS5A, and NS5B polymerase), represent key components of anti-HCV treatment, but these are associated with increased drug resistance and toxicity. Thus, the development of host-targeted antiviral agents, such as cyclophilin A inhibitors, is an alternative approach for more effective, selective, and safer treatment. Starting with the discovery of a bis-amide derivative 5 through virtual screening, the lead compound 25 was developed using molecular modeling-based design and systematic exploration of the structure-activity relationship. The lead 25 lacked cytotoxicity, had potent anti-HCV activity, and showed selective and high binding affinity for CypA. Unlike cyclosporin A, 25 lacked immunosuppressive effects, successfully inhibited the HCV replication, restored host immune responses without acute toxicity in vitro and in vivo, and exhibited a high synergistic effect in combination with other drugs. These findings suggest that the bis-amides have significant potential to extend the arsenal of HCV therapeutics. PMID:26613291

  18. Non-geometric Five-branes in Heterotic Supergravity

    CERN Document Server

    Sasaki, Shin

    2016-01-01

    We study T-duality chains of five-branes in heterotic supergravity where the first order $\\alpha'$-corrections are present. By performing the $\\alpha'$-corrected T-duality transformations of the heterotic NS5-brane solutions, we obtain the KK5-brane and the exotic $5^2_2$-brane solutions associated with the symmetric, the neutral and the gauge NS5-branes. We find that the Yang-Mills gauge field in these solutions satisfies the self-duality condition in the three- and two-dimensional transverse spaces to the brane world-volumes. The $O(2,2)$ monodromy structures of the $5^2_2$-brane solutions are investigated by the $\\alpha'$-corrected generalized metric. Our analysis shows that the symmetric $5^2_2$-brane solution, which satisfies the standard embedding condition, is a T-fold and it exhibits the non-geometric nature. We also find that the neutral $5^2_2$-brane solution is a T-fold at least at $\\mathcal{O} (\\alpha')$. On the other hand, the gauge $5^2_2$-brane solution is not a T-fold but show unusual structur...

  19. Zebrafish as a potential model organism for drug test against hepatitis C virus.

    Directory of Open Access Journals (Sweden)

    Cun-Bao Ding

    Full Text Available Screening and evaluating anti- hepatitis C virus (HCV drugs in vivo is difficult worldwide, mainly because of the lack of suitable small animal models. We investigate whether zebrafish could be a model organism for HCV replication. To achieve NS5B-dependent replication an HCV sub-replicon was designed and created with two vectors, one with HCV ns5b and fluorescent rfp genes, and the other containing HCV's 5'UTR, core, 3'UTR and fluorescent gfp genes. The vectors containing sub-replicons were co-injected into zebrafish zygotes. The sub-replicon amplified in liver showing a significant expression of HCV core RNA and protein. The sub-replicon amplification caused no abnormality in development and growth of zebrafish larvae, but induced gene expression change similar to that in human hepatocytes. As the amplified core fluorescence in live zebrafish was detectable microscopically, it rendered us an advantage to select those with replicating sub-replicon for drug experiments. Ribavirin and oxymatrine, two known anti-HCV drugs, inhibited sub-replicon amplification in this model showing reduced levels of HCV core RNA and protein. Technically, this method had a good reproducibility and is easy to operate. Thus, zebrafish might be a model organism to host HCV, and this zebrafish/HCV (sub-replicon system could be an animal model for anti-HCV drug screening and evaluation.

  20. Identifiction and Detection of Classical Swine Fever Virus in A Pig Farm of Xinxiang%新乡市某猪场猪瘟病毒的鉴别检测

    Institute of Scientific and Technical Information of China (English)

    孔令芸; 陈玲丽; 李冲; 孙相和; 李鹏; 王选年; 银梅

    2015-01-01

    新乡市某猪场发生疑似猪瘟病例,为了鉴别其为疫苗毒还是野毒,采用细胞免疫化学方法和RT-PCR,并对其NS5B基因进行序列测定,序列比对并构建进化树,结果表明,猪只为猪瘟野毒感染,且分离的猪瘟病毒与石门(Shimen)株在基因序列上未发生大的变异。%The suspicious cases of classical swine fever occurred in a pig farm of Xinxiang.The virus was i-dentified by cell immunochemistry method and RT-PCR.The results of the sequence alignment and phylo-genetic tree of NS5B gene showed that the pigs were infected with classical swine fever virus field strain, and the gene sequence variation of this isolate was not obvious.

  1. Direct anti-HCV agents

    Directory of Open Access Journals (Sweden)

    Xingquan Zhang

    2016-01-01

    Full Text Available Unlike human immunodeficiency virus (HIV and hepatitis B virus (HBV, hepatitis C virus (HCV infection is a curable disease. Current direct antiviral agent (DAA targets are focused on HCV NS3/4A protein (protease, NS5B protein (polymerase and NS5A protein. The first generation of DAAs includes boceprevir and telaprevir, which are protease inhibitors and were approved for clinical use in 2011. The cure rate for genotype 1 patients increased from 45% to 70% when boceprevir or telaprevir was added to standard PEG-IFN/ribavirin. More effective and less toxic second generation DAAs supplanted these drugs by 2013. The second generation of DAAs includes sofosbuvir (Sovaldi, simeprevir (Olysio, and fixed combination medicines Harvoni and Viekira Pak. These drugs increase cure rates to over 90% without the need for interferon and effectively treat all HCV genotypes. With these drugs the “cure HCV” goal has become a reality. Concerns remain about drug resistance mutations and the high cost of these drugs. The investigation of new HCV drugs is progressing rapidly; fixed dose combination medicines in phase III clinical trials include Viekirax, asunaprevir+daclatasvir+beclabuvir, grazoprevir+elbasvir and others.

  2. Ledipasvir/sofosbuvir fixed-dose combination for treatment of hepatitis C virus genotype 4 infection.

    Science.gov (United States)

    Nehra, V; Tan, E M; Rizza, S A; Temesgen, Z

    2016-02-01

    Hepatitis C virus (HCV) genotype 4 accounts for 8-13% of all chronic HCV infections worldwide. Patients with HCV genotype 4 have been reported to have poor treatment responses to PEGylated interferon and ribavirin regimens. Recently a single tablet, fixed-dose combination of sofosbuvir, an RNA-directed RNA polymerase (NS5B) inhibitor, and ledipasvir, a nonstructural protein 5A (NS5A) inhibitor, has been approved for treatment of chronic HCV infection. Two studies using the fixed-dose combination in chronic HCV genotype 4 for 12 weeks reported sustained virologic response rates at 12 weeks (SVR12) of 93-95%. Data also support the use of ledipasvir/sofosbuvir in chronic HCV genotype 4 and HIV co-infection. Administered as a single once-daily oral regimen, this ribavirin- and interferon-free regimen is well tolerated, with low potential for adverse effects and represents a significant advancement in the treatment of chronic HCV genotype 4 infection.

  3. Robust HCV Genotype 3a Infectious Cell Culture System Permits Identification of Escape Variants With Resistance to Sofosbuvir

    DEFF Research Database (Denmark)

    Ramirez, Santseharay; Mikkelsen, Lotte S; Gottwein, Judith M;

    2016-01-01

    to sofosbuvir-the only nucleotide analog approved for treatment of chronic HCV infection. METHODS: The developed HCV genotype 3a full-length genome (DBN3a), with a strain-DBN coding sequence, modified NS5B consensus sequence, pS52 untranslated regions, and coding mutations from a culture efficient JFH1-based...... with increasing concentrations of sofosbuvir was used to promote selection of HCV resistant variants. RESULTS: We engineered a DBN3a variant with 17 substitutions (DBN3acc) that had replication and propagation kinetics in Huh7.5 cells comparable to prototype J6/JFH1. The adaptive mutations also produced culture...... efficient DBN-based recombinants with NS5B from HCV genotype 3a strains S52 and DH11. Compared to genotype 1a, 3a was less sensitive to daclatasvir, ledipasvir and elbasvir, but equally sensitive to ombitasvir, velpatasvir, beclabuvir, dasabuvir, MK-3682, and sofosbuvir. Exposure of Huh7.5 cells infected...

  4. FDA approved hepatitis C virus drug Sovaldi (sofosbuvir)%FDA批准抗丙型肝炎新药索非布韦(sofosbuvir)上市

    Institute of Scientific and Technical Information of China (English)

    蔡巍; 陈斌; 田宁

    2014-01-01

    全球丙型肝炎病毒(HCV)的感染率高,且缺少有效的治疗药物.2013年12月6日,美国食品药物监督管理局(FDA)批准新分子实体药物索非布韦(sofosbuvir)片剂上市,商品名Sovaldi,用于慢性丙型肝炎的治疗.索非布韦是一种HCV聚合酶抑制剂,作用于病毒RNA复制的核苷酸类似物NS5B聚合酶位点,能中止病毒复制,是以NS5B聚合酶为靶点的唯一上市品种.本品与聚乙二醇干扰素/利巴韦林或单独与利巴韦林联用,与标准治疗方案相比治愈率更高且缩短给药时间,有广阔的应用前景.

  5. Dual daclatasvir and sofosbuvir for treatment of genotype 3 chronic hepatitis C virus infection.

    Science.gov (United States)

    Sundaram, Vinay; Kowdley, Kris V

    2016-01-01

    Chronic hepatitis C virus (HCV) infection is one of the most common etiologies of liver-related mortality throughout the world. Traditionally, therapy has been focused on pegylated interferon in combination with ribavirin, with clinical trials demonstrating that HCV genotype 1 had the lowest response rate (40-50%), while genotype 3 had an intermediate response rate (60-70%). Recently, significant advances have been made with all-oral direct-acting antiviral (DAA) therapy, which have significantly improved cure rates for HCV genotype 1. Accordingly, HCV genotype 3 is now potentially the most difficult to treat. One of the most potent DAA medications is sofosbuvir, a pan-genotypic nucleotide analogue that inhibits the NS5B polymerase of HCV. Daclatasvir, a pan-genotypic inhibitor of the HCV NS5A replication complex, was recently approved in the United States for treatment of HCV genotype 3 in conjunction with sofosbuvir. This combination may provide a powerful tool in the treatment of HCV genotype 3.

  6. Heterotic/type II triality and instantons on K3

    International Nuclear Information System (INIS)

    A detailed understanding of instanton effects for half-BPS couplings is pursued in theories with 16 supersymmetries. In particular, we investigate the duality between heterotic string on T4 and type IIA on K3 at the T4/Zint2 orbifold point, as well as their higher and lower dimensional versions. We present a remarkably clean quantitative test of the duality at the level of F-circumflex 4 couplings, by completely matching a purely one-loop heterotic amplitude to a purely tree-level type II result. The triality of SO(4,4) and several other miracles are shown to be crucial for the duality to hold. Exact non-perturbative new results for type I', F on K3, M on K3, and IIB on K3 are found, and the general form of D-instanton contributions in type IIA or B on T4/Zint2 is obtained. We also analyze the NS5-brane contributions in type II on K3 X T2, and predict the value mu (N)=sum(d|N) (1/d3) for the bulk contribution to the index of the NS5-brane world-volume theory on K3 X T2. (author)

  7. Distribution and heterogeneity of hepatitis C genotypes in hepatitis patients in Cameroon.

    Science.gov (United States)

    Pasquier, Christophe; Njouom, Richard; Ayouba, Ahidjo; Dubois, Martine; Sartre, Michèle Tagni; Vessière, Aurelia; Timba, Isabelle; Thonnon, Jocelyn; Izopet, Jacques; Nerrienet, Eric

    2005-11-01

    Hepatitis C virus infects humans world-wide. The virus genome varies greatly and it has several genotypes. HCV infection is highly prevalent in Central Africa and Cameroon. Initial studies on the genetic variability of HCV showed infection with HCV genotypes 1, 2, and 4. We have now sequenced the NS5b and E2 regions of 156 HCV isolates collected from patients presenting for diagnosis in Yaounde and used the data to describe the distribution of HCV genotypes and subtypes in patients with hepatitis in Cameroon. Genotype 1 was more frequent than Genotypes 4 and 2. Genotypes 1 and 4 were highly heterogeneous, containing many subtypes described previously (1b, 1c, 1e, 1h, 1l, 4f, 4t, 4p, 4k) and unsubtyped groups. There was a systematic phylogenetic concordance between NS5b and E2 sequence clustering. The Genotype 2 sequences did not vary. Neither subject age nor gender influenced HCV distribution. HCV Genotypes 1 and 4 are very heterogeneous in Cameroon, perhaps due to ancient infections. The homogeneity of HCV Genotype 2 indicates its more recent introduction from western Africa. PMID:16173014

  8. 广州地区人类白细胞抗原-Ⅰ类与丙型肝炎病毒-6a型感染相关性的研究%Study on association between hepatitis C-6a and HLA-Ⅰ allele in Guangzhou area

    Institute of Scientific and Technical Information of China (English)

    夏文杰; 叶欣; 付涌水; 王怡仲; 许茹; 徐秀章; 陈扬凯; 贝春花

    2011-01-01

    Objective :To study the association between hepatitis C-6a and HLA-Ⅰ allele in Guangzhou area .Methods :250 individuals of HCV antibodies positive and 621 health blood donors in Guangzhou area were enrolled in this study .Nested polymerase chain reaction (PCR ) was applied to detect HCV RNA in the sera .The gene sequences in E1 and NS5B area were detected for gene typing of HCV .LUMINEX SSO methods was used to detect the HLA-Ⅰ allele .The relative risk was evaluated in regular formular .Results :There were 69 samples as HCV-6a gene type in the 250 persons .RR value in A * 33 ,A * 30 was beyond 4 ,and RR value in B * 56 ,B * 54 ,B * 55 ,B * 58 ,B * 76 was also more than 4 .Conclusion :HLA-A19 and HLA-B22 are important genetic factor for infection of HCV-6a .%目的:广州地区HLA-Ⅰ类抗原和HCV-6a感染相关性的研究.方法:选取2002~2008年HCV抗体检测双试剂阳性无偿献血者250名,随机抽取621名广州地区无血缘关系的健康无偿献血者作为对照,用逆转录-套式聚合酶链反应扩增HCVE1和 NS5B基因,对E1和NS5B区扩增阳性的PCR产物核苷酸序列测定,将所测定的HCVE1、NS5B进行基因分型.LUMINEX-SSO方法检测HLA-A,B 检测样本HLA-A,B位点.根据公式对HLA型别相关性的相对危险性进行评估.结果:250名无偿献血者中有69个样本的HCVE1和NS5B区分型结果为HCV-6a,占到分析总数的27.6%.A*33、A*30与HCV-6a感染相关评估的RR值均大于4,B*56、B*54、B*55、B*58、B*76与HCV-6a感染相关评估的RR值均大于4,与HCV-6a感染具有强关联性.结论:广州地区HCV-6a的感染与A*19和B*22存在强关联性,对HCV-6a的地域性流行、治疗和预后评价有一定预见作用.

  9. Guanylate-Binding Protein 1, an Interferon-Induced GTPase, Exerts an Antiviral Activity against Classical Swine Fever Virus Depending on Its GTPase Activity

    Science.gov (United States)

    Li, Lian-Feng; Yu, Jiahui; Li, Yongfeng; Wang, Jinghan; Li, Su; Zhang, Lingkai; Xia, Shui-Li; Yang, Qian; Wang, Xiao; Yu, Shaoxiong; Luo, Yuzi; Sun, Yuan; Zhu, Yan; Munir, Muhammad

    2016-01-01

    ABSTRACT Many viruses trigger the type I interferon (IFN) pathway upon infection, resulting in the transcription of hundreds of interferon-stimulated genes (ISGs), which define the antiviral state of the host. Classical swine fever virus (CSFV) is the causative agent of classical swine fever (CSF), a highly contagious viral disease endangering the pig industry in many countries. However, anti-CSFV ISGs are poorly documented. Here we screened 20 ISGs that are commonly induced by type I IFNs against CSFV in lentivirus-delivered cell lines, resulting in the identification of guanylate-binding protein 1 (GBP1) as a potent anti-CSFV ISG. We observed that overexpression of GBP1, an IFN-induced GTPase, remarkably suppressed CSFV replication, whereas knockdown of endogenous GBP1 expression by small interfering RNAs significantly promoted CSFV growth. Furthermore, we demonstrated that GBP1 acted mainly on the early phase of CSFV replication and inhibited the translation efficiency of the internal ribosome entry site of CSFV. In addition, we found that GBP1 was upregulated at the transcriptional level in CSFV-infected PK-15 cells and in various organs of CSFV-infected pigs. Coimmunoprecipitation and glutathione S-transferase (GST) pulldown assays revealed that GBP1 interacted with the NS5A protein of CSFV, and this interaction was mapped in the N-terminal globular GTPase domain of GBP1. Interestingly, the K51 of GBP1, which is crucial for its GTPase activity, was essential for the inhibition of CSFV replication. We showed further that the NS5A-GBP1 interaction inhibited GTPase activity, which was critical for its antiviral effect. Taking our findings together, GBP1 is an anti-CSFV ISG whose action depends on its GTPase activity. IMPORTANCE Classical swine fever virus (CSFV) is the causative agent of classical swine fever (CSF), an economically important viral disease affecting the pig industry in many countries. To date, only a few host restriction factors against CSFV

  10. A highly sensitive and selective viral protein detection method based on RNA oligonucleotide nanoparticle

    Directory of Open Access Journals (Sweden)

    Changhyun Roh

    2010-04-01

    Full Text Available Changhyun Roh1, Ho-Young Lee2, Sang-Eun Kim2, Sung-Kee Jo11Radiation Research Division for Biotechnology, Advanced Radiation Technology Institute (ARTI, Korea Atomic Energy Research Institute (KAERI, Sinjeong-dong, Jeongeup, Jeonbuk, South Korea; 2Department of Nuclear Medicine, College of Medicine, Seoul National University, South KoreaAbstract: Globally, approximately 170 million people (representing approximately 3% of the population worldwide, are infected with hepatitis C virus (HCV and at risk of serious liver disease, including chronic hepatitis. We propose a new quantum dots (QDs-supported RNA oligonucleotide approach for the specific and sensitive detection of viral protein using a biochip. This method was developed by immobilizing a HCV nonstructural protein 5B (NS5B on the surface of a glass chip via the formation of a covalent bond between an amine protein group and a ProLinkerTM glass chip. The QDs-supported RNA oligonucleotide was conjugated via an amide formation reaction from coupling of a 5′-end-amine-modified RNA oligonucleotide on the surface of QDs displaying carboxyl groups via standard EDC coupling. The QDs-conjugated RNA oligonucleotide was interacted to immobilized viral protein NS5B on the biochip. The detection is based on the variation of signal of QDs-supported RNA oligonucleotide bound on an immobilized biochip. It was demonstrated that the value of the signal has a linear relationship with concentrations of the HCV NS5B viral protein in the 1 μg mL-1 to 1 ng mL-1 range with a detection limit of 1 ng mL-1. The major advantages of this RNA-oligonucleotide nanoparticle assay are its good specificity, ease of performance, and ability to perform one-spot monitoring. The proposed method could be used as a general method of HCV detection and is expected to be applicable to other types of diseases as well.Keywords: hepatitis C virus, viral protein, RNA oligonucleotide, quantum dots, biochip

  11. Directly Acting Triple Drug Anti-HCV Therapy Induces Sustained Virologic Response with a Six Week Regimen: A Proof of Concept Phase 2a Cohort Study

    Science.gov (United States)

    Kohli, Anita; Osinusi, Anuoluwapo; Sims, Zayani; Nelson, Amy; Meissner, Eric G.; Barrett, Lisa L.; Bon, Dimitra; Marti, Miriam M; Silk, Rachel; Kotb, Colleen; Gross, Chloe; Jolley, Tim A; Sidharthan, Sreetha; Petersen, Tess; Townsend, Kerry; Egerson, D’Andrea; Kapoor, Rama; Spurlin, Emily; Sneller, Michael; Proschan, Michael; Herrmann, Eva; Kwan, Richard; Teferi, Gebeyehu; Talwani, Rohit; Diaz, Gabbie; Kleiner, David E.; Wood, Brad J.; Chavez, Jose; Abbott, Stephen; Symonds, William T.; Subramanian, G. Mani; Pang, Phillip S.; McHutchison, John; Polis, Michael A.; Fauci, Anthony S; Masur, Henry; Kottilil, Shyam

    2015-01-01

    Background Direct acting anti-HCV drugs have demonstrated a high cure rate and favorable tolerability. The development of shorter courses of therapy may improve affordability and adherence. Sofosbuvir and ledipasvir together with ribavirin have yielded high efficacy when administered for 8, but not for 6 weeks. We hypothesized that addition of a third potent directly acting antiviral to sofosbuvir and ledipasvir would allow for shortened durations of therapy. Methods In this single center, open-label cohort, phase 2 atrial, sixty HCV GT-1 treatment naïve patients were sequentially enrolled onto three arms and treated with 12 weeks of sofosbuvir and ledipasvir (an NS5B nucleotide polymerase inhibitor and an NS5A inhibitor, respectively) (n=20); or 6 weeks with sofosbuvir, ledipasvir, and GS-9669 (a non-nucleoside NS5B inhibitor) (n=20) or 6 weeks with sofosbuvir, ledipasvir and GS-9451 (an NS3/4A protease inhibitor) (n=20). Patients and investigators were unmasked to treatment assignment. The primary efficacy analysis was SVR12 (HCV RNA less than the level of quantitation 12 weeks after treatment completion). Findings All subjects treated with sofosbuvir and ledipasvir for 12 weeks achieved SVR12 (95%CI: 83–100%). Nineteen of 20 patients (95% CI: 75–100%) treated with sofosbuvir, ledipasvir and GS-9669 achieved SVR12, with 1 patient relapsing 2 weeks after completion of therapy. Nineteen of 20 patients (95% CI: 75–100%) treated with sofosbuvir, ledipasvir, and GS-9451 for 6 weeks achieved SVR12, one patient was lost to follow up after achieving SVR4. There were no discontinuations of treatment due to adverse events. Interpretation In this small proof of concept study, two different three drug regimens administered for 6 weeks resulted in high cure rates for HCV infection with excellent tolerability. Funding NIAID, National Cancer Institute and Clinical Center Intramural Program. Clinical Trials.gov number NCT01805882. The study was also supported in part by

  12. Drug-Drug Interactions between Sofosbuvir and Ombitasvir-Paritaprevir-Ritonavir with or without Dasabuvir.

    Science.gov (United States)

    King, Jennifer R; Dutta, Sandeep; Cohen, Daniel; Podsadecki, Thomas J; Ding, Bifeng; Awni, Walid M; Menon, Rajeev M

    2016-02-01

    The combination of ombitasvir (an NS5A inhibitor), paritaprevir (an NS3/4A inhibitor) coadministered with ritonavir (r), and dasabuvir (an NS5B nonnucleoside polymerase inhibitor), referred to as the 3D regimen, and the combination of ombitasvir-paritaprevir-r, referred to as the 2D regimen, have demonstrated high efficacy with and without ribavirin in hepatitis C virus (HCV)-infected subjects. These regimens have potential for coadministration with sofosbuvir (nucleoside NS5B inhibitor) in the treatment of HCV. This phase 1, drug-drug interaction, open-label, multiple-dose study enrolled 32 healthy subjects to receive the 3D or 2D regimen in combination with sofosbuvir. Doses of study drugs were as follows: ombitasvir-paritaprevir-r, 25/150/100 mg daily (QD); dasabuvir, 250 mg twice daily (BID); and sofosbuvir, 400 mg QD. Blood samples were collected on study days 7, 14, and 21 for evaluating drug interaction at steady state. The effect of the 3D and 2D regimens on the pharmacokinetics of sofosbuvir and its circulating metabolite GS-331007 and vice versa was assessed by a repeated-measures analysis. Exposures of the 3D and 2D regimens were similar (≤20% change) during coadministration with sofosbuvir and during administration alone. Sofosbuvir exposures were 61% to 112% higher with the 3D regimen and 64% to 93% higher with the 2D regimen than with sofosbuvir alone. GS-331007 total exposures were 27% and 32% higher with the 3D and 2D regimens, respectively, than with sofosbuvir alone. Increases in sofosbuvir and GS-331007 exposures likely resulted from breast cancer resistance protein (BCRP) and/or P glycoprotein (P-gp) transporter inhibition by paritaprevir and ritonavir. No subjects discontinued the study due to study drug-related adverse events. No dose adjustment is recommended for 3D, 2D, or sofosbuvir in clinical trials exploring the safety and efficacy of the combination. (This study has been registered at ClinicalTrials.gov under registration no. NCT

  13. Transmission of hepatitis C virus among intravenous drug users in the Uppsala region of Sweden

    Directory of Open Access Journals (Sweden)

    Axel Danielsson

    2014-01-01

    Full Text Available Background: Epidemiology and transmission patterns of hepatitis C virus (HCV are important subjects as we enter a new era of treatment with directly acting antivirals (DAAs. The highest prevalence of HCV in developed countries is found among intravenous drug users (IDUs, where unsafe needle sharing practices provide the main route of infection. Efforts to prohibit the continuous spread of HCV among these groups have been initiated by the community services and health care providers. Our goal was to understand how HCV was transmitted among IDUs within a limited population group. We provide a retrospective study (2005–2007 of the HCV transmission patterns in a population of IDUs in the Uppsala region of Sweden. Method: Eighty-two serum samples were collected from IDUs in Uppsala County. Our reverse transcription nested polymerase chain reaction (RT-nested PCR and sequencing method enabled a comprehensive genetic analysis for a broad spectrum of genotypes of two relatively conserved regions, NS5B and NS3, that encodes for the viral polymerase and protease, respectively. HCV RNA in serum samples was amplified and sequenced with in-house primers. Sequence similarities between individuals and subgroups were analyzed with maximum likelihood (ML phylogenetic trees. Published HCV reference sequences from other geographic regions and countries were also included for clarity. Results: Phylogenetic analysis was possible for 59 NS5B (72% and 29 NS3 (35% sequences from Uppsala patients. Additionally, we also included 15 NS3 sequences from Örebro patients, making a total of 44 NS3 sequences for the analysis. By analyzing the NS3 sequences, two transmission sets were found between the IDUs (>98% sequence identity, with one set consisting of two individuals and another set consisting of three individuals. In addition, the phylogenetic analysis done with our serum samples displayed clusters that distinguished them from the reference sequences. Conclusion: Our

  14. The IR Obstruction to UV Completion for Dante's Inferno Model with Higher-Dimensional Gauge Theory Origin

    CERN Document Server

    Furuuchi, Kazuyuki

    2015-01-01

    We continue our investigation of large field inflation models obtained from higher-dimensional gauge theories, initiated in our previous study \\cite{Furuuchi:2014cwa}. We focus on Dante's Inferno model which was the most preferred model in our previous analysis. We point out the relevance of the IR obstruction to UV completion, which constrains the form of the potential of the massive vector field, under the current observational upper bound on the tensor to scalar ratio. We also show that in simple examples of the potential arising from DBI action of D5- and NS5- brane that inflation occurs in the field range which is within the convergence radius of the Taylor expansion. This is in contrast to the well known examples of axion monodromy inflation. The difference arises from the very essence of Dante's Inferno model that the effective inflaton potential is stretched in the inflaton field direction compared with the potential for the original field.

  15. Time-resolved investigation of nanosecond discharge in dense gas sustained by short and long high-voltage pulse

    Science.gov (United States)

    Yatom, S.; Gleizer, J. Z.; Levko, D.; Vekselman, V.; Gurovich, V.; Hupf, E.; Hadas, Y.; Krasik, Ya. E.

    2011-12-01

    The results of experimental and numerical studies of the generation of runaway electrons (RAE) in a pressurized air-filled diode under the application of 20 ns, 5 ns and 1 ns duration high-voltage pulses with an amplitude up to 160 kV are presented. It is shown that with a 1 ns pulse, RAE with energy >=20 keV reach the anode prior to the formation of the plasma channel between the cathode and anode. Conversely, with 20 ns or 5 ns pulses, RAE with energy >=20 keV were obtained at the anode only after the formation of the plasma channel. In addition, the high- and low-impedance stages of the development of the discharge were found. Finally, a comparison between experimental and numerical simulation results is presented.

  16. Thermodynamic Geometry and Extremal Black Holes in String Theory

    CERN Document Server

    Sarkar, Tapobrata; Tiwari, Bhupendra Nath

    2008-01-01

    We study a generalisation of thermodynamic geometry to degenerate quantum ground states at zero temperatures exemplified by charged extremal black holes in type II string theories. Several examples of extremal charged black holes with non degenerate thermodynamic geometries and finite but non zero state space scalar curvatures are established. These include black holes described by D1-D5-P and D2-D6-NS5-P brane systems and also two charged small black holes in Type II string theories. We also explore the modifications to the state space geometry and the scalar curvature due to the higher derivative contributions and string loop corrections as well as an exact entropy expression from quantum information theory. Our construction describes state space geometries arising out of a possible limiting thermodynamic characterisation of degenerate quantum ground states at zero temperatures.

  17. Remarks on brane and antibrane dynamics

    CERN Document Server

    Michel, Ben; Polchinski, Joseph; Puhm, Andrea; Saad, Philip

    2014-01-01

    We develop the point of view that brane actions should be understood in the context of effective field theory, and that this is the correct way to treat classical as well as loop divergences. We illustrate this idea in a simple model. We then consider the implications for the dynamics of antibranes in flux backgrounds, focusing on the simplest case of a single antibrane. We argue that there is no tachyonic instability at zero temperature, but there is a nonperturbative process in which an antibrane annihilates with its screening cloud. This is distinct from the NS5-brane instanton decay. Constraints on models of metastable supersymmetry breaking by antibranes may be tightened, but there is no problem of principle with this mechanism.

  18. 2d (0,2) Quiver Gauge Theories and D-Branes

    CERN Document Server

    Franco, Sebastian; Lee, Sangmin; Seong, Rak-Kyeong; Yokoyama, Daisuke

    2015-01-01

    We initiate a systematic study of 2d (0,2) quiver gauge theories on the worldvolume of D1-branes probing singular toric Calabi-Yau 4-folds. We present an algorithm for efficiently calculating the classical mesonic moduli spaces of these theories, which correspond to the probed geometries. We also introduce a systematic procedure for constructing the gauge theories for arbitrary toric singularities by means of partial resolution, which translates to higgsing in the field theory. Finally, we introduce Brane Brick Models, a novel class of brane configurations that consist of D4-branes suspended from an NS5-brane wrapping a holomorphic surface, tessellating a 3-torus. Brane Brick Models are the 2d analogues of Brane Tilings and allow a direct connection between geometry and gauge theory.

  19. High-fidelity continuous-variable quantum teleportation toward multistep quantum operations

    International Nuclear Information System (INIS)

    The progress in quantum operations of continuous-variable (CV) schemes can be reduced to that in CV quantum teleportation. The fidelity of quantum teleportation of an optical setup is limited by the finite degree of quantum correlation that can be prepared with a pair of finitely squeezed states. Reports of improvement of squeezing level have appeared recently, and we adopted the improved methods in our experimental system of quantum teleportation. As a result, we teleported a coherent state with a fidelity F=0.83±0.01, which is better than any other figures reported to date, to our knowledge. In this paper, we introduce a measure ns, the number of teleportations expected to be carried out sequentially. Our result corresponds to ns=5.0±0.4. It suggests that our improvement would enable us to proceed toward more advanced quantum operations involving multiple steps

  20. Brane polarization is no cure for tachyons

    CERN Document Server

    Bena, Iosif

    2015-01-01

    Anti-M2 and anti-D3 branes placed in regions with charges dissolved in fluxes have a tachyon in their near-horizon region, which causes these branes to repel each other. If the branes are on the Coulomb branch this tachyon gives rise to a runaway behavior, but when the branes are polarized into five-branes this tachyon only appears to lower the energy of the polarized branes, without affecting its stability. We analyze brane polarization in the presence of a brane-brane-repelling tachyon and show that when the branes are polarized along the direction of the tachyon the polarized shell is unstable. This implies that tachyons cannot be cured by brane polarization and indicates that, at least in a certain regime of parameters, anti-D3 branes polarized into NS5 branes at the bottom of the Klebanov-Strassler solution have an instability.

  1. Probing the Hydrodynamic Limit of (Super)gravity

    CERN Document Server

    Di Dato, Adriana; Pedersen, Andreas Vigand

    2015-01-01

    We study the long-wavelength effective description of two general classes of charged dilatonic (asymptotically flat) black p-branes including D/NS/M-branes in ten and eleven dimensional supergravity. In particular, we consider gravitational brane solutions in a hydrodynamic derivative expansion (to first order) for arbitrary dilaton coupling and for general brane and co-dimension and determine their effective electro-fluid-dynamic descriptions by exacting the characterizing transport coefficients. We also investigate the stability properties of the corresponding hydrodynamic systems by analyzing their response to small long-wavelength perturbations. For branes carrying unsmeared charge, we find that in a certain regime of parameter space there exists a branch of stable charged configurations. This is in accordance with the expectation that D/NS/M-branes have stable configurations, except for the D5, D6, and NS5. In contrast, we find that Maxwell charged brane configurations are Gregory-Laflamme unstable indep...

  2. The hidden seasonality of the rare biosphere in coastal marine bacterioplankton.

    Science.gov (United States)

    Alonso-Sáez, Laura; Díaz-Pérez, Laura; Morán, Xosé Anxelu G

    2015-10-01

    Rare microbial taxa are increasingly recognized to play key ecological roles, but knowledge of their spatio-temporal dynamics is lacking. In a time-series study in coastal waters, we detected 83 bacterial lineages with significant seasonality, including environmentally relevant taxa where little ecological information was available. For example, Verrucomicrobia had recurrent maxima in summer, while the Flavobacteria NS4, NS5 and NS2b clades had contrasting seasonal niches. Among the seasonal taxa, only 4 were abundant and persistent, 20 cycled between rare and abundant and, remarkably, most of them (59) were always rare (contributing biosphere, hitherto mainly characterized by dormancy and episodes of 'boom and bust', as envisioned by the seed-bank hypothesis. The predictable patterns of seasonal reoccurrence are relevant for understanding the ecology of rare bacteria, which may include key players for the functioning of marine ecosystems.

  3. Heterotic-type IIA duality and degenerations of K3 surfaces

    Science.gov (United States)

    Braun, A. P.; Watari, T.

    2016-08-01

    We study the duality between four-dimensional N = 2 compactifications of heterotic and type IIA string theories. Via adiabatic fibration of the duality in six dimensions, type IIA string theory compactified on a K3-fibred Calabi-Yau threefold has a potential heterotic dual compactification. This adiabatic picture fails whenever the K3 fibre degenerates into multiple components over points in the base of the fibration. Guided by monodromy, we identify such degenerate K3 fibres as solitons generalizing the NS5-brane in heterotic string theory. The theory of degenerations of K3 surfaces can then be used to find which solitons can be present on the heterotic side. Similar to small instanton transitions, these solitons escort singular transitions between different Calabi-Yau threefolds. Starting from well-known examples of heterotic-type IIA duality, such transitions can take us to type IIA compactifications with unknown heterotic duals.

  4. Rational sphere valued supercocycles in M-theory and type IIA string theory

    CERN Document Server

    Fiorenza, Domenico; Schreiber, Urs

    2016-01-01

    We show that supercocycles on super $L_\\infty$-algebras capture, at the rational level, the twisted cohomological charge structure of the fields of M-theory and of type IIA string theory. We show that rational 4-sphere-valued supercocycles for M-branes in M-theory descend to supercocycles in type IIA string theory to yield the Ramond-Ramond fields predicted by the rational image of twisted K-theory, with the twist given by the B-field. In particular, we derive the M2/M5 $\\leftrightarrow$ F1/Dp/NS5 correspondence via dimensional reduction of sphere-valued $L_\\infty$ supercocycles in rational homotopy theory.

  5. Subharmonic triple buncher for a high-efficiency free electron laser

    International Nuclear Information System (INIS)

    A high-efficiency free electron laser oscillator experiment is being constructed at Los Alamos National Laboratory. A buncher system has been designed to deliver 30-ps, 5-nC electron bunches to a 20-MeV standing-wave linac at the 60th subharmonic of the 1300-MHz accelerator frequency. The first 108.3-MHz buncher cavity accepts a 5-ns, 5-A peak current pulse from a triode gun. Following a 120-cm drift space, a second 108.3-MHz cavity is used, primarily to enhance the bunching of the trailing half of the bunch. A 1300-MHz cavity with 20-cm drift spaces at each end completes the beamline components. The bunching process continues into the linac's first three accelerating cells. Two thin iron-shielded lenses and seven large-diameter solenoids provide axial magnetic fields for radial focusing

  6. Cordes et D-branes dans les espaces-temps courbes

    CERN Document Server

    Ribault, S

    2003-01-01

    This thesis is devoted to the construction and study of D-branes in some curved space-times in string theory. On the one hand, those D-branes are described geometrically as submanifolds subject to Born-Infeld effective dynamics. On the other hand, they can be built microscopically using boundary conformal field theory. We use and compare those two approaches. We also improve them technically : we rewrite Born-Infeld dynamics in a gauge-invariant way, and formulate precise analyticity requirements for the density of open strings on certain D-branes. Our results include the effective description of symmetric D-branes in compact groups, the determination of the complete spectrum of open strings on AdS2 D-branes in AdS3, the exact construction of some D-branes in the cigar SL(2)/U(1), and a geometric description of all D3-branes in NS5-brane backgrounds.

  7. Two-loop partition function in the planar plane-wave matrix model

    Science.gov (United States)

    Spradlin, Marcus; Van Raamsdonk, Mark; Volovich, Anastasia

    2004-12-01

    We perform two independent calculations of the two-loop partition function for the 't Hooft large N limit of the plane-wave matrix model, conjectured to be dual to the decoupled little string theory of a single spherical type IIA NS5-brane. The first is via a direct two-loop path-integral calculation in the matrix model, while the second employs the one-loop dilatation operator of four-dimensional N = 4 Yang-Mills theory truncated to the SU (2 | 4) subsector. We find precise agreement between the results of the two calculations. Various polynomials appearing in the result have rather special properties, possibly related to the large symmetry algebra of the theory or to integrability.

  8. Two-Loop Partition Function in the Planar Plane-Wave Matrix Model

    CERN Document Server

    Spradlin, M; Volovich, A; Spradlin, Marcus; Raamsdonk, Mark Van; Volovich, Anastasia

    2004-01-01

    We perform two independent calculations of the two-loop partition function for the large N 't Hooft limit of the plane-wave matrix model, conjectured to be dual to the decoupled little string theory of a single spherical type IIA NS5-brane. The first is via a direct two-loop path-integral calculation in the matrix model, while the second employs the one-loop dilatation operator of four-dimensional N = 4 Yang-Mills theory truncated to the SU(2|4) subsector. We find precise agreement between the results of the two calculations. Various polynomials appearing in the result have rather special properties, possibly related to the large symmetry algebra of the theory or to integrability.

  9. Perturbative decay of anti-branes in flux backgrounds due to space time instabilities

    CERN Document Server

    Danielsson, Ulf H

    2015-01-01

    In this paper we suggest a new source of perturbative decay of the KPV-state, which might have consequences for the viability of the KKLT-construction. The results do not rely on any direct enhancement of the decay due to flux accumulating on the anti-brane in transverse space. Instead, we note that the system can lower its energy through a sequence of NS5-configurations all the way to the true vacuum, without encountering a barrier, if we allow for clumping of screened charge in space time. The clumping can possibly be a parallel to the Gregory-Laflamme instability of black branes. The results are obtained at large $p$, but for $p/M$ arbitrarily small. It is furthermore argued that the results extend to cases of few or single anti-branes where quantization becomes important. We believe that it is important to investigate this possible effect further to judge whether there are any fatal consequences.

  10. Evolution of dengue virus type 2 during two consecutive outbreaks with an increase in severity in southern Taiwan in 2001-2002.

    Science.gov (United States)

    Chen, Hui-Ling; Lin, Su-Ru; Liu, Hsin-Fu; King, Chwan-Chuen; Hsieh, Szu-Chia; Wang, Wei-Kung

    2008-10-01

    To investigate viral determinants and evolution linked to outbreak with increased severity, we examined dengue virus type 2 (DENV-2) sequences from plasma of 31 patients (14 dengue fever, 17 dengue hemorrhagic fever, DHF) continuously during the 2001 and 2002 outbreaks in southern Taiwan, in which both the total cases and proportion of DHF cases increased. Analysis of envelope (E) and full-genome sequences between viruses of the two outbreaks revealed 5 nucleotide changes in E, NS1, NS4A, and NS5 genes. None was identical to those reported in the DENV-2 outbreak in Cuba in 1997, suggesting viral determinants linked to severe outbreak are genotype dependent. Compared with previous reports of lineage turnover years apart, our findings that the 2002 viruses descended from a minor variant of the 2001 viruses in less than 6 months was novel, and may represent a mechanism of evolution of DENV from one outbreak to another. PMID:18840735

  11. Stable non-supersymmetric vacua in the moduli space of non-critical superstrings

    Energy Technology Data Exchange (ETDEWEB)

    Harmark, Troels [Niels Bohr Institute, Blegdamsvej 17, 2100 Copenhagen O (Denmark)]. E-mail: harmark@nbi.dk; Niarchos, Vasilis [Niels Bohr Institute, Blegdamsvej 17, 2100 Copenhagen O (Denmark)]. E-mail: niarchos@nbi.dk; Obers, Niels A. [Niels Bohr Institute, Blegdamsvej 17, 2100 Copenhagen O (Denmark)]. E-mail: obers@nbi.dk

    2006-12-18

    We study a set of asymmetric deformations of non-critical superstring theories in various dimensions. The deformations arise as Kaehler and complex structure deformations of an orthogonal two-torus comprising of a parallel and a transverse direction in the near-horizon geometry of NS5-branes. The resulting theories have the following intriguing features: Spacetime supersymmetry is broken in a continuous fashion and the masses of the lightest modes are lifted. In particular, no bulk or localized tachyons are generated in the non-supersymmetric vacua. We discuss the effects of these deformations in the context of the holographic duality between non-critical superstrings and little string theories and find solutions of rotating fivebranes in supergravity. We also comment on the generation of a one-loop cosmological constant and determine the effects of the one-loop backreaction to leading order.

  12. Stable non-supersymmetric vacua in the moduli space of non-critical superstrings

    International Nuclear Information System (INIS)

    We study a set of asymmetric deformations of non-critical superstring theories in various dimensions. The deformations arise as Kaehler and complex structure deformations of an orthogonal two-torus comprising of a parallel and a transverse direction in the near-horizon geometry of NS5-branes. The resulting theories have the following intriguing features: Spacetime supersymmetry is broken in a continuous fashion and the masses of the lightest modes are lifted. In particular, no bulk or localized tachyons are generated in the non-supersymmetric vacua. We discuss the effects of these deformations in the context of the holographic duality between non-critical superstrings and little string theories and find solutions of rotating fivebranes in supergravity. We also comment on the generation of a one-loop cosmological constant and determine the effects of the one-loop backreaction to leading order

  13. Endogenous hepatitis C virus homolog fragments in European rabbit and hare genomes replicate in cell culture.

    Directory of Open Access Journals (Sweden)

    Eliane Silva

    Full Text Available Endogenous retroviruses, non-retroviral RNA viruses and DNA viruses have been found in the mammalian genomes. The origin of Hepatitis C virus (HCV, the major cause of chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma in humans, remains unclear since its discovery. Here we show that fragments homologous to HCV structural and non-structural (NS proteins present in the European rabbit (Oryctolagus cuniculus and hare (Lepus europaeus genomes replicate in bovine cell cultures. The HCV genomic homolog fragments were demonstrated by RT-PCR, PCR, mass spectrometry, and replication in bovine cell cultures by immunofluorescence assay (IFA and immunogold electron microscopy (IEM using specific MAbs for HCV NS3, NS4A, and NS5 proteins. These findings may lead to novel research approaches on the HCV origin, genesis, evolution and diversity.

  14. Pathogenicity and genetic characterization of a duck Tembusu virus associated with egg-dropping in Muscovy ducks.

    Science.gov (United States)

    Shen, Han-Qin; Lin, Wen-Cheng; Wang, Zhan-Xin; Zhang, Kai; Yan, Zhuan-Qiang; Zhou, Qing-Feng; Qin, Jian-Ping; Xie, Qing-Mei; Bi, Ying-Zuo; Chen, Feng

    2016-09-01

    Duck Tembusu virus (DTMUV) has spread to the major duck-farming region in China, causing acute egg-production drop in Chinese duck population. In this study, we characterized a DTMUV strain (named GD2014) isolated from an egg-production drop duck farm in Guangdong province, South China. The virus was pathogenic to Muscovy duck embryos and caused severe egg production drop for laying Muscovy ducks. The genome sequence of GD2014 shared 97-99% homologies with other waterfowl-origin Tembusu viruses, and shared 89% identities with MM1775 strain isolated from mosquito. Phylogenetic analysis of entire open reading frame (ORF), E gene and NS5 gene indicated that GD2014 belonged to Ntaya group. These results have implications for understanding the orgin, emergence and pathogenicity of DTMUV as well as for the development of vaccines and diagnostics based on epidemiological data. PMID:27354303

  15. $SL(2, Z)$ invariant rotating $(m,n)$ strings in $AdS_3\\times S^3$ with mixed flux

    CERN Document Server

    Barik, Sorna Prava; Kluson, Josef; Panigrahi, Kamal L

    2016-01-01

    We study rigidly rotating and pulsating $(m,n)$ strings in $AdS_3 \\times S^3$ with mixed three form flux. The $AdS_3 \\times S^3$ background with mixed three form flux is obtained in the near horizon limit of $SL(2,Z)$-transformed solution, corresponding to the bound state of NS5-branes and fundamental strings. We study the probe $(m,n)-$string in this background by solving the manifest $SL(2,Z)-$covariant form of the action. We find out the dyonic giant magnon and single spike solutions corresponding to the equations of motion of a probe string in this background and find out various relationships among the conserved charges. We further study a class of pulsating $(m,n)$ string in $AdS_3$ with mixed three form flux.

  16. Hepatitis C virus infection and apoptosis

    Institute of Scientific and Technical Information of China (English)

    Richard Fischer; Thomas Baumert; Hubert E Blum

    2007-01-01

    Apoptosis is central for the control and elimination of viral infections. In chronic hepatitis C virus (HCV) infection,enhanced hepatocyte apoptosis and upregulation of the death inducing ligands CD95/Fas, TRAIL and TNFα occur.Nevertheless, HCV infection persists in the majority of patients. The impact of apoptosis in chronic HCV infection is not well understood. It may be harmful by triggering liver fibrosis, or essential in interferon (IFN)induced HCV elimination. For virtually all HCV proteins,pro- and anti-apoptotic effects have been described,especially for the core and NS5A protein. To date, it is not known which HCV protein affects apoptosis in vivo and whether the infectious virions act pro- or antiapoptotic. With the availability of an infectious tissue culture system, we now can address pathophysiologically relevant issues. This review focuses on the effect of HCV infection and different HCV proteins on apoptosis and of the corresponding signaling cascades.

  17. Regulatory mechanisms of viral hepatitis B and C

    Indian Academy of Sciences (India)

    G Waris; A Siddiqui

    2003-04-01

    Of all the hepatitis viruses, only the hepatitis B virus (HBV) and hepatitis C virus (HCV) cause chronic hepatitis, which can progress to cirrhosis and hepatocellular carcinoma. In this review, we discuss how these two biologically diverse viruses use common pathways to induce oxidative stress and activation of key transcription factors, known to be involved in inflammatory processes in cells. Activation of NF-B and STAT-3 most likely contribute to the progression of viral infections to chronic hepatitis and liver oncogenesis associated with HBV and HCV infections. In this review, we focus on the mechanisms of action of HBx and HCV NS5A proteins in inducing intracellular events associated with the viral infections.

  18. Transmogrifying Fuzzy Vortices

    CERN Document Server

    Murugan, J; Murugan, Jeff; Millner, Antony

    2004-01-01

    We show that the construction of vortex solitons of the noncommutative Abelian-Higgs model can be extended to a critically coupled gauged linear sigma model with Fayet-Illiopolous D-terms. Like its commutative counterpart, this fuzzy linear sigma model has a rich spectrum of BPS solutions. We offer an explicit construction of the degree$-k$ static semilocal vortex and study in some detail the infinite coupling limit in which it descends to a degree$-k$ $\\C\\Pk^{N}$ instanton. This relation between the fuzzy vortex and noncommutative lump is used to suggest an interpretation of the noncommutative sigma model soliton as tilted D-strings stretched between an NS5-brane and a stack of D3-branes in type IIB superstring theory.

  19. Anti-HCV RNA Aptamers Targeting the Genomic cis-Acting Replication Element

    Directory of Open Access Journals (Sweden)

    Alfredo Berzal-Herranz

    2011-12-01

    Full Text Available Hepatitis C virus (HCV replication is dependent on the existence of several highly conserved functional genomic RNA domains. The cis-acting replication element (CRE, located within the 3' end of the NS5B coding region of the HCV genome, has been shown essential for efficient viral replication. Its sequence and structural features determine its involvement in functional interactions with viral RNA-dependent RNA polymerase and distant RNA domains of the viral genome. This work reports the use of an in vitro selection strategy to select aptamer RNA molecules against the complete HCV-CRE. After six selection cycles, five potential target sites were identified within this domain. Inhibition assays using a sample of representative aptamers showed that the selected RNAs significantly inhibit the replication (>80% of a subgenomic HCV replicon in Huh-7 cell cultures. These results highlight the potential of aptamer RNA molecules as therapeutic antiviral agents.

  20. Daclatasvir plus peginterferon and ribavirin is noninferior to peginterferon and ribavirin alone, and reduces the duration of treatment for HCV genotype 2 or 3 infection

    DEFF Research Database (Denmark)

    Dore, Gregory J; Lawitz, Eric; Hézode, Christophe;

    2015-01-01

    BACKGROUND & AIMS: Twenty-four weeks of treatment with peginterferon and ribavirin for chronic hepatitis C virus (HCV) genotype 2 or 3 infection produces a sustained virologic response (SVR) in 70%-80% of patients. We performed a randomized, double-blind, phase 2b study to assess whether adding...... daclatasvir, a nonstructural protein 5A (NS5A) inhibitor that is active against these genotypes, improves efficacy and shortens therapy. METHODS: Patients with HCV genotype 2 or 3 infection (n = 151), enrolled at research centers in North America, Europe, or Australia, were assigned randomly to groups given...... after treatment (SVR24). RESULTS: Baseline characteristics were similar among patients within each HCV genotype group. However, the 80 patients with HCV genotype 3, compared with the 71 patients with HCV genotype 2, were younger (mean age, 45 vs 53 y, respectively), and a larger proportion had cirrhosis...

  1. Molecular design, synthesis and cell based HCV replicon assay of novel benzoxazole derivatives.

    Science.gov (United States)

    Ismail, M A H; Adel, M; Ismail, N S M; Abouzid, K A M

    2013-03-01

    Hepatitis C virus inhibitors based on benzoxazole scaffold were designed based on molecular modeling simulation study including docking into the NS5B polymerase active site. Several compounds showed significant high simulation docking scores relative to the assigned benzimidazole lead compound. The designed compounds were synthesized, structurally elucidated and their antiviral activity was evaluated through cell-based replicon in cultured Huh 5-2 cells. A number of the synthesized compounds showed significant inhibitory activity ranging from (52.2% inhibition up to 98% at<50 µg/mL). N-Benzyl-2-phenylbenzo[1,3]oxazole-5-carboxamide (8b) and N-Phenethyl-2-phenylbenzo[1,3] oxazole-5-carboxamide (8c) demonstrated genuine HCV inhibitory activity with EC50 values of 41.6 and 24.5 µg/mL respectively.

  2. Heterotic-Type IIA Duality and Degenerations of K3 Surfaces

    CERN Document Server

    Braun, Andreas P

    2016-01-01

    We study the duality between four-dimensional N=2 compactifications of Heterotic and Type IIA string theories. Via adiabatic fibration of the duality in six dimensions, Type IIA string theory compactified on a K3-fibred Calabi-Yau threefold has a potential heterotic dual compactification. This adiabatic picture fails whenever the K3 fibre degenerates into multiple components. Guided by monodromy, we identify such degenerate K3 fibres as solitons generalizing the NS5-brane in Heterotic string theory. The theory of degenerations of K3 surfaces can then be used to find which solitons can be present on the heterotic side. Similar to small instanton transitions, these solitons convoy singular transitions between different Calabi-Yau threefolds. Starting from well-known examples of Heterotic-Type IIA duality, such transitions can take us to Type IIA compactifications with unknown heterotic duals.

  3. Subharmonic buncher for the Los Alamos free-electron laser oscillator experiment

    International Nuclear Information System (INIS)

    A high efficiency free-electron laser oscillator experiment is being constructed at Los Alamos National Laboratory. A buncher system has been designed to deliver 30-ps, 5-nC electron bunches to a 20-MeV standing-wave linac at the 60th subharmonic of the 1300-MHz accelerator frequency. The first 108.3-MHz buncher cavity accepts a 5-ns, 5-A peak current pulse from a triode gun. Following a 120-cm drift space, a second 108.3-MHz cavity is used, primarily to enhance the bunching of the trailing half of the bunch. A 1300-MHz cavity with 20-cm drift spaces at the each end completes the beamline components. The bunching process continues into the linac's first three accelerating cells. Two thin iron-shielded lenses and several large-diameter solenoids provide axial magnetic fields for radial focusing

  4. Exploring String Theory Backgrounds

    CERN Document Server

    Williams, B P

    2004-01-01

    This thesis examines phenomenological and theoretical questions by exploring string theoretic backgrounds. Part I focuses on cosmology. First we propose that the induced metric along a brane moving through a curved bulk may be interpreted as the cosmology of the brane universe, providing a resolution to the apparent cosmological singularity on the brane. We then look at various decay channels of the certain meta-stable de Sitter vacua and show that there exist NS5-brane meditated decays which are much faster than decays to decompactification. Part II discusses a new class of nongeometric vacua in string theory. These backgrounds may be described locally as T2 fibrations. By enlarging the monodromy group of the fiber to include perturbative stringy duality symmetries we are able to explicitly construct nongeometric backgrounds.

  5. Detection of classical swine fever virus (CSFV) in clinical samples by RT-PCR assay in clinical samples by RT-PCR assay using different pairs of primers

    International Nuclear Information System (INIS)

    The aim was to compare the efficiency of RT-PCT assays using four pairs of primers selected from different regions of the CSFV genome for the detection of CSFV in clinical samples of swine and wild boars. The four RT-PCR assays were able to detect CSFV in all 20 clinical samples which had been collected from dead swine and wild boars during the outbreaks of CSF in Slovakia in 1993 and 1994. The quality of the selected RT-PCR primers was determined as follows: gp55L/gp55U (E2), 324/326 (5'-NC), S1/S2 (NS5B) and gp54L/gp54U (NS2 genomic region). We conclude that gp55L/gp55U primers are the most suitable for direct detection of CSFV by RT-PCR in tissue homogenates of diseased animals

  6. Sofosbuvir as backbone of interferon free treatments.

    Science.gov (United States)

    Bourlière, Marc; Oules, Valèrie; Ansaldi, Christelle; Adhoute, Xavier; Castellani, Paul

    2014-12-15

    Sofosbuvir is the first-in-class NS5B nucleotide analogues to be launched for hepatitis C virus (HCV) treatment. Its viral potency, pangenotypic activity and high barrier to resistance make it the ideal candidate to become a backbone for several IFN-free regimens. Recent data demonstrated that sofosbuvir either with ribavirin alone or in combination with other direct-acting antivirals (DAAs) as daclatasvir, ledipasvir or simeprevir are able to cure HCV in at least 90% or over of patients. Treatment experienced genotype 3 population may remain the most difficult to treat population, but ongoing DAA combination studies will help to fill this gap. Safety profile of sofosbuvir or combination with other DAAs is good. Resistance to sofosbuvir did not appear as a significant issue. The rationale for using this class of drug and the available clinical data are reviewed.

  7. Sofosbuvir-based therapy cures hepatitis C virus infection after prior treatment failures in a patient with concurrent lymphoma.

    Science.gov (United States)

    Romagnoli, Dante; Marrazzo, Alessandra; Ballestri, Stefano; Lonardo, Amedeo; Bertolotti, Marco

    2015-08-01

    We report on the first well-tolerated and successful use of sofosbuvir-based therapy in a patient in whom chronic infection with hepatitis C had preceded the development of B-cell non-Hodgkin's lymphoma. The patient had previously failed numerous attempts to clear the hepatitis C virus with traditional antiviral schedules. We demonstrate that sofosbuvir-based therapy resulted in cure of hepatitis C in a patient who had relapsed during combination therapy with an NS5A inhibitor, an NS3 protease inhibitor and ribavirin, as well as treatment failures to multiple courses of interferon-based therapy. This report also suggests that eradication of hepatitis C virus may result in the short-term prevention of B-cell non-Hodgkin's lymphoma relapse. The findings from our case require further validation in future cohorts of patients.

  8. Therapie der chronischen Hepatitis C Genotyp 1 – Update 2015

    Directory of Open Access Journals (Sweden)

    Gschwantler M

    2015-01-01

    Full Text Available Die Therapie der chronischen Hepatitis C hat sich während der vergangenen zwei Jahre fundamental verändert. Durch eine Kombination von zwei oder drei neuen DAAs („direct acting antiviral agents“ kann bei fast allen Patienten eine Elimination des Virus praktisch ohne Nebenwirkungen erzielt werden. Auch bei den meisten Patienten mit dekompensierter Leberzirrhose konnte nach virologischer Heilung innerhalb weniger Wochen eine Verbesserung der Leberfunktion beobachtet werden. Derzeit stehen in Österreich folgende neue DAAs für die Therapie zur Verfügung: Die Proteasehemmer Simeprevir und Paritaprevir, die NS5A-Inhibitoren Daclatasvir, Ledipasvir und Ombitasvir, sowie die Polymerasehemmer Sofosbuvir und Dasabuvir. Die effektivsten Therapieregime beim Genotyp 1 sind die Kombinationen Sofosbuvir/Simeprevir, Sofosbuvir/Daclatasvir, Sofosbuvir/Ledipasvir und Paritaprevir/Ritonavir/Ombitasvir/Dasabuvir.

  9. Sofosbuvir for the treatment of chronic hepatitis C virus infection.

    Science.gov (United States)

    Temesgen, Z; Talwani, R; Rizza, S A

    2014-06-01

    Sofosbuvir is a nucleotide analogue selective inhibitor of the RNA-directed RNA polymerase (NS5B) enzyme of the hepatitis C virus (HCV) genome. It has shown potent antiviral activity across all HCV genotypes and in a variety of patient populations, including treatment-naive patients; treatment-experienced patients who had failed previous standard therapy; patients with decompensated liver disease, including cirrhosis; and HIV co-infected patients. It is administered as a single, once-daily 400-mg tablet, has no food restrictions, has low potential for drug interactions, and requires no dose adjustment in mild to moderate kidney or liver impairment. When sofosbuvir is combined with pegylated interferon and/or ribavirin, its clinical and laboratory safety profile is similar to that which is expected from pegylated interferon or ribavirin alone. Rates of treatment discontinuation and dose reduction with sofosbuvir-containing regimens were lower than those commonly observed with pegylated interferon and ribavirin.

  10. Sofosbuvir for treatment of chronic hepatitis C.

    Science.gov (United States)

    Kattakuzhy, Sarah; Levy, Rachel; Kottilil, Shyam

    2015-04-01

    Chronic hepatitis C is a leading cause of liver-related morbidity and mortality worldwide. If untreated, chronic hepatitis C can progress to advanced liver fibrosis, cirrhosis, liver failure, hepatocellular carcinoma and death. Until recently, treatment of hepatitis C predominantly constituted an immunomodulatory agent, peg-interferon-alfa and ribavirin. In 2011, the first class of directly acting antiviral agents, HCV NS3/4A serine protease inhibitors, was added to peg-interferon-alfa and ribavirin with increased efficacy. In the past year, an NS5B inhibitor, sofosbuvir, has emerged as a potent agent with pangenotypic efficacy, resulting in the first interferon-free regimen for the treatment of hepatitis C. This review summarizes the data that resulted in regulatory approval of sofosbuvir and highlights the future of hepatitis C therapy with sofosbuvir as the backbone of a highly effective antiviral regimen.

  11. Further theoretical insight into the reaction mechanism of the hepatitis C NS3/NS4A serine protease

    Science.gov (United States)

    Martínez-González, José Ángel; Rodríguez, Alex; Puyuelo, María Pilar; González, Miguel; Martínez, Rodrigo

    2015-01-01

    The main reactions of the hepatitis C virus NS3/NS4A serine protease are studied using the second-order Møller-Plesset ab initio method and rather large basis sets to correct the previously reported AM1/CHARMM22 potential energy surfaces. The reaction efficiencies measured for the different substrates are explained in terms of the tetrahedral intermediate formation step (the rate-limiting process). The energies of the barrier and the corresponding intermediate are so close that the possibility of a concerted mechanism is open (especially for the NS5A/5B substrate). This is in contrast to the suggested general reaction mechanism of serine proteases, where a two-step mechanism is postulated.

  12. [Research Progress in the Core Proteins of the Classical Swine Fever Virus].

    Science.gov (United States)

    Hou, Yuzhen; Zhao, Dantong; Liu, Guoying; He, Fan; Liu, Bin; Fu, Shaoyin; Hao, Yongqing; Zhang, Wenguang

    2015-09-01

    The core protein (CP) of the classical swine fever virus (CSFV) is one of its structural proteins. Apart from forming the nucleocapsid to protect internal viral genomic RNA, this protein is involved in transcriptional regulation. Also, during viral infection, the CP is involved in interactions with many host proteins. In this review, we combine study of this protein with its disorders, structural/functional characteristics, as well as its interactions with the non-structural proteins NS3, NS5B and host proteins such as SUMO-1, UBC9, OS9 and IQGAP1. We also summarize the important part played by the CP in CSFV pathogenicity, virulence and replication of genomic RNA. We also provide guidelines for further studies in the CP of the CSFV. PMID:26738299

  13. An in vitro Flaviviridae replicase system capable of authentic RNA replication

    International Nuclear Information System (INIS)

    We have established an in vitro replication system for bovine viral diarrhea virus (BVDV), a surrogate for the closely-related hepatitis C virus. In an in vitro reaction, BVDV replication complexes synthesize vRNA and replicative form (RF) and replicative intermediate (RI) RNAs. Kinetic and heparin trapping experiments demonstrate the recycling of RF and RI products and the initiation of vRNA synthesis in this system. Consistent with this, quantitative hybridization reveals the asymmetric synthesis of positive and negative strand RNA products. These findings support the notion that RF serves as a template and RI as a precursor in the synthesis of vRNA. Furthermore, the antiviral activity of an NS5B inhibitor was similar in BVDV replicase and infectivity assays. Together, these results indicate that the in vitro activity of BVDV replicase complexes recapitulates RNA replication that occurs in infected cells, providing a system in which to study both mechanisms and inhibitors of Flaviviridae replication

  14. Molecular characterization of two Rocio flavivirus strains isolated during the encephalitis epidemic in São Paulo State, Brazil and the development of a one-step RT-PCR assay for diagnosis.

    Science.gov (United States)

    Coimbra, Terezinha Lisieux Moraes; Santos, Raimundo N; Petrella, Selma; Nagasse-Sugahara, Teresa Keico; Castrignano, Silvana Beres; Santos, Cecília L Simões

    2008-01-01

    Rocio virus (ROCV) was responsible for an explosive encephalitis epidemic in the 1970s affecting about 1,000 residents of 20 coastland counties in São Paulo State, Brazil. ROCV was first isolated in 1975 from the cerebellum of a fatal human case of encephalitis. Clinical manifestations of the illness are similar to those described for St. Louis encephalitis. ROCV shows intense antigenic cross-reactivity with Japanese encephalitis complex (JEC) viruses, particularly with Ilheus (ILHV), St. Louis encephalitis, Murray Valley and West Nile viruses. In this study, we report a specific RT-PCR assay for ROCV diagnosis and the molecular characterization of the SPAn37630 and SPH37623 strains. Partial nucleotide sequences of NS5 and E genes determined from both strains were used in phylogenetic analysis. The results indicated that these strains are closely related to JEC viruses, but forming a distinct subclade together with ILHV, in accordance with results recently reported by Medeiros et al. (2007).

  15. HCV genotyping from NGS short reads and its application in genotype detection from HCV mixed infected plasma.

    Science.gov (United States)

    Qiu, Ping; Stevens, Richard; Wei, Bo; Lahser, Fred; Howe, Anita Y M; Klappenbach, Joel A; Marton, Matthew J

    2015-01-01

    Genotyping of hepatitis C virus (HCV) plays an important role in the treatment of HCV. As new genotype-specific treatment options become available, it has become increasingly important to have accurate HCV genotype and subtype information to ensure that the most appropriate treatment regimen is selected. Most current genotyping methods are unable to detect mixed genotypes from two or more HCV infections. Next generation sequencing (NGS) allows for rapid and low cost mass sequencing of viral genomes and provides an opportunity to probe the viral population from a single host. In this paper, the possibility of using short NGS reads for direct HCV genotyping without genome assembly was evaluated. We surveyed the publicly-available genetic content of three HCV drug target regions (NS3, NS5A, NS5B) in terms of whether these genes contained genotype-specific regions that could predict genotype. Six genotypes and 38 subtypes were included in this study. An automated phylogenetic analysis based HCV genotyping method was implemented and used to assess different HCV target gene regions. Candidate regions of 250-bp each were found for all three genes that have enough genetic information to predict HCV genotypes/subtypes. Validation using public datasets shows 100% genotyping accuracy. To test whether these 250-bp regions were sufficient to identify mixed genotypes, we developed a random primer-based method to sequence HCV plasma samples containing mixtures of two HCV genotypes in different ratios. We were able to determine the genotypes without ambiguity and to quantify the ratio of the abundances of the mixed genotypes in the samples. These data provide a proof-of-concept that this random primed, NGS-based short-read genotyping approach does not need prior information about the viral population and is capable of detecting mixed viral infection.

  16. A STUDY ON COMPARISON OF INTRAVENOUS DEXMEDETOMIDINE WITH INTRAVENOUS FENTANYL FOR SUPPRESSION OF HEMODYNAMIC RESPONSES TO LARYNGOSCOPY AND ENDOTRACHEAL INTUBATION DURING GENERAL ANAESTHESIA

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    Nidhi D Patel

    2015-06-01

    Full Text Available Background: Laryngoscopy and intubation is the Gold standard for airway management but this evokes a stress response which is exhibited in the form of changes in heart rate, blood pressure and arrhythmias. This study was prospective, randomized, double blind study to determine whether the fentanyl 2 and micro;g/Kg or dexmedetomidine 1 and micro;g/Kg would decrease the attenuation of hemodynamic response during laryngoscopy and tracheal intubation during general anaesthesia. Methodology: The patients were randomly allocated into two groups. In Group D cases (n=30 received injection Dexmedetomidine 1 and micro;g/kg diluted to 10ml NS IV over 10min using syringe pump prior to intubation and 5ml of NS 5 min. prior to intubation. In Group F cases (n=30 received 2 and micro;g/kg diluted to 5ml NS 5min. prior to intubation and 20ml NS in infusion pump over 10 min., prior to intubation. Results: The age and weight of the cases in both the groups are comparable. It was observed that mean HR increased in both groups D and F immediately after endotracheal intubation. The systolic blood pressure was highly significant in group F as compared to group D during laryngoscopy and intubation, 1, 3, 5 and 10 min after intubation (p<0.000. Ramsay sedation score was and #8805; 4 in all patients in group D and was and #8804; 3 in group F. Dexmedetomidine has higher sedation score but no respiratory depression. Conclusion: We concluded that dexmedetomidine in dose 1 and micro;gm/kg i.v. is more effective in attenuating the hemodynamic pressor responses to laryngoscopy and intubation than Inj. Fentanyl 2 and micro;gm/kg i.v. when given as pre-medicant without significant side effects. [Natl J Med Res 2015; 5(2.000: 127-131

  17. Biomedical Mutation Analysis (BMA): A software tool for analyzing mutations associated with antiviral resistance

    Science.gov (United States)

    Salvatierra, Karina; Florez, Hector

    2016-01-01

    Introduction: Hepatitis C virus (HCV) is considered a major public health problem, with 200 million people infected worldwide. The treatment for HCV chronic infection with pegylated interferon alpha plus ribavirin inhibitors is unspecific; consequently, the treatment is effective in only 50% of patients infected. This has prompted the development of direct-acting antivirals (DAA) that target virus proteins. These DAA have demonstrated a potent effect in vitro and in vivo; however, virus mutations associated with the development of resistance have been described. Objective: To design and develop an online information system for detecting mutations in amino acids known to be implicated in resistance to DAA. Materials and methods:    We have used computer applications, technological tools, standard languages, infrastructure systems and algorithms, to analyze positions associated with resistance to DAA for the NS3, NS5A, and NS5B genes of HCV. Results: We have designed and developed an online information system named Biomedical Mutation Analysis (BMA), which allows users to calculate changes in nucleotide and amino acid sequences for each selected sequence from conventional Sanger and cloning sequencing using a graphical interface. Conclusion: BMA quickly, easily and effectively analyzes mutations, including complete documentation and examples. Furthermore, the development of different visualization techniques allows proper interpretation and understanding of the results. The data obtained using BMA will be useful for the assessment and surveillance of HCV resistance to new antivirals, and for the treatment regimens by selecting those DAA to which the virus is not resistant, avoiding unnecessary treatment failures. The software is available at: http://bma.itiud.org.

  18. Hepatitis C virus NS3/4A protease inhibits complement activation by cleaving complement component 4.

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    Seiichi Mawatari

    Full Text Available BACKGROUND: It has been hypothesized that persistent hepatitis C virus (HCV infection is mediated in part by viral proteins that abrogate the host immune response, including the complement system, but the precise mechanisms are not well understood. We investigated whether HCV proteins are involved in the fragmentation of complement component 4 (C4, composed of subunits C4α, C4β, and C4γ, and the role of HCV proteins in complement activation. METHODS: Human C4 was incubated with HCV nonstructural (NS 3/4A protease, core, or NS5. Samples were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and then subjected to peptide sequencing. The activity of the classical complement pathway was examined using an erythrocyte hemolysis assay. The cleavage pattern of C4 in NS3/4A-expressing and HCV-infected cells, respectively, was also examined. RESULTS: HCV NS3/4A protease cleaved C4γ in a concentration-dependent manner, but viral core and NS5 did not. A specific inhibitor of NS3/4A protease reduced C4γ cleavage. NS3/4A protease-mediated cleavage of C4 inhibited classical pathway activation, which was abrogated by a NS3/4A protease inhibitor. In addition, co-transfection of cells with C4 and wild-type NS3/4A, but not a catalytic-site mutant of NS3/4A, produced cleaved C4γ fragments. Such C4 processing, with a concomitant reduction in levels of full-length C4γ, was also observed in HCV-infected cells expressing C4. CONCLUSIONS: C4 is a novel cellular substrate of the HCV NS3/4A protease. Understanding disturbances in the complement system mediated by NS3/4A protease may provide new insights into the mechanisms underlying persistent HCV infection.

  19. Development of robust in vitro RNA-dependent RNA polymerase assay as a possible platform for antiviral drug testing against dengue.

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    Amraiz, Deeba; Zaidi, Najam-Us-Sahar Sadaf; Fatima, Munazza

    2016-10-01

    NS5 is the largest and most conserved protein among the four dengue virus (DENV) serotypes. It has been the target of interest for antiviral drug development due to its major role in replication. NS5 consists of two domains, the N-terminal methyltransferase domain and C-terminal catalytic RNA-dependent RNA polymerase (RdRp) domain. It is an unstable protein and is prone to inactivation upon prolonged incubation at room temperature, thus affecting the inhibitor screening assays. In the current study, we expressed and purified DENV RdRp alone in Esherichia coli (E. coli) cells. The N-terminally His-tagged construct of DENV RdRp was transformed into E. coli expression strain BL-21 (DE3) pLysS cells. Protein expression was induced with isopropyl-β-D-thiogalactopyranoside (IPTG) at a final concentration of 0.4mM. The induced cultures were then grown for 20h at 18°C and cells were harvested by centrifugation at 6000xg for 15min at 4°C. The recombinant protein was purified using HisTrap affinity column (Ni-NTA) and then the sample was subjected to size exclusion chromatography, which successfully removed the degradation product obtained during the previous purification step. The in vitro polymerase activity of RdRp was successfully demonstrated using homopolymeric polycytidylic acid (poly(rC)) RNA template. This study describes the high level production of enzymatically active DENV RdRp protein which can be used to develop assays for testing large number of compounds in a high-throughput manner. RdRp has the de novo initiation activity and the in vitro polymerase assays for the protein provide a platform for highly robust and efficient antiviral compound screening systems. PMID:27542741

  20. [Novel treatments for hepatitis C virus infection in chronic kidney disease].

    Science.gov (United States)

    Fabrizi, Fabrizio; Messa, Piergiorgio

    2016-01-01

    Recent evidence has been accumulated showing a negative impact of chronic hepatitis C virus infection on survival in patients with chronic kidney disease. Moreover, it appears that anti-HCV positive status has been associated with an increased risk of developing chronic kidney disease in the adult general population. These reports have emphasized the need for safe and effective therapies for hepatitis C virus infection in the chronic kidney disease population. Treatment of HCV has made considerable progress with the approval of interferon-free, direct-acting antiviral drug-based combination therapies among patients with intact kidneys; but a paucity of information exists regarding chronic kidney disease patients. The first published report on the antiviral treatment of hepatitis C among patients with chronic kidney disease (stage 4-5) and HCV genotype 1 concerns the combination of grazoprevir (NS3/4A protease inhibitor) and elbasvir (NS5A inhibitor); excellent safety and efficacy (sustained viral response, 94.3% 115/122) have been reached. In another study, the 3-D regimen (ombitasvir/ paritaprevir/ ritonavir/ dasabuvir with or without ribavirin) has been administered to CKD (stage 4-5) patients with genotype 1 (n=20); the rate of sustained viral response was excellent (90%, 18/20) and no patients discontinued treatment due to adverse events. Preliminary data on the combined treatment of sofosbuvir (NS5B inhibitor) and simeprevir (NS3/4A inhibitor) has given a viral response of 89% (34/38), but the size of the study group (n=38 patients with end-stage renal disease) was small. Thus, the evidence in the medical literature concerning use of DAAs in CKD population is encouraging even if it has a preliminary nature. Also, several points need to be addressed regarding the use of DAAs in CKD population including their impact on survival, costs, and drug-drug interactions. PMID:27545640

  1. Acute hepatitis C in a chronically HIV-infected patient: Evolution of different viral genomic regions

    Institute of Scientific and Technical Information of China (English)

    Diego Flichman; Veronica Kott; Silvia Sookoian; Rodolfo Campos

    2003-01-01

    AIM: To analyze the molecular evolution of different viral genomic regions of HCV in an acute HCV infected patient chronically infected with HIV through a 42-month follow-up.METHODS: Serum samples of a chronically HIV infected patient that seroconverted to anti HCV antibodies were sequenced, from the event of superinfection through a period of 17 months and in a late sample (42nd month). Hypervariable genomic regions of HIV (V3 loop of the gp120) and HCV (HVR-1 on the E2 glycoprotein gene) were studied. In order to analyze genomic regions involved in different biological functions and with the cellular immune response, HCV core and NS5A were also chosen to be sequenced. Amplification of the different regions was done by RT-PCR and directly sequenced. Confirmation of sequences was done on reamplified material. Nucleotide sequences of the different time points were aligned with CLUSTAL W 1.5, and the corresponding amino acid ones were deduced.RESULTS: Hypervariable genomic regions of both viruses (HVR1 and gp120 V3 loop) presented several nonsynonymous changes but, while in the gp120 V3 loop mutations were detected in the sample obtained right after HCV superinfection and maintained throughout, they occurred following a sequential and cumulative pattern in the HVR1. In the NS5A region of HCV, two amino acid changes were detected during the follow-up period, whereas the core region presented several amino acid replacements, once the HCV chronic infection had been established.CONCLUSION: During the HIV-HCV superinfection, each genomic region analyzed shows a different evolutionary pattem.Most of the nucleotide substitutions observed are nonsynonymous and clustered in previously described epitopes,thus suggesting an immune-driven evolutionary process.

  2. A Human Vaccine Strategy Based On Chimpanzee Adenoviral and MVA Vectors That Primes, Boosts and Sustains Functional HCV Specific T-Cell Memory*

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    Swadling, Leo; Capone, Stefania; Antrobus, Richard D.; Brown, Anthony; Richardson, Rachel; Newell, Evan W.; Halliday, John; Kelly, Christabel; Bowen, Dan; Fergusson, Joannah; Kurioka, Ayako; Ammendola, Virginia; Sorbo, Mariarosaria Del; Grazioli, Fabiana; Esposito, Maria Luisa; Siani, Loredana; Traboni, Cinzia; Hill, Adrian; Colloca, Stefano; Davis, Mark; Nicosia, Alfredo; Cortese, Riccardo; Folgori, Antonella; Klenerman, Paul; Barnes, Eleanor

    2015-01-01

    A protective vaccine against hepatitis C virus (HCV) remains an unmet clinical need. HCV infects millions of people worldwide and is a leading cause of liver cirrhosis and hepatocellular cancer. Animal challenge experiments, immunogenetics studies and assessment of host immunity during acute infection highlight the critical role that effective T-cell immunity plays in viral control. In this first-in-man study we have induced antiviral immunity with functional characteristics analogous to those associated with viral control in natural infection, and improved upon a vaccine based on adenoviral vectors alone. We assessed a heterologous prime-boost vaccination strategy based on a replicative defective simian adenoviral vector (ChAd3) and modified vaccinia Ankara (MVA) vector encoding the NS3, NS4, NS5A and NS5B proteins of HCV genotype-1b. Analysis employed single cell mass cytometry (CyTOF), and HLA class-I peptide tetramer technology in healthy human volunteers. We show that HCV specific T-cells induced by ChAd3 are optimally boosted with MVA, and generate very high levels of both CD8+ and CD4+ HCV specific T-cells targeting multiple HCV antigens. Sustained memory and effector T-cell populations are generated and T-cell memory evolved over time with improvement of quality (proliferation and polyfunctionality) following heterologous MVA boost. We have developed a HCV vaccine strategy, with durable, broad, sustained and balanced T-cell responses, characteristic of those associated with viral control, paving the way for the first efficacy studies of a prophylactic HCV vaccine. PMID:25378645

  3. Empirical fitness models for hepatitis C virus immunogen design

    Science.gov (United States)

    Hart, Gregory R.; Ferguson, Andrew L.

    2015-12-01

    Hepatitis C virus (HCV) afflicts 170 million people worldwide, 2%–3% of the global population, and kills 350 000 each year. Prophylactic vaccination offers the most realistic and cost effective hope of controlling this epidemic in the developing world where expensive drug therapies are not available. Despite 20 years of research, the high mutability of the virus and lack of knowledge of what constitutes effective immune responses have impeded development of an effective vaccine. Coupling data mining of sequence databases with spin glass models from statistical physics, we have developed a computational approach to translate clinical sequence databases into empirical fitness landscapes quantifying the replicative capacity of the virus as a function of its amino acid sequence. These landscapes explicitly connect viral genotype to phenotypic fitness, and reveal vulnerable immunological targets within the viral proteome that can be exploited to rationally design vaccine immunogens. We have recovered the empirical fitness landscape for the HCV RNA-dependent RNA polymerase (protein NS5B) responsible for viral genome replication, and validated the predictions of our model by demonstrating excellent accord with experimental measurements and clinical observations. We have used our landscapes to perform exhaustive in silico screening of 16.8 million T-cell immunogen candidates to identify 86 optimal formulations. By reducing the search space of immunogen candidates by over five orders of magnitude, our approach can offer valuable savings in time, expense, and labor for experimental vaccine development and accelerate the search for a HCV vaccine. Abbreviations: HCV—hepatitis C virus, HLA—human leukocyte antigen, CTL—cytotoxic T lymphocyte, NS5B—nonstructural protein 5B, MSA—multiple sequence alignment, PEG-IFN—pegylated interferon.

  4. HCV Diversity among Chinese and Burmese IDUs in Dehong, Yunnan, China

    Science.gov (United States)

    Chen, Xin; Duo, Lin; Li, Peilu; Zheng, Yong-Tang; Zhang, Chiyu

    2016-01-01

    HCV transmission is closely associated with drug-trafficking routes in China. Dehong, a prefecture of Yunnan, is the important trade transfer station linking Southeast Asia and China, as well as the drug-trafficking channel linking “Golden triangle” and other regions of China and surrounding countries. In this study, we investigated the HCV genotype diversity among IDUs in Dehong based on 259 HCV positive samples from 118 Chinese and 141 Burmese IDUs. HCV genotypes were determined based on the phylogenies of C/E2 and NS5B genomic sequences. Six HCV subtypes, including 1a, 1b, 3a, 3b, 6n and 6u, were detected. Interestingly, 4 HCV sequences from Burmese IDUs did not cluster with any known HCV subtypes, but formed a well-supported independent clade in the phylogenetic trees of both C/E2 and NS5B, suggesting a potential new HCV subtype circulating in Dehong. Subtype 3b was the predominant subtype, followed by subtypes 6n and 6u. Comparison showed that Dehong had a unique pattern of HCV subtype distribution, obviously different from other regions of China. In particular, HCV subtypes 6u and the potential new HCV subtype had a relatively high prevalence in Dehong, but were rarely detected in other regions of China. There was no significant difference in HCV subtype distribution between Burmese and Chinese IDUs. Few HCV sequences from Burmese and Chinese IDUs clustered together to form transmission clusters. Furthermore, about half of HCV sequences from Burmese IDUs formed small transmission clusters, significantly higher than that from Chinese IDUs (p<0.01). These suggest that the Chinese and Burmese IDUs were relatively isolated from each other in injection drug use behavior and the Burmese IDUs might prefer to inject drugs themselves together. The unique genotype distribution and complex diversity of genotype 6 among IDUs may be associated with the special geographical position of Dehong. PMID:27657722

  5. Identification of class I HLA T cell control epitopes for West Nile virus.

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    Saghar Kaabinejadian

    Full Text Available The recent West Nile virus (WNV outbreak in the United States underscores the importance of understanding human immune responses to this pathogen. Via the presentation of viral peptide ligands at the cell surface, class I HLA mediate the T cell recognition and killing of WNV infected cells. At this time, there are two key unknowns in regards to understanding protective T cell immunity: 1 the number of viral ligands presented by the HLA of infected cells, and 2 the distribution of T cell responses to these available HLA/viral complexes. Here, comparative mass spectroscopy was applied to determine the number of WNV peptides presented by the HLA-A*11:01 of infected cells after which T cell responses to these HLA/WNV complexes were assessed. Six viral peptides derived from capsid, NS3, NS4b, and NS5 were presented. When T cells from infected individuals were tested for reactivity to these six viral ligands, polyfunctional T cells were focused on the GTL9 WNV capsid peptide, ligands from NS3, NS4b, and NS5 were less immunogenic, and two ligands were largely inert, demonstrating that class I HLA reduce the WNV polyprotein to a handful of immune targets and that polyfunctional T cells recognize infections by zeroing in on particular HLA/WNV epitopes. Such dominant HLA/peptide epitopes are poised to drive the development of WNV vaccines that elicit protective T cells as well as providing key antigens for immunoassays that establish correlates of viral immunity.

  6. A rapid immunization strategy with a live attenuated tetravalent dengue vaccine elicits protective neutralizing antibody responses in non-human primates

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    Yuping eAmbuel

    2014-06-01

    Full Text Available Dengue viruses (DENVs cause approximately 390 million cases of DENV infections annually and over 3 billion people worldwide are at risk of infection. No dengue vaccine is currently available nor is there an antiviral therapy for DENV infections. We have developed a tetravalent live-attenuated DENV vaccine (TDV that consists of a molecularly characterized attenuated DENV-2 strain (TDV-2 and three chimeric viruses containing the pre-membrane and envelope genes of DENV-1, -3 and -4 expressed in the context of the TDV-2 genome. To impact dengue vaccine delivery in endemic areas and immunize travelers, a simple and rapid immunization strategy (RIS is preferred. We investigated RIS consisting of two full vaccine doses being administered subcutaneously or intradermally on the initial vaccination visit (day 0 at two different anatomical locations with a needle-free disposable syringe jet injection (DSJI delivery devices (PharmaJet in non-human primates (NHP. This vaccination strategy resulted in efficient priming and induction of neutralizing antibody responses to all four DENV serotypes comparable to those elicited by the traditional prime and boost (two months later vaccination schedule. In addition, the vaccine induced CD4+ and CD8+ T cells producing IFN-γ, IL-2, and TNF-α, and targeting the DENV-2 NS1, NS3 and NS5 proteins. Moreover, vaccine-specific T cells were cross-reactive with the non-structural NS3 and NS5 proteins of DENV-4. When animals were challenged with DENV-2 they were protected with no detectable viremia, and exhibited sterilizing immunity (no increase of neutralizing titers post- challenge. RIS could decrease vaccination visits and provide quick immune response to all four DENV serotypes. This strategy could increase vaccination compliance and would be especially advantageous for travelers into endemic areas.

  7. Profile of paritaprevir/ritonavir/ombitasvir plus dasabuvir in the treatment of chronic hepatitis C virus genotype 1 infection

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    Smith MA

    2015-11-01

    Full Text Available Michael A Smith, Alice LimDepartment of Pharmacy Practice and Pharmacy Administration, Philadelphia College of Pharmacy, University of the Sciences, Philadelphia, PA, USAAbstract: Over the last several years, many advances have been made in the treatment of chronic hepatitis C virus (HCV infection with the development of direct-acting antivirals. Paritaprevir/ritonavir/ombitasvir with dasabuvir (PrOD is a novel combination of a nonstructural (NS 3/4A protein inhibitor boosted by ritonavir, an NS5A protein inhibitor, and an NS5B nonnucleoside polymerase inhibitor. This review aims to discuss the pharmacology, efficacy, safety, drug interactions, and viral drug resistance of PrOD in the treatment of HCV genotype 1 infections. Phase I, II, and III human and animal studies that describe the pharmacology, pharmacokinetics, efficacy, and safety of PrOD for HCV were identified and included. Studies that evaluated patients without cirrhosis (n=2,249 and with cirrhosis (n=422 demonstrated that PrOD for 12 or 24 weeks was effective at achieving sustained virologic response rates (>90% in patients with genotype 1a or 1b HCV infection. Although indicated for the treatment of HCV genotype 1 infection, PrOD is also recommended for the treatment of HCV in patients coinfected with HIV. Additionally, promising data exist for the use of PrOD in liver-transplant recipients. The most common adverse drug events associated with PrOD included nausea, pruritus, insomnia, diarrhea, asthenia, dry skin, vomiting, and anemia. The high efficacy rates seen coupled with a favorable side effect profile seen with PrOD with or without ribavirin have led to its addition as a recommended treatment regimen for HCV genotype 1 infection.Keywords: direct-acting antiviral, interferon-free, ribavirin-free

  8. Profile of paritaprevir/ritonavir/ombitasvir plus dasabuvir in the treatment of chronic hepatitis C virus genotype 1 infection.

    Science.gov (United States)

    Smith, Michael A; Lim, Alice

    2015-01-01

    Over the last several years, many advances have been made in the treatment of chronic hepatitis C virus (HCV) infection with the development of direct-acting antivirals. Paritaprevir/ritonavir/ombitasvir with dasabuvir (PrOD) is a novel combination of a nonstructural (NS) 3/4A protein inhibitor boosted by ritonavir, an NS5A protein inhibitor, and an NS5B nonnucleoside polymerase inhibitor. This review aims to discuss the pharmacology, efficacy, safety, drug interactions, and viral drug resistance of PrOD in the treatment of HCV genotype 1 infections. Phase I, II, and III human and animal studies that describe the pharmacology, pharmacokinetics, efficacy, and safety of PrOD for HCV were identified and included. Studies that evaluated patients without cirrhosis (n=2,249) and with cirrhosis (n=422) demonstrated that PrOD for 12 or 24 weeks was effective at achieving sustained virologic response rates (>90%) in patients with genotype 1a or 1b HCV infection. Although indicated for the treatment of HCV genotype 1 infection, PrOD is also recommended for the treatment of HCV in patients coinfected with HIV. Additionally, promising data exist for the use of PrOD in liver-transplant recipients. The most common adverse drug events associated with PrOD included nausea, pruritus, insomnia, diarrhea, asthenia, dry skin, vomiting, and anemia. The high efficacy rates seen coupled with a favorable side effect profile seen with PrOD with or without ribavirin have led to its addition as a recommended treatment regimen for HCV genotype 1 infection. PMID:26622169

  9. Contribution of genome-wide HCV genetic differences to outcome of interferon-based therapy in Caucasian American and African American patients.

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    Maureen J Donlin

    Full Text Available BACKGROUND: Hepatitis C virus (HCV has six major genotypes, and patients infected with genotype 1 respond less well to interferon-based therapy than other genotypes. African American patients respond to interferon alpha-based therapy at about half the rate of Caucasian Americans. The effect of HCV's genetic variation on treatment outcome in both racial groups is poorly understood. METHODOLOGY: We determined the near full-length pre-therapy consensus sequences from 94 patients infected with HCV genotype 1a or 1b undergoing treatment with peginterferon alpha-2a and ribavirin through the Virahep-C study. The sequences were stratified by genotype, race and treatment outcome to identify HCV genetic differences associated with treatment efficacy. PRINCIPAL FINDINGS: HCV sequences from patients who achieved sustained viral response were more diverse than sequences from non-responders. These inter-patient diversity differences were found primarily in the NS5A gene in genotype 1a and in core and NS2 in genotype 1b. These differences could not be explained by host selection pressures. Genotype 1b but not 1a African American patients had viral genetic differences that correlated with treatment outcome. CONCLUSIONS & SIGNIFICANCE: Higher inter-patient viral genetic diversity correlated with successful treatment, implying that there are HCV genotype 1 strains with intrinsic differences in sensitivity to therapy. Core, NS3 and NS5A have interferon-suppressive activities detectable through in vitro assays, and hence these activities also appear to function in human patients. Both preferential infection with relatively resistant HCV variants and host-specific factors appear to contribute to the unusually poor response to therapy in African American patients.

  10. Geno2pheno[HCV] – A Web-based Interpretation System to Support Hepatitis C Treatment Decisions in the Era of Direct-Acting Antiviral Agents

    Science.gov (United States)

    Kalaghatgi, Prabhav; Sikorski, Anna Maria; Knops, Elena; Rupp, Daniel; Sierra, Saleta; Heger, Eva; Neumann-Fraune, Maria; Beggel, Bastian; Walker, Andreas; Timm, Jörg; Walter, Hauke; Obermeier, Martin; Kaiser, Rolf; Bartenschlager, Ralf; Lengauer, Thomas

    2016-01-01

    The face of hepatitis C virus (HCV) therapy is changing dramatically. Direct-acting antiviral agents (DAAs) specifically targeting HCV proteins have been developed and entered clinical practice in 2011. However, despite high sustained viral response (SVR) rates of more than 90%, a fraction of patients do not eliminate the virus and in these cases treatment failure has been associated with the selection of drug resistance mutations (RAMs). RAMs may be prevalent prior to the start of treatment, or can be selected under therapy, and furthermore they can persist after cessation of treatment. Additionally, certain DAAs have been approved only for distinct HCV genotypes and may even have subtype specificity. Thus, sequence analysis before start of therapy is instrumental for managing DAA-based treatment strategies. We have created the interpretation system geno2pheno[HCV] (g2p[HCV]) to analyse HCV sequence data with respect to viral subtype and to predict drug resistance. Extensive reviewing and weighting of literature related to HCV drug resistance was performed to create a comprehensive list of drug resistance rules for inhibitors of the HCV protease in non-structural protein 3 (NS3-protease: Boceprevir, Paritaprevir, Simeprevir, Asunaprevir, Grazoprevir and Telaprevir), the NS5A replicase factor (Daclatasvir, Ledipasvir, Elbasvir and Ombitasvir), and the NS5B RNA-dependent RNA polymerase (Dasabuvir and Sofosbuvir). Upon submission of up to eight sequences, g2p[HCV] aligns the input sequences, identifies the genomic region(s), predicts the HCV geno- and subtypes, and generates for each DAA a drug resistance prediction report. g2p[HCV] offers easy-to-use and fast subtype and resistance analysis of HCV sequences, is continuously updated and freely accessible under http://hcv.geno2pheno.org/index.php. The system was partially validated with respect to the NS3-protease inhibitors Boceprevir, Telaprevir and Simeprevir by using data generated with recombinant, phenotypic

  11. Geno2pheno[HCV] - A Web-based Interpretation System to Support Hepatitis C Treatment Decisions in the Era of Direct-Acting Antiviral Agents.

    Science.gov (United States)

    Kalaghatgi, Prabhav; Sikorski, Anna Maria; Knops, Elena; Rupp, Daniel; Sierra, Saleta; Heger, Eva; Neumann-Fraune, Maria; Beggel, Bastian; Walker, Andreas; Timm, Jörg; Walter, Hauke; Obermeier, Martin; Kaiser, Rolf; Bartenschlager, Ralf; Lengauer, Thomas

    2016-01-01

    The face of hepatitis C virus (HCV) therapy is changing dramatically. Direct-acting antiviral agents (DAAs) specifically targeting HCV proteins have been developed and entered clinical practice in 2011. However, despite high sustained viral response (SVR) rates of more than 90%, a fraction of patients do not eliminate the virus and in these cases treatment failure has been associated with the selection of drug resistance mutations (RAMs). RAMs may be prevalent prior to the start of treatment, or can be selected under therapy, and furthermore they can persist after cessation of treatment. Additionally, certain DAAs have been approved only for distinct HCV genotypes and may even have subtype specificity. Thus, sequence analysis before start of therapy is instrumental for managing DAA-based treatment strategies. We have created the interpretation system geno2pheno[HCV] (g2p[HCV]) to analyse HCV sequence data with respect to viral subtype and to predict drug resistance. Extensive reviewing and weighting of literature related to HCV drug resistance was performed to create a comprehensive list of drug resistance rules for inhibitors of the HCV protease in non-structural protein 3 (NS3-protease: Boceprevir, Paritaprevir, Simeprevir, Asunaprevir, Grazoprevir and Telaprevir), the NS5A replicase factor (Daclatasvir, Ledipasvir, Elbasvir and Ombitasvir), and the NS5B RNA-dependent RNA polymerase (Dasabuvir and Sofosbuvir). Upon submission of up to eight sequences, g2p[HCV] aligns the input sequences, identifies the genomic region(s), predicts the HCV geno- and subtypes, and generates for each DAA a drug resistance prediction report. g2p[HCV] offers easy-to-use and fast subtype and resistance analysis of HCV sequences, is continuously updated and freely accessible under http://hcv.geno2pheno.org/index.php. The system was partially validated with respect to the NS3-protease inhibitors Boceprevir, Telaprevir and Simeprevir by using data generated with recombinant, phenotypic

  12. Prevalence of hepatitis G virus infection and homology of different viral strains in Southern China

    Institute of Scientific and Technical Information of China (English)

    Gang Li; Hui-Hui Ma; Geroge KK Lau; Yin-Kit Leung; Chun-Lan Yao; Yu-Tian Chong; Wen-Hui Tang; Ji-Lu Yao

    2002-01-01

    AIM: To investigate the prevalence of hepatitis G virus (HGV) infection and to analyse the homology of different HGV strains in Southern China.METHODS: A total of 1993 sera from different groups in Guangdong, Hong Kong, and Yunnan were detected by reverse transcription polymerase chain reaction (RT-PCR). The nucleotide sequences of 5'untranslated region (5'UTR) derived from 20 strains and NS5 region from 3 strains were determined.RESULTS: The positive rate of HGV RNA was 0.89 % in community population, 2.57 % in blood donors, 17.86 % in intravenous drug abusers, 14.13 % in patients with hemodialysis, 13.66 % in those with hepatocellular carcinoma, 25.30 % in non A-E hepatitis, 7.22 % in hepatitis bone marrow transplantation, respectively. The homology was 90.40-100 % in 5'UTR among different strains, while that of NS5 region was 93.3-94 % in nucleotide sequence, and 97-99.2 % in amino acid sequence.CONCLUSION: These results showed that there was a high incidence of HGV infection in patients from Southern China, being treated for bone marrow transplantation, hepatocellular carcinoma and those on haemodialysis. Furthermore, there was also a high frequency of co-infection of HGV with HBV,HCV, non A-E viral hepatitis and that among intravenous drug abusers. The study also showed that sequence variation in different strains was associated with geographical factors but there was no significant difference in 5'UTR in circulating viruses between different patient groups. Finally, by sequential analysis of viral species present in individual patients over a three months period there was no evidence of sequence variation in the 5' UTR.

  13. Hepatitis C genotype distribution and homology among geographically disparate injecting drug users in Afghanistan.

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    Sanders-Buell, Eric; Rutvisuttinunt, Wiriya; Todd, Catherine S; Nasir, Abdul; Bradfield, Andrea; Lei, Esther; Poltavee, Kultida; Savadsuk, Hathairat; Kim, Jerome H; Scott, Paul T; de Souza, Mark; Tovanabutra, Sodsai

    2013-07-01

    Hepatitis C virus (HCV) prevalence is high among injecting drug users in Afghanistan, but transmission dynamics are poorly understood. Samples from HCV-infected injecting drug users were sequenced to determine circulating genotypes and potential transmission linkages. Serum samples were obtained from injecting drug user participants in Hirat, Jalalabad, and Mazar-i-Sharif between 2006 and 2008 with reactive anti-HCV rapid tests. Specimens with detected HCV viremia were amplified and underwent sequence analysis. Of 113 samples evaluated, 25 samples (35.2%) were only typeable in NS5B, nine samples (12.7%) were only typeable in CE1, and 37 samples (52.1%) were genotyped in both regions. Of those with typeable HCV, all were Afghan males with a mean age of 31.1 (standard deviation [SD] ± 8.0) years and mean duration of injecting of 3.9 (SD ± 4.3) years. Most reported residence outside Afghanistan in the last decade (90.1%) and prior incarceration (76.8%). HCV genotypes detected were: 1a, (35.2%, n = 25), 3a (62.0%, n = 44), and 1b (2.8%, n = 2). Cluster formation was detected in NS5B and CE1 and were generally from within the same city. All participants within clusters reported being a refugee in Iran compared to 93.5% of those outside clusters. Only 22.2% (4/11) of those within clusters had been refugees in Pakistan and these four individuals had also been refugees in Iran. Predominance of genotype 3a and the association between HCV viremia and having been a refugee in Iran potentially reflects migration between Afghanistan and Iran among IDUs from Mazar-i-Sharif and Hirat and carry implications for harm reduction programs for this migratory population. PMID:23918535

  14. Treatment of Chronic Hepatitis C in the Aged - Does It Impact Life Expectancy? A Decision Analysis.

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    Yaakov Maor

    Full Text Available Recent studies have demonstrated that the efficacy of interferon-free direct-acting antiviral agents (DAAs in patients over 70 is similar to that of younger age groups. Evidence continues to mount that life expectancy (LE increases with successful treatment of hepatitis C (HCV patients with advanced fibrosis. The evidence in older people is more limited. Our aim was to estimate the life year (LY and quality-adjusted life year (QALY gained by treatment of naïve patients with HCV as a function of patient's age and fibrosis stage.We constructed a Markov model of HCV progression toward advanced liver disease. The primary outcome was LY and QALY saved. The model and the sustained virological response of HCV infected subjects treated with a fixed-dose combination of the NS5B polymerase inhibitor Sofosbuvir and the NS5A replication complex inhibitor Ledipasvir were based on the published literature and expert opinion.Generally, both the number of LY gained and QALY gained gradually decreased with advancing age but the rate of decline was slower with more advanced fibrosis stage. For patients with fibrosis stage F1, F2 and F3, LY gained dropped below six months if treated by the age of 55, 65 or 70 years, respectively, while for a patient with fibrosis stage F4, the gain was one LY if treated by the age of 75. The QALY gained for treated over untreated elderly were reasonably high even for those treated at early fibrosis stage.There is a significant life expectancy benefit to HCV treatment in patients up to age 75 with advanced-stage fibrosis.

  15. Combination ledipasvir-sofosbuvir for the treatment of chronic hepatitis C virus infection: a review and clinical perspective

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    Nkuize M

    2016-06-01

    Full Text Available Marcel Nkuize,1 Thomas Sersté,1,2 Michel Buset,1 Jean-Pierre Mulkay11Department of Gastroenterology and Hepatology, Saint-Pierre University Hospital, 2Department of Gastroenterology, Pancreatology and Hepatology, Hôpital Academique Erasme, Université Libre de Bruxelles, Brussels, Belgium Abstract: Chronic hepatitis C treatment has continued to evolve, and interferon-free, oral treatment with direct-acting antiviral agents is the current standard of care. Recently, a new treatment, which is a combination of two direct-acting antiviral agents, ledipasvir 90 mg (anti-NS5A and sofosbuvir 400 mg (anti-NS5B, has been approved in the US and the European Union for the treatment of chronic hepatitis C viral infection. In Phase III trials among chronic hepatitis C virus genotype 1 monoinfected (treatment-naïve, treatment-experienced, and with advanced liver disease or posttransplant patients and HIV–hepatitis C virus coinfected patients, the ledipasvir-sofosbuvir fixed-dose combination is associated with a higher rate of sustained virologic response at 12 weeks after therapy has ceased. According to preliminary data, the ledipasvir-sofosbuvir combination also may be effective against hepatitis C genotype 4 virus infection. The ledipasvir-sofosbuvir combination taken orally is generally well-tolerated. Moreover, the combination treatment may suppress the effect of predictive factors of chronic hepatitis C that have historically been known to be associated with treatment failure. Thus, the fixed-dose single-tablet combination of ledipasvir-sofosbuvir offers a new era for the effective treatment of a variety of patients suffering from chronic hepatitis C virus infection.Keywords: ledipasvir, liver disease, ethnicity, DAA, HIV

  16. Geno2pheno[HCV] - A Web-based Interpretation System to Support Hepatitis C Treatment Decisions in the Era of Direct-Acting Antiviral Agents.

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    Prabhav Kalaghatgi

    Full Text Available The face of hepatitis C virus (HCV therapy is changing dramatically. Direct-acting antiviral agents (DAAs specifically targeting HCV proteins have been developed and entered clinical practice in 2011. However, despite high sustained viral response (SVR rates of more than 90%, a fraction of patients do not eliminate the virus and in these cases treatment failure has been associated with the selection of drug resistance mutations (RAMs. RAMs may be prevalent prior to the start of treatment, or can be selected under therapy, and furthermore they can persist after cessation of treatment. Additionally, certain DAAs have been approved only for distinct HCV genotypes and may even have subtype specificity. Thus, sequence analysis before start of therapy is instrumental for managing DAA-based treatment strategies. We have created the interpretation system geno2pheno[HCV] (g2p[HCV] to analyse HCV sequence data with respect to viral subtype and to predict drug resistance. Extensive reviewing and weighting of literature related to HCV drug resistance was performed to create a comprehensive list of drug resistance rules for inhibitors of the HCV protease in non-structural protein 3 (NS3-protease: Boceprevir, Paritaprevir, Simeprevir, Asunaprevir, Grazoprevir and Telaprevir, the NS5A replicase factor (Daclatasvir, Ledipasvir, Elbasvir and Ombitasvir, and the NS5B RNA-dependent RNA polymerase (Dasabuvir and Sofosbuvir. Upon submission of up to eight sequences, g2p[HCV] aligns the input sequences, identifies the genomic region(s, predicts the HCV geno- and subtypes, and generates for each DAA a drug resistance prediction report. g2p[HCV] offers easy-to-use and fast subtype and resistance analysis of HCV sequences, is continuously updated and freely accessible under http://hcv.geno2pheno.org/index.php. The system was partially validated with respect to the NS3-protease inhibitors Boceprevir, Telaprevir and Simeprevir by using data generated with recombinant

  17. Ledipasvir/Sofosbuvir: a review of its use in chronic hepatitis C.

    Science.gov (United States)

    Keating, Gillian M

    2015-04-01

    The single-tablet regimen of the hepatitis C virus (HCV) NS5A inhibitor ledipasvir and the HCV NS5B polymerase inhibitor sofosbuvir (ledipasvir/sofosbuvir; Harvoni(®)) was recently approved in the US and the EU. The phase III ION trials included treatment-naive (ION-1 and -3) or treatment-experienced (ION-2) patients with chronic HCV genotype 1 infection (≈20 % of patients in ION-1 and -2 had cirrhosis, whereas no patient in ION-3 had cirrhosis). A sustained virological response 12 weeks' post-treatment (SVR12) was seen in 99 % of treatment-naive patients receiving ledipasvir/sofosbuvir for 12 weeks in ION-1, with no additional benefit conferred by the addition of ribavirin or extending the treatment duration to 24 weeks. Moreover, in ION-3, an 8-week regimen achieved an SVR12 rate of 94 % overall and 97 % in the subgroup of patients with a baseline HCV RNA level of sofosbuvir for 12 and 24 weeks in ION-2. Data also support the use of ledipasvir/sofosbuvir in chronic HCV genotype 4 infection, in HCV and HIV co-infection and, in combination with ribavirin, in patients with chronic HCV genotype 1 or 4 infection who have decompensated cirrhosis or are liver transplant recipients and in chronic HCV genotype 3 infection. Oral ledipasvir/sofosbuvir was generally well tolerated. In conclusion, ledipasvir/sofosbuvir is an important new single-tablet regimen that represents a significant advance in the treatment of chronic hepatitis C.

  18. Daclatasvir–sofosbuvir combination therapy with or without ribavirin for hepatitis C virus infection: from the clinical trials to real life

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    Pol S

    2016-03-01

    Full Text Available Stanislas Pol, Marion Corouge, Anaïs Vallet-Pichard Université Paris Descartes, Liver Department, Assistance Publique Hôpitaux de Paris, Cochin Hospital, French Institute of Health and Medical Research UMS20, Institut Pasteur, Paris, France Abstract: The treatment of hepatitis C virus has changed dramatically with the rapid advent of numerous new antiviral agents, including direct-acting antivirals and agents with non-viral targets (cyclophilin inhibitors, interferon-lambda, vaccine therapy. Given the better safety profile and high antiviral potency of direct-acting antivirals, their combination in interferon-free oral regimens is becoming the standard of care for hepatitis C virus infection, tailored to individual patients according to the degree of disease progression (fibrosis, hepatitis C virus genotype and subtype, resistance profile, and prior therapeutic history. Results from clinical studies as well as preliminary real-life data regarding the combination of sofosbuvir (a nucleotide polymerase inhibitor and daclatasvir, a first-in-class NS5A replication complex inhibitor, demonstrate that it is one of the most promising antiviral therapies, with once-daily oral dosing, a low pill burden, good tolerability, and limited drug–drug interactions, in addition to high antiviral potency, with >90% sustained virologic response rates. This combination has high pangenotypic antiviral potency regardless of the severity and patient characteristics. The combination of sofosbuvir and an NS5A inhibitor with ribavirin for 12 weeks appears to be a very good further treatment option in both cirrhotic and treatment-experienced patients whatever the stage of fibrosis. Keywords: hepatitis C virus, direct-acting antivirals, sofosbuvir, daclatasvir

  19. Effect of Metal Chelators on γ-Secretase Indicates That Calcium and Magnesium Ions Facilitate Cleavage of Alzheimer Amyloid Precursor Substrate

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    Michael Ho

    2011-01-01

    Full Text Available Gamma-secretase is involved in the production of Aβ amyloid peptides. It cleaves the transmembrane domain of the amyloid precursor protein (APP at alternative sites to produce Aβ and the APP intracellular domain (AICD. Metal ions play an important role in Aβ aggregation and metabolism, thus metal chelators and ligands represent potential therapeutic agents for AD treatment. A direct effect of metal chelators on γ-secretase has not yet been investigated. The authors used an in vitro  γ-secretase assay consisting of cleavage of APP C100-3XFLAG by endogenous γ-secretase from rodent brains and human neuroblastoma SH-SY5Y, and detected AICD production by western blotting. Adding metalloprotease inhibitors to the reaction showed that clioquinol, phosphoramidon, and zinc metalloprotease inhibitors had no significant effect on γ-secretase activity. In contrast, phenanthroline, EDTA, and EGTA markedly decreased γ-secretase activity that could be restored by adding back calcium and magnesium ions. Mg2+ stabilized a 1,000 kDa presenilin 1 complex through blue native gel electrophoresis and size-exclusion chromatography. Data suggest that Ca2+ and Mg2+ stabilize γ-secretase and enhance its activity.

  20. Permissivity of primary human hepatocytes and different hepatoma cell lines to cell culture adapted hepatitis C virus.

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    Francois Helle

    Full Text Available Significant progress has been made in Hepatitis C virus (HCV culture since the JFH1 strain cloning. However, developing efficient and physiologically relevant culture systems for all viral genotypes remains an important goal. In this work, we aimed at producing a high titer JFH1 derived virus to test different hepatic cells' permissivity. To this end, we performed successive infections and obtained a JFH1 derived virus reaching high titers. Six potential adaptive mutations were identified (I599V in E2, R1373Q and M1611T in NS3, S2364P and C2441S in NS5A and R2523K in NS5B and the effect of these mutations on HCV replication and infectious particle production was investigated. This cell culture adapted virus enabled us to efficiently infect primary human hepatocytes, as demonstrated using the RFP-NLS-IPS reporter protein and intracellular HCV RNA quantification. However, the induction of a strong type III interferon response in these cells was responsible for HCV inhibition. The disruption of this innate immune response led to a strong infection enhancement and permitted the detection of viral protein expression by western blotting as well as progeny virus production. This cell culture adapted virus also enabled us to easily compare the permissivity of seven hepatoma cell lines. In particular, we demonstrated that HuH-7, HepG2-CD81, PLC/PRF/5 and Hep3B cells were permissive to HCV entry, replication and secretion even if the efficiency was very low in PLC/PRF/5 and Hep3B cells. In contrast, we did not observe any infection of SNU-182, SNU-398 and SNU-449 hepatoma cells. Using iodixanol density gradients, we also demonstrated that the density profiles of HCV particles produced by PLC/PRF/5 and Hep3B cells were different from that of HuH-7 and HepG2-CD81 derived virions. These results will help the development of a physiologically relevant culture system for HCV patient isolates.

  1. The history of hepatitis C virus (HCV): Basic research reveals unique features in phylogeny, evolution and the viral life cycle with new perspectives for epidemic control.

    Science.gov (United States)

    Bukh, Jens

    2016-10-01

    The discovery of hepatitis C virus (HCV) in 1989 permitted basic research to unravel critical components of a complex life cycle for this important human pathogen. HCV is a highly divergent group of viruses classified in 7 major genotypes and a great number of subtypes, and circulating in infected individuals as a continuously evolving quasispecies destined to escape host immune responses and applied antivirals. Despite the inability to culture patient viruses directly in the laboratory, efforts to define the infectious genome of HCV resulted in development of experimental recombinant in vivo and in vitro systems, including replicons and infectious cultures in human hepatoma cell lines. And HCV has become a model virus defining new paradigms in virology, immunology and biology. For example, HCV research discovered that a virus could be completely dependent on microRNA for its replication since microRNA-122 is critical for the HCV life cycle. A number of other host molecules critical for HCV entry and replication have been identified. Thus, basic HCV research revealed important molecules for development of host targeting agents (HTA). The identification and characterization of HCV encoded proteins and their functional units contributed to the development of highly effective direct acting antivirals (DAA) against the NS3 protease, NS5A and the NS5B polymerase. In combination, these inhibitors have since 2014 permitted interferon-free therapy with cure rates above 90% among patients with chronic HCV infection; however, viral resistance represents a challenge. Worldwide control of HCV will most likely require the development of a prophylactic vaccine, and numerous candidates have been pursued. Research characterizing features critical for antibody-based virus neutralization and T cell based virus elimination from infected cells is essential for this effort. If the world community promotes an ambitious approach by applying current DAA broadly, continues to develop

  2. The history of hepatitis C virus (HCV): Basic research reveals unique features in phylogeny, evolution and the viral life cycle with new perspectives for epidemic control.

    Science.gov (United States)

    Bukh, Jens

    2016-10-01

    The discovery of hepatitis C virus (HCV) in 1989 permitted basic research to unravel critical components of a complex life cycle for this important human pathogen. HCV is a highly divergent group of viruses classified in 7 major genotypes and a great number of subtypes, and circulating in infected individuals as a continuously evolving quasispecies destined to escape host immune responses and applied antivirals. Despite the inability to culture patient viruses directly in the laboratory, efforts to define the infectious genome of HCV resulted in development of experimental recombinant in vivo and in vitro systems, including replicons and infectious cultures in human hepatoma cell lines. And HCV has become a model virus defining new paradigms in virology, immunology and biology. For example, HCV research discovered that a virus could be completely dependent on microRNA for its replication since microRNA-122 is critical for the HCV life cycle. A number of other host molecules critical for HCV entry and replication have been identified. Thus, basic HCV research revealed important molecules for development of host targeting agents (HTA). The identification and characterization of HCV encoded proteins and their functional units contributed to the development of highly effective direct acting antivirals (DAA) against the NS3 protease, NS5A and the NS5B polymerase. In combination, these inhibitors have since 2014 permitted interferon-free therapy with cure rates above 90% among patients with chronic HCV infection; however, viral resistance represents a challenge. Worldwide control of HCV will most likely require the development of a prophylactic vaccine, and numerous candidates have been pursued. Research characterizing features critical for antibody-based virus neutralization and T cell based virus elimination from infected cells is essential for this effort. If the world community promotes an ambitious approach by applying current DAA broadly, continues to develop

  3. Daclatasvir with sofosbuvir and ribavirin for hepatitis C virus infection with advanced cirrhosis or post‐liver transplantation recurrence

    Science.gov (United States)

    Schiff, Eugene R.; Vierling, John M.; Landis, Charles; Fontana, Robert J.; Yang, Rong; McPhee, Fiona; Hughes, Eric A.; Noviello, Stephanie; Swenson, Eugene S.

    2016-01-01

    Chronic hepatitis C virus (HCV) infection with advanced cirrhosis or post‐liver transplantation recurrence represents a high unmet medical need with no approved therapies effective across all HCV genotypes. The open‐label ALLY‐1 study assessed the safety and efficacy of a 60‐mg once‐daily dosage of daclatasvir (pan‐genotypic NS5A inhibitor) in combination with sofosbuvir at 400 mg once daily (NS5B inhibitor) and ribavirin at 600 mg/day for 12 weeks with a 24‐week follow‐up in two cohorts of patients with chronic HCV infection of any genotype and either compensated/decompensated cirrhosis or posttransplantation recurrence. Patients with on‐treatment transplantation were eligible to receive 12 additional weeks of treatment immediately after transplantation. The primary efficacy measure was sustained virologic response at posttreatment week 12 (SVR12) in patients with a genotype 1 infection in each cohort. Sixty patients with advanced cirrhosis and 53 with posttransplantation recurrence were enrolled; HCV genotypes 1 (76%), 2, 3, 4, and 6 were represented. Child‐Pugh classifications in the advanced cirrhosis cohort were 20% A, 53% B, and 27% C. In patients with cirrhosis, 82% (95% confidence interval [CI], 67.9%‐92.0%) with genotype 1 infection achieved SVR12, whereas the corresponding rates in those with genotypes 2, 3, and 4 were 80%, 83%, and 100%, respectively; SVR12 rates were higher in patients with Child‐Pugh class A or B, 93%, versus class C, 56%. In transplant recipients, SVR12 was achieved by 95% (95% CI, 83.5%‐99.4%) and 91% of patients with genotype 1 and 3 infection, respectively. Three patients received peritransplantation treatment with minimal dose interruption and achieved SVR12. There were no treatment‐related serious adverse events. Conclusion: The pan‐genotypic combination of daclatasvir, sofosbuvir, and ribavirin was safe and well tolerated. High SVR rates across multiple HCV genotypes were achieved by patients with

  4. Increased microRNA-155 expression in the serum and peripheral monocytes in chronic HCV infection

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    Bala Shashi

    2012-07-01

    Full Text Available Abstract Background Hepatitis C Virus (HCV, a single stranded RNA virus, affects millions of people worldwide and leads to chronic infection characterized by chronic inflammation in the liver and in peripheral immune cells. Chronic liver inflammation leads to progressive liver damage. MicroRNAs (miRNA regulate inflammation (miR-155, -146a and -125b as well as hepatocyte function (miR-122. Methods Here we hypothesized that microRNAs are dysregulated in chronic HCV infection. We examined miRNAs in the circulation and in peripheral monocytes of patients with chronic HCV infection to evaluate if specific miRNA expression correlated with HCV infection. Results We found that monocytes from chronic HCV infected treatment-naïve (cHCV but not treatment responder patients showed increased expression of miR-155, a positive regulator of TNFα, and had increased TNFα production compared to monocytes of normal controls. After LPS stimulation, miR-155 levels were higher in monocytes from cHCV patients compared to controls. MiR-125b, which has negative regulatory effects on inflammation, was decreased in cHCV monocytes compared to controls. Stimulation of normal monocytes with TLR4 and TLR8 ligands or HCV core, NS3 and NS5 recombinant proteins induced a robust increase in both miR-155 expression and TNFα production identifying potential mechanisms for in vivo induction of miR-155. Furthermore, we found increased serum miR-155 levels in HCV patients compared to controls. Serum miR-125b and miR-146a levels were also increased in HCV patients. Serum levels of miR-122 were elevated in cHCV patients and correlated with increased ALT and AST levels and serum miR-155 levels. Conclusion In conclusion, our novel data demonstrate that miR-155, a positive regulator of inflammation, is upregulated both in monocytes and in the serum of patients with chronic HCV infection. Our study suggests that HCV core, NS3, and NS5 proteins or TLR4 and TLR8 ligands can mediate

  5. Spatio-temporal tracking and phylodynamics of an urban dengue 3 outbreak in Sao Paulo, Brazil.

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    Adriano Mondini

    Full Text Available The dengue virus has a single-stranded positive-sense RNA genome of approximately 10.700 nucleotides with a single open reading frame that encodes three structural (C, prM, and E and seven nonstructural (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5 proteins. It possesses four antigenically distinct serotypes (DENV 1-4. Many phylogenetic studies address particularities of the different serotypes using convenience samples that are not conducive to a spatio-temporal analysis in a single urban setting. We describe the pattern of spread of distinct lineages of DENV-3 circulating in São José do Rio Preto, Brazil, during 2006. Blood samples from patients presenting dengue-like symptoms were collected for DENV testing. We performed M-N-PCR using primers based on NS5 for virus detection and identification. The fragments were purified from PCR mixtures and sequenced. The positive dengue cases were geo-coded. To type the sequenced samples, 52 reference sequences were aligned. The dataset generated was used for iterative phylogenetic reconstruction with the maximum likelihood criterion. The best demographic model, the rate of growth, rate of evolutionary change, and Time to Most Recent Common Ancestor (TMRCA were estimated. The basic reproductive rate during the epidemics was estimated. We obtained sequences from 82 patients among 174 blood samples. We were able to geo-code 46 sequences. The alignment generated a 399-nucleotide-long dataset with 134 taxa. The phylogenetic analysis indicated that all samples were of DENV-3 and related to strains circulating on the isle of Martinique in 2000-2001. Sixty DENV-3 from São José do Rio Preto formed a monophyletic group (lineage 1, closely related to the remaining 22 isolates (lineage 2. We assumed that these lineages appeared before 2006 in different occasions. By transforming the inferred exponential growth rates into the basic reproductive rate, we obtained values for lineage 1 of R(0 = 1.53 and values for

  6. Genotypic distribution of hepatitis C virus in Thailand and Southeast Asia.

    Science.gov (United States)

    Wasitthankasem, Rujipat; Vongpunsawad, Sompong; Siripon, Nipaporn; Suya, Chutima; Chulothok, Phrutsada; Chaiear, Kasemporn; Rujirojindakul, Pairaya; Kanjana, Sawan; Theamboonlers, Apiradee; Tangkijvanich, Pisit; Poovorawan, Yong

    2015-01-01

    The majority of hepatitis C virus (HCV) infection results in chronic infection, which can lead to liver cirrhosis and hepatocellular carcinoma. Global burden of hepatitis C virus (HCV) is estimated at 150 million individuals, or 3% of the world's population. The distribution of the seven major genotypes of HCV varies with geographical regions. Since Asia has a high incidence of HCV, we assessed the distribution of HCV genotypes in Thailand and Southeast Asia. From 588 HCV-positive samples obtained throughout Thailand, we characterized the HCV 5' untranslated region, Core, and NS5B regions by nested PCR. Nucleotide sequences obtained from both the Core and NS5B of these isolates were subjected to phylogenetic analysis, and genotypes were assigned using published reference genotypes. Results were compared to the epidemiological data of HCV genotypes identified within Southeast Asian. Among the HCV subtypes characterized in the Thai samples, subtype 3a was the most predominant (36.4%), followed by 1a (19.9%), 1b (12.6%), 3b (9.7%) and 2a (0.5%). While genotype 1 was prevalent throughout Thailand (27-36%), genotype 3 was more common in the south. Genotype 6 (20.9%) constituted subtype 6f (7.8%), 6n (7.7%), 6i (3.4%), 6j and 6m (0.7% each), 6c (0.3%), 6v and 6xa (0.2% each) and its prevalence was significantly lower in southern Thailand compared to the north and northeast (p = 0.027 and p = 0.030, respectively). Within Southeast Asia, high prevalence of genotype 6 occurred in northern countries such as Myanmar, Laos, and Vietnam, while genotype 3 was prevalent in Thailand and Malaysia. Island nations of Singapore, Indonesia and Philippines demonstrated prevalence of genotype 1. This study further provides regional HCV genotype information that may be useful in fostering sound public health policy and tracking future patterns of HCV spread. PMID:25962112

  7. Genotypic distribution of hepatitis C virus in Thailand and Southeast Asia.

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    Rujipat Wasitthankasem

    Full Text Available The majority of hepatitis C virus (HCV infection results in chronic infection, which can lead to liver cirrhosis and hepatocellular carcinoma. Global burden of hepatitis C virus (HCV is estimated at 150 million individuals, or 3% of the world's population. The distribution of the seven major genotypes of HCV varies with geographical regions. Since Asia has a high incidence of HCV, we assessed the distribution of HCV genotypes in Thailand and Southeast Asia. From 588 HCV-positive samples obtained throughout Thailand, we characterized the HCV 5' untranslated region, Core, and NS5B regions by nested PCR. Nucleotide sequences obtained from both the Core and NS5B of these isolates were subjected to phylogenetic analysis, and genotypes were assigned using published reference genotypes. Results were compared to the epidemiological data of HCV genotypes identified within Southeast Asian. Among the HCV subtypes characterized in the Thai samples, subtype 3a was the most predominant (36.4%, followed by 1a (19.9%, 1b (12.6%, 3b (9.7% and 2a (0.5%. While genotype 1 was prevalent throughout Thailand (27-36%, genotype 3 was more common in the south. Genotype 6 (20.9% constituted subtype 6f (7.8%, 6n (7.7%, 6i (3.4%, 6j and 6m (0.7% each, 6c (0.3%, 6v and 6xa (0.2% each and its prevalence was significantly lower in southern Thailand compared to the north and northeast (p = 0.027 and p = 0.030, respectively. Within Southeast Asia, high prevalence of genotype 6 occurred in northern countries such as Myanmar, Laos, and Vietnam, while genotype 3 was prevalent in Thailand and Malaysia. Island nations of Singapore, Indonesia and Philippines demonstrated prevalence of genotype 1. This study further provides regional HCV genotype information that may be useful in fostering sound public health policy and tracking future patterns of HCV spread.

  8. The Novel Cyclophilin Inhibitor CPI-431-32 Concurrently Blocks HCV and HIV-1 Infections via a Similar Mechanism of Action.

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    Philippe A Gallay

    Full Text Available HCV-related liver disease is the main cause of morbidity and mortality of HCV/HIV-1 co-infected patients. Despite the recent advent of anti-HCV direct acting antivirals (DAAs, the treatment of HCV/HIV-1 co-infected patients remains a challenge, as these patients are refractory to most therapies and develop liver fibrosis, cirrhosis and liver cancer more often than HCV mono-infected patients. Until the present study, there was no suitable in vitro assay to test the inhibitory activity of drugs on HCV/HIV-1 co-infection. Here we developed a novel in vitro "co-infection" model where HCV and HIV-1 concurrently replicate in their respective main host target cells--human hepatocytes and CD4+ T-lymphocytes. Using this co-culture model, we demonstrate that cyclophilin inhibitors (CypI, including a novel cyclosporin A (CsA analog, CPI-431-32, simultaneously inhibits replication of both HCV and HIV-1 when added pre- and post-infection. In contrast, the HIV-1 protease inhibitor nelfinavir or the HCV NS5A inhibitor daclatasvir only blocks the replication of a single virus in the "co-infection" system. CPI-431-32 efficiently inhibits HCV and HIV-1 variants, which are normally resistant to DAAs. CPI-431-32 is slightly, but consistently more efficacious than the most advanced clinically tested CypI--alisporivir (ALV--at interrupting an established HCV/HIV-1 co-infection. The superior antiviral efficacy of CPI-431-32 over ALV correlates with its higher potency inhibition of cyclophilin A (CypA isomerase activity and at preventing HCV NS5A-CypA and HIV-1 capsid-CypA interactions known to be vital for replication of the respective viruses. Moreover, we obtained evidence that CPI-431-32 prevents the cloaking of both the HIV-1 and HCV genomes from cellular sensors. Based on these results, CPI-431-32 has the potential, as a single agent or in combination with DAAs, to inhibit both HCV and HIV-1 infections.

  9. Mirror symmetry in the presence of branes

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    Mertens, Adrian

    2011-10-11

    over the plain. We study complex structure monodromies of the fibers and find evidence that they are mirror to the Calabi-Yau manifold with hypersurface that defines the combined deformation space, provided an NS5 brane is wrapped on the hypersurface. This gives a simple rule how to construct mirrors to Calabi-Yau manifolds with NS5 branes wrapped on hypersurfaces. (orig.)

  10. Metabolism of phosphatidylinositol 4-kinase IIIα-dependent PI4P Is subverted by HCV and is targeted by a 4-anilino quinazoline with antiviral activity.

    Directory of Open Access Journals (Sweden)

    Annalisa Bianco

    Full Text Available 4-anilino quinazolines have been identified as inhibitors of HCV replication. The target of this class of compounds was proposed to be the viral protein NS5A, although unequivocal proof has never been presented. A 4-anilino quinazoline moiety is often found in kinase inhibitors, leading us to formulate the hypothesis that the anti-HCV activity displayed by these compounds might be due to inhibition of a cellular kinase. Type III phosphatidylinositol 4-kinase α (PI4KIIIα has recently been identified as a host factor for HCV replication. We therefore evaluated AL-9, a compound prototypical of the 4-anilino quinazoline class, on selected phosphatidylinositol kinases. AL-9 inhibited purified PI4KIIIα and, to a lesser extent, PI4KIIIβ. In Huh7.5 cells, PI4KIIIα is responsible for the phosphatidylinositol-4 phosphate (PI4P pool present in the plasma membrane. Accordingly, we observed a gradual decrease of PI4P in the plasma membrane upon incubation with AL-9, indicating that this agent inhibits PI4KIIIα also in living cells. Conversely, AL-9 did not affect the level of PI4P in the Golgi membrane, suggesting that the PI4KIIIβ isoform was not significantly inhibited under our experimental conditions. Incubation of cells expressing HCV proteins with AL-9 induced abnormally large clusters of NS5A, a phenomenon previously observed upon silencing PI4KIIIα by RNA interference. In light of our findings, we propose that the antiviral effect of 4-anilino quinazoline compounds is mediated by the inhibition of PI4KIIIα and the consequent depletion of PI4P required for the HCV membranous web. In addition, we noted that HCV has a profound effect on cellular PI4P distribution, causing significant enrichment of PI4P in the HCV-membranous web and a concomitant depletion of PI4P in the plasma membrane. This observation implies that HCV--by recruiting PI4KIIIα in the RNA replication complex--hijacks PI4P metabolism, ultimately resulting in a markedly altered

  11. Epidemic history of major genotypes of hepatitis C virus in Uruguay.

    Science.gov (United States)

    Castells, M; Bello, G; Ifrán, S; Pereyra, S; Boschi, S; Uriarte, R; Cristina, J; Colina, R

    2015-06-01

    Worldwide, more than 170 million people are chronically infected with the hepatitis C virus (HCV) and every year die more than 350,000 people from HCV-related liver diseases. Recently, HCV was reclassified into seven major genotypes and 67 subtypes. Some subtypes as 1a, 1b and 3a, have become epidemic as a result of the new parenteral transmission routes and are responsible for most HCV infections in Western countries. HCV 1a subtype have been sub-categorized into two separate sub clades. Recent studies based on the analysis of NS5B genome region, reveal that HCV epidemics in Argentina and Brazil are characterized by multiple introductions events of subtypes 1a, 1b and 3a, followed by subsequent local dispersion. There is no data about HCV genotypes circulating in Uruguay and their evolutionary and demographic history. To this end, a total of 153 HCV NS5B gene sequences were obtained from Uruguayan patients between 2005 and 2011. 86 (56%) sequences grouped with subtype 1a, 40 (26%) with subtype 3a and 27 (18%) with subtype 1b. Furthermore, subtype 1a sequences were distributed among both clades, 1 (n=62, 72%) and 2 (n=24, 28%). Four local HCV clades were found: UY-1a(I), UY-1a(II), UY-1a(III) and UY-3a; comprising a 39% of all HCV viruses analyzed in this study. HCV epidemic in Uruguay has been driving by multiple introductions of subtypes 1a, 1b and 3a and by local dissemination of a few country-specific strains. The evolutionary and demographic history of the major Uruguayan HCV clade UY-1a(I) was reconstructed under two different molecular clock rate models and displayed an epidemic history characterized by an initial phase of rapid expansion followed by a more recent reduction of growth rate since 2000-2005. This is the first comprehensive study about the molecular epidemiology and epidemic history of HCV in Uruguay.

  12. Hepatitis C and B Virus Infection in Chinese Patients with Extrahepatic Bile Duct Carcinoma

    Institute of Scientific and Technical Information of China (English)

    CHENMingyi; HUANGZhiqiang; CHENLezhen; GAOYabing; PENGRuiyun; WANGDewen

    2002-01-01

    Objective:In China, the incidence of extrahepatic bile duct carcinoma (EBDC) tends to increase over the past decades. The etiology of the noted increase in EBDC is not identified. Approximately, in a half of the overall Chinese patients with EBDC, the causative factors in the development of EBDC have not been demonstrated. There is a high prevalence of hepatitis C virus (HCV) or hepatitis B virus (HBV)in China, both of which can induce malignant transformation of infected cells and strongly associated with hepatocellular carcinoma (HCC).In this study,EBDC tissues from Chinese patients were examined for the presence of HCV and HBV infection to investigate further the potential causes of EBDC. Methods:HCV NS5 protein and HBsAg were detected by labeled streptavidin biotin (LSAB) method; HCV RNA and HBV DNA were detected by in situ polymerase chain reaction (IS-PCR) in formalin fixed, paraffin embedded specimens from 51 Chinese patients with EBDC. HCV RNA and HBV DNA were detected by IS-PCR in 34 Chinese patients with specimens of benign lesions of hepatobiliary tract(control group). Results:In 51 case tissue sections of EBDC, NS5 protein was detected in 14 (27.5%), and HBsAg in 5 (9.8%), HCV RNA in 18(35.4%) and HBV DNA in 8 (15.9%), respectively, of which HCV and HBV co-infection was detected in 2 (3.9%). In 34 case tissue sections of the control group, HCV RNA was detected in 2 (5.9%), and HBV DNA in 3 (8.8%).Conclusion:In this study using standard histochemical and PCR techniques,HCV and HBV and HBV presence in EBDC tissues than would be expected on serologic grounds.The detectable rate of HCV RNA in EBDC tissues was significantly higher than in control group(x2=9.808,P=0.002).As a result ,this study indicates that there is a correlation between the presence of HCV infection and EBDC,and HCV infection has possible ctiologic significance in the development of EBDCin China.While HBV DNA was detecled in EBDC tissues with the difference in the detectable rate of HBV

  13. Hepatitis C virus infection in Brazilian long-distance truck drivers

    Directory of Open Access Journals (Sweden)

    Freitas Nara R

    2010-08-01

    Full Text Available Abstract Hepatitis C virus (HCV infection is a global public health problem. Long-distance truck drivers live apart from their family for long periods of time, a lifestyle that favors at-risk behaviors such as unprotected sex with multiple partners and illicit drug use. As data concerning HCV infection in this population are still rare, this paper aims to investigate the prevalence, genotypes/subtypes, and the factors associated with HCV infection in long-distance truck drivers in Brazil. A cross-sectional survey was carried out with 641 Brazilian long-truck drivers who were recruited at a major truck stop located at kilometer 1,296 of the BR-153 highway, which is considered to be one of the longest roads in Brazil. All individuals were interviewed, and their serum samples were tested for the presence of antibodies to HCV (anti-HCV by ELISA and immunoblot. Anti-HCV positive samples were tested for HCV RNA by PCR amplification of the 5' NC and NS5B regions and were genotyped using the LiPA assay and nucleotide sequencing, respectively. Factors associated with HCV infection were identified with logistic regression. The prevalence of HCV infection was 1.4% (95% CI: 0.7-2.8. History of blood transfusion, sharing of personal hygiene tools, illicit drug use and HBV status were factors independently associated with HCV infection in the study population. HCV RNA was detected in 8/9 anti-HCV positive samples, in which genotypes 1 (n = 3, 2 (n = 2, and 3 (n = 3 were determined by LiPA. Using phylogenetic tree analysis of the NS5B region, subtypes 1a (n = 1, 1b (n = 2, 2b (n = 2 and 3a (n = 3 were identified. These data show that the prevalence of HCV infection among Brazilian truck drivers was similar to that observed for the general population. History of blood transfusion, sharing of personal hygiene tools, illicit drug use and HBV status were predictors of HCV infection. The HCV genotypes/subtypes identified in the study population are consistent with

  14. Hepatitis C: sexual or intrafamilial transmission? Epidemiological and phylogenetic analysis of hepatitis C virus in 24 infected couples Hepatite C: transmissão sexual ou intrafamiliar? Análise epidemiológica e filogenética do vírus da hepatite C em 24 casais infectados

    Directory of Open Access Journals (Sweden)

    Norma de Paula Cavalheiro

    2009-06-01

    Full Text Available The role of sexual or intrafamilial transmission of hepatitis C is controversial. A phylogenetic analysis was performed on the non-structural region 5B of the hepatitis C virus (NS5B-HCV. High percentages of homology (mean of 98.3% were shown between the couples. Twenty (83.3% of the 24 men but only two of the women (8.3% reported having had sexually transmitted diseases during their lives. The risk factors for HCV acquisition were blood transfusion (10 couples, use of illegal injected drugs (17, use of inhalants (15, acupuncture (5 and tattoos (5. The shared use of personal hygiene items included toothbrushes between six couples (25%, razor blades between 16 (66.7%, nail clippers between 21 (87.5% and manicure pliers between 14 (58.3%. The high degree of similarity of the hepatitis C virus genome supports the hypothesis of hepatitis C virus transmission between these couples. The shared use of personal hygiene items suggests the possibility of intrafamilial transmission of infection.O papel da transmissão sexual ou intrafamiliar da hepatite C é controverso. Foi feita análise filogenética, região não estrutural 5B do vírus da hepatite C (NS5B-HCV. Altas percentagens de homologia com média de 98,3% foi revelada entre os casais. Vinte (83,3% de 24 homens, contra apenas duas (8,3% mulheres reportaram doença sexualmente transmisível durante suas vidas. Os fatores de risco para aquisição da doença foram: transfusão de sangue para 10 casais, uso de drogas ilícitas injetáveis para 17, inalatórias para 15, acupuntura em 5 e tatuagens para 5. O compartilhamento de utensílios de higiene pessoal incluem: escova de dente para seis (25% dos casais, lâmina de barbear para 16 (66,7%, cortador de unhas para 21 (87,5% e alicate de manicure para 14 (58,3%. O alto grau de similaridade genômica entre os vírus da hepatite C suporta a hipótese de transmissão entre os casais. O uso compartilhado de utensílios de higiene pessoal sugere a

  15. 抗丙型肝炎病毒药索非布韦的临床研究进展

    Institute of Scientific and Technical Information of China (English)

    陈丹; 汤姝岚

    2015-01-01

    目的:综述抗丙型肝炎病毒(HCV)药索非布韦的临床研究进展.方法:以“Sofosbuvir"“索非布韦”“索氟布韦”“丙型肝炎”和“NS5B聚合酶抑制剂”等为关键词,组合检索2010年1月至2015年2月PubMed、万方、维普、中国知网等数据库,对索非布韦的临床药理(作用机制、药动学、药物相互作用、耐药性)、适用特殊人群、临床试验及安全性评价等内容进行综述.结果:共检索到相关文献76条,其中有效文献20条.作用机制方面,索非布韦通过与HCV的RNA核苷酸竞争HCV特异性NS5B聚合酶活化位点而发挥抗病毒作用,给药剂量为400 mg/d时对病毒的抑制作用最佳.临床应用方面,索非布韦适用于HCV初治患者和既往干扰素治疗失败的患者,不同HCV基因型感染可采用不同的给药方案;索非布韦对HCV感染合并肝硬化、肝脏移植和人类免疫缺陷病毒感染患者也有效,且给药时无需调整剂量.此外,索非布韦的耐药性较好、药物相互作用少、不良事件发生率较低.结论:索非布韦用于慢性HCV感染治疗,具有病毒学应答率高、适用人群广、不良反应发生率低、给药方式简单等特点,相信在未来会拥有良好的应用前景.

  16. Changing the face of hepatitis C management – the design and development of sofosbuvir

    Directory of Open Access Journals (Sweden)

    Noell BC

    2015-04-01

    Full Text Available Bennett C Noell,* Siddesh V Besur,* Andrew S deLemos Department of Medicine, Center for Liver Diseases and Transplantation, Carolinas Medical Center, Charlotte, NC, USA *These authors contributed equally to this work Abstract: The availability of direct-acting antiviral (DAA therapy has launched a new era in the management of chronic hepatitis C. Sofosbuvir, a uridine nucleotide analog that inhibits the hepatitis C RNA-dependent RNA polymerase, is the backbone of chronic hepatitis C therapy. Acting at the catalytic site of the polymerase, sofosbuvir is highly potent in suppressing viral replication and has a high genetic barrier to resistance. Sofosbuvir is effective across all hepatitis C genotypes, and is a mainstay of interferon-free combination therapy. In Phase II and III studies, genotype 1 patients who took sofosbuvir in combination with another DAA such as the NS3-4A protease inhibitor, simeprevir, or the NS5A replication complex inhibitors, ledipasvir or daclatasvir, achieved a sustained virologic response rate of over 90%. Harvoni®, a combination tablet of sofosbuvir and ledipasvir, dosed once daily is recommended for 24 weeks for treatment-experienced genotype 1 patients with cirrhosis, but 12 weeks of therapy is sufficient for all other populations. While genotype 2 (12 weeks or 16 weeks and treatment-naïve genotype 3 patients (24 weeks have excellent response rates with sofosbuvir and ribavirin, treatment-experienced cirrhotic genotype 3 patients may need the addition of another DAA such as daclatasvir. Sofosbuvir is efficacious in special populations such as HIV–hepatitis C virus-coinfected patients and liver transplant recipients and has already made a profound impact in these groups. Since it is renally eliminated, patients with advanced kidney disease or on dialysis must await dosing recommendations. Sofosbuvir-based regimens appear to be well tolerated with headache and fatigue being the most common side effects. The

  17. Therapie der chronischen Hepatitis C: Der Beginn einer neuen Ära

    Directory of Open Access Journals (Sweden)

    Stättermayer AF

    2014-01-01

    Full Text Available Im letzten Jahrzehnt stellte die Kombination aus pegyliertem Interferon-α (PegINF-α und Ribavirin (RBV die Standardtherapie bei Patienten mit chronischer Hepatitis C dar. Mit der Zulassung der Protease-Inhibitoren Telaprevir und Boceprevir stehen seit 2011 erstmals direkt antiviral wirksame Substanzen („direct-acting antiviral agents“ [DAA] für die Therapie des HCV-Genotyps 1 zur Verfügung. Zwar konnte hiermit der Therapieerfolg deutlich erhöht werden, gleichzeitig führte die neue Triple-Therapie allerdings auch zu vermehrten Nebenwirkungen und höheren Therapiekosten. Zusätzliche Probleme wie Virusresistenz, Medikamenteninteraktionen und eine hohe Anzahl an täglich einzunehmenden Tabletten erschweren die antivirale Therapie mit Protease-Inhibitoren der ersten Generation. Insbesondere Patienten mit fortgeschrittener Lebererkrankung, welche den dringendsten Bedarf für eine antivirale Therapie aufweisen, haben ein hohes Risiko, schwere Nebenwirkungen unter der Triple-Therapie zu entwickeln. Die Entwicklungen in der Therapie der Hepatitis C sind rasant. So stehen gegenwärtig mit der Zulassung von Sofosbuvir (Sovaldi®, NS5BInhibitor, Simeprevir (Olysio®, Protease-Inhibitor und Daclatasvir (Daklinza®, NS5A-Inhibitor in Österreich 3 weitere direkt antiviral wirkende Substanzen zur Verfügung, welche in der Kombination bei Genotyp 1 (GT1 und Genotyp 4 (GT4 somit erstmalig eine Interferon-freie Therapie erlauben. Für die HCV-Genotypen 2 und 3 (GT2, GT3 ist die Interferon-freie Therapie in Form von Sofosbuvir/Ribavirin ebenfalls bereits Realität. Eine Reihe zusätzlicher Substanzen wird in Kürze folgen. Eine Vielzahl von klinischen Studien erbrachte diesbezüglich vielversprechende Ergebnisse. Diese zusätzlichen wirksamen, nebenwirkungsarmen, hocheffektiven und kürzeren Therapien für alle Patienten mit chronischer HCV-Infektion werden in absehbarer Zeit zur Verfügung stehen.

  18. Instantons and chiral symmetry in string theory

    Science.gov (United States)

    Jensen, Steuard B.

    The study of non-perturbative effects has played an important role in many recent developments in physics. String theory has proven to be an especially fertile ground for such studies: not only is its own non-perturbative structure interesting, but it has emerged as a framework in which to study the strongly coupled behavior of a variety of models in quantum field theory as well. In this thesis, I present results demonstrating the use of string theory in both these ways. First, I discuss non-perturbative corrections to the Kaluza-Klein monopole in string theory. As usually described, this object has an isometry around a compact circle and is related by T-duality to a "smeared" NS5-brane which retains that isometry. The true NS5-brane solution is localized at a point on the circle, so duality implies that the Kaluza-Klein monopole should show some corresponding behavior. By expressing the Kaluza-Klein monopole as a gauged linear sigma model in two dimensions, I show that worldsheet instantons give corrections to its geometry. These corrections can be understood as a localization in "winding space" which could be probed by strings with winding charge around the circle. Second, I discuss a configuration of D-branes in string theory whose low energy physics corresponds to a 3+1-dimensional quantum field theory with dynamically broken chiral symmetry. In a weakly coupled region of parameter space, this theory is a non-local generalization of the Nambu-Jona-Lasinio model. Indications are given that this model dynamically breaks chiral symmetry at arbitrarily weak 't Hooft coupling. At strong coupling this field theory is no longer solvable directly, but an alternate weakly coupled description can be found from the string theory model: the dynamics is determined by replacing a stack of D-branes by their near-horizon geometry and studying the low energy theory on probe D-branes in that background. In yet another region of parameter space, this D-brane configuration gives

  19. Proteome-wide screening reveals immunodominance in the CD8 T cell response against classical swine fever virus with antigen-specificity dependent on MHC class I haplotype expression.

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    Giulia Franzoni

    Full Text Available Vaccination with live attenuated classical swine fever virus (CSFV vaccines induces a rapid onset of protection which has been associated with virus-specific CD8 T cell IFN-γ responses. In this study, we assessed the specificity of this response, by screening a peptide library spanning the CSFV C-strain vaccine polyprotein to identify and characterise CD8 T cell epitopes. Synthetic peptides were pooled to represent each of the 12 CSFV proteins and used to stimulate PBMC from four pigs rendered immune to CSFV by C-strain vaccination and subsequently challenged with the virulent Brescia strain. Significant IFN-γ expression by CD8 T cells, assessed by flow cytometry, was induced by peptide pools representing the core, E2, NS2, NS3 and NS5A proteins. Dissection of these antigenic peptide pools indicated that, in each instance, a single discrete antigenic peptide or pair of overlapping peptides was responsible for the IFN-γ induction. Screening and titration of antigenic peptides or truncated derivatives identified the following antigenic regions: core₂₄₁₋₂₅₅ PESRKKLEKALLAWA and NS3₁₉₀₂₋₁₉₁₂ VEYSFIFLDEY, or minimal length antigenic peptides: E2₉₉₆₋₁₀₀₃ YEPRDSYF, NS2₁₂₂₃₋₁₂₃₀ STVTGIFL and NS5A₃₀₇₀₋₃₀₇₈ RVDNALLKF. The epitopes are highly conserved across CSFV strains and variable sequence divergence was observed with related pestiviruses. Characterisation of epitope-specific CD8 T cells revealed evidence of cytotoxicity, as determined by CD107a mobilisation, and a significant proportion expressed TNF-α in addition to IFN-γ. Finally, the variability in the antigen-specificity of these immunodominant CD8 T cell responses was confirmed to be associated with expression of distinct MHC class I haplotypes. Moreover, recognition of NS₁₂₂₃₋₁₂₃₀ STVTGIFL and NS3₁₉₀₂₋₁₉₁₂ VEYSFIFLDEY by a larger group of C-strain vaccinated animals showed

  20. Little string theory from a double-scaled matrix model

    International Nuclear Information System (INIS)

    Following Lin and Maldacena, we find exact supergravity solutions dual to a class of vacua of the plane wave matrix model by solving an electrostatics problem. These are asymptotically near-horizon D0-brane solutions with a throat associated with NS5-brane degrees of freedom. We determine the precise limit required to decouple the asymptotic geometry and leave an infinite throat solution found earlier by Lin and Maldacena, dual to Little String Theory on S5. By matching parameters with the gauge theory, we find that this corresponds to a double scaling limit of the plane wave matrix model in which N→∞ and the 't Hooft coupling λ scales as ln4(N), which we speculate allows all terms in the genus expansion to contribute even at infinite N. Thus, the double-scaled matrix quantum mechanics gives a Lagrangian description of Little String Theory on S5, or equivalently a ten-dimensional string theory with linear dilaton background

  1. Stable non-supersymmetric supergravity solutions from deformations of the Maldacena-Nunez background

    International Nuclear Information System (INIS)

    We study a deformation of the type IIB Maldacena-Nunez background which arises as the near-horizon limit of NS5 branes wrapped on a two-cycle. This background is dual to a 'little string theory compactified on a two-sphere, a theory which at low energies includes four-dimensional N=1 super Yang-Mills theory. The deformation we study corresponds to a mass term for some of the scalar fields in this theory, and it breaks supersymmetry completely. In the language of seven-dimensional SO(4) gauged supergravity the deformation involves (at leading order) giving a VEV, depending only on the radial coordinate, to a particular scalar field. We explicitly construct the corresponding solution at leading order in the deformation, both in seven-dimensional and in ten-dimensional supergravity, and we verify that it completely breaks supersymmetry. Since the original background had a mass gap and we are performing a small deformation, the deformed background is guaranteed to be stable even though it is not supersymmetric. (author)

  2. Hyper-K\\"{a}hler with Torsion, T-duality, and Defect (p,q) Five-branes

    CERN Document Server

    Kimura, Tetsuji; Yata, Masaya

    2014-01-01

    We investigate the five-branes interpretation of a hyper-K\\"{a}hler geometry with torsion (HKT). This geometry is obtained by a conformal transformation of the Taub-NUT space which represents a single Kaluza-Klein five-brane. This HKT would represent an NS5-brane on the Taub-NUT space. In order to explore the HKT further, we compactify one transverse direction, and study the $O(2,2;{\\mathbb Z}) = SL(2,{\\mathbb Z}) \\times SL(2,{\\mathbb Z})$ monodromy structure associated with two-torus. Performing the conjugate transformation, we obtain a new solution whose physical interpretation is the defect $(p,q)$ five-branes on the ALG space. Throughout this analysis, we understand that the HKT represents the coexistent state of two kinds of five-branes. This situation is different from composite states such as $(p,q)$ five-branes or $(p,q)$ seven-branes in type IIB theory. We also study the T-dualized system of the HKT. We again find a new solution which also indicates the defect $(p,q)$ five-branes on another ALG space...

  3. Phase transitions of large N orbifold gauge theories

    Energy Technology Data Exchange (ETDEWEB)

    Hikida, Y.

    2006-10-15

    We study the phase structures of N=4 SU(N) super Yang-Mills theories on R x S{sup 3}/Z{sub k} with large N. The theory has many vacua labelled by the holonomy matrix along the non-trivial cycle on S{sup 3}/Z{sub k}, and for the fermions the periodic and the anti-periodic boundary conditions can be assigned along the cycle. We compute the partition functions of the orbifold theories and observe that phase transitions occur even in the zero 't Hooft coupling limit. With the periodic boundary condition, the vacua of the gauge theory are dual to various arrangements of k NS5-branes. With the anti-periodic boundary condition, transitions between the vacua are dual to localized tachyon condensations. In particular, the mass of a deformed geometry is compared with the Casimir energy for the dual vacuum. We also obtain an index for the supersymmetric orbifold theory. (orig.)

  4. Stability, Tunneling and Flux Changing de Sitter Transitions in the Large Volume String Scenario

    CERN Document Server

    de Alwis, S; Hatefi, E; Quevedo, F

    2013-01-01

    We study the non-perturbative stability of the Large Volume Scenario (LVS) of IIB string compactifications, by analysing transitions mediated by the Brown-Teitelboim (BT) brane nucleations and by Coleman De Luccia tunneling (CDL). We find that, as long as the effective field theory description holds, the LVS AdS minima are stable despite being non-supersymmetric. This opens the possibility of having a CFT dual. Metastable de Sitter vacua behave differently depending on the uplifting mechanism. We find explicit expressions for the different decay rates in terms of exponentials of the volume. Among the transitions of dS to dS those with increasing volume and decreasing vacuum energy are preferred, though dS decays to AdS (big-crunch sinks) have higher probability. Transitions via the CDL mechanism to decompactification are exponentially suppressed compared to these. The BT decays correspond to flux/D3 brane transitions mediated by the nucleation of D5/NS5 branes. We compare our results with previous analysis fo...

  5. An outbreak of imported dengue fever from Myanmar to the border of China, with its viral molecular epidemiological features%云南中缅边境一起输入性登革热暴发的分子流行病学研究

    Institute of Scientific and Technical Information of China (English)

    张海林; 付士红; 邓掌; 袁军; 姜红月; 李铭华; 高晓艳; 王静林; 刘永华

    2013-01-01

    Objective To understand the epidemiologic characteristics of dengue fever,imported from Myanmar to the border of Yunnan province,China.Viral molecular epidemiologic features were also studied.Methods Questionnaires were used on each diagnosed,suspected dengue fever,case or unknown cases with fever when coming from Myanmar entering the port and hospitals in Ruili city of Yunnan province.Serum samples of these patients were collected to detect IgM antibody against dengue virus and RT-PCR assay.Homology and phylogenetic tree based on the whole nucleotide sequence of PrM-C and NS5 gene of dengue virus were further analyzed.Results A total of 103 sera were collected from patients at acute stage in Ruili city in July to November 2008.Among them,49 cases were confirmed for dengue fever according to IgM and nucleic acid testings.Except one,other 48 cases were all imported into Ruili,from Myanmar.Of those,18 patients were residents from Mujie city of Myanmar and hospitalized in Ruili and the rest 30 patients were Chinese citizens who had finished business and returned from Myanmar.Two isolates of serum samples from the imported cases were identified and both homology and phylogenetic analysis were performed,using the nucleotide sequences of PrM and NS5 genes.They were divided into dengue type 1 (RLB61) and dengue type 3 (RLC31) and were closer to the dengue virus strains isolated from Southeast Asia countries.Conclusion It is confirmed that an epidemic of dengue fever which was imported from Myanmar to Ruili city of Yunnan province,China.Evidence also showed that both type Ⅰ and Ⅲ epidemic strains of dengue virus did exist in Mujie city of Myanmar in 2008.%目的 调查云南中缅边境一起输入性登革热流行状况及其流行病毒株的分子流行病学特点.方法 采集医院就诊和口岸入境人员中登革热、疑似登革热和不明原因发热患者血清标本并进行流行病学调查,采用ELISA检测登革病毒IgM抗体,RT-PCR检测登革

  6. HIV AND HCV COINFECTION: PREVALENCE, ASSOCIATED FACTORS AND GENOTYPE CHARACTERIZATION IN THE MIDWEST REGION OF BRAZIL

    Directory of Open Access Journals (Sweden)

    Solange Zacalusni Freitas

    2014-12-01

    Full Text Available A cross-sectional study on prevalence, associated factors and genotype distribution of HCV infection was conducted among 848 HIV-infected patients recruited at reference centers in the Midwest Region of Brazil. The prevalence rate of HIV-HCV coinfection was 6.9% (95% CI: 5.2 to 8.6. In multivariable analysis, increasing age, use of illicit drugs (injection and non-injection, a history of blood transfusion before 1994, and the absence of a steady partnership were significant independent associated factors for HIV-HCV coinfection. The phylogenetic analysis based on the NS5B region revealed the presence of two major circulating genotypes of HCV: genotypes 1 (58.3% and 3 (41.7%. The prevalence of HIV-HCV coinfection was lower than those reported in studies conducted with HIV-infected patients in different regions of Brazil, due to the fact that illicit drug use is not a frequent mode of HIV transmission in this region of Brazil. Serologic screening of HIV-patients for HCV before initiating antiretroviral treatment, a comprehensive identification of associated factors, and the implementation of effective harm reduction programs are highly recommended to provide useful information for treatment and to prevent HCV coinfection in these patients.

  7. Exact Thresholds and Instanton Effects in String Theory

    CERN Document Server

    Obers, N A

    2001-01-01

    In this lecture we summarize some recent work on the understanding of instanton effects in string theories with 16 supersymmetries. In particular, we consider F^4 couplings using the duality between the heterotic string on T^4 and type IIA on K_3 at an orbifold point, as well as higher and lower dimensional versions of this string-string duality. At the perturbative level a non-trivial test of the duality, requiring several miraculous identities, is presented by matching a purely one-loop heterotic amplitude to a purely tree-level type II result. A wide variety of non-perturbative effects is shown to occur in this setting, including D-brane instantons for type IIA on K_3 x S^1 and NS5-brane instantons for type IIA on K_3 x T^2. Moreover, the analysis of the three-dimensional case, which possesses a non-perturbative SO(8,24,Z) U-duality, reveals the presence of Kaluza-Klein 5-brane instanton effects, both on the heterotic and the type II side.

  8. Phylogenetic Analysis and Epidemic History of Hepatitis C Virus Genotype 2 in Tunisia, North Africa.

    Science.gov (United States)

    Rajhi, Mouna; Ghedira, Kais; Chouikha, Anissa; Djebbi, Ahlem; Cheikh, Imed; Ben Yahia, Ahlem; Sadraoui, Amel; Hammami, Walid; Azouz, Msaddek; Ben Mami, Nabil; Triki, Henda

    2016-01-01

    HCV genotype 2 (HCV-2) has a worldwide distribution with prevalence rates that vary from country to country. High genetic diversity and long-term endemicity were suggested in West African countries. A global dispersal of HCV-2 would have occurred during the 20th century, especially in European countries. In Tunisia, genotype 2 was the second prevalent genotype after genotype 1 and most isolates belong to subtypes 2c and 2k. In this study, phylogenetic analyses based on the NS5B genomic sequences of 113 Tunisian HCV isolates from subtypes 2c and 2k were carried out. A Bayesian coalescent-based framework was used to estimate the origin and the spread of these subtypes circulating in Tunisia. Phylogenetic analyses of HCV-2c sequences suggest the absence of country-specific or time-specific variants. In contrast, the phylogenetic grouping of HCV-2k sequences shows the existence of two major genetic clusters that may represent two distinct circulating variants. Coalescent analysis indicated a most recent common ancestor (tMRCA) of Tunisian HCV-2c around 1886 (1869-1902) before the introduction of HCV-2k in 1901 (1867-1931). Our findings suggest that the introduction of HCV-2c in Tunisia is possibly a result of population movements between Tunisia and European population following the French colonization. PMID:27100294

  9. The Future of HCV Therapy: NS4B as an Antiviral Target

    Directory of Open Access Journals (Sweden)

    Hadas Dvory-Sobol

    2010-11-01

    Full Text Available Chronic hepatitis C virus (HCV infection is a major worldwide cause of liver disease, including cirrhosis and hepatocellular carcinoma. It is estimated that more than 170 million individuals are infected with HCV, with three to four million new cases each year. The current standard of care, combination treatment with interferon and ribavirin, eradicates the virus in only about 50% of chronically infected patients. Notably, neither of these drugs directly target HCV. Many new antiviral therapies that specifically target hepatitis C (e.g. NS3 protease or NS5B polymerase inhibitors are therefore in development, with a significant number having advanced into clinical trials. The nonstructural 4B (NS4B protein, is among the least characterized of the HCV structural and nonstructural proteins and has been subjected to few pharmacological studies. NS4B is an integral membrane protein with at least four predicted transmembrane (TM domains. A variety of functions have been postulated for NS4B, such as the ability to induce the membranous web replication platform, RNA binding and NTPase activity. This review summarizes potential targets within the nonstructural protein NS4B, with a focus on novel classes of NS4B inhibitors.

  10. 5-Aminosalicylic acid protection against oxidative damage to synaptosomal membranes by alkoxyl radicals in vitro.

    Science.gov (United States)

    Kanski, J; Lauderback, C; Butterfield, D A

    2001-01-01

    The antioxidant properties of 5-aminosalicylic acid in vitro were evaluated in a synaptosomal membrane system prepared from gerbil cortical synaptosomes using EPR spin labeling and spectroscopic techniques. MAL-6 (2,2,6,6-tetramethyl-4-maleimidopiperidin-1-oxyl) and 5-NS (5-nitroxide stearate) spin labels were used to assess changes in protein oxidation and membrane lipid fluidity, respectively. Synaptosomal membranes were subjected to oxidative stress by incubation with 1 mM azo-bis(isobutyronitrile) (AIBN) or 1 mM 2,2'-azobis(amidino propane) dihydrochloride (AAPH) at 37 degrees C for 30 minutes. The EPR analyses of the samples showed significant oxidation of synaptosomal proteins and a decrease in membrane fluidity. 5-Aminosalicylic acid also was evaluated by means of FRAP (the ferric reducing ability of plasma) test as a potential antioxidant. 5-Aminosalicylic acid also showed protection against the oxidation in gerbil cortical synaptosomes system caused by AIBN and AAPH. These results are consistent with the notion of antioxidant protection against free radical induced oxidative stress in synaptosomal membrane system by this agent.

  11. The many faces of brane-flux annihilation

    CERN Document Server

    Gautason, Fridrik Freyr; Van Riet, Thomas

    2015-01-01

    Fluxes can decay via the nucleation of Brown-Teitelboim bubbles, but when the decaying fluxes induce D-brane charges this process must be accompanied with an annihilation of D-branes. This occurs via dynamics inside the bubble wall as was well described for (anti-)D3 branes branes annihilating against 3-form fluxes. In this paper we extend this to the other Dp branes with p smaller than seven. Generically there are two decay channels: one for the RR flux and one for the NSNS flux. The RR channel is accompanied by brane annihilation that can be understood from the Dp branes polarising into D(p+2) branes, whereas the NSNS channel corresponds to Dp branes polarising into NS5 branes or KK5 branes. We illustrate this with the decay of antibranes probing local toroidal throat geometries obtained from T-duality of the D6 solution in massive type IIA. We show that anti-Dp branes are metastable against annihilation in these backgrounds, at least at the probe level.

  12. In-silico analysis of putative HCV epitopes against Pakistani human leukocyte antigen background: An approach towards development of future vaccines for Pakistani population.

    Science.gov (United States)

    Ashraf, Naeem Mahmood; Bilal, Muhammad; Mahmood, Malik Siddique; Hussain, Aadil; Mehboob, Muhammad Zubair

    2016-09-01

    Mounting burden of HCV-infected individuals and soaring cost of treatment is a serious source of unease for developing countries. Numbers of various approaches have been anticipated to develop a vaccine against HCV but the majority of them proved ineffective. Development of vaccine by considering geographical distribution of HCV genotypes and host genetics shows potential. In this research article, we have tried to predict most putative HCV epitopes which are efficiently restricted by most common HLA alleles in Pakistani population through different computational algorithms. Thirteen selected, experimentally identified epitopes sequences were used to derived consensus sequences in all genotypes of HCV. Obtained consensus sequences were used to predict their binding affinities with most prevalent HLA alleles in Pakistani population. Two Class-I epitopes from NS4B region, one from Class-I epitope from NS5A and one Class-II epitope from NS3 region showed effective binding and proved to be highly putative to boost immune response. A cocktail of these four have been checked for population coverage and they gave 75.53% for Pakistani Asian and 70.77% for Pakistani Mixed populations with no allergenic response. Computational algorithms are robust way to shortlist potential candidate epitopes for vaccine development but further, in vivo and in-vitro studies are required to confirm their immunogenic properties. PMID:27166094

  13. Synthesis of deleobuvir, a potent hepatitis C virus polymerase inhibitor, and its major metabolites labeled with carbon-13 and carbon-14.

    Science.gov (United States)

    Latli, Bachir; Hrapchak, Matt; Chevliakov, Maxim; Li, Guisheng; Campbell, Scot; Busacca, Carl A; Senanayake, Chris H

    2015-05-30

    Deleobuvir, (2E)-3-(2-{1-[2-(5-bromopyrimidin-2-yl)-3-cyclopentyl-1-methyl-1H-indole-6-carboxamido]cyclobutyl}-1-methyl-1H-benzimidazol-6-yl)prop-2-enoic acid (1), is a non-nucleoside, potent, and selective inhibitor of hepatitis C virus NS5B polymerase. Herein, we describe the detailed synthesis of this compound labeled with carbon-13 and carbon-14. The synthesis of its three major metabolites, namely, the reduced double bond metabolite (2) and the acyl glucuronide derivatives of (1) and (2), is also reported. Aniline-(13) C6 was the starting material to prepare butyl (E)-3-(3-methylamino-4-nitrophenyl-(13) C6 )acrylate [(13) C6 ]-(11) in six steps. This intermediate was then used to obtain [(13) C6 ]-(1) and [(13) C6 ]-(2) in five and four more steps, respectively. For the radioactive synthesis, potassium cyanide-(14) C was used to prepare 1-cylobutylaminoacid [(14) C]-(23) via Buchrer-Bergs reaction. The carbonyl chloride of this acid was then used to access both [(14) C]-(1) and [(14) C]-(2) in four steps. The acyl glucuronide derivatives [(13) C6 ]-(3), [(13) C6 ]-(4) and [(14) C]-(3) were synthesized in three steps from the acids [(13) C6 ]-(1), [(13) C6 ]-(2) and [(14) C]-(1) using known procedures. PMID:25964148

  14. Robust hepatitis C genotype 3a cell culture releasing adapted intergenotypic 3a/2a (S52/JFH1) viruses

    DEFF Research Database (Denmark)

    Gottwein, J.M.; Scheel, Troels Kasper Høyer; Hoegh, A.M.;

    2007-01-01

    (immunostaining), HCV RNA titers (real-time PCR), and infectivity titers (50% tissue culture infectious dose). The role of mutations identified by sequencing of recovered S52/JFH1 viruses was analyzed by reverse genetics studies. RESULTS: S52/JFH1 and J6/JFH viruses passaged in Huh7.5 cells showed comparable......BACKGROUND & AIMS: Recently, full viral life cycle hepatitis C virus (HCV) cell culture systems were developed for strain JFH1 (genotype 2a) and an intragenotypic 2a/2a genome (J6/JFH). We aimed at exploiting the unique JFH1 replication characteristics to develop culture systems for genotype 3a......, which has a high prevalence worldwide. METHODS: Huh7.5 cells were transfected with RNA transcripts of an intergenotypic 3a/JFH1 recombinant with core, E1, E2, p7, and NS2 of the 3a reference strain S52, and released viruses were passaged. Cultures were examined for HCV core and/or NS5A expression...

  15. Indian National Association for Study of the Liver (INASL) Guidance for Antiviral Therapy Against HCV Infection: Update 2016.

    Science.gov (United States)

    Puri, Pankaj; Saraswat, Vivek A; Dhiman, Radha K; Anand, Anil C; Acharya, Subrat K; Singh, Shivaram P; Chawla, Yogesh K; Amarapurkar, Deepak N; Kumar, Ajay; Arora, Anil; Dixit, Vinod K; Koshy, Abraham; Sood, Ajit; Duseja, Ajay; Kapoor, Dharmesh; Madan, Kaushal; Srivastava, Anshu; Kumar, Ashish; Wadhawan, Manav; Goel, Amit; Verma, Abhai; Shalimar; Pandey, Gaurav; Malik, Rohan; Agrawal, Swastik

    2016-06-01

    India contributes significantly to the global burden of HCV. While the nucleoside NS5B inhibitor sofosbuvir became available in the Indian market in March 2015, the other directly acting agents (DAAs), Ledipasvir and Daclatasvir, have only recently become available in the India. The introduction of these DAA in India at a relatively affordable price has led to great optimism about prospects of cure for these patients as not only will they provide higher efficacy, but combination DAAs as all-oral regimen will result in lower side effects than were seen with pegylated interferon alfa and ribavirin therapy. Availability of these newer DAAs has necessitated revision of INASL guidelines for the treatment of HCV published in 2015. Current considerations for the treatment of HCV in India include the poorer response of genotype 3, nonavailability of many of the DAAs recommended by other guidelines and the cost of therapy. The availability of combination DAA therapy has simplified therapy of HCV with decreased reliance of evaluation for monitoring viral kinetics or drug related side effects. PMID:27493460

  16. HIV/HCV共感染合并血友病患者利巴韦林联合干扰素治疗前后特异性细胞免疫反应的研究%Study of cellular immune responses following treatment with interferon and ribavirin in patients of HIV/hepatitis C virus co-infection in combination with hemophilia

    Institute of Scientific and Technical Information of China (English)

    吕盈盈; 王江蓉; 廖晶; 谷俊朝

    2011-01-01

    Objective To study the hepatitis C virus(HCV)-specific immune responses following treatment with interferon and ribavirin in subjects with HIV-1/HCV co-infection in combination with hemophilia. Methods Immune responses were studied in a treatment trial with pegylated interferon alfa (PEG-IFN) and ribavirin(R). By using HCV core antigens,NS3 and NS5,enzyme-linked immunosorbent spots on peripheral blood mononuclear cells,products of IFN-y,IL-2,IL-4,IL-10 were measured. Immunologic,virologic and clinical variables were modeled as identifying factors associated with HCV virological response before and after 72 weeks ( SVR) treatment in 36 patients. Results There were no significant differences in baseline IFN-y and IL-2 immune responses and higher IL-10 to NS3 in subjects with VR versus non-respnnders. Subjects who had significant decreases in IL-10 responses at week 72 compared with baseline for NS3,NS5,were more likely to be VR. Using baseline immunological responses and clinical data in CART models, patients who were randomized to PEC1FN/R and had high IL-10 responses to summed HCV proteins were more likely to be VR. In SVR,IL-2 production decreased moderately, 1L-4 secreted little. The main correlation of SVR for genotype-1 subjects maintained HCV-specific IFN-7 responses from baseline to week 72. Conclusions In subjects of HIV and HCV co-infection combined with hemophilia, decrease in HCV-specific IL-10 and IL-2 responses during treatment and maintenance of IFN-y responses with IFN and ribavirin were associated with 24 or 72 week virological response.%目的 研究HIV/HCV共感染合并血友病患者在利巴韦林联合干扰素治疗过程中的细胞免疫反应,了解此类患者在抗HCV治疗过程中HCV的损伤机制和免疫重建过程.方法 收集36例HIV/HCV共感染合并血友病患者,分别在干扰素和利巴韦林治疗前、治疗结束24周后采集外周血单个核细胞( PBMC),Elispot方法检测在HCV核心抗原、NS3和NS5

  17. Large-density field theory, viscosity, and "$2k_F$" singularities from string duals

    CERN Document Server

    Polchinski, Joseph

    2012-01-01

    We analyze systems where an effective large-N expansion arises naturally in gauge theories without a large number of colors: a sufficiently large charge density alone can produce a perturbative string ('tHooft) expansion. One example is simply the well-known NS5/F1 system dual to $AdS_3\\times T^4\\times S^3$, here viewed as a 5+1 dimensional theory at finite density. This model is completely stable, and we find that the existing string-theoretic solution of this model yields two interesting results. First, it indicates that the shear viscosity is not corrected by $\\alpha'$ effects in this system. For flow perpendicular to the F1 strings the viscosity to entropy ratio take the usual value $1/4\\pi$, but for flow parallel to the F1's it vanishes as $T^2$ at low temperature. Secondly, it encodes singularities in correlation functions coming from low-frequency modes at a finite value of the momentum along the $T^4$ directions. This may provide a strong coupling analogue of finite density condensed matter systems fo...

  18. Elliptic Genus of E-strings

    CERN Document Server

    Kim, Joonho; Lee, Kimyeong; Park, Jaemo; Vafa, Cumrun

    2014-01-01

    We study a family of 2d N=(0,4) gauge theories which describes at low energy the dynamics of E-strings, the M2-branes suspended between a pair of M5 and M9 branes. The gauge theory is engineered using a duality with type IIA theory, leading to the D2-branes suspended between an NS5-brane and 8 D8-branes on an O8-plane. We compute the elliptic genus of this family of theories, and find agreement with the known results for single and two E-strings. The partition function can in principle be computed for arbitrary number of E-strings, and we compute them explicitly for low numbers. We test our predictions against the partially known results from topological strings, as well as from the instanton calculus of 5d Sp(1) gauge theory. Given the relation to topological strings, our computation provides the all genus partition function of the refined topological strings on the canonical bundle over 1/2 K3.

  19. Structure of a murine norovirus NS6 protease-product complex revealed by adventitious crystallisation.

    Directory of Open Access Journals (Sweden)

    Eoin N Leen

    Full Text Available Murine noroviruses have emerged as a valuable tool for investigating the molecular basis of infection and pathogenesis of the closely related human noroviruses, which are the major cause of non-bacterial gastroenteritis. The replication of noroviruses relies on the proteolytic processing of a large polyprotein precursor into six non-structural proteins (NS1-2, NS3, NS4, NS5, NS6(pro, NS7(pol by the virally-encoded NS6 protease. We report here the crystal structure of MNV NS6(pro, which has been determined to a resolution of 1.6 Å. Adventitiously, the crystal contacts are mediated in part by the binding of the C-terminus of NS6(pro within the peptide-binding cleft of a neighbouring molecule. This insertion occurs for both molecules in the asymmetric unit of the crystal in a manner that is consistent with physiologically-relevant binding, thereby providing two independent views of a protease-peptide complex. Since the NS6(pro C-terminus is formed in vivo by NS6(pro processing, these crystal contacts replicate the protease-product complex that is formed immediately following cleavage of the peptide bond at the NS6-NS7 junction. The observed mode of binding of the C-terminal product peptide yields new insights into the structural basis of NS6(pro specificity.

  20. CuO nanoparticles: Synthesis, characterization, optical properties and interaction with amino acids

    Energy Technology Data Exchange (ETDEWEB)

    El-Trass, A.; ElShamy, H.; El-Mehasseb, I. [Nanochemistry Laboratory, Chemistry Department, Faculty of Science, Kafrelsheikh, University, 33516 Kafr ElSheikh (Egypt); El-Kemary, M., E-mail: elkemary@yahoo.com [Nanochemistry Laboratory, Chemistry Department, Faculty of Science, Kafrelsheikh, University, 33516 Kafr ElSheikh (Egypt)

    2012-01-15

    Cupric oxide (CuO) nanoparticles with an average size of 6 nm have been successfully prepared by an alcothermal method. The prepared CuO nanoparticles were characterized by X-ray diffraction (XRD), transmission electron microscopy (TEM), Fourier-transform infrared (FT-IR) and UV-visible absorption spectroscopy. A strong sharp emission under UV excitation is reported from the prepared CuO nanoparticles. The results show that the CuO nanoparticles have high dispersion and narrow size distribution. The fluorescence emission spectra display an intense sharp emission at 365 nm and weak broad intensity emission at 470 nm. Picosecond fluorescence measurements of the nanoparticles suggest bi-exponential function giving time constants of {tau}{sub 1} (330 ps, 94.21%) and {tau}{sub 2} (4.69 ns, 5.79%). In neutral and alkaline solutions, Zeta potential values of CuO nanoparticles are negative, due to the adsorption of COO{sup -} group via the coordination of bidentate. At low pH the zeta potential value is positive due to the increased potential of H{sup +} ions in solution. Comparative UV-visible absorption experiments with the model amino acid compounds of positive and negative charges as arginine and aspartic acid, respectively confirmed the negative surface of CuO nanoparticles. The results should be extremely useful for understanding the mode of the interaction with biological systems. This binding process also affects the particle's behavior inside the body.

  1. N=(4,4) Gauged Linear Sigma Models for Defect Five-branes

    CERN Document Server

    Kimura, Tetsuji

    2015-01-01

    We study two-dimensional ${\\cal N}=(4,4)$ gauged linear sigma model (GLSM). Its low energy effective theory is a nonlinear sigma model whose target space gives rise to a configuration of five-branes in string theory. In this article we focus on sigma models for NS5-branes, KK5-branes and an exotic $5^2_2$-brane. In particular, we carefully analyze the GLSM for an exotic $5^2_2$-brane whose background configuration is multi-valued. The exotic $5^2_2$-brane is a concrete example of nongeometric configuration in string theory. We find that the exotic feature originates from the string winding coordinate in a very clear way. In order to complete this analysis, we propose a duality transformation formula which converts an ${\\cal N}=(2,2)$ chiral superfield in F-term to a twisted chiral superfield coupled to an unconstrained complex superfield. This article is a short review based on arXiv:1304.4061 in collaboration with Shin Sasaki.

  2. Hepatitis B and C prevalences among blood donors in the south region of Brazil

    Directory of Open Access Journals (Sweden)

    H. C. F. F. Vasconcelos

    1994-12-01

    Full Text Available The prevalence of hepatitis B and C infection has been determined in a seroepidemiological survey among blood donors from the south of Brazil (Florianópolis, State of Santa Catarina. These markers has also been correlated with the levels of alanine aminotransferase (ALT, a surrogate marker to prevent post-transfusion hepatitis. Sera from 5000 donors were randomly collected in the period of April to November 1991. The prevalences of HBsAg, anti-HBs and anti-HBc were respectively 0.78, 7.02 and 13.98. The anti-HCV prevalence after confirmation testing with line immunoassay (LIA, was 1.14. Normal values of ALT ( = 70 U/ml in 2.48. The positivity of anti-HCV antibodies increased with the elevation of ALT levels. This correlation was not observed in relation to HBsAg. There exists a diversity in the recognition of HCV epitopes among HCV positive donors. Via the confirmation test used, we could observe that 94.7 of donors recognize the structural core antigen. Besides that, we observed that 5.26 of the HCV reactive sera recognized only epitopes located in the NS4 and/or NS5 region, indicating the importance of these epitopes for the improvement of assays.

  3. Detection of novel insect flavivirus sequences integrated in Aedes albopictus (Diptera: Culicidae in Northern Italy

    Directory of Open Access Journals (Sweden)

    Tenorio Antonio

    2009-07-01

    Full Text Available Abstract The presence of DNA sequences integrated from a new flavivirus related to Cell Fusing Agent and Kamiti River Virus was identified in wild Aedes albopictus mosquito populations from the provinces of Trentino and Padova, Northern Italy. Field work was developed during August–October 2007 with BG-traps, and mosquitoes were screened for flavivirus and alphavirus. No alphavirus was detected, indicating that Chikungunya virus is not present in these mosquitoes in Trentino and Padova area. However, 21% of the pools were positive for flavivirus, further recognised with BLAST as similar to Kamiti River Virus. Phylogenetical analysis with 708 nucleotides from the NS5 gene identified this virus as a new member of the insect flavivirus clade, together with others like Kamiti River Virus, Cell Fusing Agent or Culex flavivirus, and in the group of those transmitted by Aedes. Furthermore, the treatment with RNAse, indicated that this flavivirus should be integrated in the genome of Ae. albopictus. These results propose that these sequences are transmitted by both sexes, and with different prevalence in the studied populations, and support the idea of a widespread distribution of integrated genomes in several mosquitoes from different areas, as first demonstrated with Cell Silent Agent. Evolutionary implications of this discovery and application in flavivirus phylogeny are discussed.

  4. Genetic Variability of Bovine Viral Diarrhea Virus and Evidence for a Possible Genetic Bottleneck during Vertical Transmission in Persistently Infected Cattle.

    Science.gov (United States)

    Dow, Natalie; Chernick, Adam; Orsel, Karin; van Marle, Guido; van der Meer, Frank

    2015-01-01

    Bovine viral diarrhea virus (BVDV), a Pestivirus in the family Flaviviridae, is an economically important pathogen of cattle worldwide. The primary propagators of the virus are immunotolerant persistently infected (PI) cattle, which shed large quantities of virus throughout life. Despite the absence of an acquired immunity against BVDV in these PI cattle there are strong indications of viral variability that are of clinical and epidemiological importance. In this study the variability of E2 and NS5B sequences in multiple body compartments of PI cattle were characterized using clonal sequencing. Phylogenetic analyses revealed that BVDV exists as a quasispecies within PI cattle. Viral variants were clustered by tissue compartment significantly more often than expected by chance alone with the central nervous system appearing to be a particularly important viral reservoir. We also found strong indications for a genetic bottleneck during vertical transmission from PI animals to their offspring. These quasispecies analyses within PI cattle exemplify the role of the PI host in viral propagation and highlight the complex dynamics of BVDV pathogenesis, transmission and evolution.

  5. PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics

    Directory of Open Access Journals (Sweden)

    Rychlewski Leszek

    2006-02-01

    Full Text Available Abstract Background The number of protein structures from structural genomics centers dramatically increases in the Protein Data Bank (PDB. Many of these structures are functionally unannotated because they have no sequence similarity to proteins of known function. However, it is possible to successfully infer function using only structural similarity. Results Here we present the PDB-UF database, a web-accessible collection of predictions of enzymatic properties using structure-function relationship. The assignments were conducted for three-dimensional protein structures of unknown function that come from structural genomics initiatives. We show that 4 hypothetical proteins (with PDB accession codes: 1VH0, 1NS5, 1O6D, and 1TO0, for which standard BLAST tools such as PSI-BLAST or RPS-BLAST failed to assign any function, are probably methyltransferase enzymes. Conclusion We suggest that the structure-based prediction of an EC number should be conducted having the different similarity score cutoff for different protein folds. Moreover, performing the annotation using two different algorithms can reduce the rate of false positive assignments. We believe, that the presented web-based repository will help to decrease the number of protein structures that have functions marked as "unknown" in the PDB file. Availability http://paradox.harvard.edu/PDB-UF and http://bioinfo.pl/PDB-UF

  6. Fate of ZN domain wall in hot holographic QCD

    International Nuclear Information System (INIS)

    We first study ZN-domain walls in a deconfined phase of Witten's D4-brane background of pure SU(N) Yang-Mills theory, motivated by a recent work in the case of N = 4 SYM. Similarly to it, we propose that for a large domain wall charge k ∼ N, it is described by k D2-branes blown up into a NS5-brane wrapping S3 inside S4 via Myers effect, and we calculate the tension by suitable U-duality. We find a precise Casimir scaling for the tension formula. We then study the fate of ZN-vacua in a presence of fundamental flavors in quenched approximation via gauge/gravity correspondence. In the case of D3/D7 system where one can vary the mass mq of flavors, we show that there is a phase transition at Tc ∼ mq, below which the ZN-vacua survive while they are lifted above the critical temperature. We analytically calculate the energy lift of k'th vacua in the massless case, both in the D3/D7 system and in the Sakai-Sugimoto model. (author)

  7. DNA Typing of Sporothrix schenckii by Analysis of Ribosomal-DNA Regions%利用核糖体基因进行申克孢子丝菌基因分型

    Institute of Scientific and Technical Information of China (English)

    张振颖; 刘晓明; 高晓蓉; 杨国玲; 金礼吉; 安利佳

    2005-01-01

    目的利用探针与DNA印迹法对申克孢子丝菌进行种内分型,探讨其基因型特征与菌种来源及临床表现的关系.方法CTAB法提取来源于不同地区31株孢子丝菌临床分离株及1株标准株的基因组DNA,以真菌通用引物ITS4、NS5扩增标准株的rDNA序列作为探针,与经限制性内切酶Apal酶切后的基因组DNA进行印迹杂交.结果杂交后形成多种清晰而稳定的带型,根据带型将31株孢子丝菌分为15种基因型(A-O型),其中A、B、C三型占51.61%.结论探针与DNA印迹法是孢子丝菌种内分型较为敏感而可靠的方法,该方法所分基因型的不同与菌种的地区来源及临床表现有一定的相关性.

  8. Z p charged branes in flux compactifications

    Science.gov (United States)

    Berasaluce-González, M.; Cámara, P. G.; Marchesano, F.; Uranga, A. M.

    2013-04-01

    We consider 4d string compactifications in the presence of fluxes, and classify particles, strings and domain walls arising from wrapped branes which have charges conserved modulo an integer p, and whose annihilation is catalized by fluxes, through the Freed-Witten anomaly or its dual versions. The Z p -valued strings and particles are associated to Z p discrete gauge symmetries, which we show are realized as discrete subgroups of 4d U(1) symmetries broken by their Chern-Simons couplings to the background fluxes. We also describe examples where the discrete gauge symmetry group is actually non-Abelian. The Z p -valued domain walls separate vacua which have different flux quanta, yet are actually equivalent by an integer shift of axion fields (or further string duality symmetries). We argue that certain examples are related by T-duality to the realization of discrete gauge symmetries and Z p charges from torsion (co)homology. At a formal level, the groups classifying these discrete charges should correspond to a generalization of K-theory in the presence of general fluxes (and including fundamental strings and NS5-branes).

  9. Sequence- and interactome-based prediction of viral protein hotspots targeting host proteins: a case study for HIV Nef.

    Directory of Open Access Journals (Sweden)

    Mahdi Sarmady

    Full Text Available Virus proteins alter protein pathways of the host toward the synthesis of viral particles by breaking and making edges via binding to host proteins. In this study, we developed a computational approach to predict viral sequence hotspots for binding to host proteins based on sequences of viral and host proteins and literature-curated virus-host protein interactome data. We use a motif discovery algorithm repeatedly on collections of sequences of viral proteins and immediate binding partners of their host targets and choose only those motifs that are conserved on viral sequences and highly statistically enriched among binding partners of virus protein targeted host proteins. Our results match experimental data on binding sites of Nef to host proteins such as MAPK1, VAV1, LCK, HCK, HLA-A, CD4, FYN, and GNB2L1 with high statistical significance but is a poor predictor of Nef binding sites on highly flexible, hoop-like regions. Predicted hotspots recapture CD8 cell epitopes of HIV Nef highlighting their importance in modulating virus-host interactions. Host proteins potentially targeted or outcompeted by Nef appear crowding the T cell receptor, natural killer cell mediated cytotoxicity, and neurotrophin signaling pathways. Scanning of HIV Nef motifs on multiple alignments of hepatitis C protein NS5A produces results consistent with literature, indicating the potential value of the hotspot discovery in advancing our understanding of virus-host crosstalk.

  10. Genotypes and viral load of hepatitis C virus among persons attending a voluntary counseling and testing center in Ethiopia.

    Science.gov (United States)

    Abreha, Tesfay; Woldeamanuel, Yimtubezinash; Pietsch, Corinna; Maier, Melanie; Asrat, Daniel; Abebe, Almaz; Hailegiorgis, Bereket; Aseffa, Abraham; Liebert, Uwe Gerd

    2011-05-01

    The prevalence of different genotypes of hepatitis C virus (HCV) in Ethiopia is not known. HCV genotypes influence the response to therapy with alpha-interferon alone or in combination with ribavirin. A cross sectional study was conducted on attendees of voluntary counseling and testing center. Serum samples from 1,954 (734 HIV positive and 1,220 HIV negative) individuals were screened for HCV antibody. Active HCV infection was confirmed by quantitative PCR in 18 of the 71 samples with anti-HCV antibodies. The HCV viral load ranged from 39,650 to 9,878,341 IU/ml (median 1,589,631 IU/ml) with no significant difference [χ(2)(17) = 18.00, P = 0.389] between persons positive or negative for HIV. The viral load of HCV was, however, higher in older study subjects (r = 0.80, P = 0.000). HCV genotypes were determined using the VERSANT HCV Genotype Assay (LiPA) and sequence analysis of the NS5b region of the HCV genome. Diverse HCV genotypes were found including genotypes 1, 2, 4, and 5. There was no difference in the distribution regarding the HIV status. As in other parts of the world, genotyping of HCV must be considered whenever HCV is incriminated as a cause of hepatitis. PMID:21351106

  11. Massive S-matrix of AdS{sub 3}×S{sup 3}×T{sup 4} superstring theory with mixed 3-form flux

    Energy Technology Data Exchange (ETDEWEB)

    Hoare, B., E-mail: ben.hoare@physik.hu-berlin.de [Institut für Physik, Humboldt-Universität zu Berlin, Newtonstraße 15, D-12489 Berlin (Germany); Tseytlin, A.A., E-mail: tseytlin@imperial.ac.uk [The Blackett Laboratory, Imperial College, London SW7 2AZ (United Kingdom)

    2013-08-11

    The type IIB supergravity AdS{sub 3}×S{sup 3}×T{sup 4} background with mixed RR and NSNS 3-form fluxes is a near-horizon limit of a non-threshold bound state of D5–D1 and NS5–NS1 branes. The corresponding superstring world-sheet theory is expected to be integrable, opening the possibility of computing its exact spectrum for any values of the coefficient q of the NSNS flux and the string tension. In (arXiv:1303.1447) we have found the tree-level S-matrix for the massive BMN excitations in this theory, which turned out to have a simple dependence on q. Here, by analyzing the constraints of symmetry and integrability, we propose an exact massive-sector dispersion relation and the exact S-matrix for this world-sheet theory. The S-matrix generalizes its recent construction in the q=0 case in (arXiv:1303.5995)

  12. Massive S-matrix of AdS3×S3×T4 superstring theory with mixed 3-form flux

    Science.gov (United States)

    Hoare, B.; Tseytlin, A. A.

    2013-08-01

    The type IIB supergravity AdS3×S3×T4 background with mixed RR and NSNS 3-form fluxes is a near-horizon limit of a non-threshold bound state of D5-D1 and NS5-NS1 branes. The corresponding superstring world-sheet theory is expected to be integrable, opening the possibility of computing its exact spectrum for any values of the coefficient q of the NSNS flux and the string tension. In arXiv:1303.1447 we have found the tree-level S-matrix for the massive BMN excitations in this theory, which turned out to have a simple dependence on q. Here, by analyzing the constraints of symmetry and integrability, we propose an exact massive-sector dispersion relation and the exact S-matrix for this world-sheet theory. The S-matrix generalizes its recent construction in the q=0 case in arXiv:1303.5995. This is a consequence of the fact that parity symmetry is broken with the introduction of the NSNS flux. However, charge conjugation composed with parity is still a symmetry.

  13. Oscillating supertubes and neutral rotating black hole microstates

    Science.gov (United States)

    Mathur, Samir D.; Turton, David

    2014-04-01

    The construction of neutral black hole microstates is an important problem, with implications for the information paradox. In this paper we conjecture a construction of non-supersymmetric supergravity solutions describing D-brane configurations which carry mass and angular momentum, but no other conserved charges. We first study a classical string solution which locally carries dipole winding and momentum charges in two compact directions, but globally carries no net winding or momentum charge. We investigate its backreaction in the D1-D5 duality frame, where this object becomes a supertube which locally carries oscillating dipole D1-D5 and NS1-NS5 charges, and again carries no net charge. In the limit of an infinite straight supertube, we find an exact supergravity solution describing this object. We conjecture that a similar construction may be carried out based on a class of two-charge non-supersymmetric D1-D5 solutions. These results are a step towards demonstrating how neutral black hole microstates may be constructed in string theory.

  14. Massive S-matrix of AdS_3 x S^3 x T^4 superstring theory with mixed 3-form flux

    CERN Document Server

    Hoare, B

    2013-01-01

    The type IIB supergravity AdS_3 x S^3 x T^4 background with mixed RR and NSNS 3-form fluxes is a near-horizon limit of a non-threshold bound state of D5-D1 and NS5-NS1 branes. The corresponding superstring world-sheet theory is expected to be integrable, opening the possibility of computing its exact spectrum for any values of the coefficient q of the NSNS flux and the string tension. In arXiv:1303.1447 we have found the tree-level S-matrix for the massive BMN excitations in this theory, which turned out to have a simple dependence on q. Here, by analyzing the constraints of symmetry and integrability, we propose an exact massive-sector dispersion relation and the exact S-matrix for this world-sheet theory. The S-matrix generalizes its recent construction in the q=0 case in arXiv:1303.5995.

  15. Effect of Retinoic Acid on Lung Injury in Hyperoxia-Exposed Newborn Rats

    Institute of Scientific and Technical Information of China (English)

    常立文; 容志惠; 张谦慎; 钱莉玲

    2003-01-01

    To investigate whether treatment with retinoic acid (RA) could improve level of lung alveolarization and influence lung collagen in newborn rats exposed to hyperoxia, newborn SpragueDawley rats aged 2 days were randomly assigned to 8 groups: (1) air, (2) O2, (3) air+NS, (4)O2 +NS, (5) air+dex, (6) O2+dex, (7) air+RA and (8) O2+RA. Group 2, 4 6 and 8 were kept in chambers containing 85 % oxygen, the values were checked 3 times a day. The other 4 groups were exposed to room air. Level of alveolarization and lung collagen were analyzed at age of 14 or 21 days through radial alveolar counts, alveolar airspace measurements, type Ⅰ , Ⅲ collagen immunohistochemical methods (SP method) and image processing system. Transforming growth factor-β receptors and procollagen mRNA accumulation were examined at age of 14 days through immunohistochemical methods and in situ hybridization. Our results showed that radial alveolar counts were increased and distal airspace was enlarged in group 8. Type I collagen was markedly increased, and transforming growth factor-β receptors and procollagen mRNA were decreased by retinoic acid in bronchial epithelial cells, alveolar epithelial cells and alveolar intersitium. It is concluded that retinoic acid can partially reverse lung development arrest during exposure to hyperoxia by increasing lung collagen.

  16. Phylogenetic analysis revealed the central roles of two African countries in the evolution and worldwide spread of Zika virus.

    Science.gov (United States)

    Shen, Shu; Shi, Junming; Wang, Jun; Tang, Shuang; Wang, Hualin; Hu, Zhihong; Deng, Fei

    2016-04-01

    Recent outbreaks of Zika virus (ZIKV) infections in Oceania's islands and the Americas were characterized by high numbers of cases and the spread of the virus to new areas. To better understand the origin of ZIKV, its epidemic history was reviewed. Although the available records and information are limited, two major genetic lineages of ZIKV were identified in previous studies. However, in this study, three lineages were identified based on a phylogenetic analysis of all virus sequences from GenBank, including those of the envelope protein (E) and non-structural protein 5 (NS5) coding regions. The spatial and temporal distributions of the three identified ZIKV lineages and the recombination events and mechanisms underlying their divergence and evolution were further elaborated. The potential migration pathway of ZIKV was also characterized. Our findings revealed the central roles of two African countries, Senegal and Cote d'Ivoire, in ZIKV evolution and genotypic divergence. Furthermore, our results suggested that the outbreaks in Asia and the Pacific islands originated from Africa. The results provide insights into the geographic origins of ZIKV outbreaks and the spread of the virus, and also contribute to a better understanding of ZIKV evolution, which is important for the prevention and control of ZIKV infections.

  17. Antibody recognition of the dengue virus proteome and implications for development of vaccines.

    Science.gov (United States)

    Fernandez, Stefan; Cisney, Emily D; Tikhonov, Alexander P; Schweitzer, Barry; Putnak, Robert J; Simmons, Monika; Ulrich, Robert G

    2011-04-01

    Dengue is a mosquito-borne infection caused by four distinct serotypes of dengue virus, each appearing cyclically in the tropics and subtropics along the equator. Although vaccines are currently under development, none are available to the general population. One of the main impediments to the successful advancement of these vaccines is the lack of well-defined immune correlates of protection. Here, we describe a protein microarray approach for measuring antibody responses to the complete viral proteome comprised of the structural (capsid, membrane, and envelope) and nonstructural (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5) components of all four dengue virus serotypes (1 to 4). We examined rhesus macaques vaccinated with tetravalent vaccines consisting of live-attenuated virus (LAV) or purified inactivated virus (PIV), followed by boosting with LAV and challenging with wild-type dengue virus. We detected temporal increases in antibodies against envelope proteins in response to either vaccine, while only the PIV/LAV vaccination strategy resulted in anticapsid antibodies. In contrast to results from vaccination, naïve macaques challenged with wild-type viruses of each serotype demonstrated a balanced response to nonstructural and structural components, including responses against the membrane protein. Our results demonstrate discriminating details concerning the nature of antibody responses to dengue virus at the proteomic level and suggest the usefulness of this information for vaccine development. PMID:21270280

  18. Hyperbolic Spaces in String and M-Theory

    International Nuclear Information System (INIS)

    We describe string-theory and d=11 supergravity solutions involving symmetric spaces of constant negative curvature. Many examples of non-supersymmetric string compactifications on hyperbolic spaces Hr of finite volume are given in terms of suitable cosets of the form Hr and Γ, where Γ is a discrete group. We describe in some detail the cases of the non-compact hyperbolic spaces F2 and F3, representing the fundamental regions of H2 and H3 under SL(2,Z) and the Picard group, respectively. By writing AdS as a U(1) fibration, we obtain new solutions where AdS2p+1 gets untwisted by T-duality to /bf RxSU(p,1)/(SU(p)xU(1)). Solutions with time-dependent dilaton field are also constructed by starting with a solution with NS5-brane flux over H3. A new class of non-supersymmetric conformal field theories can be defined via holography. (author)

  19. Closed And Open String Theories In Non-critical Backgrounds

    CERN Document Server

    Murthy, S

    2004-01-01

    This thesis is a study of closed and open string theories in low dimensional spacetimes, and the various relations between these theories. In particular, we focus on the theory of the two-dimensional black hole. We first study closed strings in the background of the Euclidean two-dimensional black hole (SL2( R )/U(1)) tensored with flat space, using the duality relating these theories to non-critical superstrings described by the supersymmetric sine-Liouville interaction on the worldsheet. We point out a subtlety in their geometric interpretation, and clarify the symmetry structure of the theories based on the understanding of these theories as near horizon limits of wrapped NS5-branes. In one such example (cigar × R6 ), we use the brave description to understand the enhancement of the global symmetry in the coset theory from U(1) to SO(3) under which the sine-Liouville and cigar interactions are related. In the same example, a worldsheet description of the moduli space R4/Z2 is presented. W...

  20. Drug: D10105 [KEGG MEDICUS

    Lifescience Database Archive (English)

    Full Text Available D10105 Drug Daclatasvir hydrochloride (JAN); Daclatasvir dihydrochloride (USAN) C40H50N8O6. 2HCl 810....3387 811.7969 D10105.gif Treatment of hepatitis C [DS:H00413] HCV NS5A inhibitor [CPD:C182...92] ko05160 Hepatitis C CAS: 1009119-65-6 PubChem: 135626823 LigandBox: D10105 ATOM 56 1 C8x C 21.4200 -21.4...900 2 C8y C 21.4200 -22.8900 3 C8x C 22.6100 -23.5900 4 C8x C 23.8700 -22.8900 5 ...C8y C 23.8700 -21.4900 6 C8x C 22.6100 -20.7900 7 C8y C 25.0600 -20.7900 8 C8x C 26.3200 -21.4900 9 C8x C 27.5800 -20.7900 10

  1. Rapid emergence of hepatitis C virus protease inhibitor resistance is expected

    Energy Technology Data Exchange (ETDEWEB)

    Rong, Libin [Los Alamos National Laboratory; Perelson, Alan S [Los Alamos National Laboratory; Ribeiro, Ruy M [Los Alamos National Laboratory

    2009-01-01

    Approximately 170 million people worldwide are infected with hepatitis C virus (HCV). Current therapy, consisting of pegylated interferon (PEG-IFN) and ribavirin (RBV), leads to sustained viral elimination in only about 45% of patients treated. Telaprevir (VX-950), a novel HCV NS3-4A serine protease inhibitor, has demonstrated substantial antiviral activity in patients with chronic hepatitis C genotype 1 infection. However, some patients experience viral breakthrough during dosing, with drug resistant variants being 5%-20% of the virus population as early as day 2 after treatment initiation. Why viral variants appear such a short time after the start of dosing is unclear, especially since this has not been seen with monotherapy for either human immunodeficiency virus or hepatitis B virus. Here, using a viral dynamic model, we explain why such rapid emergence of drug resistant variants is expected when potent HCV protease inhibitors are used as monotherapy. Surprisingly, our model also shows that such rapid emergence need not be the case with some potent HCV NS5B polymerase inhibitors. Examining the case of telaprevir therapy in detail, we show the model fits observed dynamics of both wild-type and drug-resistant variants during treatment, and supports combination therapy of direct antiviral drugs with PEG-IFN and/or RBV for hepatitis C.

  2. Oscillating supertubes and neutral rotating black hole microstates

    International Nuclear Information System (INIS)

    The construction of neutral black hole microstates is an important problem, with implications for the information paradox. In this paper we conjecture a construction of non-supersymmetric supergravity solutions describing D-brane configurations which carry mass and angular momentum, but no other conserved charges. We first study a classical string solution which locally carries dipole winding and momentum charges in two compact directions, but globally carries no net winding or momentum charge. We investigate its backreaction in the D1-D5 duality frame, where this object becomes a supertube which locally carries oscillating dipole D1-D5 and NS1-NS5 charges, and again carries no net charge. In the limit of an infinite straight supertube, we find an exact supergravity solution describing this object. We conjecture that a similar construction may be carried out based on a class of two-charge non-supersymmetric D1-D5 solutions. These results are a step towards demonstrating how neutral black hole microstates may be constructed in string theory

  3. New insights into the structure of the reaction centre from Blastochloris viridis: evolution in the laboratory.

    Science.gov (United States)

    Roszak, Aleksander W; Moulisová, Vladimíra; Reksodipuro, Adhie D P; Gardiner, Alastair T; Fujii, Ritsuko; Hashimoto, Hideki; Isaacs, Neil W; Cogdell, Richard J

    2012-02-15

    Newly determined crystal structures of the photosynthetic RC (reaction centre) from two substrains of the non-sulfur purple bacterium Blastochloris viridis strain DSM 133, together with analysis of their gene sequences, has revealed intraspecies evolutionary changes over a period of 14 years. Over 100 point mutations were identified between these two substrains in the four genes encoding the protein subunits of the RC, of which approximately one-fifth resulted in a total of 16 amino acid changes. The most interesting difference was in the M subunit where the change from a leucine residue to glycine in the carotenoid-binding pocket allowed NS5 (1,2-dihydroneurosporene) to adopt a more sterically favoured conformation, similar to the carotenoid conformation found in other related RCs. The results of the present study, together with a high rate of mutations in laboratory bacterial cultures described recently, suggest that bacteria evolve faster than has been generally recognized. The possibility that amino acid changes occur within protein sequences, without exhibiting any immediately observable phenotype, should be taken into account in studies that involve long-term continuous growth of pure bacterial cultures. The Blc. viridis RC is often studied with sophisticated biophysical techniques and changes such as those described here may well affect their outcome. In other words, there is a danger that laboratory-to-laboratory variation could well be due to different groups not realising that they are actually working with slightly different proteins. A way around this problem is suggested.

  4. Recent Immersed Bz X-ray Diode Experiments

    Science.gov (United States)

    Cooper, G. M.; McLean, J.; Davitt, R.; Goldsack, T. J.

    2002-12-01

    The immersed Bz diode is being fielded on one of the AWE Superswarf machines which provides a 55ns, 5.5MV, 35kA electron beam. The external magnetic field, up to 25Tesla, is produced by a solenoid which is driven by a 624μF, 22kV capacitor bank. The magnetic field constrains the electron beam to a small diameter at the target which results in a small x-ray source size. Recent experiments to try and reduce the source size include investigation of shaped field solenoids and the effects of reducing the cathode diameter. The inclusion of a time resolved source size diagnostic has provided more information on the behaviour of the diode. One of the better Bz shots has produced 72R@1m with a 4.0mm spot. This compares to a standard paraxial diode 80R@1m with a 5.3mm spot and the enhanced vacuum cell paraxial diode 65R@1m with a 4.0mm spot. Future investigations aimed at reducing the spot size will include providing a better vacuum in the diode and a possible reduction in the pre-pulse on the diode.

  5. Hydrogen/Deuterium Exchange Kinetics Demonstrate Long Range Allosteric Effects of Thumb Site 2 Inhibitors of Hepatitis C Viral RNA-dependent RNA Polymerase.

    Science.gov (United States)

    Deredge, Daniel; Li, Jiawen; Johnson, Kenneth A; Wintrode, Patrick L

    2016-05-01

    New nonnucleoside analogs are being developed as part of a multi-drug regimen to treat hepatitis C viral infections. Particularly promising are inhibitors that bind to the surface of the thumb domain of the viral RNA-dependent RNA polymerase (NS5B). Numerous crystal structures have been solved showing small molecule non-nucleoside inhibitors bound to the hepatitis C viral polymerase, but these structures alone do not define the mechanism of inhibition. Our prior kinetic analysis showed that nonnucleoside inhibitors binding to thumb site-2 (NNI2) do not block initiation or elongation of RNA synthesis; rather, they block the transition from the initiation to elongation, which is thought to proceed with significant structural rearrangement of the enzyme-RNA complex. Here we have mapped the effect of three NNI2 inhibitors on the conformational dynamics of the enzyme using hydrogen/deuterium exchange kinetics. All three inhibitors rigidify an extensive allosteric network extending >40 Å from the binding site, thus providing a structural rationale for the observed disruption of the transition from distributive initiation to processive elongation. The two more potent inhibitors also suppress slow cooperative unfolding in the fingers extension-thumb interface and primer grip, which may contribute their stronger inhibition. These results establish that NNI2 inhibitors act through long range allosteric effects, reveal important conformational changes underlying normal polymerase function, and point the way to the design of more effective allosteric inhibitors that exploit this new information. PMID:27006396

  6. Molecular characterization of HCV in a Swedish county over 8 years (2002–2009 reveals distinct transmission patterns

    Directory of Open Access Journals (Sweden)

    Josefine Ederth

    2016-02-01

    Full Text Available Background: Hepatitis C virus (HCV is a major public health concern and data on its molecular epidemiology in Sweden is scarce. We carried out an 8-year population-based study of newly diagnosed HCV cases in one of Sweden's centrally situated counties, Södermanland (D-county. The aim was to characterize the HCV strains circulating, analyze their genetic relatedness to detect networks, and in combination with demographic data learn more about transmission. Methods: Molecular analyses of serum samples from 91% (N=557 of all newly notified cases in D-county, 2002–2009, were performed. Phylogenetic analysis (NS5B gene, 300 bp was linked to demographic data from the national surveillance database, SmiNet, to characterize D-county transmission clusters. The linear-by-linear association test (LBL was used to analyze trends over time. Results: The most prevalent subtypes were 1a (38% and 3a (34%. Subtype 1a was most prevalent among cases transmitted via sexual contact, via contaminated blood, or blood products, while subtype 3a was most prevalent among people who inject drugs (PWIDs. Phylogenetic analysis revealed that the subtype 3a sequences formed more and larger transmission clusters (50% of the sequences clustered, while the 1a sequences formed smaller clusters (19% of the sequences clustered, possibly suggesting different epidemics. Conclusion: We found different transmission patterns in D-county which may, from a public health perspective, have implications for how to control virus infections by targeted interventions.

  7. Inflation from Supergravity with Gauged R-symmetry in de Sitter Vacuum

    CERN Document Server

    Antoniadis, I; Isono, H; Knoops, R

    2016-01-01

    We study the cosmology of a recent model of supersymmetry breaking, in the presence of a tuneable positive cosmological constant, based on a gauged shift symmetry of a string modulus that can be identified with the string dilaton. The minimal spectrum of the `hidden' supersymmetry breaking sector consists then of a vector multiplet that gauges the shift symmetry of the dilaton multiplet and when coupled to the MSSM leads to a distinct low energy phenomenology depending on one parameter. Here we study the question if this model can also lead to inflation by identifying the dilaton with the inflaton. We find that this is possible if the K\\"ahler potential is modified by a term that has the form of NS5-brane instantons, leading to an appropriate inflationary plateau around the maximum of the scalar potential, depending on two extra parameters. This model is consistent with present cosmological observations without modifying the low energy particle phenomenology associated to the minimum of the scalar potential.

  8. Short communication. Further evidence of lineage 2 West Nile Virus in Culex pipiens of North-Eastern Italy

    Directory of Open Access Journals (Sweden)

    Gioia Capelli

    2013-09-01

    Full Text Available West Nile Virus lineage 1 (WNV lin1 emerged in North-Eastern Italy in 2008 and, since then, it has been detected in animals, humans and mosquitoes. Three years later, in the same area, a lineage 2 (lin2 strain of WNV was found in birds and vectors. On August the 21st, during the 2012 WNV entomological surveillance plan, a WNV lin2 strain was detected by RT-PCR in a pool of Culex pipiens mosquitoes captured in Veneto region. According to the alignment of the partial sequences of the NS5 and NS3 genes, no differences between this Italian lineage 2 strain and the Nea Santa-Greece-2010 WNV isolate (Gr-10 were observed. Similarly to the Gr-10 strain, the putative NS3 aminoacid sequences of the Italian strain showed proline in position 249 instead of histidine (H249P. Although proline in position 249 has been suggested to increase the virulence of WNV strains, neither human nor veterinary cases associated to this strain have been reported in the region. A prompt mosquito disinfestation was organized to avoid the spread of this potential threatening virus. The simultaneous circulation of both WNV lineage 1 and 2 confirms North-Eastern Italy as a high risk area for WNV emergence and highlights the need for a continuous surveillance.

  9. Interferon-Free Hepatitis C Treatment before and after Liver Transplantation: The Role of HCV Drug Resistance

    Directory of Open Access Journals (Sweden)

    Bruno Roche

    2015-09-01

    Full Text Available Hepatitis C virus (HCV infection is one of the leading causes of end-stage liver disease and the main indication for liver transplantation (LT in most countries. All patients who undergo LT with detectable serum HCV RNA experience graft reinfection progressing to cirrhosis within five years in 20% to 30% of them. Obtaining a sustained virological response (SVR greatly improves overall and graft survival. Until 2011, standard antiviral therapy using PEGylated interferon (PEG-IFN and ribavirin (RBV was the only effective therapy, with an SVR rate around 30% in this setting. For patients infected with genotype 1, first generation NS3/4A protease inhibitors (PIs, boceprevir (BOC or telaprevir (TVR, associated with PEG-IFN and RBV for 48 weeks have increased the SVR rates to 60% in non-transplant patients. However, tolerability and drug-drug interactions with calcineurin inhibitors (CNI are both limiting factors of their use in the liver transplant setting. Over recent years, the efficacy of antiviral C therapy has improved dramatically using new direct-acting antiviral (DAA agents without PEG-IFN and/or RBV, leading to SVR rates over 90% in non-transplant patients. Results available for transplant patients showed a better efficacy and tolerability and less drug-drug interactions than with first wave PIs. However, some infrequent cases of viral resistance have been reported using PIs or NS5A inhibitors pre- or post-LT that can lead to difficulties in the management of these patients.

  10. Holographic compactifications of (1,0) theories from massive IIA supergravity

    CERN Document Server

    Apruzzi, Fabio; Passias, Achilleas; Rota, Andrea; Tomasiello, Alessandro

    2015-01-01

    We describe three analytic classes of infinitely many AdS_d BPS solutions of massive IIA supergravity, for d = 7, 5, 4. The three classes are related by simple universal maps. For example, the AdS_7 x M_3 solutions (where M_3 is topologically S^3) are mapped to AdS_5 x Sigma_2 x M'_3, where Sigma_2 is a Riemann surface of genus g >= 2 and the metric on M'_3 is obtained by distorting M_3 in a certain way. The solutions can have localized D6 or O6 sources, as well as an arbitrary number of D8-branes. The AdS_7 case (previously known only numerically) is conjecturally dual to an NS5-D6-D8 system. The field theories in three and four dimensions are not known, but their number of degrees of freedom can be computed at leading order. The AdS_4 solutions have numerical "attractor" generalizations that might be useful for flux compactification purposes.

  11. Six-Dimensional Superconformal Theories and their Compactifications from Type IIA Supergravity

    Science.gov (United States)

    Apruzzi, Fabio; Fazzi, Marco; Passias, Achilleas; Rota, Andrea; Tomasiello, Alessandro

    2015-08-01

    We describe three analytic classes of infinitely many AdSd supersymmetric solutions of massive IIA supergravity, for d =7 ,5 ,4 . The three classes are related by simple universal maps. For example, the AdS7×M3 solutions (where M3 is topologically S3 ) are mapped to AdS5×Σ2×M3' , where Σ2 is a Riemann surface of genus g ≥2 and the metric on M3' is obtained by distorting M3 in a certain way. The solutions can have localized D6 or O6 sources, as well as an arbitrary number of D8-branes. The AdS7 case (previously known only numerically) is conjecturally dual to an NS5-D6-D8 system. The field theories in three and four dimensions are not known, but their number of degrees of freedom can be computed in the supergravity approximation. The AdS4 solutions have numerical "attractor" generalizations that might be useful for flux compactification purposes.

  12. Little String Theory from a Double-Scaled Matrix Model

    CERN Document Server

    Ling, H; Shieh, H H; Van Anders, G; Van Raamsdonk, M; Ling, Henry; Mohazab, Ali Reza; Shieh, Hsien-Hang; Anders, Greg van; Raamsdonk, Mark Van

    2006-01-01

    Following Lin and Maldacena, we find exact supergravity solutions dual to a class of vacua of the plane wave matrix model by solving an electrostatics problem. These are asymptotically near-horizon D0-brane solutions with a throat associated with NS5-brane degrees of freedom. We determine the precise limit required to decouple the asymptotic geometry and leave an infinite throat solution found earlier by Lin and Maldacena, dual to Little String Theory on S^5. By matching parameters with the gauge theory, we find that this corresponds to a double scaling limit of the plane wave matrix model in which N \\to \\infty and the 't Hooft coupling \\lambda scales as \\ln^4(N), which we speculate allows all terms in the genus expansion to contribute even at infinite N. Thus, the double-scaled matrix quantum mechanics gives a Lagrangian description of Little String Theory on S^5, or equivalently a ten-dimensional string theory with linear dilaton background.

  13. PP-Wave / CFT_2 Duality

    CERN Document Server

    Gomis, J P; Strominger, A; Gomis, Jaume; Motl, Lubos; Strominger, Andrew

    2002-01-01

    We investigate the pp-wave limit of the AdS_3\\times S^3\\times K3 compactification of Type IIB string theory from the point of view of the dual Sym_N(K3) CFT. It is proposed that a fundamental string in this pp-wave geometry is dual to the c=6 effective string of the Sym_N(K3) CFT, with the string bits of the latter being composed of twist operators. The massive fundamental string oscillators correspond to certain twisted Virasoro generators in the effective string. It is shown that both the ground states and the genus expansion parameter (at least in the orbifold limit of the CFT) coincide. Surprisingly the latter scales like J^2/N rather than the J^4/N^2 which might have been expected. We demonstrate a leading-order agreement between the pp-wave and CFT particle spectra. For a degenerate special case (one NS 5-brane) an intriguing complete agreement is found.

  14. Discovery of Novel Viruses in Mosquitoes from the Zambezi Valley of Mozambique

    Science.gov (United States)

    Hayer, Juliette; Abilio, Ana Paula; Mulandane, Fernando Chanisso; Verner-Carlsson, Jenny; Falk, Kerstin I.; Fafetine, Jose M.; Berg, Mikael; Blomström, Anne-Lie

    2016-01-01

    Mosquitoes carry a wide variety of viruses that can cause vector-borne infectious diseases and affect both human and veterinary public health. Although Mozambique can be considered a hot spot for emerging infectious diseases due to factors such as a rich vector population and a close vector/human/wildlife interface, the viral flora in mosquitoes have not previously been investigated. In this study, viral metagenomics was employed to analyze the viral communities in Culex and Mansonia mosquitoes in the Zambezia province of Mozambique. Among the 1.7 and 2.6 million sequences produced from the Culex and Mansonia samples, respectively, 3269 and 983 reads were classified as viral sequences. Viruses belonging to the Flaviviridae, Rhabdoviridae and Iflaviridae families were detected, and different unclassified single- and double-stranded RNA viruses were also identified. A near complete genome of a flavivirus, tentatively named Cuacua virus, was obtained from the Mansonia mosquitoes. Phylogenetic analysis of this flavivirus, using the NS5 amino acid sequence, showed that it grouped with ‘insect-specific’ viruses and was most closely related to Nakiwogo virus previously identified in Uganda. Both mosquito genera had viral sequences related to Rhabdoviruses, and these were most closely related to Culex tritaeniorhynchus rhabdovirus (CTRV). The results from this study suggest that several viruses specific for insects belonging to, for example, the Flaviviridae and Rhabdoviridae families, as well as a number of unclassified RNA viruses, are present in mosquitoes in Mozambique. PMID:27682810

  15. Genetic Variability of Bovine Viral Diarrhea Virus and Evidence for a Possible Genetic Bottleneck during Vertical Transmission in Persistently Infected Cattle.

    Directory of Open Access Journals (Sweden)

    Natalie Dow

    Full Text Available Bovine viral diarrhea virus (BVDV, a Pestivirus in the family Flaviviridae, is an economically important pathogen of cattle worldwide. The primary propagators of the virus are immunotolerant persistently infected (PI cattle, which shed large quantities of virus throughout life. Despite the absence of an acquired immunity against BVDV in these PI cattle there are strong indications of viral variability that are of clinical and epidemiological importance. In this study the variability of E2 and NS5B sequences in multiple body compartments of PI cattle were characterized using clonal sequencing. Phylogenetic analyses revealed that BVDV exists as a quasispecies within PI cattle. Viral variants were clustered by tissue compartment significantly more often than expected by chance alone with the central nervous system appearing to be a particularly important viral reservoir. We also found strong indications for a genetic bottleneck during vertical transmission from PI animals to their offspring. These quasispecies analyses within PI cattle exemplify the role of the PI host in viral propagation and highlight the complex dynamics of BVDV pathogenesis, transmission and evolution.

  16. Monoclonal antibody-escape variant of dengue virus serotype 1: Genetic composition and envelope protein expression.

    Science.gov (United States)

    Chem, Y K; Chua, K B; Malik, Y; Voon, K

    2015-06-01

    Monoclonal antibody-escape variant of dengue virus type 1 (MabEV DEN-1) was discovered and isolated in an outbreak of dengue in Klang Valley, Malaysia from December 2004 to March 2005. This study was done to investigate whether DEN152 (an isolate of MabEV DEN-1) is a product of recombination event or not. In addition, the non-synonymous mutations that correlate with the monoclonal antibody-escape variant were determined in this study. The genomes of DEN152 and two new DEN-1 isolates, DENB04 and DENK154 were completely sequenced, aligned, and compared. Phylogenetic tree was plotted and the recombination event on DEN152 was investigated. DEN152 is sub-grouped under genotype I and is closely related genetically to a DEN-1 isolated in Japan in 2004. DEN152 is not a recombinant product of any parental strains. Four amino acid substitutions were unique only to DEN 152. These amino acid substitutions were (Ser)[326](Leu), (Ser)[340](Leu) at the deduced E protein, (Ile)[250](Thr) at NS1 protein, and (Thr)[41](Ser) at NS5 protein. Thus, DEN152 is an isolate of the emerging monoclonal antibody-escape variant DEN-1 that escaped diagnostic laboratory detection. PMID:26691263

  17. Detection of Natural Resistance-Associated Substitutions by Ion Semiconductor Technology in HCV1b Positive, Direct-Acting Antiviral Agents-Naïve Patients

    Science.gov (United States)

    Marascio, Nadia; Pavia, Grazia; Strazzulla, Alessio; Dierckx, Tim; Cuypers, Lize; Vrancken, Bram; Barreca, Giorgio Settimo; Mirante, Teresa; Malanga, Donatella; Oliveira, Duarte Mendes; Vandamme, Anne-Mieke; Torti, Carlo; Liberto, Maria Carla; Focà, Alfredo

    2016-01-01

    Naturally occurring resistance-associated substitutions (RASs) can negatively impact the response to direct-acting antivirals (DAAs) agents-based therapies for hepatitis C virus (HCV) infection. Herein, we set out to characterize the RASs in the HCV1b genome from serum samples of DAA-naïve patients in the context of the SINERGIE (South Italian Network for Rational Guidelines and International Epidemiology, 2014) project. We deep-sequenced the NS3/4A protease region of the viral population using the Ion Torrent Personal Genome Machine, and patient-specific majority rule consensus sequence summaries were constructed with a combination of freely available next generation sequencing data analysis software. We detected NS3/4A protease major and minor variants associated with resistance to boceprevir (V36L), telaprevir (V36L, I132V), simeprevir (V36L), and grazoprevir (V36L, V170I). Furthermore, we sequenced part of HCV NS5B polymerase using Sanger-sequencing and detected a natural RAS for dasabuvir (C316N). This mutation could be important for treatment strategies in cases of previous therapy failure. PMID:27618896

  18. Hepatitis C Virus Protein Interaction Network Analysis Based on Hepatocellular Carcinoma.

    Science.gov (United States)

    Han, Yuewen; Niu, Jun; Wang, Dong; Li, Yuanyuan

    2016-01-01

    Epidemiological studies have validated the association between hepatitis C virus (HCV) infection and hepatocellular carcinoma (HCC). An increasing number of studies show that protein-protein interactions (PPIs) between HCV proteins and host proteins play a vital role in infection and mediate HCC progression. In this work, we collected all published interaction between HCV and human proteins, which include 455 unique human proteins participating in 524 HCV-human interactions. Then, we construct the HCV-human and HCV-HCC protein interaction networks, which display the biological knowledge regarding the mechanism of HCV pathogenesis, particularly with respect to pathogenesis of HCC. Through in-depth analysis of the HCV-HCC interaction network, we found that interactors are enriched in the JAK/STAT, p53, MAPK, TNF, Wnt, and cell cycle pathways. Using a random walk with restart algorithm, we predicted the importance of each protein in the HCV-HCC network and found that AKT1 may play a key role in the HCC progression. Moreover, we found that NS5A promotes HCC cells proliferation and metastasis by activating AKT/GSK3β/β-catenin pathway. This work provides a basis for a detailed map tracking new cellular interactions of HCV and identifying potential targets for HCV-related hepatocellular carcinoma treatment. PMID:27115606

  19. Adaptive Mutations Enhance Assembly and Cell-to-Cell Transmission of a High-Titer Hepatitis C Virus Genotype 5a Core-NS2 JFH1-Based Recombinant

    DEFF Research Database (Denmark)

    Mathiesen, Christian K.; Prentoe, Jannick; Meredith, Luke W.;

    2015-01-01

    requiring high virus concentrations, such as studies of HCV particle composition and development of whole-virus vaccine antigens. IMPORTANCE: Hepatitis C virus (HCV) is a major global health care burden, affecting more than 150 million people worldwide. These individuals are at high risk of developing......UNLABELLED: Recombinant hepatitis C virus (HCV) clones propagated in human hepatoma cell cultures yield relatively low infectivity titers. Here, we adapted the JFH1-based Core-NS2 recombinant SA13/JFH1C3405G,A3696G (termed SA13/JFH1orig), of the poorly characterized genotype 5a, to Huh7.5 cells......, yielding a virus with greatly improved spread kinetics and an infectivity titer of 6.7 log10 focus-forming units (FFU)/ml. We identified several putative adaptive amino acid changes. In head-to-head infections at fixed multiplicities of infection, one SA13/JFH1orig mutant termed SA13/JFH1Core-NS5B...

  20. Anti-HCV fragment reagent in facilitating the diagnosis of HCV infection%抗-HCV分片段试剂在辅助诊断HCV感染中的应用

    Institute of Scientific and Technical Information of China (English)

    董小平; 陈筱华; 张洪淼; 方淑环; 孔令光

    2005-01-01

    目的探讨抗-HCV分片段试剂在辅助诊断HCV感染中的效果.方法收集常规初复检抗-HCV不符的临界样本31份,用抗-HCV分片段酶联免疫检测试剂进一步检测抗-HCV-C、NS3、NS4、NS5、膜高变区1(HVR1)抗体.结果 31份初复检不符临界样本分片段检测结果为4份阳性(12.90%),10份不确定,即仅1个抗原片段阳性(32.26%),17份阴性(54.84%).结论对抗-HCV初、复检结果不符的临界样本,用抗-HCV分片段酶联免疫检测试剂进一步作辅助检测,可降低假阳性,提高检测的特异性,具有一定的临床意义.

  1. Comparison Analysis on Reagent of Anti-HCV EIA and Anti-HCV Fragment EIA%抗-HCV EIA试剂与HCV分片段EIA试剂比较分析

    Institute of Scientific and Technical Information of China (English)

    陈莺

    2005-01-01

    [目的]探讨抗-HCV分片段试剂对抗-HCV阳性标本判断价值的可靠性.[方法]用抗-HCVEIA、MEIA及HCV分片段EIA法对23例初筛阳性标本进行检测.[结果]23例中,丙肝分片段不同基因区C区、NS3、NS4和NS5结果阳性分别为18(78.3%)、20(87.0%)、13(56.5%)和12(52.2%),判断阳性18例,可疑3例,阴性2例.23例中,16例各厂家试剂均阳性,不符7例.HCV分片段与进口雅培试剂阳性结果完全相同18例.[结论]用HCV分片段试剂对抗-HCV EIA弱阳性标本的结果判断有一定的临床使用价值.

  2. Staufen1 promotes HCV replication by inhibiting protein kinase R and transporting viral RNA to the site of translation and replication in the cells

    Science.gov (United States)

    Dixit, Updesh; Pandey, Ashutosh K.; Mishra, Priya; Sengupta, Amitabha; Pandey, Virendra N.

    2016-01-01

    Persistent hepatitis C virus (HCV) infection leads to chronic hepatitis C (CHC), which often progresses to liver cirrhosis (LC) and hepatocellular carcinoma (HCC). The molecular mechanisms that establish CHC and cause its subsequent development into LC and HCC are poorly understood. We have identified a cytoplasmic double-stranded RNA binding protein, Stau1, which is crucial for HCV replication. In this study, Stau1 specifically interacted with the variable-stem-loop region in the 3′ NTR and domain IIId of the HCV-IRES in the 5′ NTR, and promoted HCV replication and translation. Stau1 coimmunoprecipitates HCV NS5B and a cell factor, protein kinase R (PKR), which is critical for interferon-induced cellular antiviral and antiproliferative responses. Like Stau1, PKR displayed binding specificity to domain IIId of HCV-IRES. Stau1 binds to PKR and strongly inhibits PKR-autophosphorylation. We demonstrated that the transport of HCV RNA on the polysomes is Stau1-dependent, being mainly localized in the monosome fractions when Stau1 is downregulated and exclusively localized in the polysomes when Stau1 is overexpressed. Our findings suggest that HCV may appropriate Stau1 to its advantage to prevent PKR-mediated inhibition of eIF2α, which is required for the synthesis of HCV proteins for translocation of viral RNA genome to the polysomes for efficient translation and replication. PMID:27106056

  3. Oscillating supertubes and neutral rotating black hole microstates

    Energy Technology Data Exchange (ETDEWEB)

    Mathur, Samir D.; Turton, David [Department of Physics, The Ohio State University,191 W Woodruff Ave, Columbus, OH 43210 (United States)

    2014-04-10

    The construction of neutral black hole microstates is an important problem, with implications for the information paradox. In this paper we conjecture a construction of non-supersymmetric supergravity solutions describing D-brane configurations which carry mass and angular momentum, but no other conserved charges. We first study a classical string solution which locally carries dipole winding and momentum charges in two compact directions, but globally carries no net winding or momentum charge. We investigate its backreaction in the D1-D5 duality frame, where this object becomes a supertube which locally carries oscillating dipole D1-D5 and NS1-NS5 charges, and again carries no net charge. In the limit of an infinite straight supertube, we find an exact supergravity solution describing this object. We conjecture that a similar construction may be carried out based on a class of two-charge non-supersymmetric D1-D5 solutions. These results are a step towards demonstrating how neutral black hole microstates may be constructed in string theory.

  4. Oscillating supertubes and neutral rotating black hole microstates

    CERN Document Server

    Mathur, Samir D

    2014-01-01

    The construction of neutral black hole microstates is an important problem, with implications for the information paradox. In this paper we conjecture a construction of non-supersymmetric supergravity solutions describing D-brane configurations which carry mass and angular momentum, but no other conserved charges. We first study a classical string solution which locally carries dipole winding and momentum charges in two compact directions, but globally carries no net winding or momentum charge. We investigate its backreaction in the D1-D5 duality frame, where this object becomes a supertube which locally carries oscillating dipole D1-D5 and NS1-NS5 charges, and again carries no net charge. In the limit of an infinite straight supertube, we find an exact supergravity solution describing this object. We conjecture that a similar construction may be carried out based on a class of two-charge non-supersymmetric D1-D5 solutions. These results are a step towards demonstrating how neutral black hole microstates may ...

  5. Molecular mechanism of hepatitis C virus-induced glucose metabolic disorders

    Directory of Open Access Journals (Sweden)

    Ikuo eShoji

    2012-01-01

    Full Text Available Hepatitis C virus (HCV infection causes not only intrahepatic diseases but also extrahepatic manifestations, including metabolic disorders. Chronic HCV infection is often associated with type 2 diabetes. However, the precise mechanism underlying this association is still unclear. Glucose is transported into hepatocytes via glucose transporter 2 (GLUT2. Hepatocytes play a crucial role in maintaining plasma glucose homeostasis via the gluconeogenic and glycolytic pathways. We have been investigating the molecular mechanism of HCV-related type 2 diabetes using HCV RNA replicon cells and HCV J6/JFH1 system. We found that HCV replication down-regulates cell surface expression of GLUT2 at the transcriptional level. We also found that HCV infection promotes hepatic gluconeogenesis in HCV J6/JFH1-infected Huh-7.5 cells. HCV infection transcriptionally up-regulated the genes for PEPCK and G6Pase, the rate-limiting enzymes for hepatic gluconeogenesis. Gene expression of PEPCK and G6Pase was regulated by the transcription factor forkhead box O1 (FoxO1 in HCV-infected cells. Phosphorylation of FoxO1 at Ser319 was markedly diminished in HCV-infected cells, resulting in increased nuclear accumulation of FoxO1. HCV NS5A protein was directly linked with the FoxO1-dependent increased gluconeogenesis. This paper will discuss the current model of HCV-induced glucose metabolic disorders.

  6. Interpretation of the spectrum of Sn II: experimental and theoretical transition probabilities

    International Nuclear Information System (INIS)

    The optical emission a from laser produced plasma generated by 1064 nm irradiation of Sn/Pb alloys targets at a flux of 2.1010 W cm-2 was recorded and analyzed between 200 and 700 nm. The local thermodynamic equilibrium (LTE) conditions and plasma homogeneity have been checked. The analysis of Sn II was checked, with the support of parametric studies of the mixed configurations in both parities, by means of a self-consistent-field method to generate one-electron orbitals. The parametric description of the 5s5p2 configuration is improved by taking into account 5s25d, 5s26d and 5s27d mixing effects. Eigenfunctions were used to derive theoretical values of the transition probabilities. Experimental transition probabilities for 36 lines of Sn II arising from the 5s2ns, 5s2np, 5s2nd, 5s2nf, and 5s5p2 configurations of Sn II have been determined. Some values have been compared with the available data in the literature and are in a good agreement. The coincidence between several experimental and theoretical transition probabilities obtained in this work is remarked. (orig.)

  7. Detection of Natural Resistance-Associated Substitutions by Ion Semiconductor Technology in HCV1b Positive, Direct-Acting Antiviral Agents-Naïve Patients.

    Science.gov (United States)

    Marascio, Nadia; Pavia, Grazia; Strazzulla, Alessio; Dierckx, Tim; Cuypers, Lize; Vrancken, Bram; Barreca, Giorgio Settimo; Mirante, Teresa; Malanga, Donatella; Oliveira, Duarte Mendes; Vandamme, Anne-Mieke; Torti, Carlo; Liberto, Maria Carla; Focà, Alfredo; The Sinergie-Umg Study Group

    2016-01-01

    Naturally occurring resistance-associated substitutions (RASs) can negatively impact the response to direct-acting antivirals (DAAs) agents-based therapies for hepatitis C virus (HCV) infection. Herein, we set out to characterize the RASs in the HCV1b genome from serum samples of DAA-naïve patients in the context of the SINERGIE (South Italian Network for Rational Guidelines and International Epidemiology, 2014) project. We deep-sequenced the NS3/4A protease region of the viral population using the Ion Torrent Personal Genome Machine, and patient-specific majority rule consensus sequence summaries were constructed with a combination of freely available next generation sequencing data analysis software. We detected NS3/4A protease major and minor variants associated with resistance to boceprevir (V36L), telaprevir (V36L, I132V), simeprevir (V36L), and grazoprevir (V36L, V170I). Furthermore, we sequenced part of HCV NS5B polymerase using Sanger-sequencing and detected a natural RAS for dasabuvir (C316N). This mutation could be important for treatment strategies in cases of previous therapy failure. PMID:27618896

  8. PROTECTIVE EFFECTS OF PROPOLIS ON GAMMA- IRRADIATED NIGELLA SATIVA EXTRACT INDUCED BLOOD AND IMMUNE CHANGES IN WISTAR RATS

    Directory of Open Access Journals (Sweden)

    Osama Moseilhy Saleh

    2013-01-01

    Full Text Available The present study conducted to test the effect of Nigella Sativa (NS, 5 mg kg-1 of body weight, or γ-irradiated Nigella Sativa (GRNS on the changes of blood component profiles, liver, kidney functions and immune cytokines secretion in male Wistar rats. Moreover, the possible protection by propolis (200 mg kg-1 B. W. on the changes induced by NS and GRNS was examined. Results revealed that both NS and GRNS administration for two weeks induced changes in blood, GPT, GOT and urea levels and co-administration with propolis significantly ameliorated such changes. Also, liver histology showed numerous vacuolar degeneration and fatty changes in γ-irradiated groups which disappeared in presence of propolis. Kidney histology of NS administered rats showed less lymphocytic infiltration, while GRNS groups showed desquamation in the cytoplasm of the renal tubules, hemorrhage in the renal corpuscle and lymphocytic infiltration which disappeared when propolis given together with GRNS. Finally propolis induced protective effect on the changes induced in TNF-α and IL-10 secretion by either NS or GRNS in Wistar rats. In conclusion, the findings of present study clarified the protective effect of propolis on changes induced by γ-irradiated NS on blood, liver, kidney and cytokines changes in Wistar rats.

  9. Genetic variability of hepatitis C virus before and after combined therapy of interferon plus ribavirin.

    Directory of Open Access Journals (Sweden)

    José Manuel Cuevas

    Full Text Available We present an analysis of the selective forces acting on two hepatitis C virus genome regions previously postulated to be involved in the viral response to combined antiviral therapy. One includes the three hypervariable regions in the envelope E2 glycoprotein, and the other encompasses the PKR binding domain and the V3 domain in the NS5A region. We used a cohort of 22 non-responder patients to combined therapy (interferon alpha-2a plus ribavirin for which samples were obtained before initiation of therapy and after 6 or/and 12 months of treatment. A range of 25-100 clones per patient, genome region and time sample were sequenced. These were used to detect general patterns of adaptation, to identify particular adaptation mechanisms and to analyze the patterns of evolutionary change in both genome regions. These analyses failed to detect a common adaptive mechanism for the lack of response to antiviral treatment in these patients. On the contrary, a wide range of situations were observed, from patients showing no positively selected sites to others with many, and with completely different topologies in the reconstructed phylogenetic trees. Altogether, these results suggest that viral strategies to evade selection pressure from the immune system and antiviral therapies do not result from a single mechanism and they are likely based on a range of different alternatives, in which several different changes, or their combination, along the HCV genome confer viruses the ability to overcome strong selective pressures.

  10. Predominance of hepatitis C virus genotype 4 infection and rapid transmission between 1935 and 1965 in the Central African Republic.

    Science.gov (United States)

    Njouom, Richard; Frost, Eric; Deslandes, Sylvie; Mamadou-Yaya, Fleurie; Labbé, Annie-Claude; Pouillot, Régis; Mbélesso, Pascal; Mbadingai, Sylvestre; Rousset, Dominique; Pépin, Jacques

    2009-10-01

    The molecular epidemiology of hepatitis C virus (HCV) in the Central African Republic (CAR) is poorly documented. Thus, we conducted phylogenetic analyses of NS5B gene sequences from 58 HCV-infected inhabitants of a remote area of south-west CAR, which indicated that 48 (82.8%) were infected with genotype 4 (HCV-4), five (8.6%) with genotype 2 and five (8.6%) with genotype 1. HCV-4 strains were highly heterogeneous, containing previously described subtypes 4k (48%), 4c (27%), 4r (4%), 4f (4%) and unclassified subtypes (17%). To estimate the epidemic history of these HCV-4 strains, an evolutionary analysis using the coalescent approach was used. The estimated date of the most recent common ancestor of the CAR HCV-4 strains was 1539 (95% confidence intervals, 1317-1697). They exhibited a rapid, exponential spread from 1935 to 1965, simultaneously with what was recently reported in neighbouring Cameroon and Gabon. The hypothesis of a massive iatrogenic transmission during interventions for the control of endemic tropical diseases is discussed.

  11. Effects of Silymarin on Hepatitis C Virus and Heme Oxygenase-1 Gene Expression in Human Hepatoma Cells

    Science.gov (United States)

    Bonifaz, Vania; Shan, Ying; Lambrecht, Richard W.; Donohue, Susan E.; Moschenross, Darcy; Bonkovsky, Herbert L.

    2008-01-01

    Background/Aims Hepatitis C virus (HCV) infection is a global medical problem. The current standard treatment of chronic hepatitis C (CHC), pegylated interferon plus ribavirin, is prolonged, expensive, has serious side effects and, at best, is only 50% effective. Silymarin is a natural antioxidant often used by patients with CHC, although its efficacy for decreasing HCV levels or ameliorating CHC remains uncertain. HCV infection is associated with increased hepatic oxidative stress, and one of the antioxidant enzymes which protect cells against this stress is heme oxygenase-1 (HO-1). Methods We investigated effects of silymarin on HCV and HO-1 gene expression in Huh-7 cells, CNS3, and 9-13 cells (the latter two stably expressing HCV-proteins). Results Silymarin significantly down-regulated HCV core mRNA (by 20% - 36%) and protein (by 30%-60%) in CNS3 cells. In contrast, silymarin did not decrease HCV NS5A mRNA or protein expression in 9-13 cells. HO-1 mRNA was up-regulated (60%-400%) by silymarin in Huh-7, CNS3 and 9-13 cells, whereas Bach1 and Nrf2 mRNA levels were not affected. The effect of silymarin to down-regulate HCV core was not related to changes in the Jak-Stat signaling pathway. Conclusions Silymarin may be of benefit in CHC, although prospective, randomized, controlled trials are needed to be certain. PMID:18694403

  12. Isolation and genetic characterization of a tembusu virus strain isolated from mosquitoes in Shandong, China.

    Science.gov (United States)

    Tang, Y; Diao, Y; Chen, H; Ou, Q; Liu, X; Gao, X; Yu, C; Wang, L

    2015-04-01

    Tembusu virus (TMUV) is a flavivirus, presumed to be a mosquito-borne flavivirus of the Ntaya virus subgroup. To date, however, there have been no reports indicating that mosquitoes are involved in the spread of TMUV. In this study, we report the first isolation of TMUV from Culex mosquitoes. We describe the isolation and characterization of a field strain of TMUV from mosquitoes collected in Shandong Province, China. The virus isolate, named TMUV-SDMS, grows well in mosquito cell line C6/36, in Vero and duck embryo fibroblast (DEF) cell lines, and causes significant cytopathic effects in these cell cultures. The TMUV-SDMS genome is a single-stranded RNA, 10 989 nt in length, consisting of a single open reading frame encoding a polyprotein of 3410 amino acids, with 5' and 3' untranslated regions of 142 and 617 nt, respectively. Phylogenetic analysis of the E and NS5 genes revealed that the TMUV-SDMS is closely related to the TMUV YY5 and BYD strains which cause severe egg-drop in ducks. The 3'NTR of TMUV-SDMS contains two pairs of tandem repeat CS and one non-duplicate CS, which have sequence similarities to the same repeats in the YY5 and BYD strains. Our findings indicate that mosquitoes carrying the TMUV may play an important role in the spread of this virus and in disease outbreak. PMID:23711093

  13. The hidden seasonality of the rare biosphere in coastal marine bacterioplankton

    KAUST Repository

    Alonso-Sáez, Laura

    2015-04-08

    Summary: Rare microbial taxa are increasingly recognized to play key ecological roles, but knowledge of their spatio-temporal dynamics is lacking. In a time-series study in coastal waters, we detected 83 bacterial lineages with significant seasonality, including environmentally relevant taxa where little ecological information was available. For example, Verrucomicrobia had recurrent maxima in summer, while the Flavobacteria NS4, NS5 and NS2b clades had contrasting seasonal niches. Among the seasonal taxa, only 4 were abundant and persistent, 20 cycled between rare and abundant and, remarkably, most of them (59) were always rare (contributing <1% of total reads). We thus demonstrate that seasonal patterns in marine bacterioplankton are largely driven by lineages that never sustain abundant populations. A fewer number of rare taxa (20) also produced episodic \\'blooms\\', and these events were highly synchronized, mostly occurring on a single month. The recurrent seasonal growth and loss of rare bacteria opens new perspectives on the temporal dynamics of the rare biosphere, hitherto mainly characterized by dormancy and episodes of \\'boom and bust\\', as envisioned by the seed-bank hypothesis. The predictable patterns of seasonal reoccurrence are relevant for understanding the ecology of rare bacteria, which may include key players for the functioning of marine ecosystems. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

  14. Chemical diversity and antiviral potential in the pantropical Diospyros genus.

    Science.gov (United States)

    Peyrat, Laure-Anne; Eparvier, Véronique; Eydoux, Cécilia; Guillemot, Jean-Claude; Stien, Didier; Litaudon, Marc

    2016-07-01

    A screening using a dengue replicon virus-cell-based assay was performed on 3563 ethyl acetate (EtOAc) extracts from different parts of 1500 plants. The screening led to the selection of species from the genus Diospyros (Ebenaceae), among which 25 species distributed in tropical areas showed significant inhibitory activity on dengue virus replication. A metabolic analysis was conducted from the UPLC-HRMS profiles of 33 biologically active and inactive plant extracts, and their metabolic proximity is presented in the form of a dendrogram. The results of the study showed that chemical similarity is not related to plant species or organ. Overall, metabolomic profiling allowed us to define large groups of extracts, comprising both active and inactive ones. Closely related profiles from active extracts might indicate that the common major components of these extracts were responsible for the antiviral activity, while the comparison of chemically similar active and inactive extracts, will permit to find compounds of interest. Eventually, the phytochemical investigation of Diospyros glans bark EtOAc extract afforded usnic acid and 7 known ursane- and lupane-type triterpenoids, among which 5 were found significantly active against dengue virus replication. The inhibitory potency of these compounds was also evaluated on a DENV-NS5 RNA-dependant RNA polymerase assay. PMID:27126897

  15. HIV and HCV coinfection: prevalence, associated factors and genotype characterization in the Midwest Region of Brazil.

    Science.gov (United States)

    Freitas, Solange Zacalusni; Teles, Sheila Araújo; Lorenzo, Paulo Cesar; Puga, Marco Antonio Moreira; Tanaka, Tayana Serpa Ortiz; Thomaz, Danilo Yamamoto; Martins, Regina Maria Bringel; Druzian, Angelita Fernandes; Lindenberg, Andréa Siqueira Campos; Torres, Marina Sawada; Pereira, Sérgio A; Villar, Livia Melo; Lampe, Elisabete; Motta-Castro, Ana Rita Coimbra

    2014-01-01

    A cross-sectional study on prevalence, associated factors and genotype distribution of HCV infection was conducted among 848 HIV-infected patients recruited at reference centers in the Midwest Region of Brazil. The prevalence rate of HIV-HCV coinfection was 6.9% (95% CI: 5.2 to 8.6). In multivariable analysis, increasing age, use of illicit drugs (injection and non-injection), a history of blood transfusion before 1994, and the absence of a steady partnership were significant independent associated factors for HIV-HCV coinfection. The phylogenetic analysis based on the NS5B region revealed the presence of two major circulating genotypes of HCV: genotypes 1 (58.3%) and 3 (41.7%). The prevalence of HIV-HCV coinfection was lower than those reported in studies conducted with HIV-infected patients in different regions of Brazil, due to the fact that illicit drug use is not a frequent mode of HIV transmission in this region of Brazil. Serologic screening of HIV-patients for HCV before initiating antiretroviral treatment, a comprehensive identification of associated factors, and the implementation of effective harm reduction programs are highly recommended to provide useful information for treatment and to prevent HCV coinfection in these patients.

  16. Hepatitis C Virus Protein Interaction Network Analysis Based on Hepatocellular Carcinoma.

    Directory of Open Access Journals (Sweden)

    Yuewen Han

    Full Text Available Epidemiological studies have validated the association between hepatitis C virus (HCV infection and hepatocellular carcinoma (HCC. An increasing number of studies show that protein-protein interactions (PPIs between HCV proteins and host proteins play a vital role in infection and mediate HCC progression. In this work, we collected all published interaction between HCV and human proteins, which include 455 unique human proteins participating in 524 HCV-human interactions. Then, we construct the HCV-human and HCV-HCC protein interaction networks, which display the biological knowledge regarding the mechanism of HCV pathogenesis, particularly with respect to pathogenesis of HCC. Through in-depth analysis of the HCV-HCC interaction network, we found that interactors are enriched in the JAK/STAT, p53, MAPK, TNF, Wnt, and cell cycle pathways. Using a random walk with restart algorithm, we predicted the importance of each protein in the HCV-HCC network and found that AKT1 may play a key role in the HCC progression. Moreover, we found that NS5A promotes HCC cells proliferation and metastasis by activating AKT/GSK3β/β-catenin pathway. This work provides a basis for a detailed map tracking new cellular interactions of HCV and identifying potential targets for HCV-related hepatocellular carcinoma treatment.

  17. Universality of the topological string at large radius and NS-brane resurgence

    CERN Document Server

    Couso-Santamaria, Ricardo

    2015-01-01

    We show that there is a natural universal limit of the topological string free energies at the large radius point. The new free energies keep a nonholomorphic dependence on the complex structure moduli space and their functional form is the same for all Calabi-Yau geometries, compact and noncompact alike. The asymptotic nature of the free energy expansion changes in this limit due to a milder factorial growth of its coefficients, and this implies a transseries extension with instanton effects in $\\exp(- 1/g_s^2)$, of NS-brane type, rather than $\\exp(-1/g_s)$, of D-brane type. We show a relation between the instanton action of NS-brane type and the volume of the Calabi-Yau manifold which points to a possible interpretation in terms of NS5-branes. A similar rescaling limit has been considered recently leading to an Airy equation for the partition function which is here used to explain the resurgent properties of the rescaled transseries.

  18. Current status in the therapy of liver diseases.

    Science.gov (United States)

    Uhl, Philipp; Fricker, Gert; Haberkorn, Uwe; Mier, Walter

    2014-01-01

    Hepatic diseases, like viral hepatitis, autoimmune hepatitis, hereditary hemochromatosis, non-alcoholic fatty liver disease (NAFLD) and Wilson's disease, play an important role in the development of liver cirrhosis and, hence, hepatocellular carcinoma. In this review, the current treatment options and the molecular mechanisms of action of the drugs are summarized. Unfortunately, the treatment options for most of these hepatic diseases are limited. Since hepatitis B (HBV) and C (HCV) infections are the most common causes of liver cirrhosis and hepatocellular carcinoma, they are the focus of the development of new drugs. The current treatment of choice for HBV/HCV infection is an interferon-based combination therapy with oral antiviral drugs, like nucleos(t)ide analogues, which is associated with improving the therapeutic success and also preventing the development of resistances. Currently, two new protease inhibitors for HCV treatment are expected (deleobuvir, faldaprevir) and together with the promising drug, daclatasvir (NS5A-inhibitor, currently in clinical trials), adequate therapy is to be expected in due course (circumventing the requirement of interferon with its side-effects), while in contrast, efficient HBV therapeutics are still lacking. In this respect, entry inhibitors, like Myrcludex B, the lead substance of the first entry inhibitor for HBV/HDV (hepatitis D) infection, provide immense potential. The pharmacokinetics and the mechanism of action of Myrcludex B are described in detail.

  19. 抗丙型肝炎病毒药:索氟布韦(sofosbuvir)

    Institute of Scientific and Technical Information of China (English)

    陈本川

    2014-01-01

    索氟布韦(sofosbuvir)为美国FDA首次批准上市的抗丙型肝炎病毒新药,是一种口服有效的HCV NS5B聚合酶抑制剂,对HCV基因2和3型引起的慢性丙型肝炎( CHC)可全口服治疗,对基因1和4型CHC需与聚乙二醇干扰素α和利巴韦林联用。该文对索氟布韦适应证、剂量与用法、用药注意事项、非临床药理毒理学、临床药理毒理学、临床研究、不良反应及知识产权状态和国内外研究进展等进行介绍。

  20. Sofosbuvir: a review of its use in patients with chronic hepatitis C.

    Science.gov (United States)

    Keating, Gillian M

    2014-07-01

    Sofosbuvir (Sovaldi(®)) is a nucleotide hepatitis C virus (HCV) NS5B polymerase inhibitor that has pangenotypic antiviral activity and a high genetic barrier to resistance. This article reviews the clinical efficacy and tolerability of sofosbuvir in patients with chronic hepatitis C and summarizes its pharmacological properties. Interferon-free treatment with sofosbuvir plus ribavirin achieved high sustained virological response (SVR) rates in treatment-naïve and treatment-experienced patients with HCV genotype 2 or 3 infection, and also had efficacy in patients with HCV genotype 1 infection. Sofosbuvir plus ribavirin was also effective in patients co-infected with HCV and HIV, and sofosbuvir plus ribavirin administered prior to liver transplantation prevented recurrent HCV infection in the majority of patients who had HCV RNA levels below the limit of quantification at the time of transplantation. Sofosbuvir plus peginterferon-α-2a and ribavirin achieved high SVR rates in patients with HCV genotype 1 infection, and also appeared effective in patients with HCV genotype 4, 5 or 6 infection. Oral sofosbuvir was generally well tolerated in patients with chronic hepatitis C. The most commonly reported adverse events and laboratory abnormalities were consistent with those expected with ribavirin and peginterferon-α. In conclusion, sofosbuvir represents an important advance in the treatment of chronic hepatitis C.

  1. Safety, Efficacy, and Tolerability of Sofosbuvir and Ribavirin in Management of Recurrent Hepatitis C Virus Genotype 4 After Living Donor Liver Transplant in Egypt: What Have We Learned so far?

    Directory of Open Access Journals (Sweden)

    Dabbous

    2016-04-01

    Full Text Available Background Recurrence of HCV after living donor liver transplant (LDLT is nearly universal, with almost one third of recipients developing cirrhosis and graft failure within 5 years after LDLT. Different studies have been published on the effect of sofosbuvir after liver transplantation on recurrent HCV with different genotypes. Objectives The aim of this study was to evaluate the efficacy, safety, and tolerability of sofosbuvir and ribavirin in LDLT recipients with recurrent HCV genotype 4. Patients and Methods Thirty-nine Egyptian LDLT recipients were treated for recurrent HCV after LDLT with nucleos(tide analog NS5B polymerase inhibitor, sofosbuvir, and ribavirin without pegylated interferon for 6 months (November 2014 to June 2015 in this intention-to-treat analysis. Results One recipient died 1 week after starting the treatment, but the remaining 38 patients completed 24 weeks of treatment and were then followed for 12 weeks after end of treatment (EOT. The sustained virological response (SVR at week 12 after EOT was achieved in 76% (29/38 of recipients. SVR was significantly higher in treatment-naïve patients and in recipients with a low stage of fibrosis. Only 2 (5% recipients developed severe pancytopenia and acute kidney injury. Conclusions We recommend initiating treatment as soon as possible after liver transplantation with newer combinations, such as ledipasvir/sofosbuvir or sofosbuvir/simeprevir, rather than sofosbuvir with Ribavirin, to achieve higher rates of SVR.

  2. Development of sofosbuvir for the treatment of hepatitis C virus infection.

    Science.gov (United States)

    Lawitz, Eric; Jacobson, Ira M; Nelson, David R; Zeuzem, Stefan; Sulkowski, Mark S; Esteban, Rafael; Brainard, Diana; McNally, John; Symonds, William T; McHutchison, John G; Dieterich, Douglas; Gane, Edward

    2015-11-01

    The nucleotide analog NS5B polymerase inhibitor sofosbuvir was approved by the U.S. Food and Drug Administration (FDA) in December 2013 for the treatment of chronic hepatitis C virus (HCV) infection in combination with ribavirin or peginterferon and ribavirin. Sofosbuvir was developed to meet an urgent medical need for shorter, safer, simplified, more effective HCV treatment regimens and to reduce or eliminate the need for peginterferon. New treatment regimens were especially required for patient populations with limited treatment options, including patients who had failed prior HCV therapy, those with compensated and decompensated cirrhosis, and those who were either intolerant of or had contraindications to interferon. Sofosbuvir plus ribavirin for patients with genotype 2 or 3 HCV infection was the first approved all-oral treatment option. Sofosbuvir is also the backbone of the first regimen available for patients awaiting liver transplantation to prevent HCV recurrence, as well as the first oral interferon-free regimen for patients coinfected with HCV and HIV. This paper describes the development of sofosbuvir up to its original FDA approval.

  3. 治疗基因1型慢性丙型肝炎的复方制剂--HARVONITM

    Institute of Scientific and Technical Information of China (English)

    陈本川

    2015-01-01

    HarvoniTM是2种抗丙型肝炎病毒( HCV)药固定剂量的复方制剂,由HCVNS5B 聚合酶抑制药索非布韦(sofosbuvir)400 mg 和HCV蛋白酶NS5A抑制药ledipasvir(暂译名:雷迪帕韦)90 mg组合而成。是美国食品药品管理局( FDA)批准的第一个用于治疗基因1型丙型肝炎的全口服复方制剂,无需联用注射干扰素,可单药使用,也可与其他抗HCV口服药物,如利巴韦林联合使用。该文对HarvoniTM非临床药理毒理学、临床药理毒理学、临床研究、适应证、剂量与用法、用药注意事项、不良反应及知识产权状态和国内外研究进展等进行介绍。

  4. 治疗丙肝药物索非布韦的研究进展%Research progress in sofosbuvir for the treatment of hepatitis C

    Institute of Scientific and Technical Information of China (English)

    叶腾飞; 卞晓岚; 朱利明

    2015-01-01

    索非布韦(sofosbuvir,SOF)是全球首个无需同时使用干扰素即可实现全口服治疗丙肝的药物,为丙型肝炎病毒(HCV)特异性NS5B聚合酶的核苷抑制剂.临床试验表明,SOF和利巴韦林二联全口服方案可用于治疗基因2型、3型HCV的感染,用药12周总体持续病毒学应答率(SVR)为50%~78%.SOF联合聚乙二醇干扰素和利巴韦林可用于基因1型和4型HCV的感染,用药12周的SVR达90%.SOF因其服用简便,治愈率高,不良反应发生率低等特点,使其极有可能成为"重磅炸弹"型药物.

  5. Ribavirin: Past, present and future

    Institute of Scientific and Technical Information of China (English)

    2016-01-01

    Before the advent of direct acting antiviral agents (DAAs)ribavirin, associated to pegylated-interferon playeda crucial role in the treatment of chronic hepatitis C,preventing relapses and breakthroughs. In the presentera of new potent DAAs, a place is still devoted tothe drug. Ribavirin associated with sofosbuvir alone isefficient in the treatment of most cases of G2 infectedpatients. All options currently available for the lastdifficult-to-treat cirrhotic G3 patients contain ribavirin.Reducing treatment duration to 12 wk in G1 or G4cirrhotic compensated patients is feasible thanks toribavirin. Retreating patients with acquired anti NS5Aresistance-associated variants using ribavirin-basedstrategies could be useful. The addition of ribavirin withDAAs combinations however, leads to more frequentbut mild adverse events especially in cirrhotic patients.Preliminary data with interferon-free second generationDAAs combinations without ribavirin suggest thatfuture of the drug is jeopardized even in difficult-totreatpatients The optimization of ribavirin dosageaccording to an early monitoring of blood levels hasbeen suggested to be relevant in double therapy withpeginterferon or sofosbuvir but not with very potentcombinations of more than two DAAs.

  6. 丙型肝炎无干扰素全口服治疗临床Ⅲ期试验进展%Progress of interferon-free oral drugs in phase Ⅲ clinical trials for hepatitis C treatment

    Institute of Scientific and Technical Information of China (English)

    唐紫薇; 任浩; 戚中田

    2015-01-01

    Hepatitis C virus is a single stranded RNA virus categorized to the genus Flavirus.HCV infection is transmitted via blood and characterized by high chronic rate.Hepatitis C poses a major health threat worldwide with approximately 160 million chronically infected individuals.The standard therapy for HCV infection in the past decade is using pegylated IFN-α plus ribavirin.However,IFN-α treatment showed low response rate,high averse effect,and would be eventually replaced by emerging new drugs.The combination of ribavirin therapy may prevent relapse,as well as increase sustained response rate,while its usage remains to be further investigated.In 2011,FDA approved the NS3 protease and NS5B inhibitor telaprevir and boceprevir as the first generation of direct-acting antiviral agents.In 2013,the approval of sofosbuvir in hepatitis C treatment opened a new chapter for all-oral but non-interferon therapy.During the 2014 International Liver Congress,the annual meeting held by the European Association for the Study of the Liver (EASL),several promising therapies against hepatitis C infection concluded from phase Ⅲ trials were reported.The patients included treatment naive and treatment-experienced,with or without cirrhosis,as well as patients infected with type 1 HCV.The sustained virologic response rates reached over 90 %.This review summarizes the recent progresses from phase Ⅲ trials on all-oral,interferon-free anti-HCV virus treatments.

  7. Faldaprevir for the Treatment of Hepatitis C

    Directory of Open Access Journals (Sweden)

    Tatsuo Kanda

    2015-03-01

    Full Text Available The current treatments for chronic hepatitis C virus (HCV genotype 1 infection are combinations of direct-acting antivirals, and faldaprevir is one of the new generation of HCV NS3/4A protease inhibitors. At the end of 2013, the US Food and Drug Administration (FDA approved the HCV NS3/4A protease inhibitor simeprevir and the HCV NS5B polymerase inhibitor sofosbuvir. Simeprevir or sofosbuvir in combination with pegylated interferon and ribavirin are available for clinical use. Faldaprevir, another HCV NS3/4A protease inhibitor that also has fewer adverse events than telaprevir or boceprevir, is under development. Of interest, faldaprevir in combination with pegylated interferon and ribavirin, and interferon-free treatment with faldaprevir in combination with deleobuvir plus ribavirin provides high sustained virological response rates for HCV genotype 1 infection. The aim of this article is to review these data concerning faldaprevir. Faldaprevir in combination with pegylated interferon and ribavirin treatment appears to be associated with fewer adverse events than telaprevir or boceprevir in combination with pegylated interferon and ribavirin, and may be one of the therapeutic options for treatment-naive patients with HCV genotype 1. The interferon-free combination of faldaprevir and deleobuvir with ribavirin was effective for HCV genotype 1 infection and may hold promise for interferon-ineligible and interferon-intolerant patients.

  8. A new anti-hepatitis C virus drug: sofosbuvir%口服抗丙型肝炎病毒新药索福布韦

    Institute of Scientific and Technical Information of China (English)

    曾婧娉; 张弋

    2014-01-01

    面对全球约1.7亿慢性丙肝患者,现今的标准治疗方案,即聚乙二醇干扰素(Peg-IFN)联合利巴韦林(RBV),其总治愈率不足50%.因此,近年来旨在提高治愈率的直接抗病毒药物(DAAs)不断问世,其中,丙型肝炎病毒(HCV)聚合酶抑制剂索福布韦作用于病毒RNA复制的NS5B聚合酶位点,中止HCV复制.相较于标准治疗方案,基于索福布韦的联合治疗方案治愈率更高.本文就索福布韦的药理作用、药动学、临床研究及安全性等作一综述.

  9. 新型抗丙型肝炎病毒药索非布韦的研究进展%Advances in research of sofosbuvir-the new drug against hepatitis C virus

    Institute of Scientific and Technical Information of China (English)

    屈慧新; 王玉泽; 王彩霞; 史慧静; 王玲玲

    2016-01-01

    目的 评价新型抗丙型肝炎病毒(hepatitis C virus.HCV)药索非布韦的药理作用、安全药理学、药代动力学、药物相互作用、临床研究、不良反应、耐药性.方法 查阅相关文献26篇,对索非布韦基础与临床的研究进展进行了归纳与总结.结果与结论 索非布韦(sofosbuvir)是经美国食品药品管理局(FDA)批准的首个NS5B HCV聚合酶抑制剂,对所有HCV基因型均有效,本药安全性及耐受性良好,与其它药物间相互作用少,具有优良的药代动力学特性和强大的抗病毒能力,其强大的治疗效果给丙型肝炎患者带来了新希望.

  10. Sofosbuvir: A novel treatment option for chronic hepatitis C infection

    Directory of Open Access Journals (Sweden)

    Harmeet Kaur Bhatia

    2014-01-01

    Full Text Available Hepatitis C currently infects more than 170 million people around the world, leading to significant morbidity and mortality. The current standard of care for HCV infection, including one of the two protease inhibitors, telaprevir or boceprevir, for 12-32 weeks, along with pegylated interferon alfa-2a (PEG-IFN-α and ribavirin for up to 48 weeks, is unsatisfactory in many cases, either because of lack of efficacy or because of treatment-related adverse effects. There is an urgent need of new drugs with improved efficacy as well as a safety profile. Sofosbuvir, a recently approved nucleotide analog, is a highly potent inhibitor of the NS5B polymerase in the Hepatitis C virus (HCV, and has shown high efficacy in combination with several other drugs, with and without PEG-INF, against HCV. It offers many advantages due to its high potency, low side effects, oral administration, and high barrier to resistance. The efficacy and safety were demonstrated in many large and well-designed phase 2 and phase 3 clinical trials like NEUTRINO, PROTON, ELECTRON, ATOMIC, COSMOS, FUSION, FISSION, NUCLEAR, POSITRON, and the like. It is generally well-tolerated. Adverse events that occurred include: Headache, insomnia, fatigue, nausea, dizziness, pruritis, upper respiratory tract infections, rash, back pain, grade 1 anemia, and grade 4 lymphopenia; however, the exact safety profile can only be judged when this drug is actually used on a large scale.

  11. 治疗慢性丙型肝炎新药Sofosbuvir%A New Drug for Chronic Hepatitis: C-Sofosbuvir

    Institute of Scientific and Technical Information of China (English)

    吴叶红; 刘海净; 刘欢

    2014-01-01

    鉴于丙型肝炎病毒(HCV)感染全球高发趋势,目前治疗方案因禁忌、严重不良反应等导致其使用的局限性,因此需要一种更有效、安全、简便、不适宜干扰素治疗的治疗药物.Sofosbuvir是具有这些特性的直接抗病毒药物,为HCV NS5 B聚合酶的尿苷核苷酸类似物抑制药,可有效对抗多种基因型HCV感染,具有良好的安全性和耐受性.本文综述Sofosbuvir的作用机制、药动学、不良反应、药物相互作用及临床试验.

  12. 全球首个抗HCV全口服新药索非布韦%The World's First Oral Anti-hepatitis C Virus Drug Sofosbuvir

    Institute of Scientific and Technical Information of China (English)

    刘正和

    2014-01-01

    丙型肝炎病毒感染极大地威胁着公众健康,目前的标准治疗方案是聚乙二醇修饰的干扰素-α(PegIFN)与广谱抗病毒药物利巴韦林(RBV)联合,然而这种疗法的持续病毒学应答相对较低,新的研究如直接作用的抗病毒药(DAAs)提供了一种新的治疗策略,以提高疗效和耐受性.索非布韦是首个全口服抗丙型肝炎病毒药物,通过抑制NS5B聚合酶来有效抑制HCV的复制,从而达到治疗效果.本文主要就其化学合成、作用机理、药代动力学特征及临床疗效和安全性做一综述.

  13. Sofosbuvir: an all-around drug in hepatitis C treatment new era – The first phase

    Directory of Open Access Journals (Sweden)

    Alessia Ciancio

    2015-04-01

    Full Text Available Chronic hepatitis C virus (HCV infection is a slowly progressive disease affecting more than 185 million people worldwide. For many years, the combination of pegylated interferon (Peg-IFN plus ribavirin (RBV has been the backbone of treatment for patients infected with HCV. More than two years ago, the first generation direct-acting antiviral agents (DAAs – the protease inhibitors boceprevir and telaprevir – were approved for treatment of genotype 1 patients, doubling the cure rate. The new DAAs that have been developed, are effective for multiple genotypes, improve rates of sustained viral response with fewer side effects, simplify dosing and drug-drug interactions, and in some patients, offer the promise of interferon-free and/or ribavirin-free therapy. These new agents include the recently approved second generation protease inhibitor, the HCV NS5B polymerase inhibitor sofosbuvir and the NS3/4A protease inhibitor simeprevir as well as several other agents that are currently in later phases of development. With sofosbuvir-based regimens, successful interferon-free treatment is now available across all genotypes. In fact sofosbuvir is very effective in combination with Peg-interferon and ribavirine or with ribavirine alone or with other direct anti-viral agents. The following assessment evaluates the evidence on the clinical effectiveness and harms of sofosbuvir for the treatment of chronic hepatitis C.http://dx.doi.org/10.7175/rhc.v6i2.1164

  14. Biological and molecular characterization of classical swine fever challenge virus from India

    Directory of Open Access Journals (Sweden)

    Parveen Kumar

    2015-03-01

    Full Text Available Aim: The aim of this study was biological and molecular characterization of classical swine fever (CSF challenge virus from India. Materials and Methods: CSF challenge virus maintained at Division of Biological standardization was experimentally infected to two seronegative piglets. The biological characterization was done by clinical sign and symptoms along with postmortem findings. For molecular characterization 5’-nontranslated region, E2 and NS5B regions were amplified by reverse transcription polymerase chain reaction and sequenced. The sequences were compared with that of reference strains and the local field isolates to establish a phylogenetic relation. Results: The virus produced symptoms of acute disease in the piglets with typical post-mortem lesions. Phylogenetic analysis of the three regions showed that the current Indian CSF Challenge virus is having maximum similarity with the BresciaX strain (USA and Madhya Pradesh isolate (India and is belonging to subgroup 1.2 under Group 1. Conclusion: Based on biological and molecular characterization of CSF challenge virus from India is described as a highly virulent virus belonging to subgroup 1.2 under Group 1 along with some field isolates from India and Brescia strain.

  15. The IR obstruction to UV completion for Dante's Inferno model with higher-dimensional gauge theory origin

    Science.gov (United States)

    Furuuchi, Kazuyuki; Koyama, Yoji

    2016-06-01

    We continue our investigation of large field inflation models obtained from higher-dimensional gauge theories, initiated in our previous study [1]. We focus on Dante's Inferno model which was the most preferred model in our previous analysis. We point out the relevance of the IR obstruction to UV completion, which constrains the form of the potential of the massive vector field, under the current observational upper bound on the tensor to scalar ratio. We also show that in simple examples of the potential arising from DBI action of a D5-brane and that of an NS5-brane that the inflation takes place in the field range which is within the convergence radius of the Taylor expansion. This is in contrast to the well known examples of axion monodromy inflation where inflaton takes place outside the convergence radius of the Taylor expansion. This difference arises from the very essence of Dante's Inferno model that the effective inflaton potential is stretched in the inflaton field direction compared with the potential for the original field.

  16. A sensitive serodiagnosis of hepatitis C virus (HCV) infection with two non-fused peptides: comparison of antibody responses detected with a newly developed assay and a commercial second-generation test.

    Science.gov (United States)

    Sato, A; Ida, N; Ishikawa, M; Tanahashi, K; Nakamura, H; Sho, Y; Arima, T; Kunitomo, T

    1993-01-01

    An enzyme-linked immunosorbent assay (ELISA) was developed for the detection of anti-HCV antibody. We assayed for antibodies against either oligopeptide (S29-1) deduced from the nucleocapsid gene or the product of nonstructural region (NS3) synthesized in a recombinant Escherichia coli (S4). To reduce false-positive results induced by non-specific binding of antibodies with a carrier protein and to increase the sensitivity of an immunoassay, non-fused S4 peptide was prepared by the recombinant DNA technique and site-specific proteolysis (by factor Xa). In 71 non-A, non-B hepatitis patients with chronic liver disease, 70 (98.5%) were positive by S29-1/S4 ELISA as well as by a second-generation test (Abbott II). On the other hand, of 40 serum samples from blood donors, in which anti-N14 (core) and C100-3 antibodies were not detected but hepatitis C virus (HCV) RNA was detectable by polymerase chain reaction (PCR), 24 (60%) were positive by S29-1/S4 ELISA, whereas only 18 (45%) were diagnosed by Abbott II. In addition, based on results in a small group of 92 blood donors, detection of anti-S29-1/S4 antibody correlated well with HCV viremia as confirmed by PCR. These results indicated that the preparation of nonfused protein (S4) by recombinant DNA technique and a combination of S29-1 and S4 as immobilized antigens in an ELISA provide a sensitive and specific diagnosis for HCV infection with good correlation with the presence of viral RNA as confirmed by PCR. PMID:7688847

  17. Atomic scale control and understanding of cubic silicon carbide surface reconstructions, nanostructures and nanochemistry

    Science.gov (United States)

    Soukiassian, Patrick G.; Enriquez, Hanna B.

    2004-05-01

    The atomic scale ordering and properties of cubic silicon carbide (bgr-SiC) surfaces and nanostructures are investigated by atom-resolved room and high-temperature scanning tunnelling microscopy (STM) and spectroscopy (STS), synchrotron radiation-based valence band and core level photoelectron spectroscopy (VB-PES, CL-PES) and grazing incidence x-ray diffraction (GIXRD). In this paper, we review the latest results on the atomic scale understanding of (i) the structure of bgr-SiC(100) surface reconstructions, (ii) temperature-induced metallic surface phase transition, (iii) one dimensional Si(C) self-organized nanostructures having unprecedented characteristics, and on (iv) nanochemistry at SiC surfaces with hydrogen. The organization of these surface reconstructions as well as the 1D nanostructures' self-organization are primarily driven by surface stress. In this paper, we address such important issues as (i) the structure of the Si-rich 3 × 2, the Si-terminated c (4 × 2), the C-terminated c (2 × 2) reconstructions of the bgr-SiC(100) surface, (ii) the temperature-induced reversible {\\mathrm {c}}(4\\times 2) \\Leftrightarrow 2\\times 1 metallic phase transition, (iii) the formation of highly stable (up to 900 °C) Si atomic and vacancy lines, (iv) the temperature-induced sp to sp3 diamond like surface transformation, and (v) the first example of H-induced semiconductor surface metallization on the bgr-SiC (100) 3 × 2 surface. The results are discussed and compared to other experimental and theoretical investigations.

  18. First isolation and identification of Zika virus in China%我国首例寨卡病毒的分离与鉴定

    Institute of Scientific and Technical Information of China (English)

    吴德; 谈琦琪; 孙九峰; 周惠琼; 管大伟; 张欢; 宁丹; 柯昌文

    2016-01-01

    目的:建立寨卡病毒分离方法,为寨卡病毒的分离积累经验。方法将寨卡病毒血清阳性标本通过颅内注射途径接种1~3日龄BALB/c乳鼠,接种6日后处死,提取乳鼠脑、心、肝、脾、肺、肾、肌肉、皮肤和肠组织,均浆取上清提取病毒核酸,real-time RT-PCR进行核酸检测鉴定。阳性脑组织上清进行乳鼠传代接种。分离的病毒株用巢式PCR进行扩增,所获得的序列用MEGA6.0软件进行系统进化分析。结果从接种寨卡病毒的乳鼠脑、心和肝等组织中均可检测出寨卡病毒核酸,其中心和脑组织寨卡病毒Ct值最低,分别为24.4和25.3个循环。传代乳鼠病毒接种后2日可在乳鼠脑组织中检测出病毒核酸。巢式PCR成功扩增出1034个碱基大小的片段,进化分析结果显示本次分离的毒株属于亚洲族系。结论利用乳鼠颅内接种法,成功分离1株寨卡病毒,该病毒属于亚洲族系。%Objective To establish a method for the isolation of Zika virus and to gather experi-ences for viral isolation. Methods Suckling mice at age 1-3 days were inoculated with serum samples posi-tive for Zika virus through intracranial injection. All mice were sacrificed 6 days after the injection. Viral nu-cleic acids were extracted from brain, heart, liver, spleen, lung, kidney, muscle, skin and intestine tissue samples and analyzed by real-time RT-PCR. The supernatants of brain tissues positive for Zika virus were used for subculturing. Nested PCR was performed to amplify the NS5 gene of the isolated virus. The se-quences of NS5 gene were analyzed by using MEGA6. 0 software. Results All of the tissue samples were positive for Zika virus. Higher viral loads were detected in heart and brain tissue samples with cycle thresh-old (Ct) values of 24. 4 and 25. 3, respectively. The second generation of Zika virus was identified in suck-ling mice brain tissues 2 days after infection by using real-time RT-PCR. The amplified product of

  19. Development of a cell culture system with consistently expression of whole hepatitis C virus gene and Renilla luciferase and its application%丙型肝炎病毒全长基因嵌合萤光素酶重组质粒转染细胞系的建立与初步应用

    Institute of Scientific and Technical Information of China (English)

    徐洪涛; 肖丽; 咸建春; 陈亚宝

    2011-01-01

    目的 构建能产生较高效价重组病毒的HCV细胞感染模型,为HCV致病机制的研究和抗病毒药物的筛选提供一个有效的体外细胞培养系统.方法 利用PCR技术在HCV NS5A C端插入海肾萤光素酶( Renilla Luciferase,Rluc)报告基因,并引入能提高HCV效价的突变,酶切鉴定重组基因序列构建成功后,转染入肝癌细胞系Huh7.5,用细胞免疫荧光、免疫印迹法和萤光素酶活性分析检测病毒复制和感染水平.用IFNα鉴定该系统用于抗丙肝药物筛选的可行性.结果 在重组病毒JFH1-2440-Rluc RNA转染的细胞中可检测到Rluc的活性,而阴性对照JFH1-GND和野生株JFH1-wt RNA转染的细胞未检测到Rluc的活性,经连续传代,JFH 1-2440-Rluc RNA转染细胞所产生的病毒效价可达到1.5×104 FFU/mL,Rluc的活性随着IFNα浓度的增加而逐渐减低,呈现明显的剂量依赖特性.结论 构建的重组HCV-JFH1-Rluc报告基因系统具有经济、快速、敏感等优点,为抗HCV药物的筛选提供了有利平台.%Objective To develop a cell culture system with consistent expression of whole hepatitis C virus (HCV) gene and Renilla luciferase gene and to facilitate the study on HCV pathogenesis and the screening of new antiviral drugs.Methods Renilla luciferase (RLuc) reporter gene and a mutation that could yield higher virus gene expression were introduced into the C-terminus of non-structural protein 5A (NS5A) of the JFH1 viral genome by using recombinant PCR.The viral RNA was transfected into Huh7.5 cells.Naǐve Huh7.5 cells were infected by the supernatant from the viral RNA transfected cells.HCV replication and infection were determined by virus titration,Renilla luciferase assay,immunofluorescence assay and western blotting.IFN-α was used to evaluate the feasibility of this system for anti-HCV new drug screening.Results The viral RNA replicated efficiently in transfected cells.These cells could produce high titer of HCV-Rluc reporter virus and

  20. Perspectivas futuras en el tratamiento de la hepatitis crónica C Future perspective in the treatment of chronic hepatitis C

    Directory of Open Access Journals (Sweden)

    J.V. Fernández-Montero

    2011-06-01

    Full Text Available Se exponen las principales líneas de investigación en nuevos fármacos y estrategias de tratamiento contra la hepatitis vírica tipo C. Esta es una enfermedad que supone un importante problema de salud pública, con más de 700.000 afectados en España y con una importante prevalencia entre las personas privadas de libertad. Las limitaciones del actual tratamiento contra la hepatitis vírica C han forzado la investigación de nuevos fármacos que se van sustanciando en dos líneas principales de productos, algunos de ellos pronto disponibles en el mercado: los inhibidores de la serín-proteasa NS3/4ª (telaprevir, boceprevir, danoprevir o vaniprevir y los inhibidores de la RNA-polimerasa NS5B (RG-7128, RG-7227, Filibuvir, ANA-598, estos últimos en una fase de desarrollo algo más temprana. Previsiblemente habrá que utilizar estos nuevos fármacos añadidos al tratamiento estándar actual de interferón pegilado más ribavirina y en esas condiciones de uso todos estos fármacos han demostrado ya una mayor efectividad que el tratamiento estándar actual. A pesar de este esperanzador panorama, estos fármacos tienen limitaciones como el desarrollo de resistencias, la toxicidad o el poco conocimiento que tenemos de su efectividad en genotipos virales distintos del 1. No obstante su aparición abre muchas nuevas posibilidades en el tratamiento de esta enfermedad.The main lines of research into new drugs and treatment strategies against type C viral hepatitis are described. This disease is a major public health problem, with more than 700,000 people affected by the illness in Spain and with a high degree of prevalence amongst prison inmates. Limitations on current treatment for viral hepatitis C have led to research into new drugs in the form of two main product lines, some of which are soon to be available on the market: NS3/4ª serine-protease inhibitors (telaprevir, boceprevir, danoprevir and vaniprevir and the NS5B RNA polymerase inhibitors

  1. 猪源牛病毒性腹泻病毒SD0803株细胞传代研究%BIOLOGICAL CHARACTERISTICS OF PASSAGED ON MDBK CELLS BOVINE VIRAL DIARRHEA VIRUS OF PIG ORIGIN

    Institute of Scientific and Technical Information of China (English)

    孙春清; 邓宇; 张宏彪; 龙进学; 韦祖樟; 童光志; 袁世山

    2012-01-01

    To develop a Bovine viral diarrhea virus(BVDV) vaccine,the BVDV strain SD0803 of pig origin was passaged in MDBK cells for 40 times.Viral RNA was extracted from the 40th passage virus and 5 segments were amplified in RT-PCR.The complete genomic sequence was megaligned and compared with its parental virus using DNASTAR software.The results showed that the homology between the 40th passage and parental virus was 99.8% in nucleotides and 99.6 % in amino acids.Twenty three nucleotide mutations were identified,of which 15 were sense mutations.Amino acid mutations were mainly located on E2 and NS5B.To compare the growth characteristics between the parent virus and passaged viruses,supernatants were collected from infected MDCK cells at passages 1,10,20,30 and 40,and measured the amounts of released viral RNAs in RT-PCR.The multi-step growth curves showed that the parent virus and passaged viruses had high replication efficiency in MDBK cells,and shared similar growth properties.Some mutations that occurred during virus passages had no effect on the virus titers as determined by titration.%为研究猪源牛病毒性腹泻病毒(Bovine viral diarrhea virus,BVDV)生物学特性,将本实验室分离得到的SD0803毒株在马-达氏牛肾细胞(mardin-darby bovine kidney,MDBK)上连续传40代,提取第40代病毒基因组RNA,设计扩增及测序引物,用RT-PCR方法分5段扩增第40代病毒基因片段,并进行全长测序,利用DNASTAR软件进行序列拼接及分析,与亲代病毒SD0803序列比对分析;用Real-time PCR方法测定第1、10、20、30和40代细胞上清中的病毒复制效率,并绘制多步生长曲线。测序结果表明,第40代病毒与亲代病毒核苷酸序列的同源性为99.8%,氨基酸序列的同源性为99.6%,其中有23处发生核苷酸突变,14处为有义突变,氨基酸变化主要集中在E2和NS5B区域。多步生长曲线显示,传代病毒和亲本病毒均能在MDBK细胞上获得较高的复制效率,并

  2. 猪瘟病毒野毒株RT-LAMP可视化检测方法的建立%Visualized detection of wild-type classical swine fever virus using RT-LAMP

    Institute of Scientific and Technical Information of China (English)

    张兴娟; 孙元; 刘大飞; 仇华吉

    2009-01-01

    To develop a rapid and practical method to differentiate wild-type strains of classical swine fever virus (CSFV) and the attenuated C-strain, a reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay was established with a set of primers based on NS5B gene sequence. The viral cDNA generated by reverse transcription was amplified with Bst DNA polymerase at a constant temperature of 62 ℃, and the products could be visualized under the UV light with SYBR Green I dye. The RT-LAMP was able to detect different genotypes of wild-type CSFV strains, but not for the C-strain, bovine viral diarrhea virus or other swine viruses. The detection limit of the RT-LAMP assay was 2.5 TCID_(50) of CSFV, comparable to the sensitivity of the real-time RT-PCR. The agreement rate between RT-LAMP and the real-time RT-PCR or the primer-probe energy transfer real-time PCR was 100 % or 98.4 % in detecting 126 samples. Thus, the assay is a rapid, sensitive, simple and practical method for the detection of wild-type CSFV in the field.%本研究旨在建立一种可视化检测猪瘟病毒(CSFV)野毒株的反转录.环介导等温扩增方法(RT-LAMP).根据CSFV的NS5B基因序列设计一套RT-LAMP引物,以样品的cDNA为模板,利用Bsf DNA聚合酶,在62℃恒温条件下进行扩增,扩增产物中加入sYBR Green I染料直接或在紫外光下观察判定扩增结果.该方法可检测出不同基因型的CSFV厂野毒株,其检出极限为2.5 TCID_(50)的CSFV,与实时荧光定量RT.PCR方法的敏感性相当;特异性试验表明,该方法对猪瘟免化弱毒疫苗株(HCLV)、牛病毒性腹泻病毒以及其它常见猪源病毒均无扩增反应;通过对126份不同样品进行检测比较,该方法与实时荧光定量RT-LAMP检测方法的符合率达100%.与引物.探针能量转移PCR方法的符合率为98.4%.该方法无需特殊仪器,是一种适用于基层的快速、简便的CSFV野毒鉴别检测方法.

  3. 红壤侵蚀区杉木经营模式研究%Management Model of Cunninghamia lanceolata in Eroded Area of Red Soil

    Institute of Scientific and Technical Information of China (English)

    汤行昊; 李建民; 洪志猛; 范辉华; 黄石德; 游惠明

    2015-01-01

    In order to find a management model of Cunninghamia lanceolata which are suitable in eroded area of red soil,various silvicultural measures on C.lanceolata in red soil erosion area were studied.Result shows that the mean tree height & ground diameter by using the 2.5 generation seedling of C.lanceolata increase by 58.44% &51.75% than that by using normal seedlings in the testing ground.The mean tree height & ground diameter by a-dopting hole-spread with tending measures in the testing ground (NS4)increase by 19.67% and 21.39% than that in the testing ground (NS2)without tending measures.The tree height & ground diameter by adopting block tend-ing exceed 27.05% and 28.32% than that by adopting hole-spread with tending.In the testing ground (NS6)top dressed biogas manure,the mean tree height &ground diameter is 2.18 m and 3.06 cm,respectively.In the testing ground (NS5)top dressed fertilizer,the mean tree height&ground diameter is 1.89 m and 2.71cm,respectively.In the testing ground (NS3)with same seed selection and tending measures,but without dressing ,the seedling height is only 1.55 m,the mean ground diameter is only 2.22 cm.Application of biogas fertilizer can effectively promote the growth of Cunninghamia lanceolata.%为探寻适合在红壤侵蚀区应用和推广的杉木经营模式,对红壤侵蚀区的多种杉木营林措施进行了调查和研究。结果表明:采用2.5代杉木苗的试验地较采用普通苗造林的试验地,杉木植株平均树高和平均地径分别增长58.44%和51.75%。采用扩穴连带抚育措施的试验地 NS4较不抚育的试验地 NS2,平均树高和平均地径分别超出19.67%和21.39%;而采用块状抚育较扩穴连带抚育效果更佳,分别超出27.05%和28.32%。追施沼肥的NS6号试验地中,杉木平均树高为2.18 m,平均地径为3.06 cm;追施化肥的 NS5号试验地中,杉木平均树高为1.89 m,平均地径为2.71 cm;种苗选择和抚育措施相同但未进行追肥的 NS3

  4. 铁酸锌负载磷钨酸催化氧化噻吩脱硫研究%CATALYTIC OXIDATIVE DESULFURIZATION OF THIOPHENE OVER CATALYST OF PHOSPHOTUNGSTIC ACID SUPPORTED ON ZINC FERRITE

    Institute of Scientific and Technical Information of China (English)

    周二鹏; 王娟; 姚清国; 赵地顺

    2011-01-01

    以噻吩溶液为模型化合物、铁酸锌负载磷钨酸为催化剂、H2O2为氧化剂,进行催化氧化脱硫研究,考察氧化时间、氧化温度、氧化剂用量、催化剂上磷钨酸负载量、催化剂活化温度等工艺条件对脱硫率的影响.研究结果表明:催化剂上磷钨酸的最佳负载量(ω)为13%、活化温度为250℃;适宜的反应条件为:反应温度40℃,反应时间210 min,氧化剂用量n(H2O2)∶ n(S)=5.在上述条件下模型化合物的脱硫率达到90.1%.%Using F^C^as oxidation agent, oxidation/extraction desulfurization of thiophene containing model compound over catalyst of phosphotungstic acid supported on zinc ferrite was investigated including the effect of oxidation agent amount, oxidation temperature and time, the amount of phosphotungstic acid on catalyst and catalyst activation temperature on the desulfurization rate. Results showed that using catalyst activated at 250 °C and having an optimal phosphotungstic acid mass fraction of 13% , under the optimum conditions of a reaction temperature of 40 °C ,a reaction time of 210 min and H2O2/S molar ratio of 5,the sulfur removal rate of thiophene reached 90. 1%.

  5. Genetic diversity of near genome-wide hepatitis C virus sequences during chronic infection: evidence for protein structural conservation over time.

    Directory of Open Access Journals (Sweden)

    Hui Li

    Full Text Available Infection with hepatitis C virus (HCV is one of the leading causes of chronic hepatitis, liver cirrhosis and end-stage liver disease worldwide. The genetics of HCV infection in humans and the disease course of chronic hepatitis C are both remarkably variable. Although the response to interferon treatment is largely dependent on HCV genotypes, whether or not a relationship exists between HCV genome variability and clinical course of hepatitis C disease still remains unknown. To more thoroughly understand HCV genome evolution over time in association with disease course, near genome-wide HCV genomes present in 9 chronically infected participants over 83 total study years were sequenced. Overall, within HCV genomes, the number of synonymous substitutions per synonymous site (d(S significantly exceeded the number of non-synonymous substitutions per site (d(N. Although both d(S and d(N significantly increased with duration of chronic infection, there was a highly significant decrease in d(N/d(S ratio in HCV genomes over time. These results indicate that purifying selection acted to conserve viral protein structure despite persistence of high level of nucleotide mutagenesis inherent to HCV replication. Based on liver biopsy fibrosis scores, HCV genomes from participants with advanced fibrosis had significantly greater d(S values and lower d(N/d(S ratios compared to participants with mild liver disease. Over time, viral genomes from participants with mild disease had significantly greater annual changes in d(N, along with higher d(N/d(S ratios, compared to participants with advanced fibrosis. Yearly amino acid variations in the HCV p7, NS2, NS3 and NS5B genes were all significantly lower in participants with severe versus mild disease, suggesting possible pathogenic importance of protein structural conservation for these viral gene products.

  6. Phylogenetic analysis of Dengue virus 1 isolated from South Minas Gerais, Brazil

    Science.gov (United States)

    Drumond, Betania Paiva; da Silva Fagundes, Luiz Gustavo; Rocha, Raissa Prado; Fumagalli, Marcilio Jorge; Araki, Carlos Shigueru; Colombo, Tatiana Elisa; Nogueira, Mauricio Lacerda; Castilho, Thiago Elias; da Silveira, Nelson José Freitas; Malaquias, Luiz Cosme Cotta; Coelho, Luiz Felipe Leomil

    2016-01-01

    Dengue is a major worldwide public health problem, especially in the tropical and subtropical regions of the world. Primary infection with a single Dengue virus serotype causes a mild, self-limiting febrile illness called dengue fever. However, a subset of patients who experience secondary infection with a different serotype can progress to a more severe form of the disease, called dengue hemorrhagic fever. The four Dengue virus serotypes (1–4) are antigenically and genetically distinct and each serotype is composed of multiple genotypes. In this study we isolated one Dengue virus 1 serotype, named BR/Alfenas/2012, from a patient with dengue hemorrhagic fever in Alfenas, South Minas Gerais, Brazil and molecular identification was performed based on the analysis of NS5 gene. Swiss mice were infected with this isolate to verify its potential to induce histopathological alterations characteristic of dengue. Liver histopathological analysis of infected animals showed the presence of inflammatory infiltrates, hepatic steatosis, as well as edema, hemorrhage and necrosis focal points. Phylogenetic and evolutionary analyses based on the envelope gene provided evidence that the isolate BR/Alfenas/2012 belongs to genotype V, lineage I and it is probably derived from isolates of Rio de Janeiro, Brazil. The isolate BR/Alfenas/2012 showed two unique amino acids substitutions (SER222THRE and PHE306SER) when compared to other Brazilian isolates from the same genotype/lineage. Molecular models were generated for the envelope protein indicating that the amino acid alteration PHE 306 SER could contribute to a different folding in this region located within the domain III. Further genetic and animal model studies using BR/Alfenas/2012 and other isolates belonging to the same lineage/genotype could help determine the relation of these genetic alterations and dengue hemorrhagic fever in a susceptible population. PMID:26887252

  7. DENGUE OUTBREAK IN MATO GROSSO STATE, MIDWESTERN BRAZIL

    Science.gov (United States)

    HEINEN, Letícia Borges da Silva; ZUCHI, Nayara; CARDOSO, Belgath Fernandes; dos SANTOS, Marcelo Adriano Mendes; NOGUEIRA, Mauricio Lacerda; DEZENGRINI-SLHESSARENKO, Renata

    2015-01-01

    Dengue virus (DENV) is the most frequent arbovirus worldwide. In this study, we report a large outbreak in Mato Grosso State (MT). Serum samples from 604 patients with acute febrile illness for less than five days were inoculated in C6/36 cells, then infected cells were subjected to an indirect immunofluorescence test for DENV serotypes and yellow fever virus. Serum samples were submitted to a multiplex-semi-nested-RT-PCR for 11 flaviviruses. DENV-4 was isolated in 150/604 (24.8%) and DENV-1 in 19/604 (3.1%) specimens. By RT-PCR, 331 (54.8%) samples tested positive for DENV; 321 had single infections (DENV-4 n = 305; DENV-1 n = 15; DENV-3 n = 1), nine had co-infections of DENV-1/DENV-4, and one of DENV-2/DENV-4. DENV-4 was detected in 315/331 (95.2%) positive patients from 17 municipalities, and DENV-1 in 24/331 (7.2%) patients from five cities in north-central MT and the city of Cuiaba. The incidence of infection was higher in patients aged 20-39 (142/331; 42.9%). The NS5 partial nucleotide sequence of DENV-1 was most similar to that of genotype V, DENV-2 to Southeast Asian/American, DENV-3 to genotype III, and DENV-4 to genotype II strains, considered the most frequent strains in Brazil. This outbreak coincided with the introduction of DENV-4 in the state. Cuiaba was hyperendemic for the four DENV serotypes, highlighting the necessity for arbovirus surveillance in MT. PMID:27049702

  8. Changing Epidemiology of Hepatitis C Virus Genotype among Patients with Human Immunodeficiency Virus/Hepatitis C Virus Co-Infection in China

    Science.gov (United States)

    Hu, Fengyu; Nie, Jingmin; Lan, Yun; Li, Huiqin; Lu, Ruichao; Gao, Yanqing; Song, Yuxia; Zhao, Qingxia; Zheng, Yuhuang; Tang, Xiaoping; Cai, Weiping

    2016-01-01

    Background Co-infection with hepatitis C virus (HCV) has become the most common cause of death in human immunodeficiency virus (HIV) infected patients on antiretroviral therapy. The distribution of HCV genotypes varies with geographical regions and time, and limited studies have focused on the HCV genotype in HIV/HCV co-infection. Methods The distribution of HCV genotypes was evaluated in 414 patients with HIV/HCV co-infection in three regions (South, Central and Northwest) of China from 2008 to 2010. The NS5B region of HCV was characterized using nested reverse transcription polymerase chain reaction. Nucleotide sequences obtained were subjected to phylogenetic analysis, and genotypes were assigned using published reference genotypes. Results Genotype 3 was the most prevalent HCV strain (36.2%), followed by genotype 6 (30.0%), genotype 1 (28.5%), genotype 2 (5.1%), and genotype 5 (0.2%). The distribution varied geographically. Genotype 6 (37.6%) was the predominant strain while genotype 1 (20.2%) was less common in the South compared to the Central and Northwest regions (all P < 0.001). The distribution also varied temporally. There was no significant difference in genotype distribution in Guangdong (a province in the South region), between patient cohorts from 2005–2008 and 2009–2010. However, outside Guangdong, genotypes 3 and 6a became significantly more prevalent (22.4% vs.42.2%, P< 0.001; 8.0% vs. 19.8%, P = 0.004), and genotype 1 less prevalent (54.4% vs.26.6%, P< 0.001) over time. Conclusion The most dramatic shift in genotypic distribution was the movement of HCV genotypes 3 and 6a outside of Guangdong in HIV/HCV co-infected patients. This movement appeared closely associated with transmission via injected drug use. PMID:27603929

  9. Active RNA replication of hepatitis C virus downregulates CD81 expression.

    Directory of Open Access Journals (Sweden)

    Po-Yuan Ke

    Full Text Available So far how hepatitis C virus (HCV replication modulates subsequent virus growth and propagation still remains largely unknown. Here we determine the impact of HCV replication status on the consequential virus growth by comparing normal and high levels of HCV RNA expression. We first engineered a full-length, HCV genotype 2a JFH1 genome containing a blasticidin-resistant cassette inserted at amino acid residue of 420 in nonstructural (NS protein 5A, which allowed selection of human hepatoma Huh7 cells stably-expressing HCV. Short-term establishment of HCV stable cells attained a highly-replicating status, judged by higher expressions of viral RNA and protein as well as higher titer of viral infectivity as opposed to cells harboring the same genome without selection. Interestingly, maintenance of highly-replicating HCV stable cells led to decreased susceptibility to HCV pseudotyped particle (HCVpp infection and downregulated cell surface level of CD81, a critical HCV entry (coreceptor. The decreased CD81 cell surface expression occurred through reduced total expression and cytoplasmic retention of CD81 within an endoplasmic reticulum -associated compartment. Moreover, productive viral RNA replication in cells harboring a JFH1 subgenomic replicon containing a similar blasticidin resistance gene cassette in NS5A and in cells robustly replicating full-length infectious genome also reduced permissiveness to HCVpp infection through decreasing the surface expression of CD81. The downregulation of CD81 surface level in HCV RNA highly-replicating cells thus interfered with reinfection and led to attenuated viral amplification. These findings together indicate that the HCV RNA replication status plays a crucial determinant in HCV growth by modulating the expression and intracellular localization of CD81.

  10. Ledipasvir and Sofosbuvir for HCV in Patients Coinfected with HIV-1

    Science.gov (United States)

    Naggie, Susanna; Cooper, Curtis; Saag, Michael; Workowski, Kimberly; Ruane, Peter; Towner, William J.; Marks, Kristen; Luetkemeyer, Anne; Baden, Rachel P.; Sax, Paul E.; Gane, Edward; Santana-Bagur, Jorge; Stamm, Luisa M.; Yang, Jenny C.; German, Polina; Dvory-Sobol, Hadas; Ni, Liyun; Pang, Phillip S.; McHutchison, John G.; Stedman, Catherine A.M.; Morales-Ramirez, Javier O.; Bräu, Norbert; Jayaweera, Dushyantha; Colson, Amy E.; Tebas, Pablo; Wong, David K.; Dieterich, Douglas; Sulkowski, Mark

    2016-01-01

    BACKGROUND Effective treatment for hepatitis C virus (HCV) in patients coinfected with human immunodeficiency virus type 1 (HIV-1) remains an unmet medical need. METHODS We conducted a multicenter, single-group, open-label study involving patients coinfected with HIV-1 and genotype 1 or 4 HCV receiving an antiretroviral regimen of tenofovir and emtricitabine with efavirenz, rilpivirine, or raltegravir. All patients received ledipasvir, an NS5A inhibitor, and sofosbuvir, a nucleotide polymerase inhibitor, as a single fixed-dose combination for 12 weeks. The primary end point was a sustained virologic response at 12 weeks after the end of therapy. RESULTS Of the 335 patients enrolled, 34% were black, 55% had been previously treated for HCV, and 20% had cirrhosis. Overall, 322 patients (96%) had a sustained virologic response at 12 weeks after the end of therapy (95% confidence interval [CI], 93 to 98), including rates of 96% (95% CI, 93 to 98) in patients with HCV genotype 1a, 96% (95% CI, 89 to 99) in those with HCV genotype 1b, and 100% (95% CI, 63 to 100) in those with HCV genotype 4. Rates of sustained virologic response were similar regardless of previous treatment or the presence of cirrhosis. Of the 13 patients who did not have a sustained virologic response, 10 had a relapse after the end of treatment. No patient had confirmed HIV-1 viro-logic rebound. The most common adverse events were headache (25%), fatigue (21%), and diarrhea (11%). No patient discontinued treatment because of adverse events. CONCLUSIONS Ledipasvir and sofosbuvir for 12 weeks provided high rates of sustained virologic response in patients coinfected with HIV-1 and HCV genotype 1 or 4. (Funded by Gilead Sciences; ION-4 ClinicalTrials.gov number, NCT02073656.) PMID:26196665

  11. Visualization of the structures of the hepatitis C virus replication complex

    Energy Technology Data Exchange (ETDEWEB)

    Chan, Shih-Ching [Graduate Institute of Molecular and Cellular Biology, Tzu Chi University, Hualien, Taiwan (China); Lo, Shih-Yen [Graduate Institute of Medical Biotechnology, Tzu Chi University, Hualien, Taiwan (China); Graduate Institute of Medical Sciences, Tzu Chi University, Hualien, Taiwan (China); Liou, Je-Wen [Graduate Institute of Medical Sciences, Tzu Chi University, Hualien, Taiwan (China); Department of Biochemistry, Tzu Chi University, Hualien, Taiwan (China); Lin, Min-Ching [Graduate Institute of Medical Biotechnology, Tzu Chi University, Hualien, Taiwan (China); Syu, Ciao-Ling [Graduate Institute of Medical Sciences, Tzu Chi University, Hualien, Taiwan (China); Lai, Meng-Jiun; Chen, Yi- Cheng [Graduate Institute of Medical Biotechnology, Tzu Chi University, Hualien, Taiwan (China); Li, Hui-Chun, E-mail: huichun@mail.tcu.edu.tw [Graduate Institute of Molecular and Cellular Biology, Tzu Chi University, Hualien, Taiwan (China); Graduate Institute of Medical Sciences, Tzu Chi University, Hualien, Taiwan (China); Department of Biochemistry, Tzu Chi University, Hualien, Taiwan (China)

    2011-01-07

    Research highlights: {yields} Lipid rafts are known to play an important role in virus entry and virus assembly of many viruses. {yields} However, HCV is the first example of the association of lipid raft with viral RNA replication. {yields} Our results in this manuscript demonstrate that purified HCV RCs with associated lipid raft membrane appeared as distinct particles of around 0.7 um under EM and AFM. {yields} Knockdown of proteins associated with lipid raft suppressed the HCV replication and reduced the number of these particles. {yields} To our knowledge, structures of HCV RCs were demonstrated at its first time in this manuscript. -- Abstract: Hepatitis C viral RNA synthesis has been demonstrated to occur on a lipid raft membrane structure. Lipid raft membrane fraction purified by membrane flotation analysis was observed using transmission electron microscopy and atomic force microscopy. Particles around 0.7 um in size were found in lipid raft membrane fraction purified from hepatitis C virus (HCV) replicon but not their parental HuH7 cells. HCV NS5A protein was associated with these specialized particles. After several cycles of freezing-thawing, these particles would fuse into larger sizes up to 10 um. Knockdown of seven proteins associated with lipid raft (VAPA, COPG, RAB18, COMT, CDC42, DPP4, and KDELR2) of HCV replicon cells reduced the observed number of these particles and suppressed the HCV replication. Results in this study indicated that HCV replication complexes with associated lipid raft membrane form distinct particle structures of around 0.7 um as observed from transmission electron microscopy and atomic force microscopy.

  12. Evaluation and optimization of SYBR Green real-time reverse transcription polymerase chain reaction as a tool for diagnosis of the Flavivirus genus in Brazil

    Directory of Open Access Journals (Sweden)

    Marilia Farignoli Romeiro

    2016-06-01

    Full Text Available Abstract: INTRODUCTION: The genus Flavivirus includes several pathogenic species that cause severe illness in humans. Therefore, a rapid and accurate molecular method for diagnosis and surveillance of these viruses would be of great importance. Here, we evaluate and optimize a quantitative real-time reverse transcription polymerase chain reaction (RT-PCR method for the diagnosis of the Flavivirus genus. METHODS: We evaluated different commercial kits that use the SYBR Green system for real-time RT-PCR with a primer set that amplifies a fragment of the NS5 flavivirus gene. The specificity and sensitivity of the assay were tested using twelve flaviviruses and ribonucleic acid (RNA transcribed from the yellow fever virus. Additionally, this assay was evaluated using the sera of 410 patients from different regions of Brazil with acute febrile illness and a negative diagnosis for the dengue virus. RESULTS: The real-time RT-PCR amplified all flaviviruses tested at a melting temperature of 79.92 to 83.49°C. A detection limit of 100 copies per ml was determined for this assay. Surprisingly, we detected dengue virus in 4.1% (17/410 of samples from patients with febrile illness and a supposedly negative dengue infection diagnosis. The viral load in patients ranged from 2.1×107to 3.4×103copies per ml. CONCLUSIONS: The real-time RT-PCR method may be very useful for preliminary diagnoses in screenings, outbreaks, and other surveillance studies. Moreover, this assay can be easily applied to monitor viral activity and to measure viral load in pathogenesis studies.

  13. Social networks shape the transmission dynamics of hepatitis C virus.

    Directory of Open Access Journals (Sweden)

    Camila Malta Romano

    Full Text Available Hepatitis C virus (HCV infects 170 million people worldwide, and is a major public health problem in Brazil, where over 1% of the population may be infected and where multiple viral genotypes co-circulate. Chronically infected individuals are both the source of transmission to others and are at risk for HCV-related diseases, such as liver cancer and cirrhosis. Before the adoption of anti-HCV control measures in blood banks, this virus was mainly transmitted via blood transfusion. Today, needle sharing among injecting drug users is the most common form of HCV transmission. Of particular importance is that HCV prevalence is growing in non-risk groups. Since there is no vaccine against HCV, it is important to determine the factors that control viral transmission in order to develop more efficient control measures. However, despite the health costs associated with HCV, the factors that determine the spread of virus at the epidemiological scale are often poorly understood. Here, we sequenced partial NS5b gene sequences sampled from blood samples collected from 591 patients in São Paulo state, Brazil. We show that different viral genotypes entered São Paulo at different times, grew at different rates, and are associated with different age groups and risk behaviors. In particular, subtype 1b is older and grew more slowly than subtypes 1a and 3a, and is associated with multiple age classes. In contrast, subtypes 1a and 3b are associated with younger people infected more recently, possibly with higher rates of sexual transmission. The transmission dynamics of HCV in São Paulo therefore vary by subtype and are determined by a combination of age, risk exposure and underlying social network. We conclude that social factors may play a key role in determining the rate and pattern of HCV spread, and should influence future intervention policies.

  14. Validation and Application of a Liquid Chromatography-Tandem Mass Spectrometry Method To Determine the Concentrations of Sofosbuvir Anabolites in Cells.

    Science.gov (United States)

    Rower, Joseph E; Jimmerson, Leah C; Chen, Xinhui; Zheng, Jia-Hua; Hodara, Ariel; Bushman, Lane R; Anderson, Peter L; Kiser, Jennifer J

    2015-12-01

    Sofosbuvir (SOF) is a highly efficacious and well-tolerated uridine nucleotide analog that inhibits the hepatitis C virus (HCV) NS5B polymerase enzyme. SOF is administered as a prodrug, which undergoes intracellular phosphorylation by host enzymes to a monophosphate, diphosphate, and finally a pharmacologically active triphosphate. In order to fully understand the clinical pharmacology of SOF, there is a great need to determine the intracellular phosphate concentrations of the drug. We describe the validation and utilization of a method to characterize SOF's disposition into various in vivo cell types, including hepatocytes, peripheral blood mononuclear cells (PBMC), and red blood cells (RBC). Standard bioanalytical validation criteria were applied to lysed cellular matrices, with a validated linear range of 50 to 50,000 fmol/sample for each phosphate moiety. The assay was utilized to collect the first data demonstrating concentrations of phosphorylated anabolites formed in PBMC, hepatocytes, and RBC in vivo during SOF therapy. Median concentrations in PBMC were 220 (range, 51.5 to 846), 70.2 (range, 25.8 to 275), and 859 (range, 54.5 to 6,756) fmol/10(6) cells in the monophosphate, diphosphate, and triphosphate fractions, respectively. In contrast, RBC triphosphate concentrations were much lower than those of PBMC, as the median concentration was 2.91 (range, 1.14 to 10.4) fmol/10(6) cells. The PBMC triphosphate half-life was estimated at 26 h using noncompartmental approaches, while nonlinear mixed-effect modeling was used to estimate a 69 h half-life for this moiety in RBC. The validated method and the data it generates provide novel insight into the cellular disposition of SOF and its phosphorylated anabolites in vivo. PMID:26416874

  15. Nonstructural Proteins Are Preferential Positive Selection Targets in Zika Virus and Related Flaviviruses

    Science.gov (United States)

    Sironi, Manuela; Forni, Diego; Clerici, Mario; Cagliani, Rachele

    2016-01-01

    The Flavivirus genus comprises several human pathogens such as dengue virus (DENV), Japanese encephalitis virus (JEV), and Zika virus (ZIKV). Although ZIKV usually causes mild symptoms, growing evidence is linking it to congenital birth defects and to increased risk of Guillain-Barré syndrome. ZIKV encodes a polyprotein that is processed to produce three structural and seven nonstructural (NS) proteins. We investigated the evolution of the viral polyprotein in ZIKV and in related flaviviruses (DENV, Spondweni virus, and Kedougou virus). After accounting for saturation issues, alignment uncertainties, and recombination, we found evidence of episodic positive selection on the branch that separates DENV from the other flaviviruses. NS1 emerged as the major selection target, and selected sites were located in immune epitopes or in functionally important protein regions. Three of these sites are located in an NS1 region that interacts with structural proteins and is essential for virion biogenesis. Analysis of the more recent evolutionary history of ZIKV lineages indicated that positive selection acted on NS5 and NS4B, this latter representing the preferential target. All selected sites were located in the N-terminal portion of NS4B, which inhibits interferon response. One of the positively selected sites (26M/I/T/V) in ZIKV also represents a selection target in sylvatic DENV2 isolates, and a nearby residue evolves adaptively in JEV. Two additional positively selected sites are within a protein region that interacts with host (e.g. STING) and viral (i.e. NS1, NS4A) proteins. Notably, mutations in the NS4B region of other flaviviruses modulate neurovirulence and/or neuroinvasiveness. These results suggest that the positively selected sites we identified modulate viral replication and contribute to immune evasion. These sites should be prioritized in future experimental studies. However, analyses herein detected no selective events associated to the spread of the Asian

  16. Innate immunity to dengue virus infection and subversion of antiviral responses.

    Science.gov (United States)

    Green, Angela M; Beatty, P Robert; Hadjilaou, Alexandros; Harris, Eva

    2014-03-20

    Dengue is a major public health issue in tropical and subtropical regions worldwide. The four serotypes of dengue virus (DENV1-DENV4) are spread primarily by Aedes aegypti and Aedes albopictus mosquitoes, whose geographic range continues to expand. Humans are the only host for epidemic strains of DENV, and the virus has developed sophisticated mechanisms to evade human innate immune responses. The host cell's first line of defense begins with an intracellular signaling cascade resulting in production of interferon α/β (IFN-α/β), which promotes intracellular antiviral responses and helps initiates the adaptive response during the course of DENV infection. In response, DENV has developed numerous ways to subvert these intracellular antiviral responses and directly inhibit cellular signaling cascades. Specifically, DENV manipulates the unfolded protein response and autophagy to counter cellular stress and delay apoptosis. The DENV non-structural protein NS4B and subgenomic flavivirus RNA interfere with the RNA interference pathway by inhibiting the RNase Dicer. During heterotypic secondary DENV infection, subneutralizing antibodies can enable viral uptake through Fcγ receptors and down-regulate signaling cascades initiated via the pattern recognition receptors TLR-3 and MDA5/RIG-I, thus reducing the antiviral state of the cell. The DENV NS2B/3 protein cleaves human STING/MITA, interfering with induction of IFN-α/β. Finally, DENV NS2A, NS4A, and NS4B complex together to block STAT1 phosphorylation, while NS5 binds and promotes degradation of human STAT2, thus preventing formation of the STAT1/STAT2 heterodimer and its transcriptional induction of interferon stimulating genes. Here, we discuss the host innate immune response to DENV and the mechanisms of immune evasion that DENV has developed to manipulate cellular antiviral responses. PMID:24316047

  17. Antibody screening tests variably overestimate the prevalence of hepatitis C virus infection among HIV-infected adults in Ghana.

    Science.gov (United States)

    King, S; Adjei-Asante, K; Appiah, L; Adinku, D; Beloukas, A; Atkins, M; Sarfo, S F; Chadwick, D; Phillips, R O; Geretti, A M

    2015-05-01

    HIV coinfection with HCV has been poorly studied in sub-Saharan Africa, and the reliability of available seroprevalence estimates remains uncertain. The study aim was to determine HCV RNA prevalence in HIV-infected subjects receiving care in Kumasi, Ghana, and relate the findings to HCV antibody detection. From a population of 1520 HIV-infected adults, all HBsAg-positive subjects (n = 236) and a random subset of HBsAg-negative subject (n = 172) were screened for HCV RNA using pooled plasma; positive samples were genotyped by core and NS5B sequencing. HCV antibodies were detected by three commercial screening assays and confirmed by the line immunoassay. HCV RNA was detected in 4/408 subjects (1.0%, 95% confidence interval 0.0-1.9%), comprising 3/236 (1.3%; 0.0-2.8%) HBsAg-positive and 1/172 (0.6%; 0.0-1.8%) HBsAg-negative subjects. HCV RNA-positive subjects showed reactivity in all three antibody screening assays. Among HCV RNA-negative subjects, 5/67 (7.5%), 5/67 (7.5%) and 19/67 (28.4%) showed antibody reactivity by each screening assay, respectively, including two (3.0%) with reactivity by all three assays. Only one sample (1.5%) had confirmed antibody reactivity by line immunoassay indicating past HCV infection. HCV-positive subjects (three males, two females) were aged 30-46 years, by questionnaire-based interview reported surgical procedures and blood transfusion as risk factors for infection. HCV genotypes were 2 (subtypes 2j, 2l, 2k/unassigned) and 1 (subtype unassigned). Without further testing, HCV antibody screening assays variably overestimated HCV prevalence among HIV-infected subjects in Ghana. These findings inform the interpretation of previous seroprevalence estimates based upon screening assays alone.

  18. Scintillation properties of lead sulfate

    International Nuclear Information System (INIS)

    We report on the scintillation properties of lead sulfate (PbSO4), a scintillator that show promise as a high energy photon detector. It physical properties are well suited for gamma detection, as its has a density of 6.4 gm/cm3, a 1/e attenuation length for 511 keV photons of 1.2 cm, is not affected by air or moisture, and is cut and polished easily. In 99.998% pure PbSO4 crystals at room temperature excited by 511 keV annihilation photons, the fluorescence decay lifetime contains significant fast components having 1.8 ns (5%) and 19 ns (36%) decay times, but with longer components having 95 ns (36%) and 425 ns (23%) decays times. The peak emission wavelength is 335 nm, which is transmitted by borosilicate glass windowed photomultiplier tubes. The total scintillation light output increases with decreasing temperature fro 3,200 photons/MeV at +45 degrees C to 4, 900 photons/MeV at room temperature (+25 degrees C) and 68,500 photons/MeV at -145 degrees C. In an imperfect, 3 mm cube of a naturally occurring mineral form of PbSO4 (anglesite) at room temperature, a 511 keV photopeak is seen with a total light output of 60% that BGO. There are significant sample to sample variations of the light output among anglesite samples, so the light output of lead sulfate may improve when large synthetic crystals become available. 10 refs

  19. Logical design of anti-prion agents using NAGARA.

    Science.gov (United States)

    Ma, Biao; Yamaguchi, Keiichi; Fukuoka, Mayuko; Kuwata, Kazuo

    2016-01-22

    To accelerate the logical drug design procedure, we created the program "NAGARA," a plugin for PyMOL, and applied it to the discovery of small compounds called medical chaperones (MCs) that stabilize the cellular form of a prion protein (PrP(C)). In NAGARA, we constructed a single platform to unify the docking simulation (DS), free energy calculation by molecular dynamics (MD) simulation, and interfragment interaction energy (IFIE) calculation by quantum chemistry (QC) calculation. NAGARA also enables large-scale parallel computing via a convenient graphical user interface. Here, we demonstrated its performance and its broad applicability from drug discovery to lead optimization with full compatibility with various experimental methods including Western blotting (WB) analysis, surface plasmon resonance (SPR), and nuclear magnetic resonance (NMR) measurements. Combining DS and WB, we discovered anti-prion activities for two compounds and tegobuvir (TGV), a non-nucleoside non-structural protein NS5B polymerase inhibitor showing activity against hepatitis C virus genotype 1. Binding profiles predicted by MD and QC are consistent with those obtained by SPR and NMR. Free energy analyses showed that these compounds stabilize the PrP(C) conformation by decreasing the conformational fluctuation of the PrP(C). Because TGV has been already approved as a medicine, its extension to prion diseases is straightforward. Finally, we evaluated the affinities of the fragmented regions of TGV using QC and found a clue for its further optimization. By repeating WB, MD, and QC recursively, we were able to obtain the optimum lead structure.

  20. Virological confirmation of suspected dengue in a Phase 2 Latin American vaccine trial: Implications for vaccine efficacy evaluation

    Directory of Open Access Journals (Sweden)

    Mark Boaz

    2014-01-01

    Full Text Available The CYD tetravalent dengue vaccine candidate is being evaluated for protective efficacy against symptomatic dengue in Phase 3 efficacy trials. The laboratory test algorithm to confirm dengue cases was evaluated prior to Phase 3 trials. During a Phase 2 trial in Latin America a dengue epidemic occurred in the study countries. A total of 72 suspected dengue cases were reported and assessed: virological confirmation comprised qRT-PCR methods and a commercial ELISA kit for NS1 protein (Bio-Rad. The qRT-PCR included a screening assay targeting a conserved dengue region of the 3′-UTR (dengue screen assay followed by 4 individual serotype assays targeting the conserved dengue NS5 genomic region (WT dengue qRT-PCR assays. The NS1 and WT dengue qRT-PCR were endpoint assays for protocol virological confirmation (PVC. Of the 72 suspected cases, 14 were PVC. However, a unique pattern of dengue qRT-PCR results were observed in 5 suspected cases from Honduras: the dengue screen qRT-PCR assay was positive but WT dengue qRT-PCR and NS1 Ag ELISA were negative. To investigate these observations, additional molecular methods were applied: a SYBR® Green-based RT-PCR assay, sequencing assays directed at the genome regions covered by the WT dengue qRT-PCR, and a modified commercial dengue RT-PCR test (Simplexa™ Dengue, Focus Diagnostics. The exploratory data confirmed these additional cases as dengue and indicated the serotype 2 WT dengue qRT-PCR assay was unable to detect a circulating Latin American strain (DENV-2/NI/BID-V608/2006 due to a sequence variation in the isolate. The Simplexa Dengue RT-PCR test was able to detect and serotype dengue. Based on these findings an updated molecular test algorithm for the virological confirmation of dengue cases was developed and implemented in the Phase 3 efficacy trials.

  1. Development of a recombinant, chimeric tetravalent dengue vaccine candidate.

    Science.gov (United States)

    Osorio, Jorge E; Partidos, Charalambos D; Wallace, Derek; Stinchcomb, Dan T

    2015-12-10

    Dengue is a significant threat to public health worldwide. Currently, there are no licensed vaccines available for dengue. Takeda Vaccines Inc. is developing a live, attenuated tetravalent dengue vaccine candidate (TDV) that consists of an attenuated DENV-2 strain (TDV-2) and three chimeric viruses containing the prM and E protein genes of DENV-1, -3 and -4 expressed in the context of the attenuated TDV-2 genome backbone (TDV-1, TDV-3, and TDV-4, respectively). TDV has been shown to be immunogenic and efficacious in nonclinical animal models. In interferon-receptor deficient mice, the vaccine induces humoral neutralizing antibody responses and cellular immune responses that are sufficient to protect from lethal challenge with DENV-1, DENV-2 or DENV-4. In non-human primates, administration of TDV induces innate immune responses as well as long lasting antibody and cellular immunity. In Phase 1 clinical trials, the safety and immunogenicity of two different formulations were assessed after intradermal or subcutaneous administration to healthy, flavivirus-naïve adults. TDV administration was generally well-tolerated independent of dose and route. The vaccine induced neutralizing antibody responses to all four DENV serotypes: after a single administration of the higher formulation, 24-67%% of the subjects seroconverted to all four DENV and >80% seroconverted to three or more viruses. In addition, TDV induced CD8(+) T cell responses to the non-structural NS1, NS3 and NS5 proteins of DENV. TDV has been also shown to be generally well tolerated and immunogenic in a Phase 2 clinical trial in dengue endemic countries in adults and children as young as 18 months. Additional clinical studies are ongoing in preparation for a Phase 3 safety and efficacy study.

  2. Oversizing and Restenosis with Self-Expanding Stents in Iliofemoral Arteries

    Energy Technology Data Exchange (ETDEWEB)

    Saguner, Ardan M., E-mail: ardan.saguner@usz.ch; Traupe, Tobias; Raeber, Lorenz; Hess, Nina [University Hospital, Swiss Cardiovascular Center (Switzerland); Banz, Yara [University of Bern, Institute of Pathology (Switzerland); Saguner, Arhan R.; Diehm, Nicolas; Hess, Otto M. [University Hospital, Swiss Cardiovascular Center (Switzerland)

    2012-08-15

    Purpose: Uncoated self-expanding nitinol stents (NS) are commonly oversized in peripheral arteries. In current practice, 1-mm oversizing is recommended. Yet, oversizing of NS may be associated with increased restenosis. To provide further evidence, NS were implanted in porcine iliofemoral arteries with a stent-to-artery-ratio between 1.0 and 2.3. Besides conventional uncoated NS, a novel self-expanding NS with an antiproliferative titanium-nitride-oxide (TiNOX) coating was tested for safety and efficacy. Methods: Ten uncoated NS and six TiNOX-coated NS (5-6 mm) were implanted randomly in the iliofemoral artery of six mini-pigs. After implantation, quantitative angiography (QA) was performed for calculation of artery and minimal luminal diameter. Follow-up was performed by QA and histomorphometry after 5 months. Results: Stent migration, stent fracture, or thrombus formation were not observed. All stents were patent at follow-up. Based on the location of the stent (iliac/femoral) and the stent-to-artery-ratio, stent segments were divided into 'normal-sized' (stent-to-artery-ratio < 1.4, n = 12) and 'oversized' (stent-to-artery-ratio {>=} 1.4, n = 9). All stent segments expanded to their near nominal diameter during follow-up. Normal-sized stent segments increased their diameter by 6% and oversized segments by 29%. A significant correlation between oversizing and restenosis by both angiography and histomorphometry was observed. Restenosis rates were similar for uncoated NS and TiNOX-coated NS. Conclusions: TiNOX-coated NS are as safe and effective as uncoated NS in the porcine iliofemoral artery. All stents further expand to near their nominal diameter during follow-up. Oversizing is linearly and positively correlated with neointimal proliferation and restenosis, which may not be reduced by TiNOX-coating.

  3. Genetic characterization of hepatitis C virus strains in Estonia: fluctuations in the predominating subtype with time.

    Science.gov (United States)

    Tallo, Tatjana; Norder, Helene; Tefanova, Valentina; Krispin, Tõnu; Schmidt, Jelena; Ilmoja, Madis; Orgulas, Karen; Pruunsild, Kaije; Priimägi, Ludmilla; Magnius, Lars O

    2007-04-01

    During the last decade, there has been a dramatic increase in intravenous drug use in young adults in Estonia with an increased incidence of both hepatitis B and C as a consequence. Since genetic data are limited regarding hepatitis C virus (HCV) strains in Estonia, the aim of the study was to characterize HCV strains in different risk groups to determine their relatedness to strains from other geographical regions. Three hundred fifty-three anti-HCV positive sera collected during 1994-2004 from hospitalized patients, blood donors and health care workers were used as source of HCV RNA. Two hundred nine (59%) of the sera were positive for HCV RNA by PCR directed to the 5'-UTR region. For 174 strains the HCV subtype was determined by analyses of the NS5B and/or the 5'UTR-core regions. 1b (71%) was the most common subtype followed by 3a (24%), 2c (2%), 1a (1%), and 2a (1%). The 1b and 3a strains were similar to strains from other regions of the former USSR. Within genotype 1b there were several HCV lineages. However, for 3a there seemed to be two separate introductions into Estonia. There was a relative shift from subtype 1b to 3a in 1999-2000 with a further replacement of 3a with 1b in intravenous drug users in 2001 and onwards (P < 0.05). However, both subtypes were found to co-circulate in the community independent of risk factors. One patient was infected with the 2k/1b recombinant presumed to originate from St. Petersburg being the first isolate of this recombinant recovered outside Russia. PMID:17311333

  4. A novel hepatitis C virus genotyping method based on liquid microarray.

    Directory of Open Access Journals (Sweden)

    Cesar A B Duarte

    Full Text Available The strategy used to treat HCV infection depends on the genotype involved. An accurate and reliable genotyping method is therefore of paramount importance. We describe here, for the first time, the use of a liquid microarray for HCV genotyping. This liquid microarray is based on the 5'UTR - the most highly conserved region of HCV - and the variable region NS5B sequence. The simultaneous genotyping of two regions can be used to confirm findings and should detect inter-genotypic recombination. Plasma samples from 78 patients infected with viruses with genotypes and subtypes determined in the Versant™ HCV Genotype Assay LiPA (version I; Siemens Medical Solutions, Diagnostics Division, Fernwald, Germany were tested with our new liquid microarray method. This method successfully determined the genotypes of 74 of the 78 samples previously genotyped in the Versant™ HCV Genotype Assay LiPA (74/78, 95%. The concordance between the two methods was 100% for genotype determination (74/74. At the subtype level, all 3a and 2b samples gave identical results with both methods (17/17 and 7/7, respectively. Two 2c samples were correctly identified by microarray, but could only be determined to the genotype level with the Versant™ HCV assay. Genotype "1" subtypes (1a and 1b were correctly identified by the Versant™ HCV assay and the microarray in 68% and 40% of cases, respectively. No genotype discordance was found for any sample. HCV was successfully genotyped with both methods, and this is of prime importance for treatment planning. Liquid microarray assays may therefore be added to the list of methods suitable for HCV genotyping. It provides comparable results and may readily be adapted for the detection of other viruses frequently co-infecting HCV patients. Liquid array technology is thus a reliable and promising platform for HCV genotyping.

  5. Rescue of the 1947 Zika Virus Prototype Strain with a Cytomegalovirus Promoter-Driven cDNA Clone

    Science.gov (United States)

    Schwarz, Megan C.; Sourisseau, Marion; Espino, Michael M.; Gray, Essanna S.; Chambers, Matthew T.; Tortorella, Domenico

    2016-01-01

    ABSTRACT The recent Zika virus (ZIKV) outbreak has been linked to severe pathogenesis. Here, we report the construction of a plasmid carrying a cytomegalovirus (CMV) promoter-expressed prototype 1947 Uganda MR766 ZIKV cDNA that can initiate infection following direct plasmid DNA transfection of mammalian cells. Incorporation of a synthetic intron in the nonstructural protein 1 (NS1) region of the ZIKV polyprotein reduced viral cDNA-associated toxicity in bacteria. High levels of infectious virus were produced following transfection of the plasmid bearing the wild-type MR766 ZIKV genome, but not one with a disruption to the viral nonstructural protein 5 (NS5) polymerase active site. Multicycle growth curve and plaque assay experiments indicated that the MR766 virus resulting from plasmid transfection exhibited growth characteristics that were more similar to its parental isolate than previously published 2010 Cambodia and 2015 Brazil cDNA-rescued ZIKV. This ZIKV infectious clone will be useful for investigating the genetic determinants of ZIKV infection and pathogenesis and should be amenable to construction of diverse infectious clones expressing reporter proteins and representing a range of ZIKV isolates. IMPORTANCE The study of ZIKV, which has become increasingly important with the recent association of this virus with microcephaly and Guillain-Barré syndrome, would benefit from an efficient strategy to genetically manipulate the virus. This work describes a model system to produce infectious virus in cell culture. We created a plasmid carrying the prototype 1947 Uganda MR766 ZIKV genome that both was stable in bacteria and could produce high levels of infectious virus in mammalian cells through direct delivery of this DNA. Furthermore, growth properties of this rescued virus closely resembled those of the viral isolate from which it was derived. This model system will provide a simple and effective means to study how ZIKV genetics impact viral replication and

  6. First isolation of West Nile virus from a dromedary camel.

    Science.gov (United States)

    Joseph, Sunitha; Wernery, Ulrich; Teng, Jade Ll; Wernery, Renate; Huang, Yi; Patteril, Nissy Ag; Chan, Kwok-Hung; Elizabeth, Shyna K; Fan, Rachel Yy; Lau, Susanna Kp; Kinne, Jörg; Woo, Patrick Cy

    2016-01-01

    Although antibodies against West Nile virus (WNV) have been detected in the sera of dromedaries in the Middle East, North Africa and Spain, no WNV has been isolated or amplified from dromedary or Bactrian camels. In this study, WNV was isolated from Vero cells inoculated with both nasal swab and pooled trachea/lung samples from a dromedary calf in Dubai. Complete-genome sequencing and phylogenetic analysis using the near-whole-genome polyprotein revealed that the virus belonged to lineage 1a. There was no clustering of the present WNV with other WNVs isolated in other parts of the Middle East. Within lineage 1a, the dromedary WNV occupied a unique position, although it was most closely related to other WNVs of cluster 2. Comparative analysis revealed that the putative E protein encoded by the genome possessed the original WNV E protein glycosylation motif NYS at E154-156, which contained the N-linked glycosylation site at N-154 associated with increased WNV pathogenicity and neuroinvasiveness. In the putative NS1 protein, the A70S substitution observed in other cluster 2 WNVs and P250, which has been implicated in neuroinvasiveness, were present. In addition, the foo motif in the putative NS2A protein, which has been implicated in neuroinvasiveness, was detected. Notably, the amino-acid residues at 14 positions in the present dromedary WNV genome differed from those in most of the closely related WNV strains in cluster 2 of lineage 1a, with the majority of these differences observed in the putative E and NS5 proteins. The present study is the first to demonstrate the isolation of WNV from dromedaries. This finding expands the possible reservoirs of WNV and sources of WNV infection. PMID:27273223

  7. Dengue virus type 3 adaptive changes during epidemics in Sao Jose de Rio Preto, Brazil, 2006-2007.

    Directory of Open Access Journals (Sweden)

    Christian Julian Villabona-Arenas

    Full Text Available Global dengue virus spread in tropical and sub-tropical regions has become a major international public health concern. It is evident that DENV genetic diversity plays a significant role in the immunopathology of the disease and that the identification of polymorphisms associated with adaptive responses is important for vaccine development. The investigation of naturally occurring genomic variants may play an important role in the comprehension of different adaptive strategies used by these mutants to evade the human immune system. In order to elucidate this role we sequenced the complete polyprotein-coding region of thirty-three DENV-3 isolates to characterize variants circulating under high endemicity in the city of São José de Rio Preto, Brazil, during the onset of the 2006-07 epidemic. By inferring the evolutionary history on a local-scale and estimating rates of synonymous (dS and nonsynonimous (dN substitutions, we have documented at least two different introductions of DENV-3 into the city and detected 10 polymorphic codon sites under significant positive selection (dN/dS > 1 and 8 under significant purifying selection (dN/dS < 1. We found several polymorphic amino acid coding sites in the envelope (15, NS1 (17, NS2A (11, and NS5 (24 genes, which suggests that these genes may be experiencing relatively recent adaptive changes. Furthermore, some polymorphisms correlated with changes in the immunogenicity of several epitopes. Our study highlights the existence of significant and informative DENV variability at the spatio-temporal scale of an urban outbreak.

  8. Clinical outcome and genetic differences within a monophyletic Dengue virus type 2 population.

    Science.gov (United States)

    Hapuarachchi, Hapuarachchige Chanditha; Chua, Rachel Choon Rong; Shi, Yuan; Thein, Tun Lin; Lee, Linda Kay; Lee, Kim Sung; Lye, David Chien; Ng, Lee Ching; Leo, Yee Sin

    2015-01-01

    The exact mechanisms of interplay between host and viral factors leading to severe dengue are yet to be fully understood. Even though previous studies have implicated specific genetic differences of Dengue virus (DENV) in clinical severity and virus attenuation, similar studies with large-scale, whole genome screening of monophyletic virus populations are limited. Therefore, in the present study, we compared 89 whole genomes of DENV-2 cosmopolitan clade III isolates obtained from patients diagnosed with dengue fever (DF, n = 58), dengue hemorrhagic fever (DHF, n = 30) and dengue shock syndrome (DSS, n = 1) in Singapore between July 2010 and January 2013, in order to determine the correlation of observed viral genetic differences with clinical outcomes. Our findings showed no significant difference between the number of primary and secondary infections that progressed to DHF and DSS (p>0.05) in our study cohort. Despite being highly homogenous, study isolates possessed 39 amino acid substitutions of which 10 substitutions were fixed in three main groups of virus isolates. None of those substitutions were specifically associated with DHF and DSS. Notably, two evolutionarily unique virus groups possessing C-P43T+NS1-S103T+NS2A-V83I+NS3-R337K+ NS3-I600T+ NS5-P136S and NS2A-T119N mutations were exclusively found in patients with DF, the benign form of DENV infections. Those mutants were significantly associated with mild disease outcome. These observations indicated that disease progression into DHF and DSS within our patient population was more likely to be due to host than virus factors. We hypothesize that selection for potentially less virulent groups of DENV-2 in our study cohort may be an evolutionary adaptation of viral strains to extend their survival in the human-mosquito transmission cycle.

  9. Clinical outcome and genetic differences within a monophyletic Dengue virus type 2 population.

    Directory of Open Access Journals (Sweden)

    Hapuarachchige Chanditha Hapuarachchi

    Full Text Available The exact mechanisms of interplay between host and viral factors leading to severe dengue are yet to be fully understood. Even though previous studies have implicated specific genetic differences of Dengue virus (DENV in clinical severity and virus attenuation, similar studies with large-scale, whole genome screening of monophyletic virus populations are limited. Therefore, in the present study, we compared 89 whole genomes of DENV-2 cosmopolitan clade III isolates obtained from patients diagnosed with dengue fever (DF, n = 58, dengue hemorrhagic fever (DHF, n = 30 and dengue shock syndrome (DSS, n = 1 in Singapore between July 2010 and January 2013, in order to determine the correlation of observed viral genetic differences with clinical outcomes. Our findings showed no significant difference between the number of primary and secondary infections that progressed to DHF and DSS (p>0.05 in our study cohort. Despite being highly homogenous, study isolates possessed 39 amino acid substitutions of which 10 substitutions were fixed in three main groups of virus isolates. None of those substitutions were specifically associated with DHF and DSS. Notably, two evolutionarily unique virus groups possessing C-P43T+NS1-S103T+NS2A-V83I+NS3-R337K+ NS3-I600T+ NS5-P136S and NS2A-T119N mutations were exclusively found in patients with DF, the benign form of DENV infections. Those mutants were significantly associated with mild disease outcome. These observations indicated that disease progression into DHF and DSS within our patient population was more likely to be due to host than virus factors. We hypothesize that selection for potentially less virulent groups of DENV-2 in our study cohort may be an evolutionary adaptation of viral strains to extend their survival in the human-mosquito transmission cycle.

  10. Comparative genomic analysis of pre-epidemic and epidemic Zika virus strains for virological factors potentially associated with the rapidly expanding epidemic.

    Science.gov (United States)

    Zhu, Zheng; Chan, Jasper Fuk-Woo; Tee, Kah-Meng; Choi, Garnet Kwan-Yue; Lau, Susanna Kar-Pui; Woo, Patrick Chiu-Yat; Tse, Herman; Yuen, Kwok-Yung

    2016-01-01

    Less than 20 sporadic cases of human Zika virus (ZIKV) infection were reported in Africa and Asia before 2007, but large outbreaks involving up to 73% of the populations on the Pacific islands have started since 2007, and spread to the Americas in 2014. Moreover, the clinical manifestation of ZIKV infection has apparently changed, as evident by increasing reports of neurological complications, such as Guillain-Barré syndrome in adults and congenital anomalies in neonates. We comprehensively compared the genome sequences of pre-epidemic and epidemic ZIKV strains with complete genome or complete polyprotein sequences available in GenBank. Besides the reported phylogenetic clustering of the epidemic strains with the Asian lineage, we found that the topology of phylogenetic tree of all coding regions is the same except that of the non-structural 2B (NS2B) coding region. This finding was confirmed by bootscan analysis and multiple sequence alignment, which suggested the presence of a fragment of genetic recombination at NS2B with that of Spondweni virus. Moreover, the representative epidemic strain possesses one large bulge of nine bases instead of an external loop on the first stem-loop structure at the 3'-untranslated region just distal to the stop codon of the NS5 in the 1947 pre-epidemic prototype strain. Fifteen amino acid substitutions are found in the epidemic strains when compared with the pre-epidemic strains. As mutations in other flaviviruses can be associated with changes in virulence, replication efficiency, antigenic epitopes and host tropism, further studies would be important to ascertain the biological significance of these genomic changes.

  11. Neoadjuvant chemotherapy for radioinduced osteosarcoma of the extremity: The Rizzoli experience in 20 cases

    International Nuclear Information System (INIS)

    Purpose: Evaluate treatment and outcome of 20 patients with radioinduced osteosarcoma (RIO). Because of previous primary tumor treatment, RIO protocols were different from others we used for non-RIO. Patients and Methods: Between 1983 and 1998, we treated 20 RIO patients, ages 4-36 years (mean 16 years), with chemotherapy (two cycles before surgery, three postoperatively). The first preoperative cycle consisted of high-dose Methotrexate (HDMTX)/Cisplatinum (CDP)/Adriamycin (ADM) and the second of HDMTX/CDP/Ifosfamide (IFO). The three postoperative treatments were performed with cycles of MTX/CDP; IFO was used as single agent per cycle repeated three times. Results: Two patients received palliative treatment because their osteosarcoma remained unresectable after preoperative chemotherapy. The remaining 18 patients had surgery (7 amputations, 11 resections); histologic response to preoperative chemotherapy was good in 8 patients, poor in 10. At a mean follow-up of 11 years (range, 7-22 years), 9 patients remained continuously disease-free, 10 died from osteosarcoma and 1 died from a third neoplasm (myeloid acute leukemia). These results are not significantly different from those achieved in 754 patients with conventional osteosarcoma treated in the same period with protocols used for conventional treatment. However, this later group had an 18% 3-year event-free survival after treatment of relapse vs. 0% in the RIO group. Conclusion: Treated with neoadjuvant chemotherapy RIO seem to have an outcome that is not significantly different from that of comparable patients with conventional primary high grade osteosarcoma (5-year event-free survival: 40% vs. 60%, p = NS; 5-year overall survival 40% vs. 67%, p < 0.01)

  12. 2'-O methylation of the viral mRNA cap by West Nile virus evades ifit1-dependent and -independent mechanisms of host restriction in vivo.

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    Kristy J Szretter

    Full Text Available Prior studies have shown that 2'-O methyltransferase activity of flaviviruses, coronaviruses, and poxviruses promotes viral evasion of Ifit1, an interferon-stimulated innate immune effector protein. Viruses lacking 2'-O methyltransferase activity exhibited attenuation in primary macrophages that was rescued in cells lacking Ifit1 gene expression. Here, we examined the role of Ifit1 in restricting pathogenesis in vivo of wild type WNV (WNV-WT and a mutant in the NS5 gene (WNV-E218A lacking 2'-O methylation of the 5' viral RNA cap. While deletion of Ifit1 had marginal effects on WNV-WT pathogenesis, WNV-E218A showed increased replication in peripheral tissues of Ifit1⁻/⁻ mice after subcutaneous infection, yet this failed to correlate with enhanced infection in the brain or lethality. In comparison, WNV-E218A was virulent after intracranial infection as judged by increased infection in different regions of the central nervous system (CNS and a greater than 16,000-fold decrease in LD(50 values in Ifit1⁻/⁻ compared to wild type mice. Ex vivo infection experiments revealed cell-type specific differences in the ability of an Ifit1 deficiency to complement the replication defect of WNV-E218A. In particular, WNV-E218A infection was impaired in both wild type and Ifit1⁻/⁻ brain microvascular endothelial cells, which are believed to participate in blood-brain barrier (BBB regulation of virus entry into the CNS. A deficiency of Ifit1 also was associated with increased neuronal death in vivo, which was both cell-intrinsic and mediated by immunopathogenic CD8⁺ T cells. Our results suggest that virulent strains of WNV have largely evaded the antiviral effects of Ifit1, and viral mutants lacking 2'-O methylation are controlled in vivo by Ifit1-dependent and -independent mechanisms in different cell types.

  13. Illustrating and homology modeling the proteins of the Zika virus [version 2; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Sean Ekins

    2016-09-01

    Full Text Available The Zika virus (ZIKV is a flavivirus of the family Flaviviridae, which is similar to dengue virus, yellow fever and West Nile virus. Recent outbreaks in South America, Latin America, the Caribbean and in particular Brazil have led to concern for the spread of the disease and potential to cause Guillain-Barré syndrome and microcephaly. Although ZIKV has been known of for over 60 years there is very little in the way of knowledge of the virus with few publications and no crystal structures. No antivirals have been tested against it either in vitro or in vivo. ZIKV therefore epitomizes a neglected disease. Several suggested steps have been proposed which could be taken to initiate ZIKV antiviral drug discovery using both high throughput screens as well as structure-based design based on homology models for the key proteins. We now describe preliminary homology models created for NS5, FtsJ, NS4B, NS4A, HELICc, DEXDc, peptidase S7, NS2B, NS2A, NS1, E stem, glycoprotein M, propeptide, capsid and glycoprotein E using SWISS-MODEL. Eleven out of 15 models pass our model quality criteria for their further use. While a ZIKV glycoprotein E homology model was initially described in the immature conformation as a trimer, we now describe the mature dimer conformer which allowed the construction of an illustration of the complete virion. By comparing illustrations of ZIKV based on this new homology model and the dengue virus crystal structure we propose potential differences that could be exploited for antiviral and vaccine design. The prediction of sites for glycosylation on this protein may also be useful in this regard. While we await a cryo-EM structure of ZIKV and eventual crystal structures of the individual proteins, these homology models provide the community with a starting point for structure-based design of drugs and vaccines as well as a for computational virtual screening.

  14. Molecular tracing of classical swine fever viruses isolated from wild boars and pigs in France from 2002 to 2011.

    Science.gov (United States)

    Simon, Gaëlle; Le Dimna, Mireille; Le Potier, Marie-Frédérique; Pol, Françoise

    2013-10-25

    There were three outbreaks of classical swine fever (CSF) in north-eastern France between 2002 and 2011. The first two occurred in April 2002 in the Moselle department, in a wild boar and pig herd, respectively, while the third occurred in April 2003, in the Bas-Rhin department, in a wild boar. A survey was subsequently implemented in wild boar and domestic pig populations, during which 43 CSF viruses (CSFVs) were genetically characterized to provide information on virus sources, trace virus evolution and help in the monitoring of effective control measures. Phylogenetic analyses, based on fragments of the 5'NTR, E2 and NS5B genes, showed that all French CSFVs could be assigned to genotype 2, subgenotype 2.3. CSFVs isolated in Moselle were classified in the "Rostock" lineage, a strain first described in 2001 in wild boar populations in the Eifel region of north-western Rhineland-Palatinate in Germany, and in Luxemburg. In contrast, the CSFVs isolated in Bas-Rhin were homologous to strains from the "Uelzen" lineage, a strain previously isolated from wild boars in south-eastern Rhineland-Palatinate, Germany, as well as in Vosges du Nord, France, during a previous outbreak that had occurred in wild boars between 1992 and 2001. The outbreak in Moselle domestic pigs was quickly resolved as it concerned only one herd. The infection in wild boars from Moselle was extinguished after a few months whereas wild boars from Bas-Rhin remained infected until 2007. Molecular tracing showed that the Bas-Rhin index virus strain evolved slightly during the period but that no strain from a novel lineage was introduced until this outbreak ended after application of a vaccination scheme for six years.

  15. Enhancement of HCV polytope DNA vaccine efficacy by fusion to an N-terminal fragment of heat shock protein gp96.

    Science.gov (United States)

    Pishraft-Sabet, Leila; Kosinska, Anna D; Rafati, Sima; Bolhassani, Azam; Taheri, Tahereh; Memarnejadian, Arash; Alavian, Seyed-Moayed; Roggendorf, Michael; Samimi-Rad, Katayoun

    2015-01-01

    Induction of a strong hepatitis C virus (HCV)-specific immune response plays a key role in control and clearance of the virus. A polytope (PT) DNA vaccine containing B- and T-cell epitopes could be a promising vaccination strategy against HCV, but its efficacy needs to be improved. The N-terminal domain of heat shock protein gp96 (NT(gp96)) has been shown to be a potent adjuvant for enhancing immunity. We constructed a PT DNA vaccine encoding four HCV immunodominant cytotoxic T lymphocyte epitopes (two HLA-A2- and two H2-D(d)-specific motifs) from the Core, E2, NS3 and NS5B antigens in addition to a T-helper CD4+ epitope from NS3 and a B-cell epitope from E2. The NT(gp96) was fused to the C- or N-terminal end of the PT DNA (PT-NT(gp96) or NT(gp96)-PT), and their potency was compared. Cellular and humoral immune responses against the expressed peptides were evaluated in CB6F1 mice. Our results showed that immunization of mice with PT DNA vaccine fused to NT(gp96) induced significantly stronger T-cell and antibody responses than PT DNA alone. Furthermore, the adjuvant activity of NT(gp96) was more efficient in the induction of immune responses when fused to the C-terminal end of the HCV DNA polytope. In conclusion, the NT(gp96) improved the efficacy of the DNA vaccine, and this immunomodulatory effect was dependent on the position of the fusion.

  16. Cytoplasmic translocation of polypyrimidine tract-binding protein and its binding to viral RNA during Japanese encephalitis virus infection inhibits virus replication.

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    Deepika Bhullar

    Full Text Available Japanese encephalitis virus (JEV has a single-stranded, positive-sense RNA genome containing a single open reading frame flanked by the 5'- and 3'-non-coding regions (NCRs. The virus genome replicates via a negative-sense RNA intermediate. The NCRs and their complementary sequences in the negative-sense RNA are the sites for assembly of the RNA replicase complex thereby regulating the RNA synthesis and virus replication. In this study, we show that the 55-kDa polypyrimidine tract-binding protein (PTB interacts in vitro with both the 5'-NCR of the positive-sense genomic RNA--5NCR(+, and its complementary sequence in the negative-sense replication intermediate RNA--3NCR(-. The interaction of viral RNA with PTB was validated in infected cells by JEV RNA co-immunoprecipitation and JEV RNA-PTB colocalization experiments. Interestingly, we observed phosphorylation-coupled translocation of nuclear PTB to cytoplasmic foci that co-localized with JEV RNA early during JEV infection. Our studies employing the PTB silencing and over-expression in cultured cells established an inhibitory role of PTB in JEV replication. Using RNA-protein binding assay we show that PTB competitively inhibits association of JEV 3NCR(- RNA with viral RNA-dependent RNA polymerase (NS5 protein, an event required for the synthesis of the plus-sense genomic RNA. cAMP is known to promote the Protein kinase A (PKA-mediated PTB phosphorylation. We show that cells treated with a cAMP analogue had an enhanced level of phosphorylated PTB in the cytoplasm and a significantly suppressed JEV replication. Data presented here show a novel, cAMP-induced, PTB-mediated, innate host response that could effectively suppress JEV replication in mammalian cells.

  17. Thumb Site 2 Inhibitors of Hepatitis C Viral RNA-dependent RNA Polymerase Allosterically Block the Transition from Initiation to Elongation.

    Science.gov (United States)

    Li, Jiawen; Johnson, Kenneth A

    2016-05-01

    Replication of the hepatitis C viral genome is catalyzed by the NS5B (nonstructural protein 5B) RNA-dependent RNA polymerase, which is a major target of antiviral drugs currently in the clinic. Prior studies established that initiation of RNA replication could be facilitated by starting with a dinucleotide (pGG). Here we establish conditions for efficient initiation from GTP to form the dinucleotide and subsequent intermediates leading to highly processive elongation, and we examined the effects of four classes of nonnucleoside inhibitors on each step of the reaction. We show that palm site inhibitors block initiation starting from GTP but not when starting from pGG. In addition we show that nonnucleoside inhibitors binding to thumb site-2 (NNI2) lead to the accumulation of abortive intermediates three-five nucleotides in length. Our kinetic analysis shows that NNI2 do not significantly block initiation or elongation of RNA synthesis; rather, they block the transition from initiation to elongation, which is thought to proceed with significant structural rearrangement of the enzyme-RNA complex including displacement of the β-loop from the active site. Direct measurement in single turnover kinetic studies show that pyrophosphate release is faster than the chemistry step, which appears to be rate-limiting during processive synthesis. These results reveal important new details to define the steps involved in initiation and elongation during viral RNA replication, establish the allosteric mechanisms by which NNI2 inhibitors act, and point the way to the design of more effective allosteric inhibitors that exploit this new information. PMID:26851276

  18. Molecular characterization, distribution, and dynamics of hepatitis C virus genotypes in blood donors in Colombia.

    Science.gov (United States)

    Mora, Mónica Viviana Alvarado; Romano, Camila Malta; Gomes-Gouvêa, Michele Soares; Gutiérrez, Maria Fernanda; Carrilho, Flair José; Pinho, João Renato Rebello

    2010-11-01

    Hepatitis C virus (HCV) is a frequent cause of acute and chronic hepatitis and a leading cause for cirrhosis of the liver and hepatocellular carcinoma. HCV is classified in six major genotypes and more than 70 subtypes. In Colombian blood banks, serum samples were tested for anti-HCV antibodies using a third-generation ELISA. The aim of this study was to characterize the viral sequences in plasma of 184 volunteer blood donors who attended the "Banco Nacional de Sangre de la Cruz Roja Colombiana," Bogotá, Colombia. Three different HCV genomic regions were amplified by nested PCR. The first of these was a segment of 180 bp of the 5'UTR region to confirm the previous diagnosis by ELISA. From those that were positive to the 5'UTR region, two further segments were amplified for genotyping and subtyping by phylogenetic analysis: a segment of 380 bp from the NS5B region; and a segment of 391 bp from the E1 region. The distribution of HCV subtypes was: 1b (82.8%), 1a (5.7%), 2a (5.7%), 2b (2.8%), and 3a (2.8%). By applying Bayesian Markov chain Monte Carlo simulation, it was estimated that HCV-1b was introduced into Bogotá around 1950. Also, this subtype spread at an exponential rate between about 1970 to about 1990, after which transmission of HCV was reduced by anti-HCV testing of this population. Among Colombian blood donors, HCV genotype 1b is the most frequent genotype, especially in large urban conglomerates such as Bogotá, as is the case in other South American countries. PMID:20872715

  19. Epidemic History of Hepatitis C Virus among Patients with Inherited Bleeding Disorders in Iran

    Science.gov (United States)

    Samimi-Rad, Katayoun; Rahimnia, Ramin; Sadeghi, Mahdi; Malekpour, Seyed Amir; Marzban, Mona; Keshvari, Maryam; Kiani, Seyed Jalal; Alavian, Seyed-Moayed

    2016-01-01

    The high rate of hepatitis C virus (HCV) infection among transfusion related risk groups such as patients with inherited bleeding disorders highlighting the investigation on prevalent subtypes and their epidemic history among this group. In this study, 166 new HCV NS5B sequences isolated from patients with inherited bleeding disorders together with 29 sequences related to hemophiliacs obtained from a previous study on diversity of HCV in Iran were analyzed. The most prevalent subtype was 1a (65%), followed by 3a (18.7%),1b (14.5%),4(1.2%) and 2k (0.6%). Subtypes 1a and 3a showed exponential expansion during the 20th century. Whereas expansion of 3a started around 20 years earlier than 1a among the study patients, the epidemic growth of 1a revealed a delay of about 10 years compared with that found for this subtype in developed countries. Our results supported the view that the spread of 3a reached the plateau 10 years prior to the screening of blood donors for HCV. Rather, 1a reached the plateau when screening program was implemented. The differences observed in the epidemic behavior of HCV-1a and 3a may be associated with different transmission routes of two subtypes. Indeed, expansion of 1a was more commonly linked to blood transfusion, while 3a was more strongly associated to drug use and specially IDU after 1960. Our findings also showed HCV transmission through blood products has effectively been controlled from late 1990s. In conclusion, the implementation of strategies such as standard surveillance programs and subsiding antiviral treatments seems to be essential to both prevent new HCV infections and to decline the current and future HCV disease among Iranian patients with inherited bleeding disorders. PMID:27611688

  20. Dengue virus type 3 adaptive changes during epidemics in São Jose de Rio Preto, Brazil, 2006-2007.

    Science.gov (United States)

    Villabona-Arenas, Christian Julian; Mondini, Adriano; Bosch, Irene; Schimdt, Diane J; Schimitt, Diane; Calzavara-Silva, Carlos E; Zanotto, Paolo M de A; Nogueira, Maurício L

    2013-01-01

    Global dengue virus spread in tropical and sub-tropical regions has become a major international public health concern. It is evident that DENV genetic diversity plays a significant role in the immunopathology of the disease and that the identification of polymorphisms associated with adaptive responses is important for vaccine development. The investigation of naturally occurring genomic variants may play an important role in the comprehension of different adaptive strategies used by these mutants to evade the human immune system. In order to elucidate this role we sequenced the complete polyprotein-coding region of thirty-three DENV-3 isolates to characterize variants circulating under high endemicity in the city of São José de Rio Preto, Brazil, during the onset of the 2006-07 epidemic. By inferring the evolutionary history on a local-scale and estimating rates of synonymous (dS) and nonsynonimous (dN) substitutions, we have documented at least two different introductions of DENV-3 into the city and detected 10 polymorphic codon sites under significant positive selection (dN/dS > 1) and 8 under significant purifying selection (dN/dS < 1). We found several polymorphic amino acid coding sites in the envelope (15), NS1 (17), NS2A (11), and NS5 (24) genes, which suggests that these genes may be experiencing relatively recent adaptive changes. Furthermore, some polymorphisms correlated with changes in the immunogenicity of several epitopes. Our study highlights the existence of significant and informative DENV variability at the spatio-temporal scale of an urban outbreak. PMID:23667626

  1. Nonstructural Proteins Are Preferential Positive Selection Targets in Zika Virus and Related Flaviviruses.

    Science.gov (United States)

    Sironi, Manuela; Forni, Diego; Clerici, Mario; Cagliani, Rachele

    2016-09-01

    The Flavivirus genus comprises several human pathogens such as dengue virus (DENV), Japanese encephalitis virus (JEV), and Zika virus (ZIKV). Although ZIKV usually causes mild symptoms, growing evidence is linking it to congenital birth defects and to increased risk of Guillain-Barré syndrome. ZIKV encodes a polyprotein that is processed to produce three structural and seven nonstructural (NS) proteins. We investigated the evolution of the viral polyprotein in ZIKV and in related flaviviruses (DENV, Spondweni virus, and Kedougou virus). After accounting for saturation issues, alignment uncertainties, and recombination, we found evidence of episodic positive selection on the branch that separates DENV from the other flaviviruses. NS1 emerged as the major selection target, and selected sites were located in immune epitopes or in functionally important protein regions. Three of these sites are located in an NS1 region that interacts with structural proteins and is essential for virion biogenesis. Analysis of the more recent evolutionary history of ZIKV lineages indicated that positive selection acted on NS5 and NS4B, this latter representing the preferential target. All selected sites were located in the N-terminal portion of NS4B, which inhibits interferon response. One of the positively selected sites (26M/I/T/V) in ZIKV also represents a selection target in sylvatic DENV2 isolates, and a nearby residue evolves adaptively in JEV. Two additional positively selected sites are within a protein region that interacts with host (e.g. STING) and viral (i.e. NS1, NS4A) proteins. Notably, mutations in the NS4B region of other flaviviruses modulate neurovirulence and/or neuroinvasiveness. These results suggest that the positively selected sites we identified modulate viral replication and contribute to immune evasion. These sites should be prioritized in future experimental studies. However, analyses herein detected no selective events associated to the spread of the Asian

  2. Regulation of Hepatitis C Virus Replication and Gene Expression by the MAPK-ERK Pathway

    Institute of Scientific and Technical Information of China (English)

    Rongjuan Pei; Xiaoyong Zhang; Song Xu; Zhongji Meng; Michael Roggendorf; Mengji Lu; Xinwen Chen

    2012-01-01

    The mitogen activated protein kinases-extracellular signal regulated kinases (MAPK-ERK) pathway is involved in regulation of multiple cellular processes including the cell cycle.In the present study using a Huh7 cell line Con1 with an HCV replicon,we have shown that the MAPK-ERK pathway plays a significant role in the modulation of HCV replication and protein expression and might influence IFN-α signalling.Epithelial growth factor (EGF) was able to stimulate ERK activation and decreased HCV RNA load while a MAPK-ERK pathway inhibitor U0126 led to an elevated HCV RNA load and higher NS5A protein amounts in Con1 cells.It could be further demonstrated that the inhibition of the MAPK-ERK pathway facilitated the translation directed by the HCV internal ribosome entry site.Consistently,a U0126 treatment enhanced activity of the HCV reporter replicon in transient transfection assays.Thus,the MAPK-ERK pathway plays an important role in the regulation of HCV gene expression and replication.In addition,cyclin-dependent kinases (CDKs) downstream of ERK may also be involved in the modulation of HCV replication since roscovitine,an inhibitor of CDKs had a similar effect to that of U0126.Modulation of the cell cycle progression by cell cycle inhibitor or RNAi resulted consistently in changes of HCV RNA levels.Further,the replication of HCV replicon in Conl cells was inhibited by IFN-α.The inhibitory effect of IFN-α could be partly reversed by pre-incubation of Con-1 cells with inhibitors of the MAPK-ERK pathway and CDKs.It could be shown that the MAPK-ERK inhibitors are able to partially modulate the expression of interferon-stimulated genes.

  3. Phylogeography, risk factors and genetic history of hepatitis C virus in Gabon, central Africa.

    Directory of Open Access Journals (Sweden)

    Richard Njouom

    Full Text Available BACKGROUND: The epidemiological and molecular characteristics of hepatitis C virus (HCV infection in the general population have been poorly investigated in Africa. The aim of this study was to determine the prevalence, genotype distribution and epidemic history of HCV in the Gabonese general population. METHODS/PRINCIPAL FINDINGS: A total of 4042 sera collected from adults in 220 villages in all nine administrative areas of the country were screened for antibodies to HCV. HCV NS5B region sequencing was performed for molecular characterization and population genetic analyses. Of 4042 tested sera, 455 (11.2% were positive. The seroprevalence of HCV varied significantly by administrative area, with the highest rate in Ogooué-Lolo province (20.4% and the lowest in Ogooué-Maritine province (3.7%. History of parenteral injections, past hospital admission and age over 55 years were independent risk factors for HCV infection (p<0.0001. Phylogenetic analyses showed that 91.9% of the strains were genotype 4 (HCV-4, 5.7% genotype 1 and 2.2% genotype 2. HCV-4 strains were highly heterogeneous, with more than eight subtypes; subtype 4e predominated (57.3%. Coalescence analyses indicated that subtype 4e was the oldest, with an estimated most recent common ancestor of 1702 [95% CI, 1418-1884]. The epidemic profile indicated that it spread exponentially during the first part of the 20th century, probably by iatrogenic transmission. CONCLUSIONS/SIGNIFICANCE: These results confirm the endemicity of HCV subtype 4e in Gabon and show that its spread is due to a cohort effect, with previous, possibly iatrogenic events. More extensive epidemiological studies are needed to better characterize the route of transmission and the dissemination of HCV in Gabon.

  4. A novel small molecule inhibitor of hepatitis C virus entry.

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    Carl J Baldick

    Full Text Available Small molecule inhibitors of hepatitis C virus (HCV are being developed to complement or replace treatments with pegylated interferons and ribavirin, which have poor response rates and significant side effects. Resistance to these inhibitors emerges rapidly in the clinic, suggesting that successful therapy will involve combination therapy with multiple inhibitors of different targets. The entry process of HCV into hepatocytes represents another series of potential targets for therapeutic intervention, involving viral structural proteins that have not been extensively explored due to experimental limitations. To discover HCV entry inhibitors, we utilized HCV pseudoparticles (HCVpp incorporating E1-E2 envelope proteins from a genotype 1b clinical isolate. Screening of a small molecule library identified a potent HCV-specific triazine inhibitor, EI-1. A series of HCVpp with E1-E2 sequences from various HCV isolates was used to show activity against all genotype 1a and 1b HCVpp tested, with median EC50 values of 0.134 and 0.027 µM, respectively. Time-of-addition experiments demonstrated a block in HCVpp entry, downstream of initial attachment to the cell surface, and prior to or concomitant with bafilomycin inhibition of endosomal acidification. EI-1 was equally active against cell-culture adapted HCV (HCVcc, blocking both cell-free entry and cell-to-cell transmission of virus. HCVcc with high-level resistance to EI-1 was selected by sequential passage in the presence of inhibitor, and resistance was shown to be conferred by changes to residue 719 in the carboxy-terminal transmembrane anchor region of E2, implicating this envelope protein in EI-1 susceptibility. Combinations of EI-1 with interferon, or inhibitors of NS3 or NS5A, resulted in additive to synergistic activity. These results suggest that inhibitors of HCV entry could be added to replication inhibitors and interferons already in development.

  5. Hepatitis C virus (HCV genotype 1 subtype identification in new HCV drug development and future clinical practice.

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    Stéphane Chevaliez

    Full Text Available BACKGROUND: With the development of new specific inhibitors of hepatitis C virus (HCV enzymes and functions that may yield different antiviral responses and resistance profiles according to the HCV subtype, correct HCV genotype 1 subtype identification is mandatory in clinical trials for stratification and interpretation purposes and will likely become necessary in future clinical practice. The goal of this study was to identify the appropriate molecular tool(s for accurate HCV genotype 1 subtype determination. METHODOLOGY/PRINCIPAL FINDINGS: A large cohort of 500 treatment-naïve patients eligible for HCV drug trials and infected with either subtype 1a or 1b was studied. Methods based on the sole analysis of the 5' non-coding region (5'NCR by sequence analysis or reverse hybridization failed to correctly identify HCV subtype 1a in 22.8%-29.5% of cases, and HCV subtype 1b in 9.5%-8.7% of cases. Natural polymorphisms at positions 107, 204 and/or 243 were responsible for mis-subtyping with these methods. A real-time PCR method using genotype- and subtype-specific primers and probes located in both the 5'NCR and the NS5B-coding region failed to correctly identify HCV genotype 1 subtype in approximately 10% of cases. The second-generation line probe assay, a reverse hybridization assay that uses probes targeting both the 5'NCR and core-coding region, correctly identified HCV subtypes 1a and 1b in more than 99% of cases. CONCLUSIONS/SIGNIFICANCE: In the context of new HCV drug development, HCV genotyping methods based on the exclusive analysis of the 5'NCR should be avoided. The second-generation line probe assay is currently the best commercial assay for determination of HCV genotype 1 subtypes 1a and 1b in clinical trials and practice.

  6. Circulation of a Meaban-like virus in yellow-legged gulls and seabird ticks in the western Mediterranean basin.

    Directory of Open Access Journals (Sweden)

    Audrey Arnal

    Full Text Available In recent years, a number of zoonotic flaviviruses have emerged worldwide, and wild birds serve as their major reservoirs. Epidemiological surveys of bird populations at various geographical scales can clarify key aspects of the eco-epidemiology of these viruses. In this study, we aimed at exploring the presence of flaviviruses in the western Mediterranean by sampling breeding populations of the yellow-legged gull (Larus michahellis, a widely distributed, anthropophilic, and abundant seabird species. For 3 years, we sampled eggs from 19 breeding colonies in Spain, France, Algeria, and Tunisia. First, ELISAs were used to determine if the eggs contained antibodies against flaviviruses. Second, neutralization assays were used to identify the specific flaviviruses present. Finally, for colonies in which ELISA-positive eggs had been found, chick serum samples and potential vectors, culicid mosquitoes and soft ticks (Ornithodoros maritimus, were collected and analyzed using serology and PCR, respectively. The prevalence of flavivirus-specific antibodies in eggs was highly spatially heterogeneous. In northeastern Spain, on the Medes Islands and in the nearby village of L'Escala, 56% of eggs had antibodies against the flavivirus envelope protein, but were negative for neutralizing antibodies against three common flaviviruses: West Nile, Usutu, and tick-borne encephalitis viruses. Furthermore, little evidence of past flavivirus exposure was obtained for the other colonies. A subset of the Ornithodoros ticks from Medes screened for flaviviral RNA tested positive for a virus whose NS5 gene was 95% similar to that of Meaban virus, a flavivirus previously isolated from ticks of Larus argentatus in western France. All ELISA-positive samples subsequently tested positive for Meaban virus neutralizing antibodies. This study shows that gulls in the western Mediterranean Basin are exposed to a tick-borne Meaban-like virus, which underscores the need of exploring

  7. First isolation of West Nile virus from a dromedary camel

    Science.gov (United States)

    Joseph, Sunitha; Wernery, Ulrich; Teng, Jade LL; Wernery, Renate; Huang, Yi; Patteril, Nissy AG; Chan, Kwok-Hung; Elizabeth, Shyna K; Fan, Rachel YY; Lau, Susanna KP; Kinne, Jörg; Woo, Patrick CY

    2016-01-01

    Although antibodies against West Nile virus (WNV) have been detected in the sera of dromedaries in the Middle East, North Africa and Spain, no WNV has been isolated or amplified from dromedary or Bactrian camels. In this study, WNV was isolated from Vero cells inoculated with both nasal swab and pooled trachea/lung samples from a dromedary calf in Dubai. Complete-genome sequencing and phylogenetic analysis using the near-whole-genome polyprotein revealed that the virus belonged to lineage 1a. There was no clustering of the present WNV with other WNVs isolated in other parts of the Mid