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Sample records for virus samples international

  1. Influenza virus samples, international law, and global health diplomacy.

    Science.gov (United States)

    Fidler, David P

    2008-01-01

    Indonesia's decision to withhold samples of avian influenza virus A (H5N1) from the World Health Organization for much of 2007 caused a crisis in global health. The World Health Assembly produced a resolution to try to address the crisis at its May 2007 meeting. I examine how the parties to this controversy used international law in framing and negotiating the dispute. Specifically, I analyze Indonesia's use of the international legal principle of sovereignty and its appeal to rules on the protection of biological and genetic resources found in the Convention on Biological Diversity. In addition, I consider how the International Health Regulations 2005 applied to the controversy. The incident involving Indonesia's actions with virus samples illustrates both the importance and the limitations of international law in global health diplomacy.

  2. Biobanking and international interoperability: samples.

    Science.gov (United States)

    Kiehntopf, Michael; Krawczak, Michael

    2011-09-01

    In terms of sample exchange, international collaborations between biobanks, or between biobanks and their research partners, have two important aspects. First, the donors' consent usually implies that the scope and purpose of any sample transfer to third parties is subject to major constraints. Since the legal, ethical and political framework of biobanking may differ substantially, even between countries of comparable jurisdictional systems, general rules for the international sharing of biomaterial are difficult, if not impossible, to define. Issues of uncertainty include the right to transfer the material, the scope of research allowed, and intellectual property rights. Since suitable means of international law enforcement may not be available in the context of biobanking, collaborators are advised to clarify any residual uncertainty by means of bilateral contracts, for example, in the form of material transfer agreements. Second, biobank partners may rightly expect that the biomaterial they receive for further analysis attains a certain level of quality. This implies that a biobank has to implement stringent quality control measures covering, in addition to the material transfer itself, the whole process of material acquisition, transport, pre-analytical handling and storage. Again, it may be advisable for biobank partners to claim contractual warranties for the type and quality of the biomaterial they wish to acquire.

  3. Zika virus epidemic: the newest international emergency

    Directory of Open Access Journals (Sweden)

    Ruth Minamisava

    2016-03-01

    Full Text Available Infection from the Zika virus is a relatively new disease with limited publications reporting cases and research on outbreaks. It was initially described before 2007 in Africa and Asia, then later in the French Polynesia in the Pacific, and finally in the Americas, in 2015. Brazil confirmed its first case of infection from the Zika virus in March 2015(1 and since October 2015 it has recorded an explosive growth in the number of babies born with microcephaly and also an increase in neurological conditions, including Guillain-Barré syndrome. The strong suspicion that the infection from the Zika virus is related to these manifestations is what brought the Public Health Emergency Committee of the World Health Organization to declare on February 1st of 2016 that the spread of the virus is an emergency international public health problem, meaning that it is a serious, unexpected extraordinary event that could potentially require a coordinated international action(2-3. The absence of another explanation for the dramatic increase in cases of microcephaly and the Guillain-Barré syndrome, both concentrated in areas newly infected by the Zika virus, supports the recommendation of aggressive measures to prevent and reduce infection with the Zika virus, especially among pregnant women and those of reproductive age. In the same document, the World Health Organization recommends monitoring cases of microcephaly and the Guillain-Barré syndrome in the areas of risk and etiological studies of these events to determine whether infection by the Zika virus is causal and if there are other risk factors associated. Measures of additional precautions are as follows: (i             Related to the transmission of the virus: epidemiological surveillance, vector control, protection measures, information and counseling for pregnant women and to those who wish to get pregnant. (ii           Long-term measures: investment in research for vaccine

  4. Medium-term cryopreservation of rabies virus samples

    Directory of Open Access Journals (Sweden)

    Tereza D'avila de Freitas Aguiar

    2013-12-01

    Full Text Available Introduction The cryopreservation of rabies virus has been described in detail in the literature. To date, little information is available on the use of cryoprotective agents for cold preservation of this virus, and the available data focus only on short-term virus preservation. In this study, we investigated the medium-term cryopreservation of samples of rabies virus using different cryopreservation protocols. Methods The cryopreservation protocols for the rabies virus samples were performed at -20°C and were divided according to the variables of time and cryoprotectant type used. The laboratory tests (intracerebral inoculation of mice, viral titration and direct immunofluorescence were performed at regular intervals (360 and 720 days to assess the viability of the viral samples according to the different preservation techniques used. Results After 1 year of cryopreservation, the fluorescence intensity of intracellular corpuscles of the rabies virus and the median survival time of the mice differed between the positive controls and the treatments with the cryoprotectants. After 2 years, most of the samples subjected to the cryopreservation protocols (including the controls did not produce fluorescence. However, the virus samples exposed to the cryoprotectant sucrose (68% solution responded positively in the direct immunofluorescence assay and in the intracerebral inoculation of the mice. Conclusions Medium-term cryopreservation of the rabies virus inactivates the viral sample. However, the cryoprotectant agent sucrose (68% produces a preservative effect in cryopreserved rabies virus samples.

  5. Detection of influenza C virus but not influenza D virus in Scottish respiratory samples

    Science.gov (United States)

    Smith, Donald B.; Gaunt, Eleanor R.; Digard, Paul; Templeton, Kate; Simmonds, Peter

    2016-01-01

    Background A newly proposed genus of influenza virus (influenza D) is associated with respiratory disease in pigs and cattle. The novel virus is most closely related to human influenza C virus and can infect ferrets but infection has not been reported in humans. Objectives To ascertain if influenza D virus can be detected retrospectively in patient respiratory samples. Study design 3300 human respiratory samples from Edinburgh, Scotland, covering the period 2006–2008, were screened in pools of 10 by RT-PCR using primers capable of detecting both influenza C and D viruses. Results Influenza D was not detected in any sample. Influenza C was present in 6 samples (0.2%), compared with frequencies of 3.3% and 0.9% for influenza A and B viruses from RT-PCR testing of respiratory samples over the same period. Influenza C virus was detected in samples from individuals 45 years old, with cases occurring throughout the year. Phylogenetic analysis of nearly complete sequences of all seven segments revealed the presence of multiple, reassortant lineages. Conclusion We were unable to detect viruses related to influenza D virus in human respiratory samples. Influenza C virus was less prevalent than influenza A and B viruses, was associated with mild disease in the young (45 years) and comprised multiple, reassortant lineages. Inclusion of influenza C virus as part of a diagnostic testing panel for respiratory infections would be of limited additional value. PMID:26655269

  6. Prevalence of infection with dengue virus among international travelers.

    Science.gov (United States)

    Jelinek, T; Dobler, G; Hölscher, M; Löscher, T; Nothdurft, H D

    1997-11-10

    Dengue has been recognized as a potential hazard to tourists. A prospective, controlled study in the outpatient clinic of a German infectious disease clinic was conducted to assess the prevalence of dengue virus infection among international travelers. Serum samples from 130 patients with signs or recent history clinically compatible with dengue (fever, headache, muscle and joint pain, or rash), 95 matched controls with diarrhea, and 26 patients who never visited a country endemic for dengue were investigated. Nine (6.9%) of the 130 patients with compatible symptoms and 1 (1%) of the 95 controls with diarrhea developed rising antibody titers against dengue virus. Of these 10 patients with probable dengue infection, 6 had been to Thailand, 2 to Malaysia, and 1 each to Indonesia and Brazil. Infection with dengue virus appears to be a realistic threat to travelers to Southeast Asia. Symptoms commonly associated with dengue, such as fever, myalgia, arthralgia, and vomiting, can be helpful for diagnosis when present, but the absence of typical symptoms does not exclude infection.

  7. Increased detection of respiratory syncytial virus, influenza viruses, parainfluenza viruses, and adenoviruses with real-time PCR in samples from patients with respiratory symptoms

    NARCIS (Netherlands)

    van de Pol, Alma C.; van Loon, Anton M.; Wolfs, Tom F. W.; Jansen, Nicolaas J. G.; Nijhuis, Monique; Breteler, Els Klein; Schuurman, Rob; Rossen, John W. A.

    Respiratory samples (n = 267) from hospitalized patients with respiratory symptoms were tested by real-time PCR, viral culture, and direct immunofluorescence for respiratory syncytial virus, influenza virus, parainfluenza viruses, and adenoviruses. Compared with conventional diagnostic tests,

  8. Monitoring of Extraction Efficiency by a Sample Process Control Virus Added Immediately Upon Sample Receipt.

    Science.gov (United States)

    Ruhanya, Vurayai; Diez-Valcarce, Marta; D'Agostino, Martin; Cook, Nigel; Hernández, Marta; Rodríguez-Lázaro, David

    2015-12-01

    When analysing food samples for enteric viruses, a sample process control virus (SPCV) must be added at the commencement of the analytical procedure, to verify that the analysis has been performed correctly. Samples can on occasion arrive at the laboratory late in the working day or week. The analyst may consequently have insufficient time to commence and complete the complex procedure, and the samples must consequently be stored. To maintain the validity of the analytical result, it will be necessary to consider storage as part of the process, and the analytical procedure as commencing on sample receipt. The aim of this study was to verify that an SPCV can be recovered after sample storage, and thus indicate the effective recovery of enteric viruses. Two types of samples (fresh and frozen raspberries) and two types of storage (refrigerated and frozen) were studied using Mengovirus vMC0 as SPCV. SPCV recovery was not significantly different (P > 0.5) regardless of sample type or duration of storage (up to 14 days at -20 °C). Accordingly, samples can be stored without a significant effect on the performance of the analysis. The results of this study should assist the analyst by demonstrating that they can verify that viruses can be extracted from food samples even if samples have been stored.

  9. Sampling a guide for internal auditors

    CERN Document Server

    Apostolou, Barbara

    2004-01-01

    While it is possible to examine 100 percent of an audit customer's data, the time and cost associated with such a study are often prohibitive. To obtain sufficient, reliable, and relevant information with a limited data set, sampling is an efficient and effective tool. It can help you evaluate the customer's assertions, as well as reach audit conclusions and provide reasonable assurance to your organization. This handbook will help you understand sampling. It also serves as a guide for auditors and students preparing for certification. Topics include: An overview of sampling. Statistical and nonstatistical sampling issues. Sampling selection methods and risks. The pros and cons of popular sampling plans.

  10. [Internal epidemic influenza virus proteins: isolation and investigation].

    Science.gov (United States)

    Ivanova, V T; Rakutina, R O; Kordiukova, L V; Manykin, A A; Fedorova, N V; Ksenofontov, A L; Slepushkin, A N

    2006-01-01

    The internal influenza virus proteins M1 and RNP free from surface protein impurities were isolated from subviral particles (virions free from HA and NA ectomenes). The spikeless particles had no propensity to aggregate in the solution at pH 5.0 as compared with native viruses. The subviral particles of B/Hong Kong/330/01 influenza virus, which belonged to B/Victoria/2/87-lineage, were obtained by proteolytic treatment with the enzyme bromelain under the same conditions as in cases of influenza B viruses of B/Jamagata/16/88 lineage. A chromatographic analysis of the tryptic hydrolyzates obtained for matrix (M1) proteins of A(H1N1) and A(H3N2) influenza viruses revealed differences that were greatest between the protein M1 molecules isolated from influenza viruses of different subtypes of hemagglutinine. These findings suggest there are variations in the structure of this conservative internal viral protein M1 during evolution.

  11. STATE OBLIGATION ON VIRUS SAMPLE SHARING;FROM COMMON HERITAGE OF MANKIND TO STATE’S SOVEREIGN RIGHT

    Directory of Open Access Journals (Sweden)

    Nurul Barizah

    2015-06-01

    Full Text Available The tradition of free international exchange of viruses have been developed by the World Health Organization (WHO probably based on the principle of “Common Heritage of Mankind”.  This tradition lead to legal uncertainty and unfairness in the movement of resources among states and provides an opportunity for developed countries to obtain easy access to viruses of developing countries. Then, International Law has introduced a new regime of “State’s Sovereign Right.” This research focuses on whether Member States have an obligation to share pathogen materials, including viruses for preventing global public health emergency, and whether WHO Collaborating Centers has a right to  share viruses to private sectors. It examines the reason why States should apply that principle. This research is normative legal research by using conceptual approach and  statute approach. This research finds that viruses are part of genetic resources under the meaning of CBD Convention. Accordingly, there is no state obligation under International Law to share it. However, if there is an international human rights obligation to share virus, there should also be an international human rights obligation to assure the access of affordability of drugs and vaccines. Thus, each state will have an equal obligation to enhance the global public health.Key Words : Intellectual Property, Virus Sample Sharing, Common Heritage of Mankind, and State’s Sovereign Right

  12. A high diversity of Eurasian lineage low pathogenicity avian influenza A viruses circulate among wild birds sampled in Egypt.

    Directory of Open Access Journals (Sweden)

    Nancy A Gerloff

    Full Text Available Surveillance for influenza A viruses in wild birds has increased substantially as part of efforts to control the global movement of highly pathogenic avian influenza A (H5N1 virus. Studies conducted in Egypt from 2003 to 2007 to monitor birds for H5N1 identified multiple subtypes of low pathogenicity avian influenza A viruses isolated primarily from migratory waterfowl collected in the Nile Delta. Phylogenetic analysis of 28 viral genomes was performed to estimate their nearest ancestors and identify possible reassortants. Migratory flyway patterns were included in the analysis to assess gene flow between overlapping flyways. Overall, the viruses were most closely related to Eurasian, African and/or Central Asian lineage low pathogenicity viruses and belonged to 15 different subtypes. A subset of the internal genes seemed to originate from specific flyways (Black Sea-Mediterranean, East African-West Asian. The remaining genes were derived from a mixture of viruses broadly distributed across as many as 4 different flyways suggesting the importance of the Nile Delta for virus dispersal. Molecular clock date estimates suggested that the time to the nearest common ancestor of all viruses analyzed ranged from 5 to 10 years, indicating frequent genetic exchange with viruses sampled elsewhere. The intersection of multiple migratory bird flyways and the resulting diversity of influenza virus gene lineages in the Nile Delta create conditions favoring reassortment, as evident from the gene constellations identified by this study. In conclusion, we present for the first time a comprehensive phylogenetic analysis of full genome sequences from low pathogenic avian influenza viruses circulating in Egypt, underscoring the significance of the region for viral reassortment and the potential emergence of novel avian influenza A viruses, as well as representing a highly diverse influenza A virus gene pool that merits continued monitoring.

  13. Metagenomic analyses of novel viruses and plasmids from a cultured environmental sample of hyperthermophilic neutrophiles

    DEFF Research Database (Denmark)

    Garrett, Roger Antony; Prangishvili, David; Shah, Shiraz Ali

    2010-01-01

    ), and derive apparently from archaeal viruses HAV1 and HAV2. Genomic DNA was obtained from samples enriched in filamentous and tadpole-shaped virus-like particles respectively. They yielded few significant matches in public sequence databases reinforcing, further, the wide diversity of archaeal viruses...

  14. Detection and genomic characterization of Aichi viruses in stool samples from children in Monastir, Tunisia.

    Science.gov (United States)

    Sdiri-Loulizi, Khira; Hassine, Mouna; Gharbi-Khelifi, Hakima; Sakly, Nabil; Chouchane, Slaheddine; Guediche, Mohamed Neji; Pothier, Pierre; Aouni, Mahjoub; Ambert-Balay, Katia

    2009-07-01

    Aichi virus has been associated with acute gastroenteritis in adults and children. Stool samples were collected from 788 Tunisian children suffering from diarrhea. Aichi virus was found in 4.1% of the cases. The high proportion of monoinfections and the high frequency of hospitalizations support the role of Aichi virus in pediatric gastroenteritis.

  15. Dengue virus purification and sample preparation for cryo-electron microscopy.

    Science.gov (United States)

    Tan, Joanne L; Lok, Shee Mei

    2014-01-01

    Cryo-electron microscopy (cryo-EM) is a valuable tool used to study the structures of icosahedral viruses without having to resort to crystallization. During the last few decades, significant progress has been made where virus structures previously resolved only to low resolution have now breached the sub-nanometer threshold. Critical to such excellent results are the acquisition of highly purified virus samples and well-frozen samples in vitreous ice. With the virus particles locked in their native conformations, cryo-EM together with single-particle analysis can then be deployed to study the structures of the viruses in their fully hydrated states.

  16. Magnetostatic modes in ferromagnetic samples with inhomogeneous internal fields

    Science.gov (United States)

    Arias, Rodrigo

    2015-03-01

    Magnetostatic modes in ferromagnetic samples are very well characterized and understood in samples with uniform internal magnetic fields. More recently interest has shifted to the study of magnetization modes in ferromagnetic samples with inhomogeneous internal fields. The present work shows that under the magnetostatic approximation and for samples of arbitrary shape and/or arbitrary inhomogeneous internal magnetic fields the modes can be classified as elliptic or hyperbolic, and their associated frequency spectrum can be delimited. This results from the analysis of the character of the second order partial differential equation for the magnetostatic potential under these general conditions. In general, a sample with an inhomogeneous internal field and at a given frequency, may have regions of elliptic and hyperbolic character separated by a boundary. In the elliptic regions the magnetostatic modes have a smooth monotonic character (generally decaying form the surfaces (a ``tunneling'' behavior)) and in hyperbolic regions an oscillatory wave-like character. A simple local criterion distinguishes hyperbolic from elliptic regions: the sign of a susceptibility parameter. This study shows that one may control to some extent magnetostatic modes via external fields or geometry. R.E.A. acknowledges Financiamiento Basal para Centros Cientificos y Tecnologicos de Excelencia under Project No. FB 0807 (Chile), Grant No. ICM P10-061-F by Fondo de Innovacion para la Competitividad-MINECON, and Proyecto Fondecyt 1130192.

  17. Presence of enteric viruses in water samples for consumption in Colombia: Challenges for supply systems.

    Science.gov (United States)

    Peláez, Dioselina; Guzmán, Blanca Lisseth; Rodríguez, Johanna; Acero, Felipe; Nava, Gerardo

    2016-04-15

    Since drinking water can be a vehicle for the transmission of pathogens, the detection of enteric viruses in these water samples is essential to establish the appropriate measures to control and prevent associated diseases.  To analyze the results obtained for enteric viruses in water samples for human consumption received at the Colombian Instituto Nacional de Salud and establish their association with the data on water quality in Colombian municipalities.  We conducted a descriptive-retrospective analysis of the results obtained in the detection of rotavirus, enterovirus, hepatitis A virus and adenovirus in water samples received for complementary studies of enteric hepatitis, acute diarrheal disease and foodborne diseases. Data were correlated with the results of water quality surveillance determined by the national human consumption water quality index (IRCA).  Of the 288 samples processed from 102 Colombian municipalities, 50.7% were positive for viruses: 26.73% for hepatitis A virus, 20.48% for enterovirus and rotavirus and 18.05% for adenovirus. Viruses were detected in 48.26% of non-treated water samples and in 45.83% of treated water samples. The IRCA index showed no correlation with the presence of viruses.  The presence of viruses in water represents a public health risk and, therefore, the prevention of virus transmission through water requires appropriate policies to reinforce water supply systems and improve epidemiological surveillance.

  18. Effects of sodium azide on the abundance of prokaryotes and viruses in marine samples.

    Directory of Open Access Journals (Sweden)

    Christian Winter

    Full Text Available Flow cytometry is set to become the standard method for enumerating prokaryotes and viruses in marine samples. However, the samples need to be flash-frozen in liquid nitrogen directly after aldehyde fixation. Because liquid nitrogen may not always be available, we tested the potential of sodium azide as a preservative for prokaryotes and viruses in marine samples as a possible alternative. For that we conducted incubation experiments with untreated and sodium azide treated marine water samples at 4°C and room temperature. The data indicate that sodium azide cannot be used to maintain marine samples used for the enumeration of prokaryotes and viruses.

  19. HCIV-1 and Other Tailless Icosahedral Internal Membrane-Containing Viruses of the Family Sphaerolipoviridae

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    Tatiana A. Demina

    2017-02-01

    Full Text Available Members of the virus family Sphaerolipoviridae include both archaeal viruses and bacteriophages that possess a tailless icosahedral capsid with an internal membrane. The genera Alpha- and Betasphaerolipovirus comprise viruses that infect halophilic euryarchaea, whereas viruses of thermophilic Thermus bacteria belong to the genus Gammasphaerolipovirus. Both sequence-based and structural clustering of the major capsid proteins and ATPases of sphaerolipoviruses yield three distinct clades corresponding to these three genera. Conserved virion architectural principles observed in sphaerolipoviruses suggest that these viruses belong to the PRD1-adenovirus structural lineage. Here we focus on archaeal alphasphaerolipoviruses and their related putative proviruses. The highest sequence similarities among alphasphaerolipoviruses are observed in the core structural elements of their virions: the two major capsid proteins, the major membrane protein, and a putative packaging ATPase. A recently described tailless icosahedral haloarchaeal virus, Haloarcula californiae icosahedral virus 1 (HCIV-1, has a double-stranded DNA genome and an internal membrane lining the capsid. HCIV-1 shares significant similarities with the other tailless icosahedral internal membrane-containing haloarchaeal viruses of the family Sphaerolipoviridae. The proposal to include a new virus species, Haloarcula virus HCIV1, into the genus Alphasphaerolipovirus was submitted to the International Committee on Taxonomy of Viruses (ICTV in 2016.

  20. The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples.

    Directory of Open Access Journals (Sweden)

    Shannon J Williamson

    Full Text Available Viruses are the most abundant biological entities on our planet. Interactions between viruses and their hosts impact several important biological processes in the world's oceans such as horizontal gene transfer, microbial diversity and biogeochemical cycling. Interrogation of microbial metagenomic sequence data collected as part of the Sorcerer II Global Ocean Expedition (GOS revealed a high abundance of viral sequences, representing approximately 3% of the total predicted proteins. Cluster analyses of the viral sequences revealed hundreds to thousands of viral genes encoding various metabolic and cellular functions. Quantitative analyses of viral genes of host origin performed on the viral fraction of aquatic samples confirmed the viral nature of these sequences and suggested that significant portions of aquatic viral communities behave as reservoirs of such genetic material. Distributional and phylogenetic analyses of these host-derived viral sequences also suggested that viral acquisition of environmentally relevant genes of host origin is a more abundant and widespread phenomenon than previously appreciated. The predominant viral sequences identified within microbial fractions originated from tailed bacteriophages and exhibited varying global distributions according to viral family. Recruitment of GOS viral sequence fragments against 27 complete aquatic viral genomes revealed that only one reference bacteriophage genome was highly abundant and was closely related, but not identical, to the cyanomyovirus P-SSM4. The co-distribution across all sampling sites of P-SSM4-like sequences with the dominant ecotype of its host, Prochlorococcus supports the classification of the viral sequences as P-SSM4-like and suggests that this virus may influence the abundance, distribution and diversity of one of the most dominant components of picophytoplankton in oligotrophic oceans. In summary, the abundance and broad geographical distribution of viral

  1. Human virus and microbial indicator occurrence in public-supply groundwater systems: meta-analysis of 12 international studies

    Science.gov (United States)

    Fout, G. Shay; Borchardt, Mark A.; Kieke, Burney A.; Karim, Mohammad R.

    2017-06-01

    Groundwater quality is often evaluated using microbial indicators. This study examines data from 12 international groundwater studies (conducted 1992-2013) of 718 public drinking-water systems located in a range of hydrogeological settings. Focus was on testing the value of indicator organisms for identifying virus-contaminated wells. One or more indicators and viruses were present in 37 and 15% of 2,273 samples and 44 and 27% of 746 wells, respectively. Escherichia coli ( E. coli) and somatic coliphage are 7-9 times more likely to be associated with culturable virus-positive samples when the indicator is present versus when it is absent, while F-specific and somatic coliphages are 8-9 times more likely to be associated with culturable virus-positive wells. However, single indicators are only marginally associated with viruses detected by molecular methods, and all microbial indicators have low sensitivity and positive predictive values for virus occurrence, whether by culturable or molecular assays, i.e., indicators are often absent when viruses are present and the indicators have a high false-positive rate. Wells were divided into three susceptibility subsets based on presence of (1) total coliform bacteria or (2) multiple indicators, or (3) location of wells in karst, fractured bedrock, or gravel/cobble settings. Better associations of some indicators with viruses were observed for (1) and (3). Findings indicate the best indicators are E. coli or somatic coliphage, although both indicators may underestimate virus occurrence. Repeat sampling for indicators improves evaluation of the potential for viral contamination in a well.

  2. International Committee on Taxonomy of Viruses and the 3,142 unassigned species

    Directory of Open Access Journals (Sweden)

    Fargette D

    2005-08-01

    Full Text Available Abstract In 2005, ICTV (International Committee on Taxonomy of Viruses, the official body of the Virology Division of the International Union of Microbiological Societies responsible for naming and classifying viruses, will publish its latest report, the state of the art in virus nomenclature and taxonomy. The book lists more than 6,000 viruses classified in 1,950 species and in more than 391 different higher taxa. However, GenBank contains a staggering additional 3,142 "species" unaccounted for by the ICTV report. This paper reviews the reasons for such a situation and suggests what might be done in the near future to remedy this problem, particularly in light of the potential for a ten-fold increase in virus sequencing in the coming years that would generate many unclassified viruses. A number of changes could be made both at ICTV and GenBank to better handle virus taxonomy and classification in the future.

  3. Transfection of RNA from organ samples of infected animals represents a highly sensitive method for virus detection and recovery of classical swine fever virus.

    Science.gov (United States)

    Meyer, Denise; Schmeiser, Stefanie; Postel, Alexander; Becher, Paul

    2015-01-01

    Translation and replication of positive stranded RNA viruses are directly initiated in the cellular cytoplasm after uncoating of the viral genome. Accordingly, infectious virus can be generated by transfection of RNA genomes into susceptible cells. In the present study, efficiency of conventional virus isolation after inoculation of cells with infectious sample material was compared to virus recovery after transfection of total RNA derived from organ samples of pigs infected with Classical swine fever virus (CSFV). Compared to the conventional method of virus isolation applied in three different porcine cell lines used in routine diagnosis of CSF, RNA transfection showed a similar efficiency for virus rescue. For two samples, recovery of infectious virus was only possible by RNA transfection, but not by the classical approach of virus isolation. Therefore, RNA transfection represents a valuable alternative to conventional virus isolation in particular when virus isolation is not possible, sample material is not suitable for virus isolation or when infectious material is not available. To estimate the potential risk of RNA prepared from sample material for infection of pigs, five domestic pigs were oronasally inoculated with RNA that was tested positive for virus rescue after RNA transfection. This exposure did not result in viral infection or clinical disease of the animals. In consequence, shipment of CSFV RNA can be regarded as a safe alternative to transportation of infectious virus and thereby facilitates the exchange of virus isolates among authorized laboratories with appropriate containment facilities.

  4. Standard methods for sampling freshwater fishes: Opportunities for international collaboration

    Science.gov (United States)

    Bonar, Scott A.; Mercado-Silva, Norman; Hubert, Wayne A.; Beard, Douglas; Dave, Göran; Kubečka, Jan; Graeb, Brian D. S.; Lester, Nigel P.; Porath, Mark T.; Winfield, Ian J.

    2017-01-01

    With publication of Standard Methods for Sampling North American Freshwater Fishes in 2009, the American Fisheries Society (AFS) recommended standard procedures for North America. To explore interest in standardizing at intercontinental scales, a symposium attended by international specialists in freshwater fish sampling was convened at the 145th Annual AFS Meeting in Portland, Oregon, in August 2015. Participants represented all continents except Australia and Antarctica and were employed by state and federal agencies, universities, nongovernmental organizations, and consulting businesses. Currently, standardization is practiced mostly in North America and Europe. Participants described how standardization has been important for management of long-term data sets, promoting fundamental scientific understanding, and assessing efficacy of large spatial scale management strategies. Academics indicated that standardization has been useful in fisheries education because time previously used to teach how sampling methods are developed is now more devoted to diagnosis and treatment of problem fish communities. Researchers reported that standardization allowed increased sample size for method validation and calibration. Group consensus was to retain continental standards where they currently exist but to further explore international and intercontinental standardization, specifically identifying where synergies and bridges exist, and identify means to collaborate with scientists where standardization is limited but interest and need occur.

  5. First molecular detection of Aichi virus in sewage and shellfish samples in the Monastir region of Tunisia.

    Science.gov (United States)

    Sdiri-Loulizi, K; Hassine, M; Aouni, Z; Gharbi-Khelifi, H; Sakly, N; Chouchane, S; Guédiche, M N; Pothier, P; Aouni, M; Ambert-Balay, K

    2010-09-01

    The aims of our investigations were (1) to look for Aichi virus in environmental samples and (2) to compare the Aichi virus strains in both clinical and environmental samples in order to evaluate the role of environmental contamination as a possible vehicle for viral transmission. Aichi virus was detected in 15 (6%) sewage samples and in 4 (6.6%) shellfish samples. Aichi virus was identified for the first time in water samples. Phylogenetic analysis revealed several clusters that occurred sequentially in time, suggesting some parallelism in the evolution of environmental and human strains. Aichi virus present in sewage reflects the viruses circulating in the community.

  6. Vesicular exanthema of swine virus: isolation and serotyping of field samples.

    OpenAIRE

    Edwards, J F; Yedloutschnig, R J; Dardiri, A H; Callis, J. J.

    1987-01-01

    Virus isolation was attempted from 262 field samples of vesicular material collected during the outbreaks of vesicular exanthema of swine in the U.S.A. from 1952-54. Using primary swine kidney culture, viral cytopathogenic agents were isolated from 76.3% of the samples. However, an overall recovery rate of 82.1% was obtained after samples negative in tissue culture were inoculated intradermally in susceptible swine. All vesicular exanthema of swine virus isolates were identified as serotype B...

  7. RNA interference inhibits herpes simplex virus type 1 isolated from saliva samples and mucocutaneous lesions.

    Science.gov (United States)

    Silva, Amanda Perse da; Lopes, Juliana Freitas; Paula, Vanessa Salete de

    2014-01-01

    The aim of this study was to evaluate the use of RNA interference to inhibit herpes simplex virus type-1 replication in vitro. For herpes simplex virus type-1 gene silencing, three different small interfering RNAs (siRNAs) targeting the herpes simplex virus type-1 UL39 gene (sequence si-UL 39-1, si-UL 39-2, and si-UL 39-3) were used, which encode the large subunit of ribonucleotide reductase, an essential enzyme for DNA synthesis. Herpes simplex virus type-1 was isolated from saliva samples and mucocutaneous lesions from infected patients. All mucocutaneous lesions' samples were positive for herpes simplex virus type-1 by real-time PCR and by virus isolation; all herpes simplex virus type-1 from saliva samples were positive by real-time PCR and 50% were positive by virus isolation. The levels of herpes simplex virus type-1 DNA remaining after siRNA treatment were assessed by real-time PCR, whose results demonstrated that the effect of siRNAs on gene expression depends on siRNA concentration. The three siRNA sequences used were able to inhibit viral replication, assessed by real-time PCR and plaque assays and among them, the sequence si-UL 39-1 was the most effective. This sequence inhibited 99% of herpes simplex virus type-1 replication. The results demonstrate that silencing herpes simplex virus type-1 UL39 expression by siRNAs effectively inhibits herpes simplex virus type-1 replication, suggesting that siRNA based antiviral strategy may be a potential therapeutic alternative. Copyright © 2014. Published by Elsevier Editora Ltda.

  8. Antibodies to H5 subtype avian influenza virus and Japanese encephalitis virus in northern pintails (Anas acuta) sampled in Japan

    Science.gov (United States)

    Ramey, Andy M.; Spackman, Erica; Yeh, Jung-Yong; Fujita, Go; Konishi, Kan; Reed, John A.; Wilcox, Benjamin R.; Brown, Justin D.; Stallknecht, David E.

    2013-01-01

    Blood samples from 105 northern pintails (Anas acuta) captured on Hokkaido, Japan were tested for antibodies to avian influenza virus (AIV), Japanese encephalitis virus (JEV), and West Nile virus (WNV) to assess possible involvement of this species in the spread of economically important and potentially zoonotic pathogens. Antibodies to AIV were detected in 64 of 105 samples (61%). Of the 64 positives, 95% and 81% inhibited agglutination of two different H5 AIV antigens (H5N1 and H5N9), respectively. Antibodies to JEV and WNV were detected in five (5%) and none of the samples, respectively. Results provide evidence for prior exposure of migrating northern pintails to H5 AIV which couldhave implications for viral shedding and disease occurrence. Results also provide evidence for limited involvement of this species in the transmission and spread of flaviviruses during spring migration.

  9. Aerosol Sampling Experiment on the International Space Station

    Science.gov (United States)

    Meyer, Marit E.

    2017-01-01

    The International Space Station (ISS) is a unique indoor environment which serves as both home and workplace to the astronaut crew. There is currently no particulate monitoring, although particulate matter requirements exist. An experiment to collect particles in the ISS cabin was conducted recently. Two different aerosol samplers were used for redundancy and to collect particles in two size ranges spanning from 10 nm to hundreds of micrometers. The Active Sampler is a battery operated thermophoretic sampler with an internal pump which draws in air and collects particles directly on a transmission electron microscope grid. This commercial-off-the-shelf device was modified for operation in low gravity. The Passive Sampler has five sampling surfaces which were exposed to air for different durations in order to collect at least one sample with an optimal quantity of particles for microscopy. These samples were returned to Earth for analysis with a variety of techniques to obtain long-term average concentrations and identify particle emission sources. Results are compared with the inventory of ISS aerosols which was created based on sparse data and the literature. The goal of the experiment is to obtain data on indoor aerosols on ISS for future particulate monitor design and development.

  10. Novel circular DNA viruses in stool samples of wild-living chimpanzees.

    Science.gov (United States)

    Blinkova, Olga; Victoria, Joseph; Li, Yingying; Keele, Brandon F; Sanz, Crickette; Ndjango, Jean-Bosco N; Peeters, Martine; Travis, Dominic; Lonsdorf, Elizabeth V; Wilson, Michael L; Pusey, Anne E; Hahn, Beatrice H; Delwart, Eric L

    2010-01-01

    Viral particles in stool samples from wild-living chimpanzees were analysed using random PCR amplification and sequencing. Sequences encoding proteins distantly related to the replicase protein of single-stranded circular DNA viruses were identified. Inverse PCR was used to amplify and sequence multiple small circular DNA viral genomes. The viral genomes were related in size and genome organization to vertebrate circoviruses and plant geminiviruses but with a different location for the stem-loop structure involved in rolling circle DNA replication. The replicase genes of these viruses were most closely related to those of the much smaller (approximately 1 kb) plant nanovirus circular DNA chromosomes. Because the viruses have characteristics of both animal and plant viruses, we named them chimpanzee stool-associated circular viruses (ChiSCV). Further metagenomic studies of animal samples will greatly increase our knowledge of viral diversity and evolution.

  11. How Does Sampling Methodology Influence Molecular Detection and Isolation Success in Influenza A Virus Field Studies?

    Science.gov (United States)

    Latorre-Margalef, Neus; Avril, Alexis; Tolf, Conny; Olsen, Björn; Waldenström, Jonas

    2015-12-11

    Wild waterfowl are important reservoir hosts for influenza A virus (IAV) and a potential source of spillover infections in other hosts, including poultry and swine. The emergence of highly pathogenic avian influenza (HPAI) viruses, such as H5N1 and H5N8, and subsequent spread along migratory flyways prompted the initiation of several programs in Europe, North America, and Africa to monitor circulation of HPAI and low-pathogenicity precursor viruses (low-pathogenicity avian influenza [LPAI] viruses). Given the costs of maintaining such programs, it is essential to establish best practice for field methodologies to provide robust data for epidemiological interpretation. Here, we use long-term surveillance data from a single site to evaluate the influence of a number of parameters on virus detection and isolation of LPAI viruses. A total of 26,586 samples (oropharyngeal, fecal, and cloacal) collected from wild mallards were screened by real-time PCR, and positive samples were subjected to isolation in embryonated chicken eggs. The LPAI virus detection rate was influenced by the sample type: cloacal/fecal samples showed a consistently higher detection rate and lower cycle threshold (Ct) value than oropharyngeal samples. Molecular detection was more sensitive than isolation, and virus isolation success was proportional to the number of RNA copies in the sample. Interestingly, for a given Ct value, the isolation success was lower in samples from adult birds than in those from juveniles. Comparing the results of specific real-time reverse transcriptase (RRT)-PCRs and of isolation, it was clear that coinfections were common in the investigated birds. The effects of sample type and detection methods warrant some caution in interpretation of the surveillance data. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  12. International naming of viruses - a digest of recent developments

    NARCIS (Netherlands)

    Bos, L.

    2002-01-01

    With the impressive series of illustrative examples ¿ including viruses of all sorts of organisms from humans to bacteria ¿ given by Van Regenmortel [12], there seem to be no further obstructions towards the implication of ¿a single universal system applicable to all viruses¿ (Art. 3.1 of the Code).

  13. Inhibition of influenza virus internalization by (-)-epigallocatechin-3-gallate.

    Science.gov (United States)

    Kim, Meehyein; Kim, So-Yeon; Lee, Hye Won; Shin, Jin Soo; Kim, Pilho; Jung, Young-Sik; Jeong, Hyeong-Seop; Hyun, Jae-Kyung; Lee, Chong-Kyo

    2013-11-01

    (-)-Epigallocatechin-3-gallate (EGCG), one of the major flavonoid components of green tea, is known to have a broad antiviral activity against several enveloped viruses, including the influenza virus. However, its mode of action and the mechanism that allows it to target influenza virus molecules have not been fully elucidated. Thus, this study investigated the molecular mechanism by which EGCG suppresses influenza virus infections. EGCG was found to block an early step in the influenza viral life cycle, but it did not affect viral adsorption to target cells or viral RNA replication. However, EGCG inhibited hemifusion events between virus particles and the cellular membrane by reducing the viral membrane integrity, thereby resulting in the loss of the cell penetration capacity of the influenza virus. EGCG also marginally suppressed the viral and nonviral neuraminidase (NA) activity in an enzyme-based assay system. In conclusion, it is suggested that the anti-influenza viral efficacy of EGCG is attributable to damage to the physical properties of the viral envelope and partial inhibition of the NA surface glycoprotein. These results may facilitate future investigations of the antiviral activity of EGCG against other enveloped viruses as well as influenza virus. Copyright © 2013 Elsevier B.V. All rights reserved.

  14. Metadata from 12 international groundwater studies: virus and microbial indicator occurrence

    Data.gov (United States)

    U.S. Environmental Protection Agency — This data set contains raw data from 12 international groundwater studies that monitored for human viruses and microbial indicators. Please see the first worksheet...

  15. Dissecting virus entry: replication-independent analysis of virus binding, internalization, and penetration using minimal complementation of β-galactosidase.

    Directory of Open Access Journals (Sweden)

    Christine Burkard

    Full Text Available Studies of viral entry into host cells often rely on the detection of post-entry parameters, such as viral replication or the expression of a reporter gene, rather than on measuring entry per se. The lack of assays to easily detect the different steps of entry severely hampers the analysis of this key process in virus infection. Here we describe novel, highly adaptable viral entry assays making use of minimal complementation of the E. coli β-galactosidase in mammalian cells. Enzyme activity is reconstituted when a small intravirion peptide (α-peptide is complementing the inactive mutant form ΔM15 of β-galactosidase. The method allows to dissect and to independently detect binding, internalization, and fusion of viruses during host cell entry. Here we use it to confirm and extend current knowledge on the entry process of two enveloped viruses: vesicular stomatitis virus (VSV and murine hepatitis coronavirus (MHV.

  16. Global Unique Identification of Geoscience Samples: The International Geo Sample Number (IGSN) and the System for Earth Sample Registration (SESAR)

    Science.gov (United States)

    Lehnert, K. A.; Goldstein, S. L.; Vinayagamoorthy, S.; Lenhardt, W. C.

    2005-12-01

    Data on samples represent a primary foundation of Geoscience research across disciplines, ranging from the study of climate change, to biogeochemical cycles, to mantle and continental dynamics and are key to our knowledge of the Earth's dynamical systems and evolution. Different data types are generated for individual samples by different research groups, published in different papers, and stored in different databases on a global scale. The utility of these data is critically dependent on their integration. Such integration can be achieved within a Geoscience Cyberinfrastructure, but requires unambiguous identification of samples. Currently, naming of samples is arbitrary and inconsistent and therefore severely limits our ability to share, link, and integrate sample-based data. Major problems include name duplication, and changing of names as a sample is passed along over many years to different investigators. SESAR, the System for Earth Sample Registration (http://www.geosamples.org), addresses this problem by building a registry that generates and administers globally unique identifiers for Geoscience samples: the International Geo Sample Number (IGSN). Implementation of the IGSN in data publication and digital data management will dramatically advance interoperability among information systems for sample-based data, opening an extensive range of new opportunities for discovery and for interdisciplinary approaches in research. The IGSN will also facilitate the ability of investigators to build on previously collected data on samples as new measurements are made or new techniques are developed. With potentially broad application to all types of Geoscience samples, SESAR is global in scope. It is a web-based system that can be easily accessed by individual users through an interactive web interface and by distributed client systems via standard web services. Samples can be registered individually or in batches and at various levels of granularity from entire cores

  17. VENOUS SAMPLING FOR CUSHING DISEASE: COMPARISON OF INTERNAL JUGULAR VEIN AND INFERIOR PETROSAL SINUS SAMPLING.

    Science.gov (United States)

    Radvany, Martin G; Quinones-Hinojosa, Alfredo; Gallia, Gary L; Wand, Gary S; Salvatori, Roberto

    2016-09-01

    Because magnetic resonance imaging (MRI) fails to detect many adrenocorticotropic hormone (ACTH)-secreting pituitary adenomas, inferior petrosal sinus sampling (IPSS) is considered the gold standard to differentiate Cushing disease (CD) from ectopic ACTH secretion syndrome (EAS). Some authors have suggested internal jugular vein sampling (IJVS) as an alternative to IPSS. We simultaneously compared IJVS to IPSS in 30 consecutive patients referred for ACTH-dependent Cushing syndrome and equivocal MRI exams. Five sites were simultaneously sampled in each patient (right and left IPS, right and left IJV, and femoral vein) before and after the administration of corticotrophin-releasing hormone or desmopressin. The test was considered consistent with CD when the IPS to peripheral ratio was >2 at baseline or >3 after stimulus and the IJV to peripheral ratio was >1.7 at baseline or >2 after stimulus. In 27 of 30 patients, IPSS results were consistent with a central source of ACTH. Two of the other 3 patients had EAS (one lung carcinoid and one occult), and 1 patient had pathology-proven CD. The sensitivity of IPSS was 96.4%. Only 64.2% of these patients had results meeting criteria for a central source of ACTH by IJVS criteria. Twenty patients with centralizing IPPS have undergone pituitary surgery. Of these, the central origin of excessive ACTH was confirmed with certainty in 16 patients. Among these 16 patients, the IPSS sensitivity was 93.8%, whereas 5 patients had false-negative IJVS (68.7% sensitivity). These results do not support the routine use of IJVS in establishing if the pituitary is the source of excessive ACTH. ACTH = adrenocorticotropic hormone CD = Cushing disease CRH = corticotrophin-releasing hormone CS = Cushing syndrome DDAVP = desmopressin EAS = ectopic ACTH secretion IJVS = internal jugular vein sampling IPSS = inferior petrosal sinus sampling JVS = jugular venous sampling MRI = magnetic resonance imaging.

  18. Error baseline rates of five sample preparation methods used to characterize RNA virus populations.

    Science.gov (United States)

    Kugelman, Jeffrey R; Wiley, Michael R; Nagle, Elyse R; Reyes, Daniel; Pfeffer, Brad P; Kuhn, Jens H; Sanchez-Lockhart, Mariano; Palacios, Gustavo F

    2017-01-01

    Individual RNA viruses typically occur as populations of genomes that differ slightly from each other due to mutations introduced by the error-prone viral polymerase. Understanding the variability of RNA virus genome populations is critical for understanding virus evolution because individual mutant genomes may gain evolutionary selective advantages and give rise to dominant subpopulations, possibly even leading to the emergence of viruses resistant to medical countermeasures. Reverse transcription of virus genome populations followed by next-generation sequencing is the only available method to characterize variation for RNA viruses. However, both steps may lead to the introduction of artificial mutations, thereby skewing the data. To better understand how such errors are introduced during sample preparation, we determined and compared error baseline rates of five different sample preparation methods by analyzing in vitro transcribed Ebola virus RNA from an artificial plasmid-based system. These methods included: shotgun sequencing from plasmid DNA or in vitro transcribed RNA as a basic "no amplification" method, amplicon sequencing from the plasmid DNA or in vitro transcribed RNA as a "targeted" amplification method, sequence-independent single-primer amplification (SISPA) as a "random" amplification method, rolling circle reverse transcription sequencing (CirSeq) as an advanced "no amplification" method, and Illumina TruSeq RNA Access as a "targeted" enrichment method. The measured error frequencies indicate that RNA Access offers the best tradeoff between sensitivity and sample preparation error (1.4-5) of all compared methods.

  19. First international external quality assessment of molecular detection of Crimean-Congo hemorrhagic fever virus.

    Directory of Open Access Journals (Sweden)

    Camille Escadafal

    Full Text Available Crimean-Congo hemorrhagic fever (CCHF is a zoonosis caused by a Nairovirus of the family Bunyaviridae. Infection is transmitted to humans mostly by Hyalomma ticks and also by direct contact with the blood or tissues of infected humans or viremic livestock. Clinical features usually include a rapid progression characterized by hemorrhage, myalgia and fever, with a lethality rate up to 30%. CCHF is one of the most widely distributed viral hemorrhagic fevers and has been reported in Africa, the Middle East and Asia, as well as parts of Europe. There is no approved vaccine or specific treatment against CCHF virus (CCHFV infections. In this context, an accurate diagnosis as well as a reliable surveillance of CCHFV infections is essential. Diagnostic techniques include virus culture, serology and molecular methods, which are now increasingly used. The European Network for the Diagnostics of "Imported" Viral Diseases organized the first international external quality assessment of CCHVF molecular diagnostics in 2011 to assess the efficiency and accurateness of CCHFV molecular methods applied by expert laboratories. A proficiency test panel of 15 samples was distributed to the participants including 10 different CCHFV preparations generated from infected cell cultures, a preparation of plasmid cloned with the nucleoprotein of CCHFV, two CCHFV RNA preparations and two negative controls. Forty-four laboratories worldwide participated in the EQA study and 53 data sets were received. Twenty data sets (38% met all criteria with optimal performance, 10 (19% with acceptable performance, while 23 (43% reported results showing a need for improvement. Differences in performance depended on the method used, the type of strain tested, the concentration of the sample tested and the laboratory performing the test. These results indicate that there is still a need for improving testing conditions and standardizing protocols for the molecular detection of Crimean

  20. Sampling Indoor Aerosols on the International Space Station

    Science.gov (United States)

    Meyer, Marit E.

    2016-01-01

    In a spacecraft cabin environment, the size range of indoor aerosols is much larger and they persist longer than on Earth because they are not removed by gravitational settling. A previous aerosol experiment in 1991 documented that over 90 of the mass concentration of particles in the NASA Space Shuttle air were between 10 m and 100 m based on measurements with a multi-stage virtual impactor and a nephelometer (Liu et al. 1991). While the now-retired Space Shuttle had short duration missions (less than two weeks), the International Space Station (ISS) has been continually inhabited by astronauts for over a decade. High concentrations of inhalable particles on ISS are potentially responsible for crew complaints of respiratory and eye irritation and comments about 'dusty' air. Air filtration is the current control strategy for airborne particles on the ISS, and filtration modeling, performed for engineering and design validation of the air revitalization system in ISS, predicted that PM requirements would be met. However, aerosol monitoring has never been performed on the ISS to verify PM levels. A flight experiment is in preparation which will provide data on particulate matter in ISS ambient air. Particles will be collected with a thermophoretic sampler as well as with passive samplers which will extend the particle size range of sampling. Samples will be returned to Earth for chemical and microscopic analyses, providing the first aerosol data for ISS ambient air.

  1. Quantification and Genotyping of Aichi Virus 1 in Water Samples in the Kathmandu Valley, Nepal.

    Science.gov (United States)

    Haramoto, Eiji; Kitajima, Masaaki

    2017-02-09

    Aichi virus 1 genomes were detected by quantitative PCR in groundwater from shallow dug (10/22) and tube wells (1/15), river water (14/14), and sewage (1/1), with the maximum concentration of 4.0 × 10(9) copies/l. Nucleotide sequencing analysis demonstrated the prevalence of genotype B in the virus positive samples.

  2. Zika virus disease: a public health emergency of international concern.

    Science.gov (United States)

    Lupton, Kelly

    The emergence of Zika virus disease (ZIKV) in the Americas, mainly Brazil, has required the World Health Organization to take action to halt the spread of the virus by implementing preventive measures. This has resulted in increased surveillance of the virus and its potential complications. In the UK, cases of ZIKV have been reported in returning travellers. With the importance of this disease increasing, it is vital that nurses and other health professionals take the time to learn about ZIKV in order to pass on this knowledge to patients, enabling them to make informed choices about travel to affected areas. This article will discuss the ZIKV, its complications and what to advise travellers, including pregnant women, to prevent transmission and spread.

  3. Nucleic Acid, Antibody, and Virus Culture Methods to Detect Xenotropic MLV-Related Virus in Human Blood Samples

    Directory of Open Access Journals (Sweden)

    M. F. Kearney

    2011-01-01

    Full Text Available The MLV-related retrovirus, XMRV, was recently identified and reported to be associated with both prostate cancer and chronic fatigue syndrome. At the National Cancer Institute-Frederick, MD (NCI-Frederick, we developed highly sensitive methods to detect XMRV nucleic acids, antibodies, and replication competent virus. Analysis of XMRV-spiked samples and/or specimens from two pigtail macaques experimentally inoculated with 22Rv1 cell-derived XMRV confirmed the ability of the assays used to detect XMRV RNA and DNA, and culture isolatable virus when present, along with XMRV reactive antibody responses. Using these assays, we did not detect evidence of XMRV in blood samples ( or prostate specimens ( from two independent cohorts of patients with prostate cancer. Previous studies detected XMRV in prostate tissues. In the present study, we primarily investigated the levels of XMRV in blood plasma samples collected from patients with prostate cancer. These results demonstrate that while XMRV-related assays developed at the NCI-Frederick can readily measure XMRV nucleic acids, antibodies, and replication competent virus, no evidence of XMRV was found in the blood of patients with prostate cancer.

  4. [Knowledge of human papilloma virus (HPV) and acceptance of vaginal self-sampling among Mexican woman].

    Science.gov (United States)

    Hernández-Márquez, Clara I; Salinas-Urbina, Addis A; Cruz-Valdez, Aurelio; Hernández-Girón, Carlos

    2014-01-01

    To analyze the relationship between the level of knowledge about human papilloma virus and the acceptance of vaginal self-sampling as a cervical cancer diagnostic test among Mexican women who have already experienced vaginal self-sampling at home. A structured questionnaire consisting of 22 questions was applied to 690 women in the state of Morelos who had taken a vaginal self-sample at home. The aspects explored were the level of knowledge about transmission of the human papilloma virus, identification of the virus as a necessary cause of cervical cancer, and clinical manifestations of infection and treatment. A knowledge index was constructed, identifying the relationship between the index and the women's acceptance of self-sampling, and their degree of trust in the procedure. The statistical analysis included a logistic regression with estimates of measures of association and their respective 95% confidence intervals. The level of knowledge about human papillomavirus showed a positive association with the degree of acceptance of vaginal self-sampling (OR 2.9; 95% CI 1.0-5.01) and the women's level of confidence (OR 2.9; 95% CI 1.8-4.67). The level of knowledge increased with level of education and was higher in younger women. In order for women with an increased risk of cervical cancer to continue participating in vaginal self-sampling, they must be well informed about the virus. This is especially true for older women, those with lower levels of education, and those in lower socioeconomic levels.

  5. No Evidence of Rat Hepatitis E Virus Excretion in Urine Samples of Rats.

    Science.gov (United States)

    Li, Tian-Cheng; Yoshizaki, Sayaka; Ami, Yasushi; Suzaki, Yuriko; Johne, Reimar; Wakita, Takaji

    2017-05-24

    To investigate whether rat hepatitis E virus (rat HEV) is excreted in the urine of HEV-infected rats, we infected 3 Wistar and 6 nude rats with rat HEV and examined the rat-HEV RNA in serum, fecal, and urine samples. We detected rat-HEV RNA in the serum and fecal samples of all 9 rats but not in any of the urine samples. Our results suggest that in rats, rat HEV is not transmitted via urine.

  6. Vesicular exanthema of swine virus: isolation and serotyping of field samples.

    Science.gov (United States)

    Edwards, J F; Yedloutschnig, R J; Dardiri, A H; Callis, J J

    1987-01-01

    Virus isolation was attempted from 262 field samples of vesicular material collected during the outbreaks of vesicular exanthema of swine in the U.S.A. from 1952-54. Using primary swine kidney culture, viral cytopathogenic agents were isolated from 76.3% of the samples. However, an overall recovery rate of 82.1% was obtained after samples negative in tissue culture were inoculated intradermally in susceptible swine. All vesicular exanthema of swine virus isolates were identified as serotype B51 using complement fixation and serum neutralization tests. Two isolates did not react with antisera to known vesicular agents of swine and failed to produce vesicles or clinical signs of disease upon inoculation in swine. One vesicular exanthema of swine virus isolate from tissue of equine origin was pathogenic for swine but produced limited vesiculation at the site of intradermalingual inoculation in the tongue of a pony infected experimentally. Type B51 virus was reisolated from lesions produced in the pony and the pony became seropositive for virus type B51. PMID:3651889

  7. Field Methods and Sample Collection Techniques for the Surveillance of West Nile Virus in Avian Hosts.

    Science.gov (United States)

    Wheeler, Sarah S; Boyce, Walter M; Reisen, William K

    2016-01-01

    Avian hosts play an important role in the spread, maintenance, and amplification of West Nile virus (WNV). Avian susceptibility to WNV varies from species to species thus surveillance efforts can focus both on birds that survive infection and those that succumb. Here we describe methods for the collection and sampling of live birds for WNV antibodies or viremia, and methods for the sampling of dead birds. Target species and study design considerations are discussed.

  8. The Use of Bioaerosol Sampling for Airborne Virus Surveillance in Swine Production Facilities: A Mini Review

    Directory of Open Access Journals (Sweden)

    Benjamin D. Anderson

    2017-07-01

    Full Text Available Modern swine production facilities typically house dense populations of pigs and may harbor a variety of potentially zoonotic viruses that can pass from one pig generation to another and periodically infect human caretakers. Bioaerosol sampling is a common technique that has been used to conduct microbial risk assessments in swine production, and other similar settings, for a number of years. However, much of this work seems to have been focused on the detection of non-viral microbial agents (i.e., bacteria, fungi, endotoxins, etc., and efforts to detect viral aerosols in pig farms seem sparse. Data generated by such studies would be particularly useful for assessments of virus transmission and ecology. Here, we summarize the results of a literature review conducted to identify published articles related to bioaerosol generation and detection within swine production facilities, with a focus on airborne viruses. We identified 73 scientific reports, published between 1991 and 2017, which were included in this review. Of these, 19 (26.7% used sampling methodology for the detection of viruses. Our findings show that bioaerosol sampling methodologies in swine production settings have predominately focused on the detection of bacteria and fungi, with no apparent standardization between different approaches. Information, specifically regarding virus aerosol burden in swine production settings, appears to be limited. However, the number of viral aerosol studies has markedly increased in the past 5 years. With the advent of new sampling technologies and improved diagnostics, viral bioaerosol sampling could be a promising way to conduct non-invasive viral surveillance among swine farms.

  9. Assessment of the RNASound RNA Sampling Card for the preservation of influenza virus RNA

    Directory of Open Access Journals (Sweden)

    Hilda Lau

    2016-11-01

    Full Text Available Shipping influenza virus specimens, isolates or purified RNA is normally conducted at ultra-low temperatures using dry ice to ensure minimal degradation of the samples but this is expensive and requires special packaging and shipping conditions. Therefore, alternative methods for shipping influenza viruses or RNA at ambient temperatures would be desirable.The RNASound RNA Sampling Card (FortiusBio LLC, CA, USA is a device that enables specimens or isolates to be applied to a card, whereby viruses are inactivated, while RNA is preserved and purified RNA can also easily be eluted. To evaluate this card, we applied influenza virus cell culture isolate supernatants to either the RNASound card or Whatman Grade No. 1 filter paper (GE Healthcare, NSW, Australia and compared the preservation to that of material stored in liquid form. Preservation was tested using influenza A and B viruses at two different storage temperatures (cool 2-8oC or room temperature 18-22oC and these were compared with control material stored at -80°C, for 7, 14 or 28 days. The quality of the RNA recovered was assessed using real time RT-PCR and Sanger sequencing. The RNASound card was effective in preserving influenza RNA at room temperature for up to 28 days, with only a minor change in real-time RT-PCR cycle threshold values for selected gene targets when comparing between viruses applied to the card or stored at -80°C. Similar results were obtained with filter paper, whilst virus in liquid form performed the worst. Nevertheless, as the RNASound card also has the capability to inactivate viruses in addition to preserving RNA at room temperature for many weeks, this makes it feasible to send samples to laboratories using regular mail, and thus avoid the need for expensive shipping conditions requiring biohazard containers and dry ice. Moreover, the quick and simple RNA recovery from the RNASound card allows recipient labs to obtain RNA without the need for special reagents

  10. The xenotropic murine leukemia virus-related retrovirus debate continues at first international workshop

    NARCIS (Netherlands)

    J.P. Stoye (Jonathan); R.H. Silverman (Robert); C.A.B. Boucher (Charles); S.F.J. Le Grice

    2010-01-01

    textabstractThe 1stInternational Workshop on Xenotropic Murine Leukemia Virus-Related Retrovirus (XMRV), co-sponsored by the National Institutes of Health, The Department of Health and Human Services and Abbott Diagnostics, was convened on September 7/8, 2010 on the NIH campus, Bethesda, MD.

  11. Antigenic typing of brazilian rabies virus samples isolated from animals and humans, 1989-2000

    Directory of Open Access Journals (Sweden)

    FAVORETTO Silvana Regina

    2002-01-01

    Full Text Available Animal and human rabies samples isolated between 1989 and 2000 were typified by means of a monoclonal antibody panel against the viral nucleoprotein. The panel had been previously established to study the molecular epidemiology of rabies virus in the Americas. Samples were isolated in the Diagnostic Laboratory of the Pasteur Institute and in other rabies diagnostic centers in Brazil. In addition to the fixed virus samples CVS-31/96-IP, preserved in mouse brain, and PV-BHK/97, preserved in cell culture, a total of 330 rabies virus samples were isolated from dogs, cats, cattle, horses, bats, sheep, goat, swine, foxes, marmosets, coati and humans. Six antigenic variants that were compatible with the pre-established monoclonal antibodies panel were defined: numbers 2 (dog, 3 (Desmodus rotundus, 4 (Tadarida brasiliensis, 5 (vampire bat from Venezuela, 6 (Lasiurus cinereus and Lab (reacted to all used antibodies. Six unknown profiles, not compatible with the panel, were also found. Samples isolated from insectivore bats showed the greatest variability and the most commonly isolated variant was variant-3 (Desmodus rotundus. These findings may be related to the existence of multiple independent transmission cycles, involving different bat species.

  12. Buffer AVL Alone Does Not Inactivate Ebola Virus in a Representative Clinical Sample Type.

    Science.gov (United States)

    Smither, Sophie J; Weller, Simon A; Phelps, Amanda; Eastaugh, Lin; Ngugi, Sarah; O'Brien, Lyn M; Steward, Jackie; Lonsdale, Steve G; Lever, Mark S

    2015-10-01

    Rapid inactivation of Ebola virus (EBOV) is crucial for high-throughput testing of clinical samples in low-resource, outbreak scenarios. The EBOV inactivation efficacy of Buffer AVL (Qiagen) was tested against marmoset serum (EBOV concentration of 1 × 10(8) 50% tissue culture infective dose per milliliter [TCID50 · ml(-1)]) and murine blood (EBOV concentration of 1 × 10(7) TCID50 · ml(-1)) at 4:1 vol/vol buffer/sample ratios. Posttreatment cell culture and enzyme-linked immunosorbent assay (ELISA) analysis indicated that treatment with Buffer AVL did not inactivate EBOV in 67% of samples, indicating that Buffer AVL, which is designed for RNA extraction and not virus inactivation, cannot be guaranteed to inactivate EBOV in diagnostic samples. Murine blood samples treated with ethanol (4:1 [vol/vol] ethanol/sample) or heat (60°C for 15 min) also showed no viral inactivation in 67% or 100% of samples, respectively. However, combined Buffer AVL and ethanol or Buffer AVL and heat treatments showed total viral inactivation in 100% of samples tested. The Buffer AVL plus ethanol and Buffer AVL plus heat treatments were also shown not to affect the extraction of PCR quality RNA from EBOV-spiked murine blood samples. © Crown copyright 2015.

  13. Exhaled breath condensate sampling is not a new method for detection of respiratory viruses

    Directory of Open Access Journals (Sweden)

    Maes Piet

    2011-03-01

    Full Text Available Abstract Background Exhaled breath condensate (EBC sampling has been considered an inventive and novel method for the isolation of respiratory viruses. Methods In our study, 102 volunteers experiencing upper airway infection were recruited over the winter and early spring of 2008/2009 and the first half of the winter of 2009/2010. Ninety-nine EBCs were successfully obtained and screened for 14 commonly circulating respiratory viruses. To investigate the efficiency of virus isolation from EBC, a nasal swab was taken in parallel from a subset of volunteers. The combined use of the ECoVent device with the RTube™ allowed the registration of the exhaled volume and breathing frequency during collection. In this way, the number of exhaled viral particles per liter air or per minute can theoretically be estimated. Results Viral screening resulted in the detection of 4 different viruses in EBC and/or nasal swabs: Rhinovirus, Human Respiratory Syncytial Virus B, Influenza A and Influenza B. Rhinovirus was detected in 6 EBCs and 1 EBC was Influenza B positive. We report a viral detection rate of 7% for the EBCs, which is much lower than the detection rate of 46.8% observed using nasal swabs. Conclusion Although very promising, EBC collection using the RTube™ is not reliable for diagnosis of respiratory infections.

  14. Prevalence and genetic diversity of Aichi virus strains in stool samples from community and hospitalized patients.

    Science.gov (United States)

    Ambert-Balay, K; Lorrot, M; Bon, F; Giraudon, H; Kaplon, J; Wolfer, M; Lebon, P; Gendrel, D; Pothier, P

    2008-04-01

    Aichi virus has been proposed as a causative agent of gastroenteritis. A total of 457 stool specimens from children hospitalized with acute diarrhea and 566 stool specimens from adults and children involved in 110 gastroenteritis outbreaks were screened for the presence of Aichi virus by reverse transcription-PCR (RT-PCR) amplification of the genomic region of the 3C and 3D (3CD) nonstructural proteins. Our results show a low incidence of Aichi virus in pediatric samples and the existence of mixed infections with other microbiological agents in some cases. From the outbreak survey, it appears that the presence of Aichi virus is an indicator of mixed infections causing gastroenteritis outbreaks and that it could be involved in half of the oyster-associated outbreaks. A second RT-PCR was developed to amplify a part of the VP1 gene. The phylogenetic analysis showed a good correlation between the two classifications based on 3CD and VP1 gene sequences and revealed the prevalence of genotype A in France. It also allowed us to partially describe an Aichi virus strain that could represent a new genotype, thus suggesting the existence of a certain diversity.

  15. Simultaneous detection of four foodborne viruses in food samples using a one-step multiplex reverse transcription PCR.

    Science.gov (United States)

    Lee, Shin-Young; Kim, Mi-Ju; Kim, Hyun-Joong; Jeong, KwangCheol Casey; Kim, Hae-Yeong

    2017-11-15

    A one-step multiplex reverse transcription PCR (RT-PCR) method comprising six primer sets (for the detection of norovirus GI and GII, hepatitis A virus, rotavirus, and astrovirus) was developed to simultaneously detect four kinds of pathogenic viruses. The size of the PCR products for norovirus GI and GII, hepatitis A virus (VP3/VP1 and P2A regions), rotavirus, and astrovirus were 330, 164, 244, 198, 629, and 449 bp, respectively. The RT-PCR with the six primer sets showed specificity for the pathogenic viruses. The detection limit of developed multiplex RT-PCR, as evaluated using serially diluted viral RNAs, was comparable to that of one-step single RT-PCR. Also, this multiplex RT-PCR was evaluated using food samples such as water, oysters, lettuce, and vegetable product. These food samples were artificially spiked with four kinds of viruses in diverse combinations, and the spiked viruses in all food samples were detected successfully.

  16. The effect of maternal antibodies on the detection of bovine virus diarrhoea virus in peripheral blood samples

    NARCIS (Netherlands)

    Zimmer, G.M.; Maanen, van C.; Goey, de I.; Brinkhof, J.; Wentink, G.H.

    2004-01-01

    Persistently infected animals (PI animals), that is those animals born after an intrauterine infection of the dam during the first 120 days of gestation, are the main source of bovine virus diarrhoea virus (BVD virus) in a cattle population. The success of any BVD virus eradication programme depends

  17. Application of viability PCR to discriminate the infectivity of hepatitis A virus in food samples.

    Science.gov (United States)

    Moreno, L; Aznar, R; Sánchez, G

    2015-05-18

    Transmitted through the fecal-oral route, the hepatitis A virus (HAV) is acquired primarily through close personal contact and foodborne transmission. HAV detection in food is mainly carried out by quantitative RT-PCR (RT-qPCR). The discrimination of infectious and inactivated viruses remains a key obstacle when using RT-qPCR to quantify enteric viruses in food samples. Initially, viability dyes, propidium monoazide (PMA) and ethidium monoazide (EMA), were evaluated for the detection and quantification of infectious HAV in lettuce wash water. Results showed that PMA combined with 0.5% Triton X-100 (Triton) was the best pretreatment to assess HAV infectivity and completely eliminated the signal of thermally inactivated HAV in lettuce wash water. This procedure was further evaluated in artificially inoculated foods (at concentrations of ca. 6×10(4), 6×10(3) and 6×10(2)TCID50) including lettuce, parsley, spinach, cockles and coquina clams. The PMA-0.5% Triton pretreatment reduced the signal of thermally inactivated HAV between 0.5 and 2 logs, in lettuce and spinach concentrates. Moreover, this pretreatment reduced the signal of inactivated HAV by more than 1.5 logs, in parsley and ten-fold diluted shellfish samples inoculated at the lowest concentration. Overall, this pretreatment (50 μM PMA-0.5% Triton) significantly reduced the detection of thermally inactivated HAV, depending on the initial virus concentration and the food matrix. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. Internal control for real-time polymerase chain reaction based on MS2 bacteriophage for RNA viruses diagnostics

    Directory of Open Access Journals (Sweden)

    Miriam Ribas Zambenedetti

    Full Text Available BACKGROUND Real-time reverse transcription polymerase chain reaction (RT-PCR is routinely used to detect viral infections. In Brazil, it is mandatory the use of nucleic acid tests to detect hepatitis C virus (HCV, hepatitis B virus and human immunodeficiency virus in blood banks because of the immunological window. The use of an internal control (IC is necessary to differentiate the true negative results from those consequent from a failure in some step of the nucleic acid test. OBJECTIVES The aim of this study was the construction of virus-modified particles, based on MS2 bacteriophage, to be used as IC for the diagnosis of RNA viruses. METHODS The MS2 genome was cloned into the pET47b(+ plasmid, generating pET47b(+-MS2. MS2-like particles were produced through the synthesis of MS2 RNA genome by T7 RNA polymerase. These particles were used as non-competitive IC in assays for RNA virus diagnostics. In addition, a competitive control for HCV diagnosis was developed by cloning a mutated HCV sequence into the MS2 replicase gene of pET47b(+-MS2, which produces a non-propagating MS2 particle. The utility of MS2-like particles as IC was evaluated in a one-step format multiplex real-time RT-PCR for HCV detection. FINDINGS We demonstrated that both competitive and non-competitive IC could be successfully used to monitor the HCV amplification performance, including the extraction, reverse transcription, amplification and detection steps, without compromising the detection of samples with low target concentrations. In conclusion, MS2-like particles generated by this strategy proved to be useful IC for RNA virus diagnosis, with advantage that they are produced by a low cost protocol. An attractive feature of this system is that it allows the construction of a multicontrol by the insertion of sequences from more than one pathogen, increasing its applicability for diagnosing different RNA viruses.

  19. Direct detection of Trichomonas vaginalis virus in Trichomonas vaginalis positive clinical samples from the Netherlands.

    Science.gov (United States)

    Jehee, Ivo; van der Veer, Charlotte; Himschoot, Michelle; Hermans, Mirjam; Bruisten, Sylvia

    2017-12-01

    Trichomonas vaginalis is the most common sexually transmitted parasitical infection worldwide. T. vaginalis can carry a virus: Trichomonas vaginalis virus (TVV). To date, four TVV species have been described. Few studies have investigated TVV prevalence and its clinical importance. We have developed a nested reverse-transcriptase PCR, with novel, type specific primers to directly detect TVV RNA in T. vaginalis positive clinical samples. A total of 119T. vaginalis positive clinical samples were collected in Amsterdam and "s-Hertogenbosch, the Netherlands, from 2012 to 2016. For all samples T. vaginalis was genotyped using multi-locus sequence typing. The T. vaginalis positive samples segregated into a two-genotype population: type I (n=64) and type II (n=55). All were tested for TVV with the new TVV PCR. We detected 3 of the 4 TVV species. Sequencing of the amplified products showed high homology with published TVV genomes (82-100%). Half of the T. vaginalis clinical samples (n=60, 50.4%) were infected with one or more TVV species, with a preponderance for TVV infections in T. vaginalis type I (n=44, 73.3%). Clinical data was available for a subset of samples (n=34) and we observed an association between testing positive for (any) TVV and reporting urogenital symptoms (p=0.023). The nested RT-PCR allowed for direct detection of TVV in T. vaginalis positive clinical samples. This may be helpful in studies and clinical settings, since T. vaginalis disease and/or treatment outcome may be influenced by the protozoa"s virus. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Low prevalence of Aichi virus in molluscan shellfish samples from Galicia (NW Spain).

    Science.gov (United States)

    Rivadulla, E; Varela, M F; Romalde, J L

    2017-02-01

    The aim of this study was to detect and quantify Aichi virus (AiV) in shellfish from three estuaries in Galicia, the main producer of molluscs in Europe. A total of 249 shellfish samples were analysed using a reverse transcription-quantitative PCR procedure. AiV was detected in 15 of 249 (6·02%) samples. Ría de Ares-Betanzos showed the highest prevalence (11·1%), followed by Ría do Burgo (3·7%) and Ría de Vigo, (2·56%). AiV quantifications ranged from nonquantifiable (under the limit of quantification of the method) to 6·9 × 10 3 RNAc per g DT, with a mean value of 1·9 × 10 2 RNAc per g DT. Results obtained indicated that the prevalence of this enteric virus in the studied area is considerably lower than those of other enteric viruses, such as Norovirus, Sapovirus, HAV or HEV. This is the first study that detects the presence of AiV in shellfish from authorized harvesting areas in Spain. Further studies with clinical samples are needed to determine the potential risk of AiV for human health in Galicia. © 2016 The Society for Applied Microbiology.

  1. Hepatitis E virus in liver and bile samples from slaughtered pigs of Brazil

    Directory of Open Access Journals (Sweden)

    Noemi Rovaris Gardinali

    2012-11-01

    Full Text Available The objective of this study was to detect and identify hepatitis E virus (HEV strains in liver and bile samples from slaughtered pigs in the state of Paraná, Brazil. Liver and bile samples were collected from 118 asymptomatic adult pigs at a slaughterhouse in a major Brazilian pork production area. The samples were assayed using a nested reverse transcription-polymerase chain reaction protocol with primer sets targeting open reading frames (ORF1 and 2 of the HEV genome. HEV RNA was detected in two (1.7% liver samples and one (0.84% bile sample using both primers sets. The HEV strains were classified as genotype 3b on the basis of their nucleotide sequences. These data suggest that healthy pigs may be a source of HEV infection for consumers of pig liver and slaughterhouse workers in Brazil.

  2. Stability of Bovine viral diarrhea virus antigen in ear punch samples collected from bovine fetuses.

    Science.gov (United States)

    Ridpath, Julia F; Chiang, Yu-Wei; Waldbillig, Jill; Neill, John D

    2009-05-01

    Fourteen first-calf heifers were tested free of antibodies against Bovine viral diarrhea viruses (BVDV) by serum neutralization and free of BVDV by polymerase chain reaction. Twelve were exposed to BVDV-1b strain CA0401186a at 84-86 days of gestation, and 2 were exposed to mock inoculum and served as negative controls. Fetuses were harvested by cesarean section at 115-117 days of gestation. The 12 fetuses removed from the BVDV-exposed heifers were BVDV positive based on virus isolation from kidney, thymus, cerebellum, and spleen. It can be assumed that these fetuses would have developed into persistently infected calves had they been allowed to go to term. Virus was not isolated from the fetuses of control animals. Ear punch samples were collected from all fetuses at time of harvest. Antigen capture enzyme-linked immunosorbent assay (ACE), using a commercial kit, was performed on ear punch samples that were frozen within 5 hr of collection and stored at -20 degrees C until tested, tested after storage for 7 days at room temperature (18-25 degrees C), or tested after storage for 7 days at 37 degrees C. Samples stored for 7 days at room temperature or 37 degrees C lost an average of 34% of their starting weight. All samples from BVDV isolation-positive fetuses tested positive by ACE, whereas samples from nonexposed fetuses tested negative, regardless of storage conditions. These results suggest that ACE testing of skin samples collected from aborted fetuses and stillborn calves found in the field may represent a practical surveillance method for BVDV-induced reproductive disease.

  3. Human papillomavirus detection from human immunodeficiency virus-infected Colombian women's paired urine and cervical samples.

    Science.gov (United States)

    Munoz, Marina; Camargo, Milena; Soto-De Leon, Sara C; Sanchez, Ricardo; Parra, Diana; Pineda, Andrea C; Sussmann, Otto; Perez-Prados, Antonio; Patarroyo, Manuel E; Patarroyo, Manuel A

    2013-01-01

    Infection, coinfection and type-specific human papillomavirus (HPV) distribution was evaluated in human immunodeficiency virus (HIV)-positive women from paired cervical and urine samples. Paired cervical and urine samples (n = 204) were taken from HIV-positive women for identifying HPV-DNA presence by using polymerase chain reaction (PCR) with three generic primer sets (GP5+/6+, MY09/11 and pU1M/2R). HPV-positive samples were typed for six high-risk HPV (HR-HPV) (HPV-16, -18, -31, -33, -45 and -58) and two low-risk (LR-HPV) (HPV-6/11) types. Agreement between paired sample results and diagnostic performance was evaluated. HPV infection prevalence was 70.6% in cervical and 63.2% in urine samples. HPV-16 was the most prevalent HPV type in both types of sample (66.7% in cervical samples and 62.0% in urine) followed by HPV-31(47.2%) in cervical samples and HPV-58 (35.7%) in urine samples. There was 55.4% coinfection (infection by more than one type of HPV) in cervical samples and 40.2% in urine samples. Abnormal Papanicolau smears were observed in 25.3% of the women, presenting significant association with HPV-DNA being identified in urine samples. There was poor agreement of cervical and urine sample results in generic and type-specific detection of HPV. Urine samples provided the best diagnosis when taking cytological findings as reference. In conclusion including urine samples could be a good strategy for ensuring adherence to screening programs aimed at reducing the impact of cervical cancer, since this sample is easy to obtain and showed good diagnostic performance.

  4. Human papillomavirus detection from human immunodeficiency virus-infected Colombian women's paired urine and cervical samples.

    Directory of Open Access Journals (Sweden)

    Marina Munoz

    Full Text Available Infection, coinfection and type-specific human papillomavirus (HPV distribution was evaluated in human immunodeficiency virus (HIV-positive women from paired cervical and urine samples. Paired cervical and urine samples (n = 204 were taken from HIV-positive women for identifying HPV-DNA presence by using polymerase chain reaction (PCR with three generic primer sets (GP5+/6+, MY09/11 and pU1M/2R. HPV-positive samples were typed for six high-risk HPV (HR-HPV (HPV-16, -18, -31, -33, -45 and -58 and two low-risk (LR-HPV (HPV-6/11 types. Agreement between paired sample results and diagnostic performance was evaluated. HPV infection prevalence was 70.6% in cervical and 63.2% in urine samples. HPV-16 was the most prevalent HPV type in both types of sample (66.7% in cervical samples and 62.0% in urine followed by HPV-31(47.2% in cervical samples and HPV-58 (35.7% in urine samples. There was 55.4% coinfection (infection by more than one type of HPV in cervical samples and 40.2% in urine samples. Abnormal Papanicolau smears were observed in 25.3% of the women, presenting significant association with HPV-DNA being identified in urine samples. There was poor agreement of cervical and urine sample results in generic and type-specific detection of HPV. Urine samples provided the best diagnosis when taking cytological findings as reference. In conclusion including urine samples could be a good strategy for ensuring adherence to screening programs aimed at reducing the impact of cervical cancer, since this sample is easy to obtain and showed good diagnostic performance.

  5. Hepatitis E virus in swine and effluent samples from slaughterhouses in Brazil.

    Science.gov (United States)

    dos Santos, Debora Regina Lopes; de Paula, Vanessa Salete; de Oliveira, Jaqueline Mendes; Marchevsky, Renato Sérgio; Pinto, Marcelo Alves

    2011-04-21

    Hepatitis E is an infectious disease which virus (HEV) is highly disseminated in swine herd populations. Sporadic acute human hepatitis E cases have been associated to genotype 3 and 4 strains of HEV also reported in swine populations of endemic and non-endemic areas. With the aim to evaluate the incidence of animals with current infection of HEV, 115 bile samples were collected from three slaughterhouses under inspection by Animal Sanitary Protection Agency of Rio de Janeiro, Brazil. In parallel, effluent samples were collected from six sewage pipe exit sites of two slaughterhouses. HEV RNA was detected in 11 out of 115 (9.6%) bile samples collected and three waste samples from one slaughterhouse. Viral loads observed for bile samples varied from 10(1)-10(5) genome copies/mL and for effluent samples mean load was 10(2) genome copies/mL. Sequencing and phylogenetic analysis classified samples within genotype 3 subtype 3b closely related to the sample obtained from the first reported autochthonous human case and samples from swine of commercial herds in Brazil. Our data demonstrates that although most animals achieve slaughter age (around 20 weeks old) already immune to HEV, a significant number of animals are with current infection at commercial age. Further studies should be addressed to consider risk analysis and possible evaluation of inspection regulations considering food safety measures regarding hepatitis E zoonotic aspect in Brazil. Copyright © 2010 Elsevier B.V. All rights reserved.

  6. Benefits and Limits of Egg Yolk vs. Serum Samples for Avian Influenza Virus Serosurveillance.

    Science.gov (United States)

    Abdelwhab, E M; Grund, Christian; Aly, Mona M; Beer, Martin; Harder, Timm C; Hafez, Hafez M

    2016-06-01

    Serologic tests are a valuable tool for retrospective surveillance of avian influenza viruses (AIV) and monitoring of postvaccination host immune response. Yet collection of serum samples, particularly in adult breeder chickens, is laborious, intrusive to birds, and may pose a serious risk to the biosecurity of a flock. In this study we compared the level of AIV-specific antibody titers in eggs and serum samples obtained from broiler breeder chickens vaccinated at 6, 12, and 18 wk of age with H5N2-inactivated vaccine. Nucleocapsid protein-specific ELISA and hemagglutination inhibition test (HI) against homologous as well as heterologous antigens were used. The eggs and sera were collected at 22, 30, 45, and 50 wk of age (i.e., 4, 12, 27, and 32 wk after the third and final immunization, respectively). Using ELISA, the number of positive egg yolk samples decreased over time after vaccination, from 97% to 47%, while the seropositivity rate of serum samples was 97%-100% during the whole investigation period. No antibody titers were detected in egg white. By HI, antibody titers in serum samples were higher than in egg yolk samples. Compared to the homologous H5N2 antigen, significantly lower HI titers were obtained by using a heterologous H5N1 virus of clade 2.2.1.2. In addition, no HI titers were detected in egg yolk and/or serum samples tested against the antigen of an Egyptian H5N1 antigenic drift variant of clade 2.2.1.1. This study indicates that egg yolk may be used to monitor the postvaccination immune status of broiler breeder chickens and retrospective serosurveillance-by HI when a matching antigen is available as well as by ELISA-particularly for up to 12 wk postvaccination.

  7. Oncolytic viruses on the cusp of success?: proceedings of the 9th International Conference on Oncolytic Virus Therapeutics

    Directory of Open Access Journals (Sweden)

    Cole Peters

    2016-01-01

    Full Text Available Boston, Massachusetts, was the site of the 9th International Conference on Oncolytic Virus Therapeutics held 13–16 June 2015. An overarching theme of the meeting was the continued development of combinatorial treatment regimens to bolster the therapeutic potential of oncolytic viruses (OVs. Several talks focused on combining OVs with immune checkpoint inhibitors in a wide array of tumors, signaling an experimental and thematic shift toward driving immune activation to clear a tumor versus relying on direct viral oncolysis. An important aspect of the meeting was the variety of ongoing OV clinical trials. Topics ranged from basic virology to clinical trials and from academic research to intellectual property and biotechnology. There was much excitement due to the US Food and Drug Administration’s recent consideration of talimogene laherparepvec (T-VEC for the treatment of advanced melanoma (T-VEC was approved in October, following the conference. Here, we summarize the meeting’s primary themes, which reflect the current state of the field.

  8. Phylogenetic analysis of Austrian canine distemper virus strains from clinical samples from dogs and wild carnivores.

    Science.gov (United States)

    Benetka, V; Leschnik, M; Affenzeller, N; Möstl, K

    2011-04-09

    Austrian field cases of canine distemper (14 dogs, one badger [Meles meles] and one stone marten [Martes foina]) from 2002 to 2007 were investigated and the case histories were summarised briefly. Phylogenetic analysis of fusion (F) and haemagglutinin (H) gene sequences revealed different canine distemper virus (CDV) lineages circulating in Austria. The majority of CDV strains detected from 2002 to 2004 were well embedded in the European lineage. One Austrian canine sample detected in 2003, with a high similarity to Hungarian sequences from 2005 to 2006, could be assigned to the Arctic group (phocine distemper virus type 2-like). The two canine sequences from 2007 formed a clearly distinct group flanked by sequences detected previously in China and the USA on an intermediate position between the European wildlife and the Asia-1 cluster. The Austrian wildlife strains (2006 and 2007) could be assigned to the European wildlife group and were most closely related to, yet clearly different from, the 2007 canine samples. To elucidate the epidemiological role of Austrian wildlife in the transmission of the disease to dogs and vice versa, H protein residues related to receptor and host specificity (residues 530 and 549) were analysed. All samples showed the amino acids expected for their host of origin, with the exception of a canine sequence from 2007, which had an intermediate position between wildlife and canine viral strains. In the period investigated, canine strains circulating in Austria could be assigned to four different lineages reflecting both a high diversity and probably different origins of virus introduction to Austria in different years.

  9. The challenge of detecting classical swine fever virus circulation in wild boar (Sus scrofa): Simulation of sampling options

    DEFF Research Database (Denmark)

    Schulz, Jana; Schulz, Katja; Blome, Sandra

    2016-01-01

    investigations play a major role in the early detection of new introductions and in regions immunized with a conventional vaccine. The required financial resources and personnel for reliable testing are often large, and sufficient sample sizes to detect low virus prevalences are difficult to obtain. We conducted...... a simulation to model the possible impact of changes in sample size and sampling intervals on the probability of CSF virus detection based on a study area of 65 German hunting grounds. A 5-yr period with 4,652 virologic investigations was considered. Results suggest that low prevalences could not be detected...... with a justifiable effort. The simulation of increased sample sizes per sampling interval showed only a slightly better performance but would be unrealistic in practice, especially outside the main hunting season. Further studies on other approaches such as targeted or risk-based sampling for virus detection...

  10. Rescue of foot-and-mouth disease viruses that are pathogenic for cattle from preserved viral RNA samples

    DEFF Research Database (Denmark)

    Belsham, Graham; Jamal, Syed Muhammad; Tjørnehøj, Kirsten

    2011-01-01

    of the rescued viruses (of serotype O and Asia 1) were inoculated into bull calves under high containment conditions. Acute clinical disease was observed in each case which spread rapidly from the inoculated calves to in-contact animals. Thus the rescued viruses were highly pathogenic. The availability......Background: Foot and mouth disease is an economically important disease of cloven-hoofed animals including cattle, sheep and pigs. It is caused by a picornavirus, foot-and-mouth disease virus (FMDV), which has a positive sense RNA genome which, when introduced into cells, can initiate virus...... replication. Principal Findings: A system has been developed to rescue infectious FMDV from RNA preparations generated from clinical samples obtained under experimental conditions and then applied to samples collected in the ‘‘field’’. Clinical samples from suspect cases of foot-and-mouth disease (FMD) were...

  11. Mannosylation of virus-like particles enhances internalization by antigen presenting cells.

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    Farah Al-Barwani

    Full Text Available Internalization of peptides by antigen presenting cells is crucial for the initiation of the adaptive immune response. Mannosylation has been demonstrated to enhance antigen uptake through mannose receptors, leading to improved immune responses. In this study we test the effect of surface mannosylation of protein-based virus-like particles (VLP derived from Rabbit hemorrhagic disease virus (RHDV on uptake by murine and human antigen presenting cells. A monomannoside and a novel dimannoside were synthesized and successfully conjugated to RHDV VLP capsid protein, providing approximately 270 mannose groups on the surface of each virus particle. VLP conjugated to the mannoside or dimannoside exhibited significantly enhanced binding and internalization by murine dendritic cells, macrophages and B cells as well as human dendritic cells and macrophages. This uptake was inhibited by the inclusion of mannan as a specific inhibitor of mannose specific uptake, demonstrating that mannosylation of VLP targets mannose receptor-based uptake. Consistent with mannose receptor-based uptake, partial retargeting of the intracellular processing of RHDV VLP was observed, confirming that mannosylation of VLP provides both enhanced uptake and modified processing of associated antigens.

  12. Use of dried blood samples for monitoring hepatitis B virus infection

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    Muñoz Onofre

    2009-09-01

    Full Text Available Abstract Background Hepatitis B virus (HBV infection is a problem in several regions of the world with limited resources. Blood samples dried on filter paper (DBS have been successfully used to diagnose and monitor several infectious diseases. In Mexico there is an urgent need for an affordable and easy sampling method for viral load (VL testing and monitoring of chronic HBV infection. The purpose of this work was to validate the utility of DBS samples for monitoring HBV infection in patients from Mexico City. Methods Matched samples of plasma and DBS on filter paper from 47 HBV infected patients from the Instituto Mexicano del Seguro Social (IMSS, were included. To evaluate the DNA stability and purity from DBS stored at different temperature conditions, samples from ten patients were stored at 4 degree, 25 degree, and 37 degree C for 7 days. After DBS elution and DNA extraction, the purity of these samples was determined measuring the O.D. rate 260/280. The DBS utility for molecular studies was assessed with PCR assays to amplify a 322 bp fragment from the "a" determinant region of the HBV "S" gene. The VL from all samples was determined to evaluate the correlation between plasma and DBS matched samples. Results The quality of the DNA from DBS specimen is not adversely affected by storage at 4 degree, 25 degree and 37 degree C for up 7 days. Statistical ANOVA analyses did not show any significant difference. The same amplification efficiency was observed between DNA templates from samples stored at different temperatures. The Pearson correlation between the VL from DBS and plasma matched samples was 0.93 (p = 0.01. The SD was 1.48 for DBS vs.1.32 for Plasma, and an average of log10 copies/mL of 5.32 vs. 5.53. ANOVA analysis did not show any statistically significant difference between the analyzed groups (p = 0.92. Conclusion The results provide strong evidence that the isolation and quantification of DNA-HBV from DBS is a viable alternative

  13. Use of dried blood samples for monitoring hepatitis B virus infection

    Science.gov (United States)

    Lira, Rosalia; Maldonado-Rodriguez, Angelica; Rojas-Montes, Othon; Ruiz-Tachiquin, Martha; Torres-Ibarra, Rocio; Cano-Dominguez, Carlos; Valdez-Salazar, Hilda; Gomez-Delgado, Alejandro; Muñoz, Onofre; Alvarez-Muñoz, Ma-Teresa

    2009-01-01

    Background Hepatitis B virus (HBV) infection is a problem in several regions of the world with limited resources. Blood samples dried on filter paper (DBS) have been successfully used to diagnose and monitor several infectious diseases. In Mexico there is an urgent need for an affordable and easy sampling method for viral load (VL) testing and monitoring of chronic HBV infection. The purpose of this work was to validate the utility of DBS samples for monitoring HBV infection in patients from Mexico City. Methods Matched samples of plasma and DBS on filter paper from 47 HBV infected patients from the Instituto Mexicano del Seguro Social (IMSS), were included. To evaluate the DNA stability and purity from DBS stored at different temperature conditions, samples from ten patients were stored at 4 degree, 25 degree, and 37 degree C for 7 days. After DBS elution and DNA extraction, the purity of these samples was determined measuring the O.D. rate 260/280. The DBS utility for molecular studies was assessed with PCR assays to amplify a 322 bp fragment from the "a" determinant region of the HBV "S" gene. The VL from all samples was determined to evaluate the correlation between plasma and DBS matched samples. Results The quality of the DNA from DBS specimen is not adversely affected by storage at 4 degree, 25 degree and 37 degree C for up 7 days. Statistical ANOVA analyses did not show any significant difference. The same amplification efficiency was observed between DNA templates from samples stored at different temperatures. The Pearson correlation between the VL from DBS and plasma matched samples was 0.93 (p = 0.01). The SD was 1.48 for DBS vs.1.32 for Plasma, and an average of log10 copies/mL of 5.32 vs. 5.53. ANOVA analysis did not show any statistically significant difference between the analyzed groups (p = 0.92). Conclusion The results provide strong evidence that the isolation and quantification of DNA-HBV from DBS is a viable alternative for patient monitoring

  14. CONVERGENCE OF INTERNATIONAL AUDIT STANDARDS AND AMERICAN AUDIT STANDARDS REGARDING SAMPLING

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    Chis Anca Oana

    2013-07-01

    Full Text Available Abstract: Sampling is widely used in market research, scientific analysis, market analysis, opinion polls and not least in the financial statement audit. We wonder what is actually sampling and how did it appear? Audit sampling involves the application of audit procedures to less than 100% of items within an account balance or class of transactions. Nowadays the technique is indispensable, the economic entities operating with sophisticated computer systems and large amounts of data. Economic globalization and complexity of capital markets has made possible not only the harmonization of international accounting standards with the national ones, but also the convergence of international accounting and auditing standards with the American regulations. International Standard on Auditing 530 and Statement on Auditing Standard 39 are the two main international and American normalized referentials referring to audit sampling. This article discusses the origin of audit sampling, mentioning a brief history of the method and different definitions from literature review. The two standards are studied using Jaccard indicators in terms of the degree of similarity and dissimilarity concerning different issues. The Jaccard coefficient measures the degree of convergence of international auditing standards (ISA 530 and U.S. auditing standards (SAS 39. International auditing standards and American auditing standards, study the sampling problem, both regulations presenting common points with regard to accepted sampling techniques, factors influencing the audit sample, treatment of identified misstatements and the circumstances in which sampling is appropriate. The study shows that both standards agree on application of statistical and non-statistical sampling in auditing, that sampling is appropriate for tests of details and controls, the factors affecting audit sampling being audit risk, audit objectives and population\\'s characteristics.

  15. The Diabetes Regimen Responsibility Scale: Information on Internal Consistency and Validity in a Pediatric Sample.

    Science.gov (United States)

    Carey, Tracy; Reid, Graham; Ruggiero, Laurie; Horner, James; Dubow, Eric

    1997-01-01

    The internal consistency and validity of the Diabetes Regimen Responsibility Scale (DRRS) (L. Ruggiero and others, 1991) were examined in a sample of 49 youths. The DRRS demonstrated adequate internal consistency, and most subscales correlated significantly with diabetes knowledge (health education issue). Only two reports correlated with…

  16. A modified RNA-Seq approach for whole genome sequencing of RNA viruses from faecal and blood samples.

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    Elizabeth M Batty

    Full Text Available To date, very large scale sequencing of many clinically important RNA viruses has been complicated by their high population molecular variation, which creates challenges for polymerase chain reaction and sequencing primer design. Many RNA viruses are also difficult or currently not possible to culture, severely limiting the amount and purity of available starting material. Here, we describe a simple, novel, high-throughput approach to Norovirus and Hepatitis C virus whole genome sequence determination based on RNA shotgun sequencing (also known as RNA-Seq. We demonstrate the effectiveness of this method by sequencing three Norovirus samples from faeces and two Hepatitis C virus samples from blood, on an Illumina MiSeq benchtop sequencer. More than 97% of reference genomes were recovered. Compared with Sanger sequencing, our method had no nucleotide differences in 14,019 nucleotides (nt for Noroviruses (from a total of 2 Norovirus genomes obtained with Sanger sequencing, and 8 variants in 9,542 nt for Hepatitis C virus (1 variant per 1,193 nt. The three Norovirus samples had 2, 3, and 2 distinct positions called as heterozygous, while the two Hepatitis C virus samples had 117 and 131 positions called as heterozygous. To confirm that our sample and library preparation could be scaled to true high-throughput, we prepared and sequenced an additional 77 Norovirus samples in a single batch on an Illumina HiSeq 2000 sequencer, recovering >90% of the reference genome in all but one sample. No discrepancies were observed across 118,757 nt compared between Sanger and our custom RNA-Seq method in 16 samples. By generating viral genomic sequences that are not biased by primer-specific amplification or enrichment, this method offers the prospect of large-scale, affordable studies of RNA viruses which could be adapted to routine diagnostic laboratory workflows in the near future, with the potential to directly characterize within-host viral diversity.

  17. Hepatitis E virus genotypes 1 and 3 in wastewater samples in Tunisia.

    Science.gov (United States)

    Béji-Hamza, A; Hassine-Zaafrane, M; Khélifi-Gharbi, H; Della Libera, S; Iaconelli, M; Muscillo, M; Petricca, S; Ciccaglione, A R; Bruni, R; Taffon, S; Aouni, M; La Rosa, G

    2015-01-01

    Hepatitis E represents an important public-health concern throughout the world. It is one of the leading causes of hepatitis in North Africa, Asia and the Middle East. In Tunisia, the true burden of HEV infection is still unknown. The objectives of the present study were to assess the occurrence of hepatitis E virus in Tunisia through the monitoring of urban sewage and to characterize the strains identified using molecular assays. A total of 150 sewage samples (raw and treated) were collected from three wastewater treatment plants located in the regions of Monastir and Mahdia and analyzed by nested RT-PCR using a qualitative assay targeting the methyltransferase gene in ORF1. Of these, only three samples (2 %) were found to be positive for HEV, one belonging to genotype 1 and two to genotype 3. The results of the present study indicate a low level of virus excretion among the Tunisian population. Both genotypes 1 and 3 are circulating in this country, however, possibly causing sporadic infections. The presence of the zoonotic genotype 3, known to be transmitted to humans mainly by swine and demonstrated in Tunisia for the first time in this work, raises the question of possible reservoir species, since pork products are not consumed in this country, pigs are not bred, and wild boar is not endemic. Further studies will be needed to gather information on the occurrence and diversity of HEV strains circulating among humans and animals in Tunisia, and on possible animal reservoirs.

  18. Influenza A virus: sampling of the unique shorebird habitat at Delaware Bay, USA.

    Science.gov (United States)

    Poulson, Rebecca L; Luttrell, Page M; Slusher, Morgan J; Wilcox, Benjamin R; Niles, Lawrence J; Dey, Amanda D; Berghaus, Roy D; Krauss, Scott; Webster, Robert G; Stallknecht, David E

    2017-11-01

    Delaware (DE) Bay, in the northeastern USA, has long been recognized as a hotspot for avian influenza A virus (IAV); every spring, this coastal region serves as a brief stopover site for thousands of long-distance migrating shorebirds, en route to breeding grounds in the Arctic. During these stopovers, IAV has been consistently recovered from ruddy turnstones (Arenaria interpres) that are likely to become infected as they feed by probing sand and cobble in search of food. In May 2010-2012, we successfully isolated 19 IAV from environmental samples (sand, n = 18; horseshoe crab eggs, n = 1) obtained from DE Bay sites. Two of these viruses were subjected to laboratory conditions similar to those in the DE Bay spring-time environment, and remained infectious for 7 days. Here, through the recovery of IAV from environmental samples, temperature monitoring at and below the sand surface and simulated laboratory trials, we provide evidence that the beach environment may enable localized transmission and short-term maintenance of IAV in this unique ecosystem.

  19. An Internationally Coordinated Science Management Plan for Samples Returned from Mars

    Science.gov (United States)

    Haltigin, T.; Smith, C. L.

    2015-12-01

    Mars Sample Return (MSR) remains a high priority of the planetary exploration community. Such an effort will undoubtedly be too large for any individual agency to conduct itself, and thus will require extensive global cooperation. To help prepare for an eventual MSR campaign, the International Mars Exploration Working Group (IMEWG) chartered the international Mars Architecture for the Return of Samples (iMARS) Phase II working group in 2014, consisting of representatives from 17 countries and agencies. The overarching task of the team was to provide recommendations for progressing towards campaign implementation, including a proposed science management plan. Building upon the iMARS Phase I (2008) outcomes, the Phase II team proposed the development of an International MSR Science Institute as part of the campaign governance, centering its deliberations around four themes: Organization: including an organizational structure for the Institute that outlines roles and responsibilities of key members and describes sample return facility requirements; Management: presenting issues surrounding scientific leadership, defining guidelines and assumptions for Institute membership, and proposing a possible funding model; Operations & Data: outlining a science implementation plan that details the preliminary sample examination flow, sample allocation process, and data policies; and Curation: introducing a sample curation plan that comprises sample tracking and routing procedures, sample sterilization considerations, and long-term archiving recommendations. This work presents a summary of the group's activities, findings, and recommendations, highlighting the role of international coordination in managing the returned samples.

  20. Virome profiling of bats from Myanmar by metagenomic analysis of tissue samples reveals more novel Mammalian viruses.

    Directory of Open Access Journals (Sweden)

    Biao He

    Full Text Available Bats are reservoir animals harboring many important pathogenic viruses and with the capability of transmitting these to humans and other animals. To establish an effective surveillance to monitor transboundary spread of bat viruses between Myanmar and China, complete organs from the thorax and abdomen from 853 bats of six species from two Myanmar counties close to Yunnan province, China, were collected and tested for their virome through metagenomics by Solexa sequencing and bioinformatic analysis. In total, 3,742,314 reads of 114 bases were generated, and over 86% were assembled into 1,649,512 contigs with an average length of 114 bp, of which 26,698 (2% contigs were recognizable viral sequences belonging to 24 viral families. Of the viral contigs 45% (12,086/26,698 were related to vertebrate viruses, 28% (7,443/26,698 to insect viruses, 27% (7,074/26,698 to phages and 95 contigs to plant viruses. The metagenomic results were confirmed by PCR of selected viruses in all bat samples followed by phylogenetic analysis, which has led to the discovery of some novel bat viruses of the genera Mamastrovirus, Bocavirus, Circovirus, Iflavirus and Orthohepadnavirus and to their prevalence rates in two bat species. In conclusion, the present study aims to present the bat virome in Myanmar, and the results obtained further expand the spectrum of viruses harbored by bats.

  1. Multiplex PCR for simultaneous detection and differentiation of sheeppox, goatpox and orf viruses from clinical samples of sheep and goats.

    Science.gov (United States)

    Venkatesan, G; Balamurugan, V; Bhanuprakash, V

    2014-01-01

    A multiplex polymerase chain reaction (mPCR) was developed and evaluated for detection of pox viral infections simultaneously using clinical samples from sheep and goats. Specific primers for three pox viruses of sheep and goats including sheeppox virus (SPPV), goatpox virus (GTPV) and orf virus (ORFV) were designed targeting conserved sequences of the DNA binding phosphoprotein (I3L) coding gene of Capripoxvirus (CaPV) and the DNA polymerase (E9L) gene of parapoxvirus for identification of these viruses. The mPCR assay was found to be sensitive for detecting as low as 350 pg of viral genomic DNA or 10(2) copies of standard plasmid of individual targets; and 10(3) copies of plasmid in a mixture of two or three viruses. The assay was specific for detecting one or more of the viruses in various combinations from clinical specimens. Two hundred and thirty five (n=235) clinical samples from sheep and goats received from different geographical regions of the country for diagnosis of pox infection were evaluated by developed uniplex and mPCR assays. The assay had improved diagnostic sensitivity and specificity over to in-use laboratory diagnostic methods and can be useful for clinical differential diagnosis of these infections in sheep and goats. Copyright © 2013 Elsevier B.V. All rights reserved.

  2. Time clustered sampling can inflate the inferred substitution rate in foot-and-mouth disease virus analyses

    DEFF Research Database (Denmark)

    Pedersen, Casper-Emil Tingskov; Frandsen, Peter; Wekesa, Sabenzia N.

    2015-01-01

    through a study of the foot-and-mouth (FMD) disease virus serotypes SAT 1 and SAT 2. Our study shows that clustered temporal sampling in phylogenetic analyses of FMD viruses will strongly bias the inferences of substitution rates and tMRCA because the inferred rates in such data sets reflect a rate closer......With the emergence of analytical software for the inference of viral evolution, a number of studies have focused on estimating important parameters such as the substitution rate and the time to the most recent common ancestor (tMRCA) for rapidly evolving viruses. Coupled with an increasing...... to the mutation rate rather than the substitution rate. Estimating evolutionary parameters from viral sequences should be performed with due consideration of the differences in short-term and longer-term evolutionary processes occurring within sets of temporally sampled viruses, and studies should carefully...

  3. Development of internal forest soil reference samples and testing of digestion methods

    Science.gov (United States)

    J.E. Hislop; J.W. Hornbeck; S.W. Bailey; R.A. Hallett

    1998-01-01

    Our research requires determinations of total elemental concentrations of forest soils. The lack of certified forest soil reference materials led us to develop internal reference samples. Samples were collected from three soil horizons (Oa, B, and C) at three locations having forested, acidic soils similar to those we commonly analyze. A shatterbox was used to...

  4. Flexible Analog Front Ends of Reconfigurable Radios Based on Sampling and Reconstruction with Internal Filtering

    Directory of Open Access Journals (Sweden)

    Poberezhskiy Yefim S.

    2005-01-01

    Full Text Available Bandpass sampling, reconstruction, and antialiasing filtering in analog front ends potentially provide the best performance of software defined radios. However, conventional techniques used for these procedures limit reconfigurability and adaptivity of the radios, complicate integrated circuit implementation, and preclude achieving potential performance. Novel sampling and reconstruction techniques with internal filtering eliminate these drawbacks and provide many additional advantages. Several ways to overcome the challenges of practical realization and implementation of these techniques are proposed and analyzed. The impact of sampling and reconstruction with internal filtering on the analog front end architectures and capabilities of software defined radios is discussed.

  5. Detection and genetic characterization of foot‐and‐mouth disease viruses in samples from clinically healthy animals in endemic settings

    DEFF Research Database (Denmark)

    Jamal, Syed Muhammad; Ferrari, G.; Hussain, M.

    2012-01-01

    A total of 1501 oral swab samples from Pakistan, Afghanistan and Tajikistan were collected from clinically healthy animals between July 2008 and August 2009 and assayed for the presence of foot‐and‐mouth disease virus (FMDV) RNA. The oral swab samples from two (of four) live animal markets in Pak...

  6. Rapid detection of avian influenza virus in chicken fecal samples by immunomagnetic capture reverse transcriptase–polymerase chain reaction assay

    DEFF Research Database (Denmark)

    Dhumpa, Raghuram; Handberg, Kurt; Jørgensen, Poul Henrik

    2011-01-01

    Avian influenza virus (AIV) causes great economic losses for the poultry industry worldwide and threatens the human population with a pandemic. The conventional detection method for AIV involves sample preparation of viral RNA extraction and purification from raw sample such as bird droppings...

  7. Internal calibration on adjacent samples (InCAS) with Fourier transform mass spectrometry.

    Science.gov (United States)

    O'Connor, P B; Costello, C E

    2000-12-15

    Using matrix-assisted laser desorption/ionization (MAL DI) on a trapped ion mass spectrometer such as a Fourier transform mass spectrometer (FTMS) allows accumulation of ions in the cell from multiple laser shots prior to detection. If ions from separate MALDI samples are accumulated simultaneously in the cell, ions from one sample can be used to calibrate ions from the other sample. Since the ions are detected simultaneously in the cell, this is, in effect, internal calibration, but there are no selective desorption effects in the MALDI source. This method of internal calibration with adjacent samples is demonstrated here on cesium iodide clusters, peptides, oligosaccharides, poly(propylene glycol), and fullerenes and provides typical FTMS internal calibration mass accuracy of < 1 ppm.

  8. Defining a sample preparation workflow for advanced virus detection and understanding sensitivity by next-generation sequencing.

    Science.gov (United States)

    Wang, Christopher J; Feng, Szi Fei; Duncan, Paul

    2014-01-01

    The application of next-generation sequencing (also known as deep sequencing or massively parallel sequencing) for adventitious agent detection is an evolving field that is steadily gaining acceptance in the biopharmaceutical industry. In order for this technology to be successfully applied, a robust method that can isolate viral nucleic acids from a variety of biological samples (such as host cell substrates, cell-free culture fluids, viral vaccine harvests, and animal-derived raw materials) must be established by demonstrating recovery of model virus spikes. In this report, we implement the sample preparation workflow developed by Feng et. al. and assess the sensitivity of virus detection in a next-generation sequencing readout using the Illumina MiSeq platform. We describe a theoretical model to estimate the detection of a target virus in a cell lysate or viral vaccine harvest sample. We show that nuclease treatment can be used for samples that contain a high background of non-relevant nucleic acids (e.g., host cell DNA) in order to effectively increase the sensitivity of sequencing target viruses and reduce the complexity of data analysis. Finally, we demonstrate that at defined spike levels, nucleic acids from a panel of model viruses spiked into representative cell lysate and viral vaccine harvest samples can be confidently recovered by next-generation sequencing. © PDA, Inc. 2014.

  9. The xenotropic murine leukemia virus-related retrovirus debate continues at first international workshop

    Directory of Open Access Journals (Sweden)

    Boucher Charles A

    2010-12-01

    Full Text Available Abstract The 1st International Workshop on Xenotropic Murine Leukemia Virus-Related Retrovirus (XMRV, co-sponsored by the National Institutes of Health, The Department of Health and Human Services and Abbott Diagnostics, was convened on September 7/8, 2010 on the NIH campus, Bethesda, MD. Attracting an international audience of over 200 participants, the 2-day event combined a series of plenary talks with updates on different aspects of XMRV research, addressing basic gammaretrovirus biology, host response, association of XMRV with chronic fatigue syndrome and prostate cancer, assay development and epidemiology. The current status of XMRV research, concerns among the scientific community and suggestions for future actions are summarized in this meeting report.

  10. The xenotropic murine leukemia virus-related retrovirus debate continues at first international workshop.

    Science.gov (United States)

    Stoye, Jonathan P; Silverman, Robert H; Boucher, Charles A; Le Grice, Stuart F J

    2010-12-22

    The 1st International Workshop on Xenotropic Murine Leukemia Virus-Related Retrovirus (XMRV), co-sponsored by the National Institutes of Health, The Department of Health and Human Services and Abbott Diagnostics, was convened on September 7/8, 2010 on the NIH campus, Bethesda, MD. Attracting an international audience of over 200 participants, the 2-day event combined a series of plenary talks with updates on different aspects of XMRV research, addressing basic gammaretrovirus biology, host response, association of XMRV with chronic fatigue syndrome and prostate cancer, assay development and epidemiology. The current status of XMRV research, concerns among the scientific community and suggestions for future actions are summarized in this meeting report.

  11. [DETECTION OF VENEZUELAN EQUINE ENCEPHALOMYELITIS VIRUS RNA IN BIOLOGICAL SAMPLES BY REVERSE-TRANSCRIPTION POLYMERASE CHAIN REACTION].

    Science.gov (United States)

    Petrov, A A; Pyshnaya, N S; Lebedev, V N; Kulish, V S; Stovba, L F; Kazantsev, A V; Borisevich, S V

    2015-01-01

    Detection-and identification of Venezuelan equine encephalomyelitis (VEE) virus RNA in biological samples by reverse-transcription polymerase chain reaction (RT-PCR) and RT-PCR in real time (rRT-PCR). VEE, Sindbis, West Nile, Japanese and tick-borne encephalitis viruses were studied. Cell culture of chicken fibroblasts, outbred mice and rats, Javanese macaques were used in the experiments. Biological activity determination of the running culture of causative agents used in the experiments was carried out by negative colony method in monolayer cell culture under agar coating. and using intra-cerebral infection of mice. Reagent kits developed in the 48th Central Research Institute and Institute of Analytical Instrument Engineering were used during execution of experiments of VEE virus RNA detection by RT-PCR and rRT-PCR. VEE virus was detected in biological samples by various methods. Data from RT-PCR and rRT-PCR are in accordance with the results of virus detection in samples using sensitive animals. Use of molecular-diagnostics methods for detection in biological samples of a causative agent of a dangerous infectious disease is important for procuring biological safety of Russian Federation.

  12. Detection and Evaluate the Frequency of Cytomegalovirus and Epstein-Barr Virus in Bladder Tumor Samples in Hamedan Province, 1392

    Directory of Open Access Journals (Sweden)

    Zohreh Alinezhad

    2015-04-01

    Full Text Available Background and Aim: Some unknown reasons as the cytomegalovirus (CMV and Epstein-Barr virus (EBV in the incidence of bladder cancer has been much discussed in recent years. The purpose of this study was to identify and Evaluate the frequency CMV and EBV in bladder tumors. Materials and Methods: Fourty samlps of TCC bladder carcinoma collected from the pathology department of the dr Gharazi hospital in hamedan during summer 2012. samples deparaffinized and DNA extracted  by tissue kit (Qiagen. The human beta-globin gene amplified to ensure the accuracy and integrity of the extracted DNA. To perform the PCR, primers amplified BRLF1 gene for EPV and UL123 for CMV.  Therefore amplified fragments were observed on 1.5% agarose gel. Finaly  the chi-square test were used to assess the relationship between viruses and their relationship to the incidence of bladder cancer. Results: From 40 carcinoma samples studied 4 (10% were infected with the CMV virus and 29 samples (72.5% were infected with EBV. Four samples were simultaneously infected with both viruses. The relationship between age, tumor stage, CMV and EBV virus wasn’t observed (P <0.05.. Conclusions: CMV and EBV can be detected by optimized PCR protocol from bladder cancer. No significant association was observed. The high prevalence of EBV develops this theory that EBV was a factor in bladder cancer.

  13. Rapid detection of bluetongue virus in blood and organ samples using a capture enzyme-linked immunosorbent assay.

    Science.gov (United States)

    Portanti, O; Luciani, M; Ronchi, G F

    2005-01-01

    An antigen capture ELISA for bluetongue (BT) virus was developed using tissue culture supernatant to identify different BT virus (BTV) serotypes 1, 2, 4, 9 and 16, which have been incriminated in the current epidemic in the Mediterranean Basin. To obtain a positive result and after amplification in tissue culture, the minimum amount of infecting virus required was 100 TCID(50). Results from the antigen capture ELISA were compared with conventional methods for virus isolation and identification, such as virus amplification on embryonated chicken eggs (ECEs), followed by tissue culture and the direct immunofluorescence test. The sensitivity and specificity of the ELISA in infected tissue culture supernatant using homogenates of BTV-positive ovine and bovine organs and blood, without a previous step in ECEs, were 100%. The assay was also applied to homogenates of chicken embryo tissues, which had been infected with different BTV serotypes. This method enabled detection of the virus with 100% sensitivity and specificity rates, also using amplification in ECEs. Furthermore, among the various embryo tissues tested, liver was found to be the most suitable for use with ELISA. In experimentally infected ovine blood samples, the ELISA revealed the presence of the virus. Given the high sensitivity and specificity obtained with the BTV serotypes in this trial, the method should greatly facilitate BT diagnosis.

  14. Validation and clinical use of a sensitive HIV-2 viral load assay that uses a whole virus internal control.

    Science.gov (United States)

    Styer, Linda M; Miller, Thomas T; Parker, Monica M

    2013-12-01

    Human immunodeficiency virus type 2 (HIV-2) is distantly related to the more widespread HIV-1. Although HIV-2 infection is rare in the U.S., cases are concentrated in the Northeast. No FDA-approved HIV-2 viral load assays exist. A clinically validated laboratory-developed assay is currently available in the U.S., however it is not currently approved for use on New York State patients. To develop a sensitive viral load assay to quantify HIV-2 RNA in plasma and to validate it for clinical use. The real-time RT-PCR assay simultaneously amplifies HIV-2 and a whole virus internal control, added during the lysis step. Two extraction volumes can be used. Results are reported in HIV-2 RNA International Units (IU). The assay has a limit of detection of 7 IU/mL and a lower limit of quantification of 29 IU/mL. The assay detects multiple strains of HIV-2 group A and B and generates reproducible results. Samples exchanged with a comparator laboratory produced similar viral load results, with 74% of positives differing by loads (range: 1.63-5.14 log10 IU/mL), 10 (19%) were positive but not quantifiable, and 14 were negative. HIV-2 RNA was detected in at least one specimen from 19 of 25 (76%) individuals tested. We developed a sensitive and accurate HIV-2 viral load assay. Validation data indicate the assay is suitable for clinical use and its availability in New York State will improve clinical monitoring of HIV-2 infected patients. Copyright © 2013 Elsevier B.V. All rights reserved.

  15. Prevalence of rotavirus, adenovirus, hepatitis A virus and enterovirus in water samples collected from different region of Peshawar, Pakistan.

    Science.gov (United States)

    Ahmad, Tahir; Arshad, Najma; Adnan, Fazal; Sadaf Zaidi, Najam-Us-Sahar; Shahid, Muhammad Talha; Zahoor, Usman; Afzal, Muhammad S; Anjum, Sadia

    2016-12-23

    Viral gastroenteritis and other water-borne diseases are the most neglected areas of research in Pakistan. To determine the quality of water, 4 enteric viruses were studied from different localities of Peshawar, Pakistan. The study validates the viral detection method for Rotavirus (RV), Human adenovirus (HAdV), Enterovirus (EV) and Hepatitis A virus (HAV), directly from water sources of rural areas of Peshawar, KPK, Pakistan. Overall, 95 five water samples were tested; among them, 9.47% were positive for RV, 38.94% for HAdV, 48.42% for EV and 12.63% for HAV. The presence of these viruses in water was directly correlated with meteorological data. High prevalence of EV and HAdV was detected frequently in the wet season from May - September, which can be the potential cause of spreading of gastroenteritis in the population. Environmental surveillance is an additional tool to evaluate the epidemiology of enteric viruses circulating in a given community.

  16. Metagenomic detection of viruses in aerosol samples from workers in animal slaughterhouses.

    Science.gov (United States)

    Hall, Richard J; Leblanc-Maridor, Mily; Wang, Jing; Ren, Xiaoyun; Moore, Nicole E; Brooks, Collin R; Peacey, Matthew; Douwes, Jeroen; McLean, David J

    2013-01-01

    Published studies have shown that workers in animal slaughterhouses are at a higher risk of lung cancers as compared to the general population. No specific causal agents have been identified, and exposures to several chemicals have been examined and found to be unrelated. Evidence suggests a biological aetiology as the risk is highest for workers who are exposed to live animals or to biological material containing animal faeces, urine or blood. To investigate possible biological exposures in animal slaughterhouses, we used a metagenomic approach to characterise the profile of organisms present within an aerosol sample. An assessment of aerosol exposures for individual workers was achieved by the collection of personal samples that represent the inhalable fraction of dust/bioaerosol in workplace air in both cattle and sheep slaughterhouses. Two sets of nine personal aerosol samples were pooled for the cattle processing and sheep processing areas respectively, with a total of 332,677,346 sequence reads and 250,144,492 sequence reads of 85 bp in length produced for each. Eukaryotic genome sequence was found in both sampling locations, and bovine, ovine and human sequences were common. Sequences from WU polyomavirus and human papillomavirus 120 were detected in the metagenomic dataset from the cattle processing area, and these sequences were confirmed as being present in the original personal aerosol samples. This study presents the first metagenomic description of personal aerosol exposure and this methodology could be applied to a variety of environments. Also, the detection of two candidate viruses warrants further investigation in the setting of occupational exposures in animal slaughterhouses.

  17. Metagenomic detection of viruses in aerosol samples from workers in animal slaughterhouses.

    Directory of Open Access Journals (Sweden)

    Richard J Hall

    Full Text Available Published studies have shown that workers in animal slaughterhouses are at a higher risk of lung cancers as compared to the general population. No specific causal agents have been identified, and exposures to several chemicals have been examined and found to be unrelated. Evidence suggests a biological aetiology as the risk is highest for workers who are exposed to live animals or to biological material containing animal faeces, urine or blood. To investigate possible biological exposures in animal slaughterhouses, we used a metagenomic approach to characterise the profile of organisms present within an aerosol sample. An assessment of aerosol exposures for individual workers was achieved by the collection of personal samples that represent the inhalable fraction of dust/bioaerosol in workplace air in both cattle and sheep slaughterhouses. Two sets of nine personal aerosol samples were pooled for the cattle processing and sheep processing areas respectively, with a total of 332,677,346 sequence reads and 250,144,492 sequence reads of 85 bp in length produced for each. Eukaryotic genome sequence was found in both sampling locations, and bovine, ovine and human sequences were common. Sequences from WU polyomavirus and human papillomavirus 120 were detected in the metagenomic dataset from the cattle processing area, and these sequences were confirmed as being present in the original personal aerosol samples. This study presents the first metagenomic description of personal aerosol exposure and this methodology could be applied to a variety of environments. Also, the detection of two candidate viruses warrants further investigation in the setting of occupational exposures in animal slaughterhouses.

  18. Test and validation of methods to sample and detect human virus from environmental surfaces using norovirus as a model virus

    DEFF Research Database (Denmark)

    Ibfelt, T.; Frandsen, T.; Permin, Anders

    2016-01-01

    : To validate and test efficient and reliable procedures to detect multiple human pathogenic viruses on surfaces. Methods: The study was divided into two parts. In Part A, six combinations of three different swabs (consisting of cotton, foamed cotton, or polyester head) and two different elution methods (direct...

  19. "ISA-Lation" of Single-Stranded Positive-Sense RNA Viruses from Non-Infectious Clinical/Animal Samples.

    Directory of Open Access Journals (Sweden)

    Fabien Aubry

    Full Text Available Isolation of viral pathogens from clinical and/or animal samples has traditionally relied on either cell cultures or laboratory animal model systems. However, virus viability is notoriously susceptible to adverse conditions that may include inappropriate procedures for sample collection, storage temperature, support media and transportation. Using our recently described ISA method, we have developed a novel procedure to isolate infectious single-stranded positive-sense RNA viruses from clinical or animal samples. This approach, that we have now called "ISA-lation", exploits the capacity of viral cDNA subgenomic fragments to re-assemble and produce infectious viral RNA in susceptible cells. Here, it was successfully used to rescue enterovirus, Chikungunya and Tick-borne encephalitis viruses from a variety of inactivated animal and human samples. ISA-lation represents an effective option to rescue infectious virus from clinical and/or animal samples that may have deteriorated during the collection and storage period, but also potentially overcomes logistic and administrative difficulties generated when complying with current health and safety and biosecurity guidelines associated with shipment of infectious viral material.

  20. Micronuclei formation in liver fibrosis samples from patients infected by hepatitis C virus

    Science.gov (United States)

    2010-01-01

    Genetic research on fibrosis outset and its progression in chronic hepatitis (CH) by hepatitis C virus (HCV) are limited. The lack of cytogenetic data led us to investigate the presence of micronuclei (MNi), as a sign of genomic damage. Hepatocytes of hepatic parenchyma from 62 cases diagnosed with CH associated with HCV and displaying different degrees of fibrosis (F1-F4) were analyzed. These data were compared to 15 cases without fibrosis (F0). Twelve healthy liver parenchyma samples were included as control. All samples were obtained from paraffin-embedded archival material. Micronucleated hepatocytes (MN-Heps) were analyzed through Feulgen/Fast-green staining. Results showed that the rates of MN-Heps in the F4 group were statistically significant (p 0.05) on comparing F0, F1, F2, F3, one against the other, as well as individual versus control. Although chromosomal losses in CH were detected, it was shown that liver parenchyma with fibrosis in the initial stages (F1-F3) cannot be considered cytogenetically abnormal. PMID:21637406

  1. Bullying, internalized hepatitis (Hepatitis C virus) stigma, and self-esteem: Does spirituality curtail the relationship in the workplace.

    Science.gov (United States)

    Noor, Ayesha; Bashir, Sajid; Earnshaw, Valerie A

    2016-09-01

    The objective of this study was to examine the impact of workplace bullying on self-esteem, including the mediating effect of internalized stigma and the moderating effect of spirituality, among hepatitis C virus patients. Data were collected from 228 employed hepatitis C virus patients who had been admitted to Gastroenterology and Hepatology wards in Pakistani hospitals. We found support for the hypothesis that workplace bullying is associated with low self-esteem via internalized stigma. In addition, spirituality moderated the association such that participants with greater spirituality were buffered from the impact of stigma on self-esteem. © The Author(s) 2015.

  2. The detection of lumpy skin disease virus in samples of experimentally infected cattle using different diagnostic techniques

    Directory of Open Access Journals (Sweden)

    E.S.M. Tuppurainen

    2005-09-01

    Full Text Available Lumpy skin disease (LSD is a disease of cattle, primarily in Africa and Madagascar and rarely in the Middle East. It is caused by a capripoxvirus that belongs to the family Poxviridae. The disease is of economic importance in endemic areas. Effective control of LSD requires accurate and rapid laboratory techniques to confirm a tentative clinical diagnosis. Comparative studies on different diagnostic tests used at different stages of the disease have not been done. The aim of this study was to compare several of these tests. Six seronegative bulls, between 11 and 20 months of age, were infected intravenously and kept in an insect-free facility. The course of the infection was monitored. During a 3-month period blood samples and skin biopsies were collected for virus isolation and polymerase chain reaction (PCR. Skin biopsies were also examined using transmission electron microscopy (TEM. The incubation period in infected animals varied from 4-5 days. The length of the viraemic period did not correlate with the severity of clinical disease. Viraemia was detected from 1-12 days using virus isolation and from 4-11 days using the PCR, which is longer than has previously been reported. Virus was isolated from skin biopsies until Day 39 post infection (p.i. and PCR could demonstrate viral DNA until Day 92 p.i. Transmission electron microscopy of negatively stained skin biopsies detected LSD virus only in one of the four bulls that developed skin lesions until Day 33 p.i. The PCR was a fast and sensitive method to demonstrate viral DNA in blood and skin samples. It could detect viral nucleic acid in skin lesions 53 days longer than virus isolation. Virus isolation from blood and skin samples was sensitive and reliable, but as a single test it may be too time-consuming to use although this depends on how rapidly the diagnosis must be confirmed. In conclusion, this study showed the PCR to be superior in detecting LSD virus from blood and skin samples

  3. International external quality assessment study for molecular detection of Lassa virus.

    Directory of Open Access Journals (Sweden)

    Sergejs Nikisins

    2015-05-01

    Full Text Available Lassa virus (LASV is a causative agent of hemorrhagic fever in West Africa. In recent years, it has been imported several times to Europe and North America. The method of choice for early detection of LASV in blood is RT-PCR. Therefore, the European Network for Diagnostics of 'Imported' Viral Diseases (ENIVD performed an external quality assessment (EQA study for molecular detection of LASV. A proficiency panel of 13 samples containing various concentrations of inactivated LASV strains Josiah, Lib-1580/121, CSF, or AV was prepared. Samples containing the LASV-related lymphocytic choriomeningitis virus (LCMV and negative sera were included as specificity controls. Twenty-four laboratories from 17 countries (13 European, one African, one Asian, two American countries participated in the study. Thirteen laboratories (54% reported correct results, 4 (17% laboratories reported 1 to 2 false-negative results, and 7 (29% laboratories reported 3 to 5 false-negative results. This EQA study indicates that most participating laboratories have a good or acceptable performance in molecular detection of LASV. However, several laboratories need to review and improve their diagnostic procedures.

  4. Analysis of the activity of virus internal ribosome entry site in silkworm Bombyx mori.

    Science.gov (United States)

    Ye, Lupeng; Zhuang, Lanfang; Li, Jisheng; You, Zhengying; Liang, Jianshe; Wei, Hao; Lin, Jianrong; Zhong, Boxiong

    2013-07-01

    Internal ribosome entry site (IRES) has been widely used in genetic engineering; however, the application in silkworm (Bombyx mori) has hardly been reported. In this study, the biological activity of partial sequence of Encephalomyocarditis virus (EMCV) IRES, Rhopalosiphum padi virus (RhPV) IRES, and the hybrid of IRES of EMCV and RhPV were investigated in Spodoptera frugiperda (Sf9) cell line and silkworm tissues. The hybrid IRES of EMCV and RhPV showed more effective than EMCV IRES or RhPV IRES in promoting downstream gene expression in insect and silkworm. The activities of all IRESs in middle silk gland of silkworm were higher than those in the fat body and posterior silk gland. The hybrid IRES of EMCV and RhPV was integrated into silkworm genome by transgenic technology to test biological activity of IRES. Each of the positive transgenic individuals had significant expression of report gene EGFP. These results suggested that IRES has a potential to be used in the genetic engineering research of silkworm.

  5. Kecenderungan Objektivitas Pemberitaan Epidemi Virus H5N1 dalam International Herald Tribune Online

    Directory of Open Access Journals (Sweden)

    Birgitta Bestari Puspita

    2013-11-01

    Full Text Available Abstract: Newspapers have to be objective in representing the news to the audience. This research wanted to measure the objectivity’s tendency of the news about H5N1 virus, which attacked Indonesia in year 2003. The news’ objectivities on International Herald Tribune from January 2005 until December 2006 were being measured with the Westerstahl’s Objectivity’s Principle and content analysis as the method. There are 2 dimensions in Westerstahl’s Objectivity’s Principle. First is factuality, which consists of truth and relevance, and the second one is impartiality which consists of balance and neutral presentation.  Abstrak: Surat kabar harus obyektif dalam menyajikan berita kepada audiens. Riset ini ingin mengukur kecenderungan obyektivitas berita tentang virus H5N1 yang melanda Indonesia pada tahun 2003. Obyektivitas berita diukur berdasar prinsip-prinsip obyektivitas Westerstahl dan menggunakan metode analisis isi. Ada dua dimensi dalam prinsip-prinsip obyektivitas Westerstahl. Pertama adalah faktualitas yang terdiri dari kebenaran dan relevansi, dan yang kedua adalah imparsialitas yang terdiri dari keseimbangan dan penyajian yang netral.

  6. Refractoriness of hepatitis C virus internal ribosome entry site to processing by Dicer in vivo

    Directory of Open Access Journals (Sweden)

    Boissonneault Vincent

    2009-08-01

    Full Text Available Abstract Background Hepatitis C virus (HCV is a positive-strand RNA virus harboring a highly structured internal ribosome entry site (IRES in the 5' nontranslated region of its genome. Important for initiating translation of viral RNAs into proteins, the HCV IRES is composed of RNA structures reminiscent of microRNA precursors that may be targeted by the host RNA silencing machinery. Results We report that HCV IRES can be recognized and processed into small RNAs by the human ribonuclease Dicer in vitro. Furthermore, we identify domains II, III and VI of HCV IRES as potential substrates for Dicer in vitro. However, maintenance of the functional integrity of the HCV IRES in response to Dicer overexpression suggests that the structure of the HCV IRES abrogates its processing by Dicer in vivo. Conclusion Our results suggest that the HCV IRES may have evolved to adopt a structure or a cellular context that is refractory to Dicer processing, which may contribute to viral escape of the host RNA silencing machinery.

  7. PCR assay with host specific internal control forStaphylococcus aureus from bovine milk samples

    Directory of Open Access Journals (Sweden)

    Zafer Cantekin

    2015-03-01

    Full Text Available Staphylococcus aureus is considered as one of the most important and common pathogens of bovine mastitis. Polymerase Chain Reaction is frequently proposed in the diagnosis of S. aureus directly from milk samples instead of classical culture. However, false-negative results may occur in the polymerase chain reaction analysis performed directly from clinical material. For the purpose of disclosing the false negative results, the use of internal amplification controls can be beneficial. Therefore, in this study a new polymerase chain reaction technique with host specific internal amplification control was developed by optimizing S. aureus-specific primers in combination with bovine specific primers. The effectiveness of the developed technique in this study was attempted in milk samples from bovine subclinical mastitis. This technique has the potential to detect S. aureus from bovine milk samples or dairy products.

  8. Clinical trials with nested subgroups: Analysis, sample size determination and internal pilot studies.

    Science.gov (United States)

    Placzek, Marius; Friede, Tim

    2017-01-01

    The importance of subgroup analyses has been increasing due to a growing interest in personalized medicine and targeted therapies. Considering designs with multiple nested subgroups and a continuous endpoint, we develop methods for the analysis and sample size determination. First, we consider the joint distribution of standardized test statistics that correspond to each (sub)population. We derive multivariate exact distributions where possible, providing approximations otherwise. Based on these results, we present sample size calculation procedures. Uncertainties about nuisance parameters which are needed for sample size calculations make the study prone to misspecifications. We discuss how a sample size review can be performed in order to make the study more robust. To this end, we implement an internal pilot study design where the variances and prevalences of the subgroups are reestimated in a blinded fashion and the sample size is recalculated accordingly. Simulations show that the procedures presented here do not inflate the type I error significantly and maintain the prespecified power as long as the sample size of the smallest subgroup is not too small. We pay special attention to the case of small sample sizes and attain a lower boundary for the size of the internal pilot study.

  9. Direct detection of Trichomonas vaginalis virus in Trichomonas vaginalis positive clinical samples from the Netherlands

    NARCIS (Netherlands)

    Jehee, Ivo; van der Veer, Charlotte; Himschoot, Michelle; Hermans, Mirjam; Bruisten, Sylvia

    2017-01-01

    Trichomonas vaginalis is the most common sexually transmitted parasitical infection worldwide. T. vaginalis can carry a virus: Trichomonas vaginalis virus (TVV). To date, four TVV species have been described. Few studies have investigated TVV prevalence and its clinical importance. We have developed

  10. [Detection of Aichi virus in stool samples from children in Lanzhou].

    Science.gov (United States)

    Li, Bo-Wen; Liang, Sha; Xie, Jin-Xin; Li, Jie; Lan, Bei; Li, Yong-Qing; Li, Hui-Ying; Cheng, Wei-Xia; Li, Dan-Di; Jin, Yu; Duan, Zhao-Jun

    2010-02-01

    To identification and analysis Aichi virus from diarrhea and normal children in Lanzhou, and discuss the relationship between Aichi virus and Infant Diarrhea. According to the literature published data, Using RT-PCR method to amplified Aichi virus 3CD fragment and the positive products were sequenced and determined, and made the alignment analysis between the nucleotide sequences of the amplified fragment with the known sequence of this virus. There was 1 case detection of Aichi virus in the 46 hospitalized children with diarrhea and 299 children with diarrhea out-patients specifically, Overall detection rate was 0.06%, and there was no Aichi virus was detected in normal control children. 2 viral 3CD gene and the known reference strains of nucleotide sequences were 97%, while phylogenetic analysis showed that genotype of 2 viral belongs to the B. There existed B Genotype of Aichi virus in China, and more research is needed to clarified the etiology and epidemiology of Aichi virus characteristics.

  11. The sequence context of the initiation codon in the encephalomyocarditis virus leader modulates efficiency of internal translation initiation.

    OpenAIRE

    Davies, M V; Kaufman, R J

    1992-01-01

    Translation initiation on poliovirus and encephalomyocarditis virus (EMCV) mRNAs occurs by a cap-independent mechanism utilizing an internal ribosomal entry site (IRES). However, no unifying mechanism for AUG initiation site selection has been proposed. Analysis of initiation of mRNAs translated in vitro has suggested that initiation of poliovirus mRNA translation likely involves both internal binding of ribosomes and scanning to the first AUG which is in a favorable context for initiation. I...

  12. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples.

    Science.gov (United States)

    Quick, Joshua; Grubaugh, Nathan D; Pullan, Steven T; Claro, Ingra M; Smith, Andrew D; Gangavarapu, Karthik; Oliveira, Glenn; Robles-Sikisaka, Refugio; Rogers, Thomas F; Beutler, Nathan A; Burton, Dennis R; Lewis-Ximenez, Lia Laura; de Jesus, Jaqueline Goes; Giovanetti, Marta; Hill, Sarah C; Black, Allison; Bedford, Trevor; Carroll, Miles W; Nunes, Marcio; Alcantara, Luiz Carlos; Sabino, Ester C; Baylis, Sally A; Faria, Nuno R; Loose, Matthew; Simpson, Jared T; Pybus, Oliver G; Andersen, Kristian G; Loman, Nicholas J

    2017-06-01

    Genome sequencing has become a powerful tool for studying emerging infectious diseases; however, genome sequencing directly from clinical samples (i.e., without isolation and culture) remains challenging for viruses such as Zika, for which metagenomic sequencing methods may generate insufficient numbers of viral reads. Here we present a protocol for generating coding-sequence-complete genomes, comprising an online primer design tool, a novel multiplex PCR enrichment protocol, optimized library preparation methods for the portable MinION sequencer (Oxford Nanopore Technologies) and the Illumina range of instruments, and a bioinformatics pipeline for generating consensus sequences. The MinION protocol does not require an Internet connection for analysis, making it suitable for field applications with limited connectivity. Our method relies on multiplex PCR for targeted enrichment of viral genomes from samples containing as few as 50 genome copies per reaction. Viral consensus sequences can be achieved in 1-2 d by starting with clinical samples and following a simple laboratory workflow. This method has been successfully used by several groups studying Zika virus evolution and is facilitating an understanding of the spread of the virus in the Americas. The protocol can be used to sequence other viral genomes using the online Primal Scheme primer designer software. It is suitable for sequencing either RNA or DNA viruses in the field during outbreaks or as an inexpensive, convenient method for use in the lab.

  13. Environmental sampling for avian influenza virus A (H5N1) in live-bird markets, Indonesia.

    Science.gov (United States)

    Indriani, Risa; Samaan, Gina; Gultom, Anita; Loth, Leo; Irianti, Sri; Indryani, Sri; Adjid, Rma; Dharmayanti, Ni Luh Putu Indi; Weaver, John; Mumford, Elizabeth; Lokuge, Kamalini; Kelly, Paul M; Darminto

    2010-12-01

    To identify environmental sites commonly contaminated by avian influenza virus A (H5N1) in live-bird markets in Indonesia, we investigated 83 markets in 3 provinces in Indonesia. At each market, samples were collected from up to 27 poultry-related sites to assess the extent of contamination. Samples were tested by using real-time reverse transcription-PCR and virus isolation. A questionnaire was used to ascertain types of birds in the market, general infrastructure, and work practices. Thirty-nine (47%) markets showed contamination with avian influenza virus in ≥ 1 of the sites sampled. Risk factors were slaughtering birds in the market and being located in West Java province. Protective factors included daily removal of waste and zoning that segregated poultry-related work flow areas. These results can aid in the design of evidence-based programs concerning environmental sanitation, food safety, and surveillance to reduce the risk for avian influenza virus A (H5N1) transmission in live-bird markets.

  14. Serological Status of Rubella Virus in Cord Blood Samples of Newborn in Hospitals Affiliated to Tehran University of Medical Sciences

    Directory of Open Access Journals (Sweden)

    S.H. Monavari

    2012-04-01

    Full Text Available Introduction & Objective: Rubella is a disease caused by the rubella virus and is usually mild and self-limiting. Infection of a developing fetus is serious and important because the child may be born with congenital rubella syndrome. Its symptoms include mental retardation, heart defects, cataract, etc. In 2003, mass vaccination against measles and rubella in individuals 5-25 years old was done. One of the main objectives of this study was to survey congenital rubella infection status with the presence of IgM antibodies against rubella virus in cord blood samples and also the immunity assessment of maternal IgG antibodies against rubella virus in the samples.Materials & Methods: In this cross-sectional study 358 cord blood samples were collected in hospitals affiliated to Tehran University of Medical Sciences in 2008-2009. The collected samples were analyzed by two ELISA methods for detection of IgG and IgM antibodies and RT-nested PCR tests on samples of IgG–negative and IgM-positive. In this study two groups of mothers were tested, one consisted of the ones29 with the frequency of 29.1%.Results: The mean age of subjects was 22.6 years old. Out of 358 samples, 326 (91.1% were IgG positive, and 10 (2.8% were IgM positive against rubella virus. All of the samples with negative result for IgG antibody, and positive result for IgM antibody against rubella virus were tested for the presence of rubella genome with RT-nested PCR method. None of these samples were positive according to the presence of the virus genome.Conclusion: According to the high immunity of mothers, the probability of congenital rubella transmission is low, but because of low immunity of mothers being >29 years old, it is highly reccommended to upgrade the age of vaccination to 28.(Sci J Hamadan Univ Med Sci 2012;19(1:16-21

  15. Virus isolation vs RT-PCR: which method is more successful in detecting VHSV and IHNV in fish tissue sampled under field conditions?

    DEFF Research Database (Denmark)

    Knüsel, R.; Bergmann, S. M.; Einer-Jensen, Katja

    2007-01-01

    (total of 859 fish) originating from a field survey on the occurrence of VHSV and IHNV in farmed and wild salmonids in Switzerland. These samples represented all sites with fish that were either identified as virus-positive by means of virus isolation (three sites, four positive tissue sample pools) and...

  16. Screening for Chikungunya virus infection in aged people: Development and internal validation of a new score.

    Directory of Open Access Journals (Sweden)

    Lidvine Godaert

    Full Text Available This study aimed to derive and validate a score for Chikungunya virus (CHIKV infection screening in old people admitted to acute care units.This study was performed in the Martinique University Hospitals from retrospective cases. Patients were aged 65+, admitted to acute care units for suspected CHIKV infection in 2014, with biological testing using Reverse Transcription Polymerase Chain Reaction (RT-PCR. RT-PCR was used as the gold standard. A screening score was created using adjusted odds ratios of factors associated with positive RT-PCR derived from a multivariable logistic regression model. A ROC curve was used to determine the best cut-off of the score. Bootstrap analysis was used to evaluate its internal validity.In all, 687 patients were included, 68% with confirmed CHIKV infection, and 32% with laboratory-unconfirmed CHIKV infection. Mean age was 80±8 years, 51% were women. Four variables were found to be independently associated with positive RT-PCR (fever: 3 points; arthralgia of the ankle: 2 points; lymphopenia: 6 points; absence of neutrophil leucocytosis: 10 points. The best cut-off was score ≥12; sensitivity was 87% (83%-90% and specificity was 70% (63%-76%.This score shows good diagnostic performance and good internal validation and could be helpful to screen aged people for CHIKV infection.

  17. Rapid sample preparation for detection and identification of avian influenza virus from chicken faecal samples using magnetic bead microsystem

    DEFF Research Database (Denmark)

    Dhumpa, Raghuram; Bu, Minqiang; Handberg, Kurt

    2010-01-01

    -PCR is a sensitive method for detection of AIV, it requires sample preparation including separation and purification of AIV and concentrate viral RNA. It is laborious and complex process especially for diagnosis using faecal sample. In this study, magnetic beads were used for immunoseparation of AIV in chicken...... faecal sample by a magnetic microsystem. Using this system, all the 16 hemagglutinin (H) and 9 neuraminidase (N) subtypes of AIV were separated and detected in spiked faecal samples using RT-PCR, without an RNA extraction step. This rapid sample preparation method can be integrated with a total analysis...

  18. Characterization of Decommissioned PWR Vessel Internals Materials Samples: Material Certification, Fluence, and Temperature (Nonproprietary Version)

    Energy Technology Data Exchange (ETDEWEB)

    M. Krug; R. Shogan; A. Fero; M. Snyder

    2004-11-01

    Pressurized water reactor (PWR) cores, operate under extreme environmental conditions due to coolant chemistry, operating temperature, and neutron exposure. Extending the life of PWRs require detailed knowledge of the changes in mechanical and corrosion properties of the structural austenitic stainless steel components adjacent to the fuel. This report contains basic material characterization information of the as-installed samples of reactor internals material which were harvested from a decommissioned PWR.

  19. Development of a Reverse Genetic System for Infectious Salmon Anemia Virus: Rescue of Recombinant Fluorescent Virus by Using Salmon Internal Transcribed Spacer Region 1 as a Novel Promoter

    Science.gov (United States)

    Toro-Ascuy, Daniela; Tambley, Carolina; Beltran, Carolina; Mascayano, Carolina; Sandoval, Nicolas; Olivares, Eduardo; Medina, Rafael A.; Spencer, Eugenio

    2014-01-01

    Infectious salmon anemia (ISA) is a serious disease of marine-farmed Atlantic salmon (Salmo salar) caused by ISA virus (ISAV), belonging to the genus Isavirus, family Orthomyxoviridae. There is an urgent need to understand the virulence factors and pathogenic mechanisms of ISAV and to develop new vaccine approaches. Using a recombinant molecular biology approach, we report the development of a plasmid-based reverse genetic system for ISAV, which includes the use of a novel fish promoter, the Atlantic salmon internal transcribed spacer region 1 (ITS-1). Salmon cells cotransfected with pSS-URG-based vectors expressing the eight viral RNA segments and four cytomegalovirus (CMV)-based vectors that express the four proteins of the ISAV ribonucleoprotein complex allowed the generation of infectious recombinant ISAV (rISAV). We generated three recombinant viruses, wild-type rISAV901_09 and rISAVrS6-NotI-HPR containing a NotI restriction site and rISAVS6/EGFP-HPR harboring the open reading frame of enhanced green fluorescent protein (EGFP), both within the highly polymorphic region (HPR) of segment 6. All rescued viruses showed replication activity and cytopathic effect in Atlantic salmon kidney-infected cells. The fluorescent recombinant viruses also showed a characteristic cytopathic effect in salmon cells, and the viruses replicated to a titer of 6.5 × 105 PFU/ml, similar to that of the wild-type virus. This novel reverse genetics system offers a powerful tool to study the molecular biology of ISAV and to develop a new generation of ISAV vaccines to prevent and mitigate ISAV infection, which has had a profound effect on the salmon industry. PMID:25480750

  20. Quantification of Human and Animal Viruses to Differentiate the Origin of the Fecal Contamination Present in Environmental Samples

    Directory of Open Access Journals (Sweden)

    Sílvia Bofill-Mas

    2013-01-01

    Full Text Available Many different viruses are excreted by humans and animals and are frequently detected in fecal contaminated waters causing public health concerns. Classical bacterial indicator such as E. coli and enterococci could fail to predict the risk for waterborne pathogens such as viruses. Moreover, the presence and levels of bacterial indicators do not always correlate with the presence and concentration of viruses, especially when these indicators are present in low concentrations. Our research group has proposed new viral indicators and methodologies for determining the presence of fecal pollution in environmental samples as well as for tracing the origin of this fecal contamination (microbial source tracking. In this paper, we examine to what extent have these indicators been applied by the scientific community. Recently, quantitative assays for quantification of poultry and ovine viruses have also been described. Overall, quantification by qPCR of human adenoviruses and human polyomavirus JC, porcine adenoviruses, bovine polyomaviruses, chicken/turkey parvoviruses, and ovine polyomaviruses is suggested as a toolbox for the identification of human, porcine, bovine, poultry, and ovine fecal pollution in environmental samples.

  1. Limited interlaboratory comparison of Schmallenberg virus antibody detection in serum samples.

    NARCIS (Netherlands)

    Poel, van der W.H.M.; Cay, B.; Zientara, S.; Steinbach, F.; Valarcher, J.F.; Botner, A.; Mars, M.H.; Hakze-van der Honing, van der R.W.; Schirrmeier, H.; Beer, M.

    2014-01-01

    Eight veterinary institutes in seven different countries in Europe participated in a limited interlaboratory comparison trial to evaluate laboratory performances of Schmallenberg virus (SBV) antibody detection in serum. Seven different sheep sera and three different cattle sera were circulated, and

  2. Use of chimeric influenza viruses as a novel internal control for diagnostic rRT-PCR assays.

    Science.gov (United States)

    Wang, Xueliang; Liu, Fen; Jiang, Lingli; Bao, Yun; Xiao, Yanqun; Wang, Hualiang

    2016-02-01

    Real-time quantitative reverse transcriptase polymerase chain reaction (rRT-PCR) is now widely used to detect viral pathogens in various human specimens. The application of internal controls to validate the entire process of these assays is necessary to prevent false-negative results caused by unexpected inhibition or inefficient extraction. In the present study, we describe a strategy to produce a stable internal control for rRT-PCR by packaging foreign RNA into influenza virions using plasmid-based reverse genetics technology. The envelope structure of influenza virus can effectively protect RNA segments from RNase digestion, which provides an advantage for its routine use as an internal control. Utilizing this approach, we successfully generated a recombinant influenza virus (rPR8-HCV) containing the 5′ untranslated region (5′UTR) of the hepatitis C virus (HCV) RNA genome. After inactivation and purification, the rPR8-HCV particles were demonstrated to be RNase resistant and stable at 4 °C for at least 252 days in human plasma, with no degradation even after being frozen and thawed multiple times. These results were reproducible in the COBAS TaqMan HCV test for 164 days. Moreover, the chimeric influenza virus particles could be easily produced in embryonated eggs and were noninfectious after inactivation treatment. Additionally, this strategy could also be adapted for real-time clinical applications of other RNA targets, providing a universal approach with broad clinical applications in rRT-PCR assays.

  3. International Standardisation of a Method for Detection of Human Pathogenic Viruses in Molluscan Shellfish

    DEFF Research Database (Denmark)

    Lees, David; Schultz, Anna Charlotte

    2010-01-01

    The viruses primarily associated with shellfish-borne illness are norovirus, causing gastroenteritis and hepatitis A virus (HAV). Recent years have seen a proliferation of publications on methods for detection of these viruses in shellfish using polymerase chain reaction (PCR). However, currently...

  4. Infective respiratory syncytial virus is present in human cord blood samples and most prevalent during winter months.

    Directory of Open Access Journals (Sweden)

    Angela Mary Fonceca

    Full Text Available Human respiratory syncytial virus (RSV remains the most common cause of severe lower respiratory tract disease amongst infants, and continues to cause annual epidemics of respiratory disease every winter worldwide. Demonstrating placental transmission of viable RSV in human samples is a major paradigm shift in respiratory routes considered likely for RSV transmission.Droplet digital PCR (ddPCR was used to identify RSV present in cord blood mononucleocytes (CBM. CBMs testing positive for RSV were treated with phytohemagglutinin (PHA, PHA and nitric oxide (NO or PHA, NO and palivizumab, and co-cultured with HeLa cell monolayers. Subsequent immuno-staining for RSV was used to visualize infective viral plaques.RSV was detected in 26 of 45 samples (57.7% by ddPCR. CBM's collected in winter were more likely to test positive for RSV (17/21 samples, risk = 80%, OR = 7.08; 95% CI 1.80-27.80; p = 0.005 compared to non-winter months (9/24 samples, 37.5%. RSV plaques were observed in non-treated and treated co-cultured HeLa monolayers.Demonstrating active RSV in CBMs suggests in utero transmission of infective virus to the fetus without causing overt disease. This is likely to have an important impact on immune development as well as future virus-host interactions, thereby warranting further investigation.

  5. Infective respiratory syncytial virus is present in human cord blood samples and most prevalent during winter months.

    Science.gov (United States)

    Fonceca, Angela Mary; Chopra, Abha; Levy, Avram; Noakes, Paul Stanton; Poh, Matthew Wee-Peng; Bear, Natasha Leanne; Prescott, Susan; Everard, Mark Lloyd

    2017-01-01

    Human respiratory syncytial virus (RSV) remains the most common cause of severe lower respiratory tract disease amongst infants, and continues to cause annual epidemics of respiratory disease every winter worldwide. Demonstrating placental transmission of viable RSV in human samples is a major paradigm shift in respiratory routes considered likely for RSV transmission. Droplet digital PCR (ddPCR) was used to identify RSV present in cord blood mononucleocytes (CBM). CBMs testing positive for RSV were treated with phytohemagglutinin (PHA), PHA and nitric oxide (NO) or PHA, NO and palivizumab, and co-cultured with HeLa cell monolayers. Subsequent immuno-staining for RSV was used to visualize infective viral plaques. RSV was detected in 26 of 45 samples (57.7%) by ddPCR. CBM's collected in winter were more likely to test positive for RSV (17/21 samples, risk = 80%, OR = 7.08; 95% CI 1.80-27.80; p = 0.005) compared to non-winter months (9/24 samples, 37.5%). RSV plaques were observed in non-treated and treated co-cultured HeLa monolayers. Demonstrating active RSV in CBMs suggests in utero transmission of infective virus to the fetus without causing overt disease. This is likely to have an important impact on immune development as well as future virus-host interactions, thereby warranting further investigation.

  6. Internal Hydrolysis Indicator for Sample Specific Monitoring of β-Glucuronidase Activity.

    Science.gov (United States)

    Taylor, Lacy L; Flint, Noah A; Ma, Vinh; Hill, Brandy M; Clark, Chantry J; Strathmann, Frederick G

    2017-06-01

    Metabolized forms of benzodiazepines (benzos) can cause issues with mass spectrometry identification. Benzodiazepines undergo a process called glucuronidation during metabolism that attaches a glucuronic acid for increased solubility. Often in clinical testing an enzymatic hydrolysis step is implemented to increase the sensitivity of benzodiazepines by hydrolyzing β-D-glucuronic acid from benzodiazepine-glucuronide conjugates in urine samples using the β-Glucuronidase enzyme. In this study resorufin β-D-glucuronide, a substrate of the β-Glucuronidase enzyme, was added to patient samples to determine if proper hydrolysis had occurred. The presence of resorufin as an Internal Hydrolysis Indicator (IHI) shows the activity and efficiency of the enzyme in each patient sample. Synthetic/patient urine samples were obtained and mixed with hydrolysis buffer containing resorufin β-D-glucuronide. The β-Glucuronidase enzyme was used to hydrolyze the benzodiazepine analytes as well as resorufin β-D-glucuronide. The enzymatic hydrolysis addition increased the positivity rate of benzodiazepines by 42.5%. The β-Glucuronidase substrate resorufin (IHI) displayed variability in area counts between patient samples. Comparative studies with internal standards and resorufin (IHI) showed no correlation between recovery and analyte variability. Hydrolysis reactions greatly improved the sensitivity of benzodiazepines by liquid chromatography time-of-flight mass spectrometry analysis. The large variation in resorufin (IHI) area counts amongst patient samples indicates possible variability in enzymatic hydrolysis activity. The enzymatic hydrolysis step is a part of the extraction procedure and should be controlled for in each patient sample. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  7. High pressure sample cell for total internal reflection fluorescence spectroscopy at pressures up to 2500 bar

    Science.gov (United States)

    Koo, Juny; Czeslik, Claus

    2012-08-01

    Total internal reflection fluorescence (TIRF) spectroscopy is a surface sensitive technique that is widely used to characterize the structure and dynamics of molecules at planar liquid-solid interfaces. In particular, biomolecular systems, such as protein adsorbates and lipid membranes can easily be studied by TIRF spectroscopy. Applying pressure to molecular systems offers access to all kinds of volume changes occurring during assembly of molecules, phase transitions, and chemical reactions. So far, most of these volume changes have been characterized in bulk solution, only. Here, we describe the design and performance of a high pressure sample cell that allows for TIRF spectroscopy under high pressures up to 2500 bar (2.5 × 108 Pa), in order to expand the understanding of volume effects from the bulk phase to liquid-solid interfaces. The new sample cell is based on a cylindrical body made of Nimonic 90 alloy and incorporates a pressure transmitting sample cuvette. This cuvette is composed of a fused silica prism and a flexible rubber gasket. It contains the sample solution and ensures a complete separation of the sample from the liquid pressure medium. The sample solution is in contact with the inner wall of the prism forming the interface under study, where fluorescent molecules are immobilized. In this way, the new high pressure TIRF sample cell is very useful for studying any biomolecular layer that can be deposited at a planar water-silica interface. As examples, high pressure TIRF data of adsorbed lysozyme and two phospholipid membranes are presented.

  8. VIRUSES

    Indian Academy of Sciences (India)

    and-mouth disease in livestock was an infectious particle smaller than any bacteria. This was the first clue to the nature of viruses, genetic entities that lie somewhere in the gray area between living and non-living states.

  9. Implementation of immunohistochemistry on frozen ear notch tissue samples in diagnosis of bovine viral diarrhea virus in persistently infected cattle.

    Science.gov (United States)

    Bedeković, Tomislav; Lemo, Nina; Lojkić, Ivana; Beck, Ana; Lojkić, Mirko; Madić, Josip

    2011-12-05

    Bovine viral diarrhea is a contagious disease of domestic and wild ruminants and one of the most economically important diseases in cattle. Bovine viral diarrhea virus belongs to the genus Pestivirus, within the family Flaviviridae. The identification and elimination of the persistently infected animals from herds is the initial step in the control and eradication programs. It is therefore necessary to have reliable methods for diagnosis of bovine viral diarrhea virus. One of those methods is immunohistochemistry. Immunohistochemistry on formalin fixed, paraffin embedded tissue is a routine technique in diagnosis of persistently infected cattle from ear notch tissue samples. However, such technique is inappropriate due to complicated tissue fixation process and it requires more days for preparation. On the contrary, immunohistochemistry on frozen tissue was usually applied on organs from dead animals. In this paper, for the first time, the imunohistochemistry on frozen ear notch tissue samples was described. Seventeen ear notch tissue samples were obtained during the period 2008-2009 from persistently infected cattle. Samples were fixed in liquid nitrogen and stored on -20°C until testing. Ear notch tissue samples from all persistently infected cattle showed positive results with good section quality and possibility to determinate type of infected cells. Although the number of samples was limited, this study indicated that immunohistochemistry on formalin fixed paraffin embedded tissue can be successfully replaced with immunohistochemistry on frozen ear notch tissue samples in diagnosis of persistently infected cattle.

  10. Implementation of immunohistochemistry on frozen ear notch tissue samples in diagnosis of bovine viral diarrhea virus in persistently infected cattle

    Directory of Open Access Journals (Sweden)

    Bedeković Tomislav

    2011-12-01

    Full Text Available Abstract Background Bovine viral diarrhea is a contagious disease of domestic and wild ruminants and one of the most economically important diseases in cattle. Bovine viral diarrhea virus belongs to the genus Pestivirus, within the family Flaviviridae. The identification and elimination of the persistently infected animals from herds is the initial step in the control and eradication programs. It is therefore necessary to have reliable methods for diagnosis of bovine viral diarrhea virus. One of those methods is immunohistochemistry. Immunohistochemistry on formalin fixed, paraffin embedded tissue is a routine technique in diagnosis of persistently infected cattle from ear notch tissue samples. However, such technique is inappropriate due to complicated tissue fixation process and it requires more days for preparation. On the contrary, immunohistochemistry on frozen tissue was usually applied on organs from dead animals. In this paper, for the first time, the imunohistochemistry on frozen ear notch tissue samples was described. Findings Seventeen ear notch tissue samples were obtained during the period 2008-2009 from persistently infected cattle. Samples were fixed in liquid nitrogen and stored on -20°C until testing. Ear notch tissue samples from all persistently infected cattle showed positive results with good section quality and possibility to determinate type of infected cells. Conclusions Although the number of samples was limited, this study indicated that immunohistochemistry on formalin fixed paraffin embedded tissue can be successfully replaced with immunohistochemistry on frozen ear notch tissue samples in diagnosis of persistently infected cattle.

  11. Evaluation of feline monocyte-derived dendritic cells loaded with internally inactivated virus as a vaccine against feline immunodeficiency virus.

    Science.gov (United States)

    Freer, Giulia; Matteucci, Donatella; Mazzetti, Paola; Tarabella, Francesca; Catalucci, Valentina; Ricci, Enrica; Merico, Antonio; Bozzacco, Leonia; Pistello, Mauro; Bendinelli, Mauro

    2008-03-01

    Dendritic cells are the only antigen-presenting cells that can present exogenous antigens to both helper and cytolytic T cells and prime Th1-type or Th2-type cellular immune responses. Given their unique immune functions, dendritic cells are considered attractive "live adjuvants" for vaccination and immunotherapy against cancer and infectious diseases. The present study was carried out to assess whether the reinjection of autologous monocyte-derived dendritic cells loaded with an aldithriol-2-inactivated primary isolate of feline immune deficiency virus (FIV) was able to elicit protective immune responses against the homologous virus in naive cats. Vaccine efficacy was assessed by monitoring immune responses and, finally, by challenge with the homologous virus of vaccinated, mock-vaccinated, and healthy cats. The outcome of challenge was followed by measuring cellular and antibody responses and viral and proviral loads and quantitating FIV by isolation and a count of CD4(+)/CD8(+) T cells in blood. Vaccinated animals exhibited clearly evident FIV-specific peripheral blood mononuclear cell proliferation and antibody titers in response to immunization; however, they became infected with the challenge virus at rates comparable to those of control animals.

  12. Immunotherapy with internally inactivated virus loaded dendritic cells boosts cellular immunity but does not affect feline immunodeficiency virus infection course.

    Science.gov (United States)

    Freer, Giulia; Matteucci, Donatella; Mazzetti, Paola; Tarabella, Francesca; Ricci, Enrica; Bozzacco, Leonia; Merico, Antonio; Pistello, Mauro; Ceccherini-Nelli, Luca; Bendinelli, Mauro

    2008-04-17

    Immunotherapy of feline immunodeficiency virus (FIV)-infected cats with monocyte-derived dendritic cells (MDCs) loaded with aldrithiol-2 (AT2)-inactivated homologous FIV was performed. Although FIV-specific lymphoproliferative responses were markedly increased, viral loads and CD4+ T cell depletion were unaffected, thus indicating that boosting antiviral cell-mediated immunity may not suffice to modify infection course appreciably.

  13. Rapid Detection/pathotyping of Newcastle disease virus isolates in clinical samples using real time polymerase chain reaction assay

    OpenAIRE

    sprotocols

    2014-01-01

    Authors: Abdul Wajid, Muhammad Wasim, Tahir Yaqub, Shafqat F Rehmani, Tasra Bibi, Nadia Mukhtar, Javed Muhammad, Umar Bacha, Suliman Qadir Afridi, Muhammad Nauman Zahid, Zia u ddin, Muhammad Zubair Shabbir, Kamran Abbas & Muneer Ahmad ### Abstract In the present protocol we describe the real time reverse transcription polymerase chain reaction (rRT-PCR) assay for the rapid detection/pathotyping of Newcastle disease virus (NDV) isoaltes in clinical samples. Fusion gene and matrix gene...

  14. [Detection of West Nile virus in human samples: follow-up studies during the 2015 seasonal period].

    Science.gov (United States)

    Nagy, Anna; Nagy, Orsolya; Bán, Enikő; Molnár, Eszter; Müller, Zsófia; Orbán, Márton; Kecskés, Borbála; Harsányi, Emese Henriett; Kővágó, Levente; Jobbágy, Lajos; Németh, Zoltán; Várnai, Zsuzsanna; Takács, Mária

    2017-05-01

    West Nile virus, a mosquito-borne viral zoonosis is responsible for human infections in Hungary. Laboratory diagnosis is based on serological tests, however the application of molecular methods has been appreciated. The aim of the study was to investigate blood, cerebrospinal-fluid and urine samples of acutely ill patients and to follow-up PCR positive cases to ascertain the length of virus excretion. Clinical specimens were examined by indirect-immunofluorescent, haemagglutination-inhibition, two PCR tests and Sanger-sequencing. Virus isolation in case of two patients was successful. A follow-up study could be carried out in case of 5 patients. Viral nucleic acid was detectable in urine even for several weeks after symptom onset and viral RNA was present at higher concentration compared with other samples. PCR analysis of urine could provide useful epidemiological and diagnostic information. Therefore, it is recommended to collect urine samples in order to supplement the serological diagnosis. Orv Hetil. 2017; 158(20): 791-796.

  15. Identification of a suitable internal control for fluorescence analysis on canine peripheral blood samples.

    Science.gov (United States)

    Riondato, F; Martini, V; Poggi, A; Rota, A; Comazzi, S; Sulce, M; Bruno, B; Borrelli, A; Miniscalco, B

    2016-04-01

    Reliable detection of fluorescence intensity (FI) by flow cytometry (FC) is fundamental. FI depends on instrument settings and sample processing procedures: thus, measurements should be done using internal controls with known FI. Commercially available beads-based standards are expensive, thus reducing their usability in the veterinary practice. Cell subsets with stable mean FI (MFI) within the population have been proposed as acceptable surrogates in human medicine. In veterinary medicine, no data exist about stability of antigen expression among different subjects or upon sample storage. The aim of the present study was to evaluate MFI variability of main lymphocytes antigens among the lymphoid cells within each subject, among different subjects, and upon 24-h storage, in order to identify the antigen most suitable as stable internal control in MFI analyses. Peripheral blood samples from 18 healthy dogs were analysed by FC within 3h from sampling to assess the expression of CD3, CD5, CD4, CD8, CD21 and cyCD79b using conjugated monoclonal antibodies. Analyses were restricted to the lymphoid population. Fluorescent microbeads were added to each tube, and antigen MFI was calculated as Relative Fluorescence Intensity RFI (CD/beads). Fluorescence histogram CV (fhCV) for each CD was regarded as an index of the variability of expression among lymphocytes within each subject (cell-to-cell variability); whereas the CV of RFI was regarded as an index of inter-subjects variability (dog-to-dog variability). In 11 cases, FC analyses were repeated after 24h storage at 4°C and RFI and CVs of fresh and stored samples were compared to assess variability linked to storage. CD4 was identified as the best antigen to be used as an internal control for MFI analyses in canine peripheral blood samples because of low cell-to-cell and dog-to-dog variability, and optimal stability upon 24-h storage. Blood samples from a second group of 21 healthy dogs were labelled only with CD4, in order

  16. Origin and characteristics of internal genes affect infectivity of the novel avian-origin influenza A (H7N9) virus.

    Science.gov (United States)

    Feng, Yan; Mao, Haiyan; Xu, Changping; Jiang, Jianmin; Chen, Yin; Yan, Juying; Gao, Jian; Li, Zhen; Xia, Shichang; Lu, Yiyu

    2013-01-01

    Human infection with a novel avian-origin influenza A (H7N9) virus occurred continuously in China during the first half of 2013, with high infectivity and pathogenicity to humans. In this study, we investigated the origin of internal genes of the novel H7N9 virus and analyzed the relationship between internal genes and infectivity of the virus. We tested the environmental specimens using real-time RT-PCR assays and isolated five H9N2 viruses from specimens that were positive for both H7 and H9. Results of recombination and phylogeny analysis, performed based on the entire sequences of 221 influenza viruses, showed that one of the Zhejiang avian H9N2 isolates, A/environment/Zhejiang/16/2013, shared the highest identities on the internal genes with the novel H7N9 virus A/Anhui/1/2013, ranging from 98.98% to 100%. Zhejiang avian H9N2 isolates were all reassortant viruses, by acquiring NS gene from A/chicken/Dawang/1/2011-like viruses and other five internal genes from A/brambling/Beijing/16/2012-like viruses. Compared to A/Anhui/1/2013 (H7N9), the homology on the NS gene was 99.16% with A/chicken/Dawang/1/2011, whereas only 94.27-97.61% with A/bramnling/Beijing/16/2012-like viruses. Analysis on the relationship between internal genes and the infectivity of novel H7N9 viruses were performed by comparing amino acid sequences with the HPAI H5N1 viruses, the H9N2 and the earlier H7N9 avian influenza viruses. There were nine amino acids on the internal genes found to be possibly associated with the infectivity of the novel H7N9 viruses. These findings indicate that the internal genes, sharing the highest similarities with A/environment/Zhejiang/16/2013-like (H9N2) viruses, may affect the infectivity of the novel H7N9 viruses.

  17. Powassan (POW) Virus Basics

    Science.gov (United States)

    ... Professionals Related Topics For International Travelers Powassan (POW) Virus Basics Download this fact sheet formatted for print: ... POW) Virus Fact Sheet (PDF) What is Powassan virus? Powassan (POW) virus is a flavivirus that is ...

  18. Characterization of Posa and Posa-like virus genomes in fecal samples from humans, pigs, rats, and bats collected from a single location in Vietnam.

    Science.gov (United States)

    Oude Munnink, Bas B; Phan, My V T; Simmonds, Peter; Koopmans, Marion P G; Kellam, Paul; van der Hoek, Lia; Cotten, Matthew

    2017-07-01

    Porcine stool-associated RNA virus (posavirus), and Human stool-associated RNA virus (husavirus) are viruses in the order Picornavirales recently described in porcine and human fecal samples. The tentative group (Posa and Posa-like viruses: PPLVs) also includes fish stool-associated RNA virus (fisavirus) as well as members detected in insects (Drosophila subobscura and Anopheles sinensis) and parasites (Ascaris suum). As part of an agnostic deep sequencing survey of animal and human viruses in Vietnam, we detected three husaviruses in human fecal samples, two of which share 97-98% amino acid identity to Dutch husavirus strains and one highly divergent husavirus with only 25% amino acid identity to known husaviruses. In addition, the current study found forty-seven complete posavirus genomes from pigs, ten novel rat stool-associated RNA virus genomes (tentatively named rasavirus), and sixteen novel bat stool-associated RNA virus genomes (tentatively named basavirus). The five expected Picornavirales protein domains (helicase, 3C-protease, RNA-dependent RNA polymerase, and two Picornavirus capsid domain) were found to be encoded by all PPLV genomes. In addition, a nucleotide composition analysis revealed that the PPLVs shared compositional properties with arthropod viruses and predicted non-mammalian hosts for all PPLV lineages. The study adds seventy-six genomes to the twenty-nine PPLV genomes currently available and greatly extends our sequence knowledge of this group of viruses within the Picornavirales order.

  19. Detection and partial characterization of simian immunodeficiency virus SIVsm strains from bush meat samples from rural Sierra Leone.

    Science.gov (United States)

    Apetrei, Cristian; Metzger, Michael J; Richardson, David; Ling, Binhua; Telfer, Paul T; Reed, Patricia; Robertson, David L; Marx, Preston A

    2005-02-01

    Human immunodeficiency virus type 2 (HIV-2) originated from simian immunodeficiency viruses (SIVs) that naturally infect sooty mangabeys (SMs; Cercocebus atys). In order to further investigate the relationship between HIV-2 and SIVsm, the SIV specific to the SM, we characterized seven new SIVsm strains from SMs sold in Sierra Leone markets as bush meat. The gag, pol, and env sequences showed that, while the viruses of all seven SMs belonged to the SIVsm-HIV-2 lineage, they were highly divergent viruses, in spite of the fact that most of the samples originated from the same geographical region. They clustered in three lineages, two of which have been previously reported. Two of the new SIVsm strains clustered differently in gag and env phylogenetic trees, suggesting SIVsm recombination that had occurred in the past. In spite of the fact that our study doubles the number of known SIVsm strains from wild SMs, none of the simian strains were close to the groups in which HIV-2 was epidemic (groups A and B).

  20. Genomic RNAs of Borna disease virus are elongated on internal template motifs after realignment of the 3' termini.

    Science.gov (United States)

    Martin, Arnold; Hoefs, Nadja; Tadewaldt, Josefine; Staeheli, Peter; Schneider, Urs

    2011-04-26

    The terminal structures of the Borna disease virus (BDV) genome (vRNA) and antigenome (cRNA) differ from those of other negative strand RNA viruses, as both molecules possess four nucleotides at the 3' terminus without an apparent template at the 5' end of the opposite strand. Consequently, the v- and cRNA molecules are not perfect mirror images, a situation that is not compatible with conventional strategies to maintain genetic information. We show here that recombinant viruses recovered from cDNA lacking the nontemplated nucleotides efficiently reconstitute the 3' overhangs. Analyses of recombinant viruses encoding genetic markers in potential alternative template sequences demonstrated that the BDV v- and cRNA molecules are extended by a realign-and-elongation process on internal template motifs located in close proximity to the 3' ends of v- and cRNA, respectively. The data further suggest that cRNA elongation is restricted to a single template motif of the nascent strand, whereas elongation of vRNA might use multiple template motifs. We propose that the elongation of the 3' termini supports the terminal integrity of the genomic RNA molecules during BDV persistence, and furthermore provides an elegant strategy to eliminate the triphosphate groups from the 5' termini of the BDV v- and cRNA without compromising the genetic information of the virus.

  1. Genomic RNAs of Borna disease virus are elongated on internal template motifs after realignment of the 3′ termini

    Science.gov (United States)

    Martin, Arnold; Hoefs, Nadja; Tadewaldt, Josefine; Staeheli, Peter; Schneider, Urs

    2011-01-01

    The terminal structures of the Borna disease virus (BDV) genome (vRNA) and antigenome (cRNA) differ from those of other negative strand RNA viruses, as both molecules possess four nucleotides at the 3′ terminus without an apparent template at the 5′ end of the opposite strand. Consequently, the v- and cRNA molecules are not perfect mirror images, a situation that is not compatible with conventional strategies to maintain genetic information. We show here that recombinant viruses recovered from cDNA lacking the nontemplated nucleotides efficiently reconstitute the 3′ overhangs. Analyses of recombinant viruses encoding genetic markers in potential alternative template sequences demonstrated that the BDV v- and cRNA molecules are extended by a realign-and-elongation process on internal template motifs located in close proximity to the 3′ ends of v- and cRNA, respectively. The data further suggest that cRNA elongation is restricted to a single template motif of the nascent strand, whereas elongation of vRNA might use multiple template motifs. We propose that the elongation of the 3′ termini supports the terminal integrity of the genomic RNA molecules during BDV persistence, and furthermore provides an elegant strategy to eliminate the triphosphate groups from the 5′ termini of the BDV v- and cRNA without compromising the genetic information of the virus. PMID:21482759

  2. Broadly reactive nested reverse transcription-PCR using an internal RNA standard control for detection of noroviruses in stool samples.

    Science.gov (United States)

    Medici, Maria Cristina; Martinelli, Monica; Ruggeri, Franco Maria; Abelli, Laura Anna; Bosco, Simona; Arcangeletti, Maria Cristina; Pinardi, Federica; De Conto, Flora; Calderaro, Adriana; Chezzi, Carlo; Dettori, Giuseppe

    2005-08-01

    We developed a nested reverse transcription-PCR (nRT-PCR) for the detection of noroviruses in stools, using random primers for RT, the JV12/JV13 primer pair in the first round of nPCR, and a set of nine inner primers for the second, comprising the reverse sequences of primers SR46, SR48, SR50, and SR52, and five novel oligonucleotide sequences (113-1, 113-2, 115-1, 115-2, and 115-3). The specificity of the nRT-PCR was confirmed by testing 61 stools containing enteric viruses other than noroviruses. In comparative assays on either stools or RNA dilutions from two genogroup I and three genogroup II (GII) norovirus-positive samples, nRT-PCR was always at least as sensitive as RT-PCR and Southern hybridization. With some of the samples tested, the increase in sensitivity was 10-fold or higher. For GII viruses, the detectable range of nRT-PCR was estimated to be 8.4 x 10(4) to 2 RNA viral particles. When used on 85 stools from pediatric patients with acute gastroenteritis negative for viruses by electron microscopy and cell culture, the nRT-PCR detected norovirus in 19 samples (22.3%), while it failed to detect one reference RT-PCR-positive sample containing a Desert Shield strain. Sixteen of the 19 nRT-PCR-positive samples gave concordant results with reference RT-PCR and Southern hybridization, and all with sequence analysis. Partial sequencing of the polymerase region revealed that from January to April 2000 all GII strains except two (Rotterdam- and Leeds-like viruses) formed a tight cluster related to Hawaii virus. The nRT-PCR described could prove suitable for large epidemiological studies and for specialized clinical laboratories performing routine molecular testing.

  3. Broadly Reactive Nested Reverse Transcription-PCR Using an Internal RNA Standard Control for Detection of Noroviruses in Stool Samples

    Science.gov (United States)

    Medici, Maria Cristina; Martinelli, Monica; Ruggeri, Franco Maria; Abelli, Laura Anna; Bosco, Simona; Arcangeletti, Maria Cristina; Pinardi, Federica; De Conto, Flora; Calderaro, Adriana; Chezzi, Carlo; Dettori, Giuseppe

    2005-01-01

    We developed a nested reverse transcription-PCR (nRT-PCR) for the detection of noroviruses in stools, using random primers for RT, the JV12/JV13 primer pair in the first round of nPCR, and a set of nine inner primers for the second, comprising the reverse sequences of primers SR46, SR48, SR50, and SR52, and five novel oligonucleotide sequences (113-1, 113-2, 115-1, 115-2, and 115-3). The specificity of the nRT-PCR was confirmed by testing 61 stools containing enteric viruses other than noroviruses. In comparative assays on either stools or RNA dilutions from two genogroup I and three genogroup II (GII) norovirus-positive samples, nRT-PCR was always at least as sensitive as RT-PCR and Southern hybridization. With some of the samples tested, the increase in sensitivity was 10-fold or higher. For GII viruses, the detectable range of nRT-PCR was estimated to be 8.4 × 104 to 2 RNA viral particles. When used on 85 stools from pediatric patients with acute gastroenteritis negative for viruses by electron microscopy and cell culture, the nRT-PCR detected norovirus in 19 samples (22.3%), while it failed to detect one reference RT-PCR-positive sample containing a Desert Shield strain. Sixteen of the 19 nRT-PCR-positive samples gave concordant results with reference RT-PCR and Southern hybridization, and all with sequence analysis. Partial sequencing of the polymerase region revealed that from January to April 2000 all GII strains except two (Rotterdam- and Leeds-like viruses) formed a tight cluster related to Hawaii virus. The nRT-PCR described could prove suitable for large epidemiological studies and for specialized clinical laboratories performing routine molecular testing. PMID:16081909

  4. Immunotherapy with internally inactivated virus loaded dendritic cells boosts cellular immunity but does not affect feline immunodeficiency virus infection course

    Directory of Open Access Journals (Sweden)

    Pistello Mauro

    2008-04-01

    Full Text Available Abstract Immunotherapy of feline immunodeficiency virus (FIV-infected cats with monocyte-derived dendritic cells (MDCs loaded with aldrithiol-2 (AT2-inactivated homologous FIV was performed. Although FIV-specific lymphoproliferative responses were markedly increased, viral loads and CD4+ T cell depletion were unaffected, thus indicating that boosting antiviral cell-mediated immunity may not suffice to modify infection course appreciably.

  5. Assessing the risk of international spread of yellow fever virus: a mathematical analysis of an urban outbreak in Asuncion, 2008.

    Science.gov (United States)

    Johansson, Michael A; Arana-Vizcarrondo, Neysarí; Biggerstaff, Brad J; Gallagher, Nancy; Marano, Nina; Staples, J Erin

    2012-02-01

    Yellow fever virus (YFV), a mosquito-borne virus endemic to tropical Africa and South America, is capable of causing large urban outbreaks of human disease. With the ease of international travel, urban outbreaks could lead to the rapid spread and subsequent transmission of YFV in distant locations. We designed a stochastic metapopulation model with spatiotemporally explicit transmissibility scenarios to simulate the global spread of YFV from a single urban outbreak by infected airline travelers. In simulations of a 2008 outbreak in Asunción, Paraguay, local outbreaks occurred in 12.8% of simulations and international spread in 2.0%. Using simple probabilistic models, we found that local incidence, travel rates, and basic transmission parameters are sufficient to assess the probability of introduction and autochthonous transmission events. These models could be used to assess the risk of YFV spread during an urban outbreak and identify locations at risk for YFV introduction and subsequent autochthonous transmission.

  6. Screening for plant viruses by next generation sequencing using a modified double strand RNA extraction protocol with an internal amplification control.

    Science.gov (United States)

    Kesanakurti, Prasad; Belton, Mark; Saeed, Hanaa; Rast, Heidi; Boyes, Ian; Rott, Michael

    2016-10-01

    The majority of plant viruses contain RNA genomes. Detection of viral RNA genomes in infected plant material by next generation sequencing (NGS) is possible through the extraction and sequencing of total RNA, total RNA devoid of ribosomal RNA, small RNA interference (RNAi) molecules, or double stranded RNA (dsRNA). Plants do not typically produce high molecular weight dsRNA, therefore the presence of dsRNA makes it an attractive target for plant virus diagnostics. The sensitivity of NGS as a diagnostic method demands an effective dsRNA protocol that is both representative of the sample and minimizes sample cross contamination. We have developed a modified dsRNA extraction protocol that is more efficient compared to traditional protocols, requiring reduced amounts of starting material, that is less prone to sample cross contamination. This was accomplished by using bead based homogenization of plant material in closed, disposable 50ml tubes. To assess the quality of extraction, we also developed an internal control by designing a real-time (quantitative) PCR (qPCR) assay that targets endornaviruses present in Phaseolus vulgaris cultivar Black Turtle Soup (BTS). Crown Copyright © 2016. Published by Elsevier B.V. All rights reserved.

  7. Prevalence of Protective Measles Virus Antibody Levels in Umbilical Cord Blood Samples in Catalonia, Spain▿

    Science.gov (United States)

    Plans, Pedro; Costa, Josep; Domínguez, Angela; Torner, Núria; Borras, Eva; Plasència, Antoni

    2010-01-01

    The prevalence of protective antibody levels (>160 mIU/ml) in neonates was 98.5%. The mean measles virus antibody level was 3,406 mIU/ml and increased with maternal age. Measles vaccination was reported by 42% of pregnant women and decreased with age. PMID:20164254

  8. Alcohol dependence is related to overall internalizing psychopathology load rather than to particular internalizing disorders: evidence from a national sample.

    Science.gov (United States)

    Kushner, Matt G; Wall, Melanie M; Krueger, Robert F; Sher, Kenneth J; Maurer, Eric; Thuras, Paul; Lee, Susanne

    2012-02-01

    Alcohol dependence is more prevalent among those with any one of several anxiety or depressive ("internalizing") disorders than among those in the general population. However, because internalizing disorders are highly intercorrelated, it is ambiguous whether alcohol dependence is related to internalizing psychopathology components that are: (i) unique to a particular internalizing disorder ("specific"); versus (ii) shared across a number of internalizing disorders ("general"). To clarify this ambiguity, we employed structural equation and logistic models to decompose the specific versus general components of internalizing psychopathology and then related these components separately to alcohol dependence. The data were based on face-to-face interviews of U.S. community residents collected in the 2001 to 2002 National Epidemiologic Survey on Alcohol and Related Conditions (NESARC; N = 43,093). Both analytic approaches demonstrated that increases in the general internalizing psychopathology load are accompanied by increases in the prevalence of alcohol dependence. Once the general internalizing psychopathology load is accounted for, knowing whether a particular internalizing disorder is present or absent provides little additional information regarding the prevalence of alcohol dependence. The components of internalizing psychopathology that are associated with alcohol dependence are shared and cumulative among common anxiety and depressive disorders. These findings have the potential to influence clinical and scientific conceptualizations of the association between alcohol dependence and internalizing psychopathology. Copyright © 2011 by the Research Society on Alcoholism.

  9. Early Detection of Foot-And-Mouth Disease Virus from Infected Cattle Using A Dry Filter Air Sampling System.

    Science.gov (United States)

    Pacheco, J M; Brito, B; Hartwig, E; Smoliga, G R; Perez, A; Arzt, J; Rodriguez, L L

    2017-04-01

    Foot-and-mouth disease (FMD) is a highly contagious livestock disease of high economic impact. Early detection of FMD virus (FMDV) is fundamental for rapid outbreak control. Air sampling collection has been demonstrated as a useful technique for detection of FMDV RNA in infected animals, related to the aerogenous nature of the virus. In the current study, air from rooms housing individual (n = 17) or two groups (n = 4) of cattle experimentally infected with FDMV A24 Cruzeiro of different virulence levels was sampled to assess the feasibility of applying air sampling as a non-invasive, screening tool to identify sources of FMDV infection. Detection of FMDV RNA in air was compared with first detection of clinical signs and FMDV RNA levels in serum and oral fluid. FMDV RNA was detected in room air samples 1-3 days prior (seven animals) or on the same day (four animals) as the appearance of clinical signs in 11 of 12 individually housed cattle. Only in one case clinical signs preceded detection in air samples by one day. Overall, viral RNA in oral fluid or serum preceded detection in air samples by 1-2 days. Six individually housed animals inoculated with attenuated strains did not show clinical signs, but virus was detected in air in one of these cases 3 days prior to first detection in oral fluid. In groups of four cattle housed together, air detection always preceded appearance of clinical signs by 1-2 days and coincided more often with viral shedding in oral fluid than virus in blood. These data confirm that air sampling is an effective non-invasive screening method for detecting FMDV infection in confined to enclosed spaces (e.g. auction barns, milking parlours). This technology could be a useful tool as part of a surveillance strategy during FMD prevention, control or eradication efforts. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.

  10. Internalizing and externalizing personality and subjective effects in a sample of adolescent cannabis users.

    Science.gov (United States)

    García-Sánchez, Sara; Matalí, Josep Lluís; Martín-Fernández, María; Pardo, Marta; Lleras, Maria; Castellano-Tejedor, Carmina; Haro, Josep Maria

    2016-10-06

    Cannabis is the illicit substance most widely used by adolescents. Certain personality traits such as impulsivity and sensation seeking, and the subjective effects experienced after substance use (e.g. euphoria or relaxation) have been identified as some of the main etiological factors of consumption. This study aims to categorize a sample of adolescent cannabis users based on their most dominant personality traits (internalizing and externalizing profile). Then, to make a comparison of both profiles considering a set of variables related to consumption, clinical severity and subjective effects experienced. From a cross-sectional design, 173 adolescents (104 men and 69 women) aged 13 to 18 asking for treatment for cannabis use disorder in an Addictive Behavior Unit (UCAD) from the hospital were recruited. For the assessment, an ad hoc protocol was employed to register consumption, the Millon Adolescent Clinical Inventory (MACI) and the Addiction Research Center Inventory (ARCI) 49-item short form were also administered. Factor analysis suggested a two-profile solution: Introverted, Inhibited, Doleful, Dramatizing (-), Egotistic (-), Self-demeaning and Borderline tendency scales composed the internalizing profile, and Submissive (-), Unruly, Forceful, Conforming (-) and Oppositional scales composed the externalizing profile. The comparative analysis showed that the internalizing profile has higher levels of clinical severity and more subjective effects reported than the externalizing profile. These results suggest the need to design specific intervention strategies for each profile.

  11. Sexual risk taking in a community sample of international backpackers visiting Brisbane, Australia.

    Science.gov (United States)

    Fischer, Jane A; Debattista, Joseph; Rostami, Soulmaz; Peet, Anthony R; Dean, Judith A; Allen, Kate E; Stewart, Mary

    2015-03-01

    We sought to examine correlations between international backpackers' alcohol consumption and sexual behaviors and determine the prevalence of Chlamydia trachomatis and Neisseria gonorrhoea in this population. A cross-sectional study design consisting of a convenience sample (N = 168) of non-treatment-seeking international backpackers visiting Brisbane, Australia was recruited. Participants were asked to self-complete a questionnaire on sexual behavior and to undertake a urine-based polymerase chain reaction test for C trachomatis and N gonorrhoea. Since arriving in Australia, 73.2% reported having had sex, with a median number of 2 different sex partners (range = 0-21). Most participants had consumed alcohol (53.7%) and used condoms (46.3%) the last time they had sex. In our sample, there was a 4.3% prevalence of C trachomatis and a 0% prevalence of N gonorrhoea. This study identified a variable pattern of risk among backpackers, with those spending longer periods in the country more likely to have sex with Australians. © 2013 APJPH.

  12. A network approach for provisional assay recognition of a Hendra virus antibody ELISA: test validation with low sample numbers from infected horses.

    Science.gov (United States)

    Colling, Axel; Lunt, Ross; Bergfeld, Jemma; McNabb, Leanne; Halpin, Kim; Juzva, Susan; Newberry, Kim; Morrissy, Chris; Loomes, Cameron; Warner, Simone; Diallo, Ibrahim; Kirkland, Peter; Broder, Christopher C; Carlile, Gemma; Loh, Mai Hlaing; Waugh, Caryll; Wright, Lynda; Watson, James; Eagles, Debbie; Zuelke, Kurt; McCullough, Sam; Daniels, Peter

    2018-02-01

    Obtaining statistically sound numbers of sera from Hendra virus (HeV)-infected horses is problematic because affected individuals usually die or are euthanized before developing a serum antibody response. As a consequence, test validation becomes a challenge. Our approach is an extension of OIE principles for provisional recognition and included 7 validation panels tested across multiple laboratories that provided estimates for test performance characteristics. At a 0.4 S/P cutoff, 16 of 19 sera from HeV-infected horses gave positive results in the HeV soluble G, indirect ELISA (HeVsG iELISA; DSe 84.2% [95% CI: 60.4-96.6%]); 463 of 477 non-infected horse sera tested negative (DSp 97.1% [95% CI: 95.1-98.4%]). The HeVsG iELISA eliminated almost all false-positive results from the previously used HeV iELISA, with marginally decreased relative sensitivity. Assay robustness was evaluated in inter-laboratory and proficiency testing panels. The HeVsG iELISA is considered to be fit for purpose for serosurveillance and international movement of horses when virus neutralization is used for follow-up testing of positive or inconclusive serum samples.

  13. Comparison of Selected Nonlethal Samples from Adult Steelhead for Detection of Infectious Hematopoietic Necrosis Virus Using Cell Culture.

    Science.gov (United States)

    Burbank, David R; Fehringer, Tyson R; Chiaramonte, Luciano V

    2017-06-01

    Nonlethal sampling techniques have previously been evaluated for detection of a variety of viral salmonid pathogens. However, many of these studies have used molecular assays in lieu of widely accepted cell culture techniques to evaluate the sampled tissues. Samples were collected from female steelhead Oncorhynchus mykiss broodstock using three potential nonlethal sampling methods (mucus/skin scrape, pectoral fin clip, and gill tissue biopsy) and evaluated for the presence of infectious hematopoietic necrosis virus (IHNV) via cell culture techniques. The results were compared with those from samples collected using a standard lethal sampling method (pooled anterior kidney and spleen tissues) applied to the same fish. Of the three nonlethal sampling techniques that were evaluated, fin clipping was the easiest and least invasive method. Furthermore, fin tissue was as sensitive as or more sensitive than kidney/spleen tissue for detecting IHNV in this population of fish. However, with the exception of gill tissue, the nonlethal samples did not appear to be appropriate surrogates for lethally collected tissues with regard to identifying an active infection in a particular fish. Nevertheless, nonlethal sampling coupled with cell culture appears to be suitable for helping to define the IHNV status of a steelhead population. Received July 27, 2016; accepted December 11, 2016.

  14. Utilizing the International GeoSample Number Concept during ICDP Expedition COSC

    Science.gov (United States)

    Conze, Ronald; Lorenz, Henning; Ulbricht, Damian; Gorgas, Thomas; Elger, Kirsten

    2016-04-01

    The concept of the International GeoSample Number (IGSN) was introduced to uniquely identify and register geo-related sample material, and make it retrievable via electronic media (e.g., SESAR - http://www.geosamples.org/igsnabout). The general aim of the IGSN concept is to improve accessing stored sample material worldwide, enable the exact identification, its origin and provenance, and also the exact and complete citation of acquired samples throughout the literature. The ICDP expedition COSC (Collisional Orogeny in the Scandinavian Caledonides, http://cosc.icdp-online.org) prompted for the first time in ICDP's history to assign and register IGSNs during an ongoing drilling campaign. ICDP drilling expeditions are using commonly the Drilling Information System DIS (http://doi.org/10.2204/iodp.sd.4.07.2007) for the inventory of recovered sample material. During COSC IGSNs were assigned to every drill hole, core run, core section, and sample taken from core material. The original IGSN specification has been extended to achieve the required uniqueness of IGSNs with our offline-procedure. The ICDP name space indicator and the Expedition ID (5054) are forming an extended prefix (ICDP5054). For every type of sample material, an encoded sequence of characters follows. This sequence is derived from the DIS naming convention which is unique from the beginning. Thereby every ICDP expedition has an unlimited name space for IGSN assignments. This direct derivation of IGSNs from the DIS database context ensures the distinct parent-child hierarchy of the IGSNs among each other. In the case of COSC this method of inventory-keeping of all drill cores was done routinely using the ExpeditionDIS during field work and subsequent sampling party. After completing the field campaign, all sample material was transferred to the "Nationales Bohrkernlager" in Berlin-Spandau, Germany. Corresponding data was subsequently imported into the CurationDIS used at the aforementioned core storage

  15. Evaluation of a single-tube fluorogenic RT-PCR assay for detection of bovine respiratory syncytial virus in clinical samples

    DEFF Research Database (Denmark)

    Hakhverdyan, Mikhayil; Hägglund, Sara; Larsen, Lars Erik

    2005-01-01

    Bovine respiratory syncytial virus (BRSV) causes severe disease in naive cattle of all ages and is a common pathogen in the respiratory disease complex of calves. Simplified methods for rapid BRSV diagnosis would encourage sampling during outbreaks and would consequently lead to an extended......, antigen ELISA (Ag-ELISA) and virus isolation (VI). Interspersed negative control samples, samples from healthy animals and eight symptomatically or genetically related viruses were all negative, confirming a high specificity of the assay. Taken together, the data indicated that the fRT-PCR assay can...... understanding of the virus. In this study, a BRSV fluorogenic reverse transcription PCR (fRT-PCR) assay, based on TaqMan principle, was developed and evaluated on a large number of clinical samples, representing various cases of natural and experimental BRSV infections. By using a single-step closed-tube format...

  16. Epidemiology of human parechovirus, Aichi virus and salivirus in fecal samples from hospitalized children with gastroenteritis in Hong Kong.

    Science.gov (United States)

    Yip, Cyril C Y; Lo, Kin-Land; Que, Tak-Lun; Lee, Rodney A; Chan, Kwok-Hung; Yuen, Kwok-Yung; Woo, Patrick C Y; Lau, Susanna K P

    2014-10-18

    Emerging human picornaviruses, including human parechovirus (HPeV), Aichi virus (AiV) and salivirus (SalV) were found to be associated with gastroenteritis, but their roles in enteric infections are not fully understood. In addition, no report on the circulation of these viruses in Hong Kong is available. The objective of this study was to investigate the prevalence and genetic diversity of HPeV, AiV and SalV in fecal samples from hospitalized children with gastroenteritis in Hong Kong. Fecal samples from hospitalized children with gastroenteritis were subject to detection of HPeV, AiV and SalV by RT-PCR using consensus primers targeted to their 5'UTRs. Positive samples were subject to capsid and/or 3CD region analysis for genotype determination. The epidemiology of HPeV, AiV and SalV infections was analyzed. Among 1,708 fecal samples subjected to RT-PCR using primers targeted to 5'UTR of HPeV, AiV and SalV, viruses were detected in 55 samples, with 50 positive for HPeV only, 3 positive for AiV only, 1 positive for both HPeV and AiV, and 1 positive for both HPeV and SalV. Phylogenetic analysis of the partial VP1 gene of the 33 HPeV strains revealed the presence of genotypes of HPeV- 1, 3, 4, 5, 7, 10, among which HPeV-1 was the predominant genotype circulating in our population. The peak activity of HPeV infection was in fall. Of the 3 children with AiV infection, the 3 AiV strains were found to belong to genotype A based on the phylogenetic analysis of their partial VP1 and 3CD regions. The genotype of a SalV strain detected in this study could not be determined. Co-detection of different pathogens was observed in 24 samples (43.6%) of 55 fecal samples positive for HPeV, AiV and SalV. HPeV, AiV and SalV were detected in fecal samples of hospitalized children with gastroenteritis in Hong Kong, with the former having the highest prevalence. HPeV-1 was the predominant genotype among HPeVs, while genotype A was the predominant genotype among AiVs in this study.

  17. Plasma membrane phosphatidylinositol 4,5 bisphosphate is required for internalization of foot-and-mouth disease virus and vesicular stomatitis virus.

    Directory of Open Access Journals (Sweden)

    Angela Vázquez-Calvo

    Full Text Available Phosphatidylinositol-4,5-bisphosphate, PI(4,5P(2, is a phospholipid which plays important roles in clathrin-mediated endocytosis. To investigate the possible role of this lipid on viral entry, two viruses important for animal health were selected: the enveloped vesicular stomatitis virus (VSV - which uses a well characterized clathrin mediated endocytic route - and two different variants of the non-enveloped foot-and-mouth disease virus (FMDV with distinct receptor specificities. The expression of a dominant negative dynamin, a PI(4,5P(2 effector protein, inhibited the internalization and infection of VSV and both FMDV isolates. Depletion of PI(4,5P(2 from plasma membrane using ionomycin or an inducible system, and inhibition of its de novo synthesis with 1-butanol revealed that VSV as well as FMDV C-S8c1, which uses integrins as receptor, displayed a high dependence on PI(4,5P(2 for internalization. Expression of a kinase dead mutant (KD of phosphatidylinositol-4-phosphate-5-kinase Iα (PIP5K-Iα, an enzyme responsible for PI(4,5P(2 synthesis that regulates clathrin-dependent endocytosis, also impaired entry and infection of VSV and FMDV C-S8c1. Interestingly FMDV MARLS variant that uses receptors other than integrins for cell entry was less sensitive to PI(4,5P(2 depletion, and was not inhibited by the expression of the KD PIP5K-Iα mutant suggesting the involvement of endocytic routes other than the clathrin-mediated on its entry. These results highlight the role of PI(4,5P(2 and PIP5K-Iα on clathrin-mediated viral entry.

  18. Egg sampling as a possible alternative to blood sampling when monitoring the exposure of yellow-legged gulls (Larus michahellis) to avian influenza viruses.

    Science.gov (United States)

    Hammouda, Abdessalem; Pearce-Duvet, Jessica; Boulinier, Thierry; Selmi, Slaheddine

    2014-01-01

    We explored whether antibody detection in egg yolks could serve as an alternative to antibody detection in plasma samples when monitoring yellow-legged gulls (Larus michahellis) for exposure to avian influenza viruses (AIVs). We tested female plasma and eggs for anti-AIV antibodies and used the data we obtained to check whether the two sample types yielded the same antibody status (positive or negative) and to compare the antibody prevalence estimated from the blood data with that estimated from the yolk data. Our results showed that sampling one egg per clutch, regardless of that egg's position in the laying sequence, is sufficient to provide an unbiased estimate of antibody prevalence across clutches. The results also showed that almost 25% of the clutches laid by positive females contained only antibody-negative eggs, which suggests that yolk samples might underestimate female antibody prevalence. However, this result may stem from differences in the methods used to assess plasma versus yolk antibody status. Further research is needed to clarify this issue; while the number of false negatives could be reduced by adapting antibody detection techniques, it may be that they are an unavoidable consequence of natural avian maternal transfer dynamics.

  19. Testing the Effect of Internal Genes Derived from a Wild-Bird-Origin H9N2 Influenza A Virus on the Pathogenicity of an A/H7N9 Virus

    Directory of Open Access Journals (Sweden)

    Wen Su

    2015-09-01

    Full Text Available Since 2013, avian influenza A(H7N9 viruses have diversified into multiple lineages by dynamically reassorting with other viruses, especially H9N2, in Chinese poultry. Despite concerns about the pandemic threat posed by H7N9 viruses, little is known about the biological properties of H7N9 viruses that may recruit internal genes from genetically distinct H9N2 viruses circulating among wild birds. Here, we generated 63 H7N9 reassortants derived from an avian H7N9 and a wild-bird-origin H9N2 virus. Compared with the wild-type parent, 25/63 reassortants had increased pathogenicity in mice. A reassortant containing PB1 of the H9N2 virus was highly lethal to mice and chickens but was not transmissible to guinea pigs by airborne routes; however, three substitutions associated with adaptation to mammals conferred airborne transmission to the virus. The emergence of the H7N9-pandemic reassortant virus highlights that continuous monitoring of H7N9 viruses is needed, especially at the domestic poultry/wild bird interface.

  20. Correlates of homophobia, transphobia, and internalized homophobia in gay or lesbian and heterosexual samples.

    Science.gov (United States)

    Warriner, Katrina; Nagoshi, Craig T; Nagoshi, Julie L

    2013-01-01

    This research assessed the correlates of homophobia and transphobia in heterosexual and homosexual individuals, based on a theory of different sources of perceived symbolic threat to social status. Compared to 310 heterosexual college students, a sample of 30 gay male and 30 lesbian college students scored lower on homophobia, transphobia, and religious fundamentalism. Mean gender differences were smaller for gay men and lesbians for homophobia, aggressiveness, benevolent sexism, masculinity, and femininity. Fundamentalism, right-wing authoritarianism, and hostile and benevolent sexism were correlated only with homophobia in lesbians, whereas fundamentalism and authoritarianism were correlated only with transphobia in gay men. Correlates of internalized homophobia were different than those found for homophobia and transphobia, which was discussed in terms of gender differences in threats to status based on sexual orientation versus gender identity.

  1. Social Distancing of Depressive and Panic Disorders in an International Sample of Social Work Students

    Directory of Open Access Journals (Sweden)

    Donna S. Wang

    2014-06-01

    Full Text Available : Using an international sample, this study examined what variables were associated with social distancing among social work students. A total of 1,042 students from seven universities in the United States, United Kingdom, and Australia participated in a cross-sectional paper and pencil survey that applied the Social Distancing Scale to case vignettes describing an individual with panic disorder or major depressive disorder. The results show that levels of social distancing were related to age, knowing someone with a mental illness, type of disorder, level of conservatism, race, country, professional interest in mental health, level of student, and sex. Overall, 16.8% of the variance was accounted for with these significant variables. Implications for social work education and future research are discussed.

  2. Parent discipline practices in an international sample: associations with child behaviors and moderation by perceived normativeness.

    Science.gov (United States)

    Gershoff, Elizabeth T; Grogan-Kaylor, Andrew; Lansford, Jennifer E; Chang, Lei; Zelli, Arnaldo; Deater-Deckard, Kirby; Dodge, Kenneth A

    2010-01-01

    This study examined the associations of 11 discipline techniques with children's aggressive and anxious behaviors in an international sample of mothers and children from 6 countries and determined whether any significant associations were moderated by mothers' and children's perceived normativeness of the techniques. Participants included 292 mothers and their 8- to 12-year-old children living in China, India, Italy, Kenya, Philippines, and Thailand. Parallel multilevel and fixed effects models revealed that mothers' use of corporal punishment, expressing disappointment, and yelling were significantly related to more child aggression symptoms, whereas giving a time-out, using corporal punishment, expressing disappointment, and shaming were significantly related to greater child anxiety symptoms. Some moderation of these associations was found for children's perceptions of normativeness.

  3. Parent Discipline Practices in an International Sample: Associations With Child Behaviors and Moderation by Perceived Normativeness

    Science.gov (United States)

    Gershoff, Elizabeth T.; Grogan-Kaylor, Andrew; Lansford, Jennifer E.; Chang, Lei; Zelli, Arnaldo; Deater-Deckard, Kirby; Dodge, Kenneth A.

    2010-01-01

    This study examined the associations of 11 discipline techniques with children's aggressive and anxious behaviors in an international sample of mothers and children from 6 countries and determined whether any significant associations were moderated by mothers’ and children's perceived normativeness of the techniques. Participants included 292 mothers and their 8- to 12-year-old children living in China, India, Italy, Kenya, Philippines, and Thailand. Parallel multilevel and fixed effects models revealed that mothers’ use of corporal punishment, expressing disappointment, and yelling were significantly related to more child aggression symptoms, whereas giving a time out, using corporal punishment, expressing disappointment, and shaming were significantly related to greater child anxiety symptoms. Some moderation of these associations was found for children's perceptions of normativeness. PMID:20438455

  4. The Relationship between Motor Skills, Perceived Social Support, and Internalizing Problems in a Community Adolescent Sample

    Directory of Open Access Journals (Sweden)

    Vincent Oreste Mancini

    2016-04-01

    Full Text Available Objectives: Poor motor skills are associated with a range of psychosocial consequences, including internalizing (anxious and depressive symptoms. The Elaborated Environmental Stress Hypothesis provides a causal framework to explain this association. The framework posits that motor skills impact internalizing problems through an indirect effect via perceived social support. However, empirical evaluation is required. We examined whether motor skills has an indirect effect on anxious and depressive symptoms via perceived family support domains. Methods: This study used a community sample of 93 adolescents (12-16 years. Participants completed measures of motor skills, perceived social support across three dimensions (family, friend, and significant other, depressive symptoms, and anxious symptoms. Age, gender, verbal IQ, and ADHD symptoms were included as control variables.Results: Regression analysis using PROCESS revealed that motor skills had an indirect effect on depressive symptoms via perceived family support, but not by perceived friend support or significant other support. The negative association between motor skills and anxious symptoms was not mediated by any perceived social support domain. Conclusions: Findings are consistent with previous literature indicating an association between motor skills and internalizing problems. However, we identified a different pattern of relationships across anxious and depressive symptoms. While anxiety and depressive symptoms were highly correlated, motor skills had an indirect effect on depressive symptoms via perceived family support only. Our findings highlight the importance of family support as a potential protective factor in the onset of depressive symptoms. This study provides partial support for the Elaborated Environmental Stress Hypothesis, however further research is required.

  5. Factor Structure, Internal Consistency, and Screening Sensitivity of the GARS-2 in a Developmental Disabilities Sample

    Directory of Open Access Journals (Sweden)

    Martin A. Volker

    2016-01-01

    Full Text Available The Gilliam Autism Rating Scale-Second Edition (GARS-2 is a widely used screening instrument that assists in the identification and diagnosis of autism. The purpose of this study was to examine the factor structure, internal consistency, and screening sensitivity of the GARS-2 using ratings from special education teaching staff for a sample of 240 individuals with autism or other significant developmental disabilities. Exploratory factor analysis yielded a correlated three-factor solution similar to that found in 2005 by Lecavalier for the original GARS. Though the three factors appeared to be reasonably consistent with the intended constructs of the three GARS-2 subscales, the analysis indicated that more than a third of the GARS-2 items were assigned to the wrong subscale. Internal consistency estimates met or exceeded standards for screening and were generally higher than those in previous studies. Screening sensitivity was .65 and specificity was .81 for the Autism Index using a cut score of 85. Based on these findings, recommendations are made for instrument revision.

  6. Histological and Transcriptomic Analysis of Adult Japanese Medaka Sampled Onboard the International Space Station.

    Directory of Open Access Journals (Sweden)

    Yasuhiko Murata

    Full Text Available To understand how humans adapt to the space environment, many experiments can be conducted on astronauts as they work aboard the Space Shuttle or the International Space Station (ISS. We also need animal experiments that can apply to human models and help prevent or solve the health issues we face in space travel. The Japanese medaka (Oryzias latipes is a suitable model fish for studying space adaptation as evidenced by adults of the species having mated successfully in space during 15 days of flight during the second International Microgravity Laboratory mission in 1994. The eggs laid by the fish developed normally and hatched as juveniles in space. In 2012, another space experiment ("Medaka Osteoclast" was conducted. Six-week-old male and female Japanese medaka (Cab strain osteoblast transgenic fish were maintained in the Aquatic Habitat system for two months in the ISS. Fish of the same strain and age were used as the ground controls. Six fish were fixed with paraformaldehyde or kept in RNA stabilization reagent (n = 4 and dissected for tissue sampling after being returned to the ground, so that several principal investigators working on the project could share samples. Histology indicated no significant changes except in the ovary. However, the RNA-seq analysis of 5345 genes from six tissues revealed highly tissue-specific space responsiveness after a two-month stay in the ISS. Similar responsiveness was observed among the brain and eye, ovary and testis, and the liver and intestine. Among these six tissues, the intestine showed the highest space response with 10 genes categorized as oxidation-reduction processes (gene ontogeny term GO:0055114, and the expression levels of choriogenin precursor genes were suppressed in the ovary. Eleven genes including klf9, klf13, odc1, hsp70 and hif3a were upregulated in more than four of the tissues examined, thus suggesting common immunoregulatory and stress responses during space adaptation.

  7. Exploring the concurrent presence of hepatitis A virus genome in serum, stool, saliva, and urine samples of hepatitis A patients.

    Science.gov (United States)

    Joshi, Madhuri S; Bhalla, Shilpa; Kalrao, Vijay R; Dhongade, Ramchandra K; Chitambar, Shobha D

    2014-04-01

    The use of saliva and urine as an alternative to serum samples for detection of anti-hepatitis A virus (HAV) IgM antibodies has been documented. However, these samples remain underreported or unexplored for shedding of HAV. To address this issue, paired serum, stool, saliva, and urine samples collected from hepatitis A patients were screened by reverse transcription polymerase chain reaction for detection of HAV RNA. HAV RNA was detected in 67.6% (44/65), 52.3% (34/65), 8.7% (5/57), and 12.3% (8/65) of the serum, stool, saliva, and urine samples, respectively. Phylogenetic analysis of nucleotide sequences obtained for partial RNA polymerase region grouped HAV strains from all of the clinical samples of the study in subgenotype IIIA. Low frequency of HAV nucleic acid in saliva and urine samples indicates limited utility of these samples in genomic studies on HAV but suggests its potential for transmission and infection of hepatitis A. Copyright © 2014 Elsevier Inc. All rights reserved.

  8. Direct polymerase chain reaction from blood and tissue samples for rapid diagnosis of bovine leukemia virus infection.

    Science.gov (United States)

    Nishimori, Asami; Konnai, Satoru; Ikebuchi, Ryoyo; Okagawa, Tomohiro; Nakahara, Ayako; Murata, Shiro; Ohashi, Kazuhiko

    2016-06-01

    Bovine leukemia virus (BLV) infection induces bovine leukemia in cattle and causes significant financial harm to farmers and farm management. There is no effective therapy or vaccine; thus, the diagnosis and elimination of BLV-infected cattle are the most effective method to eradicate the infection. Clinical veterinarians need a simpler and more rapid method of diagnosing infection, because both nested polymerase chain reaction (PCR) and real-time PCR are labor intensive, time-consuming, and require specialized molecular biology techniques and expensive equipment. In this study, we describe a novel PCR method for amplifying the BLV provirus from whole blood, thus eliminating the need for DNA extraction. Although the sensitivity of PCR directly from whole blood (PCR-DB) samples as measured in bovine blood containing BLV-infected cell lines was lower than that of nested PCR, the PCR-DB technique showed high specificity and reproducibility. Among 225 clinical samples, 49 samples were positive by nested PCR, and 37 samples were positive by PCR-DB. There were no false positive samples; thus, PCR-DB sensitivity and specificity were 75.51% and 100%, respectively. However, the provirus loads of the samples detected by nested PCR and not PCR-DB were quite low. Moreover, PCR-DB also stably amplified the BLV provirus from tumor tissue samples. PCR-DB method exhibited good reproducibility and excellent specificity and is suitable for screening of thousands of cattle, thus serving as a viable alternative to nested PCR and real-time PCR.

  9. Hepatitis B virus DNA stability in plasma samples under short-term storage at 42°C

    Directory of Open Access Journals (Sweden)

    R.W. de Almeida

    2015-06-01

    Full Text Available We evaluated the stability of hepatitis B virus (HBV DNA in plasma samples stored at 42°C for external quality assessment (EQA panels of viral load. To assess the stability of plasma samples containing different concentrations of HBV DNA, serial dilutions of HBV-infected samples with a viral load of 6.40 log(10 IU/mL were made to yield viral loads of 5, 4, and 3 log(10 IU/mL. These were incubated at 42°C for up to 7 days and then frozen at -70°C. Viral load testing for HBV DNA was performed for all samples using COBAS¯ AmpliPrep/COBAS¯ TaqMan¯ HBV Test (v.2.0, Roche, Switzerland. Results were compared with fresh frozen plasma samples as a benchmark to establish acceptable measurements on the days following sample collection. Although the results of this study demonstrated a decrease in HBV DNA viral load ranging from 0.005 to 0.30 log(10 IU/mL after storage at 42°C for up to 7 days, these values did not exceed 0.5 log(10, which is the estimated intra-assay variation for molecular tests. Thus, the insignificant decrease in viral load suggests that shipment of HBV in plasma samples at temperatures of up to 42°C is permissible if they are frozen within 7 days.

  10. Sample Selectivity and the Validity of International Student Achievement Tests in Economic Research. NBER Working Paper No. 15867

    Science.gov (United States)

    Hanushek, Eric A.; Woessmann, Ludger

    2010-01-01

    Critics of international student comparisons argue that results may be influenced by differences in the extent to which countries adequately sample their entire student populations. In this research note, we show that larger exclusion and non-response rates are related to better country average scores on international tests, as are larger…

  11. The picornavirus avian encephalomyelitis virus possesses a hepatitis C virus-like internal ribosome entry site element

    DEFF Research Database (Denmark)

    Bakhshesh, M.; Groppelli, E.; Willcocks, M.A.

    2008-01-01

    evidence that the 494-nucleotide-long 5' untranslated region of the AEV genome contains an internal ribosome entry site (IRES) element that functions efficiently in vitro and in mammalian cells. Unlike the HAV IRES, the AEV IRES is relatively short and functions in the presence of cleaved eIF4G...

  12. Identification of an internal RNA element essential for replication and translational enhancement of tobacco necrosis virus A(C.

    Directory of Open Access Journals (Sweden)

    Heng Pu

    Full Text Available Different regulatory elements function are involved in plant virus gene expression and replication by long-distance RNA-RNA interactions. A cap-independent functional element of the Barley yellow dwarf virus (BYDV - like translational enhancer (BTE is present in Tobacco necrosis virus A (TNV-A, a Necrovirus member in the Tombusviridae family. In this paper, an RNA stretch flanking the 5' proximal end of the TNV-A(C coat protein (CP gene was shown to be essential for viral replication in Chenopodium amaranticolor plants and tobacco cells. This internal sequence functioned in transient expression of β-glucuronidase (GUS when present at either the 5' or 3' sides of the GUS open reading frame. Serial deletion analyses revealed that nine nucleotides from nt 2609 to 2617 (-3 to +6 of the CP initiation site within TNV-A(C RNA are indispensable for viral replication in whole plants and tobacco cells. Fusion of this RNA element in mRNAs translated in tobacco cells resulted in a remarkable enhancement of luciferase expression from in vitro synthesised chimaeric RNAs or DNA expression vectors. Interestingly, the element also exhibited increased translational activity when fused downstream of the reporter genes, although the efficiency was lower than with upstream fusions. These results provide evidence that an internal RNA element in the genomic (g RNA of TNV-A(C, ranging approximately from nt 2543 to 2617, plays a bifunctional role in viral replication and translation enhancement during infection, and that this element may use novel strategies differing from those previously reported for other viruses.

  13. Sampling

    CERN Document Server

    Thompson, Steven K

    2012-01-01

    Praise for the Second Edition "This book has never had a competitor. It is the only book that takes a broad approach to sampling . . . any good personal statistics library should include a copy of this book." —Technometrics "Well-written . . . an excellent book on an important subject. Highly recommended." —Choice "An ideal reference for scientific researchers and other professionals who use sampling." —Zentralblatt Math Features new developments in the field combined with all aspects of obtaining, interpreting, and using sample data Sampling provides an up-to-date treat

  14. Molecular detection of mixed infections with multiple dengue virus serotypes in suspected dengue samples in Tamaulipas, Mexico

    Directory of Open Access Journals (Sweden)

    Rocío Requena-Castro

    Full Text Available This study aimed to detect dengue virus (DENV serotypes in serum samples obtained in Matamoros Tamaulipas, Mexico, and to determine the concordance of conventional nested reverse transcriptase polymerase chain reaction (RT-PCR and a serological test [enzyme-linked immunosorbent assay (ELISA NS1]. Here, we detected mixed infections consisting of four serotypes of DENV. The most prevalent serotype was DENV-1, followed by DENV-4. This is the first report of DENV-4 in our region. Mixed infections were also detected in 21.5% of samples, and the predominant coinfection consisted of DENV-1 and DENV-2. Therefore, continuous epidemiological surveillance of DENV in this area is required to predict future forms of dengue heterologous infections and the effect of this on health care.

  15. Molecular detection of mixed infections with multiple dengue virus serotypes in suspected dengue samples in Tamaulipas, Mexico.

    Science.gov (United States)

    Requena-Castro, Rocío; Reyes-López, Miguel Ángel; Rodríguez-Reyna, Rosa Eminé; Palma-Nicolás, Prisco; Bocanegra-García, Virgilio

    2017-07-01

    This study aimed to detect dengue virus (DENV) serotypes in serum samples obtained in Matamoros Tamaulipas, Mexico, and to determine the concordance of conventional nested reverse transcriptase polymerase chain reaction (RT-PCR) and a serological test [enzyme-linked immunosorbent assay (ELISA NS1)]. Here, we detected mixed infections consisting of four serotypes of DENV. The most prevalent serotype was DENV-1, followed by DENV-4. This is the first report of DENV-4 in our region. Mixed infections were also detected in 21.5% of samples, and the predominant coinfection consisted of DENV-1 and DENV-2. Therefore, continuous epidemiological surveillance of DENV in this area is required to predict future forms of dengue heterologous infections and the effect of this on health care.

  16. Hepatitis C virus and GBV-C virus prevalence among patients with B-cell lymphoma in different European regions: a case-control study of the International Extranodal Lymphoma Study Group.

    Science.gov (United States)

    Nicolosi Guidicelli, Sabrina; Lopez-Guillermo, Armando; Falcone, Umberto; Conconi, Annarita; Christinat, Alexandre; Rodriguez-Abreu, Delvys; Grisanti, Salvatore; Lobetti-Bodoni, Chiara; Piffaretti, Jean Claude; Johnson, Peter W; Mombelli, Giorgio; Cerny, Andreas; Montserrat, Emili; Cavalli, Franco; Zucca, Emanuele

    2012-09-01

    Hepatitis C virus (HCV) infection is associated with some B-cell non-Hodgkin lymphoma (B cell-NHLs). Patients with HCV infection frequently show co-infections with GB virus C (GBV-C, formerly known as hepatitis G virus), and some studies have suggested a higher incidence of GBV-C infection in patients with B cell-NHLs. The aim of this study was to prospectively evaluate the association between HCV and/or GBV-C infection and B cell-NHLs in different geographic areas. One hundred thirty-seven lymphoma cases and 125 non-lymphoma matched controls were enrolled in an international case-control study conducted in Switzerland (Bellinzona), Spain (Barcelona) and England (Southampton) on samples collected from 2001 to 2002. In Bellinzona (41 cases and 81 controls), the overall prevalence of HCV was 3.3% (4.9% in NHLs), and the overall prevalence of GBV-C was 24% (22% in NHLs). In Barcelona (46 cases and 44 controls), the prevalence of HCV was 10% (8.7% in NHLs) and the prevalence of GBV-C 20% (13% in NHLs). There was no statistically significant difference in the frequency of both infections between patients with NHL and controls. In Southampton, 50 NHL cases were analysed, none of them was found to be HCV-positive; therefore, no control group was analysed and GBV-C analysis was not performed, too. Both in Bellinzona and in Barcelona, the seropositivity rate was significantly lower for HCV than for GBV-C, suggesting that their transmission can be independent. The incidence of HCV was significantly higher in Barcelona than that in Bellinzona. This study confirmed the existence of marked geographic differences in the prevalence of HCV in NHL but cannot provide any significant evidence for an association between HCV and/or GBV-C and B-cell NHLs. Copyright © 2011 John Wiley & Sons, Ltd.

  17. Molecular detection and nucleotide sequence analysis of a new Aichi virus closely related to canine kobuvirus in sewage samples.

    Science.gov (United States)

    Yamashita, Teruo; Adachi, Hirokazu; Hirose, Emi; Nakamura, Noriko; Ito, Miyabi; Yasui, Yoshihiro; Kobayashi, Shinichi; Minagawa, Hiroko

    2014-05-01

    Between 2001 and 2005, 207 raw sewage samples were collected at the inflow of a sewage treatment plant in Aichi Prefecture, Japan. Of the 207 sewage samples, 137 (66.2 %) were found to be positive for amplification of Aichi virus (AiV) nucleotide using reverse transcription (RT)-PCR with 10 forward and 10 reverse primers in the 3D region corresponding to the nucleotide sequence of all kobuviruses. AiV genotype A sequences were detected in all 137 samples. New sequences of AiV were detected in nine samples, exhibiting 83 % similarity with AiV A846/88, but 95 % similarity with canine kobuvirus (CKV) US-PC0082 in this region. The nucleotide sequences from the VP3 region to the 3' untranslated region (UTR) of sewage sample Y12/2004 were determined. The number of nucleotides in each region was the same as that of CKV. The similarity of the nucleotide (amino acid) identity of a complete VP1 region was 90.5 % (94.8 %) between Y12/2004 and CKV US-PC0082. The phylogenic analyses based on the nucleotide and the deduced amino acid sequences of VP1 and 3D showed that Y12/2004 was independent from AiV, but closely related to CKV. These results suggested that CKV is present in Aichi Prefecture, Japan.

  18. Rapid detection and subtyping of European swine influenza viruses in porcine clinical samples by haemagglutinin- and neuraminidase-specific tetra- and triplex real-time RT-PCRs

    DEFF Research Database (Denmark)

    Henritzi, Dinah; Zhao, Na; Starick, Elke

    2016-01-01

    Background A diversifying pool of mammalian-adapted influenza A viruses (IAV) with largely unknown zoonotic potential is maintained in domestic swine populations worldwide. The most recent human influenza pandemic in 2009 was caused by a virus with genes originating from IAV isolated from swine....... Swine influenza viruses (SIV) are widespread in European domestic pig populations and evolve dynamically. Knowledge regarding occurrence, spread and evolution of potentially zoonotic SIV in Europe is poorly understood. Objectives Efficient SIV surveillance programmes depend on sensitive and specific...... algorithm is proposed for the combined detection in clinical samples and subtyping of SIV strains currently circulating in Europe that is based on a generic, M-gene-specific influenza A virus RT-qPCR. In a second step, positive samples are examined by tetraplex HA- and triplex NA-specific RT...

  19. Influenza virus isolation.

    Science.gov (United States)

    Krauss, Scott; Walker, David; Webster, Robert G

    2012-01-01

    The isolation of influenza viruses is important for the diagnosis of respiratory diseases in lower animals and humans, for the detection of the infecting agent in surveillance programs, and is an essential element in the development and production of vaccine. Since influenza is caused by a zoonotic virus it is necessary to do surveillance in the reservoir species (aquatic waterfowls), intermediate hosts (quails, pigs), and in affected mammals including humans. Two of the hemagglutinin (HA) subtypes of influenza A viruses (H5 and H7) can evolve into highly pathogenic (HP) strains for gallinaceous poultry; some HP H5 and H7 strains cause lethal infection of humans. In waterfowls, low pathogenic avian influenza (LPAI) isolates are obtained primarily from the cloaca (or feces); in domestic poultry, the virus is more often recovered from the respiratory tract than from cloacal samples; in mammals, the virus is most often isolated from the respiratory tract, and in cases of high pathogenic avian influenza (HPAI) from the blood and internal organs of infected birds. Virus isolation procedures are performed by inoculation of clinical specimens into embryonated eggs (primarily chicken eggs) or onto a variety of primary or continuous tissue culture systems. Successful isolation of influenza virus depends on the quality of the sample and matching the appropriate culture method to the sample type.

  20. The Ras-PI3K signaling pathway is involved in clathrin-independent endocytosis and the internalization of influenza viruses.

    Directory of Open Access Journals (Sweden)

    Yoichiro Fujioka

    Full Text Available BACKGROUND: Influenza virus infection causes highly contagious, severe respiratory disorders and gives rise to thousands of deaths every year; however, the efficacy of currently approved defense strategies, including vaccines and neuraminidase inhibitors, is limited because the virus frequently acquires resistance via antigen drift and reassortment. It is therefore important to establish a novel, effective therapeutic strategy that is effective irrespective of viral subtype. METHODOLOGY/PRINCIPAL FINDINGS: Here, we identify the Ras-phosphoinositide 3-kinase (PI3K signaling pathway as a host-cell regulatory mechanism for influenza virus entry. The binding of Ras to PI3K is specifically involved in clathrin-independent endocytosis, endosomal maturation, and intracellular transport of viruses, which result in decreased infectious efficacy of different subtypes of influenza viruses in cells lacking the Ras-PI3K interaction. Moreover, influenza virus infection indeed triggered Ras activation and subsequent PI3K activation in early endosomes. CONCLUSIONS/SIGNIFICANCE: Taken together, these results demonstrate that the Ras-PI3K signaling axis acts as a host-oriented mechanism for viral internalization. Given that virus incorporation is a process conserved among virus subtypes and species, this signaling pathway may provide a target for potent, well-tolerated prophylactics and therapeutics against a broad range of viruses.

  1. A Sequence-Independent, Unstructured Internal Ribosome Entry Site Is Responsible for Internal Expression of the Coat Protein of Turnip Crinkle Virus.

    Science.gov (United States)

    May, Jared; Johnson, Philip; Saleem, Huma; Simon, Anne E

    2017-04-15

    To maximize the coding potential of viral genomes, internal ribosome entry sites (IRES) can be used to bypass the traditional requirement of a 5' cap and some/all of the associated translation initiation factors. Although viral IRES typically contain higher-order RNA structure, an unstructured sequence of about 84 nucleotides (nt) immediately upstream of the Turnip crinkle virus (TCV) coat protein (CP) open reading frame (ORF) has been found to promote internal expression of the CP from the genomic RNA (gRNA) both in vitro and in vivo An absence of extensive RNA structure was predicted using RNA folding algorithms and confirmed by selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) RNA structure probing. Analysis of the IRES region in vitro by use of both the TCV gRNA and reporter constructs did not reveal any sequence-specific elements but rather suggested that an overall lack of structure was an important feature for IRES activity. The CP IRES is A-rich, independent of orientation, and strongly conserved among viruses in the same genus. The IRES was dependent on eIF4G, but not eIF4E, for activity. Low levels of CP accumulated in vivo in the absence of detectable TCV subgenomic RNAs, strongly suggesting that the IRES was active in the gRNA invivo Since the TCV CP also serves as the viral silencing suppressor, early translation of the CP from the viral gRNA is likely important for countering host defenses. Cellular mRNA IRES also lack extensive RNA structures or sequence conservation, suggesting that this viral IRES and cellular IRES may have similar strategies for internal translation initiation.IMPORTANCE Cap-independent translation is a common strategy among positive-sense, single-stranded RNA viruses for bypassing the host cell requirement of a 5' cap structure. Viral IRES, in general, contain extensive secondary structure that is critical for activity. In contrast, we demonstrate that a region of viral RNA devoid of extensive secondary

  2. Gender and Direction of Effect of Alcohol Problems and Internalizing Symptoms in a Longitudinal Sample of College Students.

    Science.gov (United States)

    Homman, Lina E; Edwards, Alexis C; Cho, Seung Bin; Dick, Danielle M; Kendler, Kenneth S

    2017-03-21

    Alcohol problems and internalizing symptoms are consistently found to be associated but how they relate to each other is unclear. The present study aimed to address limitations in the literature of comorbidity of alcohol problems and internalizing symptoms by investigating the direction of effect between the phenotypes and possible gender differences in college students. We utilized data from a large longitudinal study of college students from the United States (N = 2607). Three waves of questionnaire-based data were collected over the first two years of college (in 2011-2013). Cross-lagged models were applied to examine the possible direction of effect of internalizing symptoms and alcohol problems. Possible effects of gender were investigated using multigroup modeling. There were significant correlations between alcohol problems and internalizing symptoms. A direction of effect was found between alcohol problems and internalizing symptoms but differed between genders. A unidirectional relationship varying with age was identified for males where alcohol problems initially predicted internalizing symptoms followed by internalizing symptoms predicting alcohol problems. For females, a unidirectional relationship existed wherein alcohol problems predicted internalizing symptoms. Conclusions/Importance: We conclude that the relationship between alcohol problems and internalizing symptoms is complex and differ between genders. In males, both phenotypes are predictive of each other, while in females the relationship is driven by alcohol problems. Importantly, our study examines a population-based sample, revealing that the observed relationships between alcohol problems and internalizing symptoms are not limited to individuals with clinically diagnosed mental health or substance use problems.

  3. Detection of African Swine Fever Virus DNA in Blood Samples Stored on FTA Cards from Asymptomatic Pigs in Mbeya Region, Tanzania

    DEFF Research Database (Denmark)

    Braae, U. C.; Johansen, M. V.; Ngowi, H. A.

    2015-01-01

    The aim of the study was to assess whether blood samples collected onto FTA® cards could be used in combination with real-time PCR for the detection of African swine fever virus (ASFV) DNA in samples from resource-poor settings under the assumption that asymptomatically (sub-clinically) infected ...

  4. Sampling of sea ducks for influenza A viruses in Alaska during winter provides lack of evidence for epidemiological peak of infection.

    Science.gov (United States)

    Ramey, Andy M.; Reeves, Andrew B.; Poulson, Rebecca L.; Wasley, Jeff; Esler, Daniel N.; Stalknecht, David E.

    2015-01-01

    Sampling of sea ducks for influenza A viruses in Alaska during winter provided no evidence for an epidemiologic peak of infection. Isolates were recovered, however, that provide information on viral diversity and dispersal that may not be realized through sampling efforts focused on other avian taxa.

  5. Modulation of Cytokine mRNA Expression in Pharyngeal Epithelial Samples obtained from Cattle Infected with Foot-and-Mouth Disease Virus

    DEFF Research Database (Denmark)

    Stenfeldt, Anna Carolina; Heegaard, Peter M. H.; Stockmarr, Anders

    2012-01-01

    A novel technique of endoscopical collection of small tissue samples was used to obtain sequential tissue samples from the dorsal soft palate (DSP) of individual cattle infected with foot-and-mouth disease virus (FMDV) at different phases of the infection. Levels of mRNA encoding interferon (IFN...

  6. Detection of infectious spleen and kidney necrosis virus (ISKNV) and turbot reddish body iridovirus (TRBIV) from archival ornamental fish samples.

    Science.gov (United States)

    Go, J; Waltzek, T B; Subramaniam, K; Yun, S C; Groff, J M; Anderson, I G; Chong, R; Shirley, I; Schuh, J C L; Handlinger, J H; Tweedie, A; Whittington, R J

    2016-12-21

    Although infections caused by megalocytiviruses have been reported from a wide range of finfish species for several decades, molecular characterisation of the viruses involved has been undertaken only on more recent cases. Sequence analysis of the major capsid protein and adenosine triphosphatase genes is reported here from formalin-fixed, paraffin-embedded material from 2 archival ornamental fish cases from 1986 and 1988 in conjunction with data for a range of genes from fresh frozen tissues from 5 cases obtained from 1991 through to 2010. Turbot reddish body iridovirus (TRBIV) genotype megalocytiviruses, previously not documented in ornamental fish, were detected in samples from 1986, 1988 and 1991. In contrast, megalocytiviruses from 1996 onwards, including those characterised from 2002, 2006 and 2010 in this study, were almost indistinguishable from infectious spleen and kidney necrosis virus (ISKNV). Three of the species infected with TRBIV-like megalocytiviruses from 1986 to 1991, viz. dwarf gourami Trichogaster lalius (formerly Colisa lalia), freshwater angelfish Pterophyllum scalare and oscar Astronotus ocellatus, were infected with ISKNV genotype megalocytiviruses from 2002 to 2010. The detection of a TRBIV genotype isolate in ornamental fish from 1986 represents the index case, confirmed by molecular sequence data, for the genus Megalocytivirus.

  7. The mediating role of internalized racism in the relationship between racist experiences and anxiety symptoms in a Black American sample.

    Science.gov (United States)

    Graham, Jessica R; West, Lindsey M; Martinez, Jennifer; Roemer, Lizabeth

    2016-07-01

    The current study explores the potential mediating role of internalized racism in the relationship between racist experiences and anxiety symptomology in a Black American sample. One hundred and 73 Black American participants, between 18 and 62 years of age, completed a questionnaire packet containing measures of anxious arousal and stress symptoms, internalized racism, and experiences of racist events. Results indicated that internalized racism mediated the relationship between past-year frequency of racist events and anxious arousal as well as past-year frequency of racist events and stress symptoms. Internalized racism may be 1 mechanism that underlies the relationship between racism and anxious symptomology for Black Americans. These preliminary findings suggest that internalized racism may be an avenue through which clinicians can target the anxiety elicited by racist experiences. The clinical implications of these findings and future research directions are discussed. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

  8. Prevalence of xenotropic murine leukaemia virus-related virus in patients with chronic fatigue syndrome in the Netherlands: retrospective analysis of samples from an established cohort.

    NARCIS (Netherlands)

    Kuppeveld, F.J.M. van; Jong, A.S. de; Lanke, K.H.W.; Verhaegh, G.W.C.T.; Melchers, W.J.G.; Swanink, C.M.A.; Bleijenberg, G.; Netea, M.G.; Galama, J.M.D.; Meer, J.W.M. van der

    2010-01-01

    OBJECTIVE: The presence of the retrovirus xenotropic murine leukaemia virus-related virus (XMRV) has been reported in peripheral blood mononuclear cells of patients with chronic fatigue syndrome. Considering the potentially great medical and social relevance of such a discovery, we investigated

  9. Personal Digital Assistant-Based Self-Work Sampling Study of Pediatric Interns Quantifies Workday and Educational Value.

    Science.gov (United States)

    Campbell, Joyce K; Ortiz, Michael V; Ottolini, Mary C; Birch, Sarah; Agrawal, Dewesh

    2017-04-01

    Optimizing clinical proficiency and education of residents has become more important with restricted residency duty hours. Our objective was to investigate how interns spend their time on inpatient rotations and the perceived educational value of workday activities. We performed a descriptive self-work sampling study using a personal digital assistant (PDA) to randomly query interns on inpatient rotations in real time regarding their activity and the perceived educational value of that activity on a 4-point Likert scale. A total of 31 interns participated on 88 workdays over a 5-month period, generating 2082 samples from which the average workday was modeled. Time spent using the electronic health record (EHR) accounted for 33% of intern time, communicating with the health care team 23%, educational activities 17%, and time with patients and families 12%. Time with patients and families was perceived to be the most educational part of clinical service. Time spent using the EHR was perceived as the least educational. Interns perceived clinical service as excellent or good 37% of the time, while planned educational activities were perceived as excellent or good 81% of the time. Interns spend the majority of their time using the EHR and communicating with the health care team. Interns perceive time spent in planned educational activities has more educational value than time spent in clinical service. The distribution of daily activities is discordant with the perceived educational value of those activities. Copyright © 2016 Academic Pediatric Association. Published by Elsevier Inc. All rights reserved.

  10. Geographical distribution of hepatitis C virus genotypes in blood donors: an international collaborative survey.

    OpenAIRE

    McOmish, F; Yap, P L; Dow, B C; Follett, E A; Seed, C; Keller, A J; Cobain, T J; Krusius, T; Kolho, E; Naukkarinen, R; Lin, C.; Lai, C; Leong, S.; Medgyesi, G A; Hejjas, M

    1994-01-01

    The frequency of infection with the six classified major genotypes of hepatitis C virus (HCV) was investigated in 447 infected volunteer blood donors from the following nine countries: Scotland, Finland, The Netherlands, Hungary, Australia, Egypt, Japan, Hong Kong, and Taiwan. Viral sequences in plasma from blood donors infected with HCV were amplified in the 5'-noncoding region and were typed by restriction fragment length polymorphism analysis. Electrophoresis of DNA fragments produced by c...

  11. Correlates of internalized homophobia and homosexual identity formation in a sample of gay men.

    Science.gov (United States)

    Rowen, Christopher J; Malcolm, James P

    2002-01-01

    Eighty-six behaviourally homosexual men, at various stages of homosexual identity formation (HIF), were participants in a study that examined correlates of internalized homophobia (IH) and HIF. Results indicated higher levels of internalized homophobia were correlated with lower stages of HIF. In addition, internalized homophobia was significantly related to lower levels of self-esteem, to lower levels of self-concepts of physical appearance and emotional stability, and to higher levels of sex guilt. Post hoc regression analysis revealed that perceived level of repression against homosexuals predicted internalized homophobia and sex-guilt, which were mediator variables to the resolution of HIF. This research supports theory, that suggests internalized homophobia is a major developmental difficulty in gay men.

  12. Comparative Effectiveness of Dried-Plasma Hepatitis B Virus Viral Load (VL) Testing in Three Different VL Commercial Platforms Using ViveST for Sample Collection

    OpenAIRE

    Zanoni, Michelle; Giron, Leila B. [UNIFESP; Vilhena, Cintia; Sucupira, Maria Cecilia; Lloyd, Robert M.; Diaz, Ricardo Sobhie

    2012-01-01

    Ninety-six samples from hepatitis B virus (HBV)-infected individuals were used to compare ViveST samples to frozen samples in COBAS TaqMan, RealArt, and VERSANT. Correlation (r) between ViveST samples and frozen samples was 0.99 in all three platforms. Correlations among tests using frozen samples were 0.96 for COBAS and RealArt, 0.94 for COBAS and VERSANT, and 0.97 for VERSANT and RealArt. The results indicate that ViveST may be useful in clinical practice. Different HBV-VL platforms correla...

  13. Comparative effectiveness of dried-plasma hepatitis B virus viral load (VL) testing in three different VL commercial platforms using ViveST for sample collection.

    Science.gov (United States)

    Zanoni, Michelle; Giron, Leila B; Vilhena, Cintia; Sucupira, Maria Cecilia; Lloyd, Robert M; Diaz, Ricardo Sobhie

    2012-01-01

    Ninety-six samples from hepatitis B virus (HBV)-infected individuals were used to compare ViveST samples to frozen samples in COBAS TaqMan, RealArt, and VERSANT. Correlation (r) between ViveST samples and frozen samples was 0.99 in all three platforms. Correlations among tests using frozen samples were 0.96 for COBAS and RealArt, 0.94 for COBAS and VERSANT, and 0.97 for VERSANT and RealArt. The results indicate that ViveST may be useful in clinical practice. Different HBV-VL platforms correlated well with one another.

  14. IGSN at Geoscience Australia: implementation and promotion of international sample identifiers system to forster collaboration in Australia and beyond.

    Science.gov (United States)

    Bastrakova, I.; Car, N. J.

    2016-12-01

    The International Geo-Sample Number (IGSN) is a globally unique resolvable identifier for physical samples. It provides a mechanism for linking physical samples with analytical data derived from them and even related publications. Geoscience Australia (GA) is one of the largest Australian repositories of geoscientific samples and derived data. Since becoming an IGSN allocating agent in 2014, GA has put significant effort into adopting and promoting IGSN and its benefits internally and across Australia. Since August 2015, GA has registered 1,966,384 samples which represent approximately 1/3 of the international IGSN collection. GA supports the development of the Australian National Specimen Portal (ANSP) lead by the CSIRO aiming to enhance the discoverability of all Australian samples. GA is also collaborating with Curtin University in testing the assumptions of re-use of IGSN-registered sample metadata by linking GA samples with the new analytical data produced by the University. Future plans for GA include: implementing an IGSN minting service for Australian Geological Surveys; promoting wider IGSN use in Australia, particularly among universities; and integrating IGSN systems and metadata with Linked Data and Semantic Web systems including standardised vocabularies and ontologies. The IGSN project, given its standardised mechanisms and metadata and the collaborative way in which it is being conducted, enables a common approach across organisations in Australia for the unique identification and discovery of geoscience samples. It will bring physical sample identification and use into line with many electronic data initiatives allowing the standardised representation of information flows from samples through laboratory work and computation to publications.

  15. The microbial detection array for detection of emerging viruses in clinical samples--a useful panmicrobial diagnostic tool

    DEFF Research Database (Denmark)

    Rosenstierne, Maiken W; McLoughlin, Kevin S; Olesen, Majken Lindholm

    2014-01-01

    Emerging viruses are usually endemic to tropical and sub-tropical regions of the world, but increased global travel, climate change and changes in lifestyle are believed to contribute to the spread of these viruses into new regions. Many of these viruses cause similar disease symptoms as other...... emerging viruses or common infections, making these unexpected pathogens difficult to diagnose. Broad-spectrum pathogen detection microarrays containing probes for all sequenced viruses and bacteria can provide rapid identification of viruses, guiding decisions about treatment and appropriate case...... management. We report a modified Whole Transcriptome Amplification (WTA) method that increases unbiased amplification, particular of RNA viruses. Using this modified WTA method, we tested the specificity and sensitivity of the Lawrence Livermore Microbial Detection Array (LLMDA) against a wide range...

  16. Strategic Approach To Produce Low-Cost, Efficient, and Stable Competitive Internal Controls for Detection of RNA Viruses by Use of Reverse Transcription-PCR▿

    Science.gov (United States)

    Villanova, Gabriela V.; Gardiol, Daniela; Taborda, Miguel A.; Reggiardo, Virginia; Tanno, Hugo; Rivadeneira, Emilia D.; Perez, Germán R.; Giri, Adriana A.

    2007-01-01

    Molecular diagnostics based on reverse transcription (RT)-PCR are routinely complicated by the lack of stable internal controls, leading to falsely negative results. We describe a strategy to produce a stable competitive internal control (CIC) based on a Qβ phage derivative (recombinant Qβ [rQβ]) bearing primers KY78 and KY80, which are widely used in the detection of hepatitis C virus (HCV). rQβ was RNase resistant and stable at 4°C for 452 days in SM medium (0.1 M NaCl, 8 mM MgSO4·7H2O, 50 mM Tris HCl [pH 7.5], 2% gelatin) and for 125 days after lyophilization and reconstitution. rQβ performance as a CIC was evaluated. rQβ was added to HCV-positive samples, followed by RNA extraction and a CIC-HCV RT-PCR assay. This method combines RT-PCR, liquid hybridization with nonradioactive probes, and enzyme immunoanalysis. No influence of the CIC on qualitative HCV detection was observed independently of viral load, and results had high concordance with those of commercial kits. In conclusion, we describe a versatile, low-cost alternative strategy to armored RNA technology that can be adapted for detection or real-time applications of any RNA target. Moreover, the CIC reported here is an essential reagent for HCV screening in blood banks in resource-limited settings. PMID:17699653

  17. Parental internalizing problems in a community sample : association with child psychosocial problems

    NARCIS (Netherlands)

    Spijkers, Willem; Jansen, Danielle E. M. C.; Reijneveld, Sijmen A.

    Background: Offspring of depressed, anxious and stressed parents are at increased risk of developing mental disorders. However, most studies investigating this association concentrate on clinical symptoms. The objective of this study is to examine the association between parental internalizing

  18. TIMSS 2011 User Guide for the International Database. Supplement 4: TIMSS 2011 Sampling Stratification Information

    Science.gov (United States)

    Foy, Pierre, Ed.; Arora, Alka, Ed.; Stanco, Gabrielle M., Ed.

    2013-01-01

    This supplement contains documentation on the explicit and implicit stratification variables included in the TIMSS 2011 data files. The explicit strata are smaller sampling frames, created from the national sampling frames, from which national samples of schools were drawn. The implicit strata are nested within the explicit strata, and were used…

  19. A Confirmatory Factor Analysis of the Wong and Law Emotional Intelligence Scale in a Sample of International College Students

    Science.gov (United States)

    Ng, Kok-Mun; Wang, Chuang; Zalaquett, Carlos P.; Bodenhorn, Nancy

    2007-01-01

    There is the need for a reliable and valid measure to facilitate emotional intelligence (EI) research on international college students (ICSs). The present study examined the factorial invariance of the Wong and Law Emotional Intelligence Scale (WLEIS), a trait EI measure, in a sample of 628 ICSs. A web-based survey was developed to facilitate…

  20. Direct sample preparation methods for the detection of Plum pox virus by real-time RT-PCR.

    Science.gov (United States)

    Capote, Nieves; Bertolini, Edson; Olmos, Antonio; Vidal, Eduardo; Martínez, Maria Carmen; Cambra, Mariano

    2009-03-01

    Direct systems to process plant materials allowed high-throughput testing of Plum pox virus (PPV) by real-time reverse transcription (RT)-PCR without nucleic acids purification. Crude plant extracts were diluted in buffer or spotted on membranes to be used as templates. Alternatively, immobilized PPV targets were amplified from fresh sections of plant tissues printed or squashed onto the same supports, without extract preparation. Spot real-time RT-PCR was validated as a PPV diagnostic method in samples collected during the dormancy period and showed high sensitivity (93.6%), specificity (98.0%), and post-test probability (97.9%) towards sharka disease. In an analysis of 2919 Prunus samples by spot real-time RT-PCR and DASI-ELISA 90.8% of the results coincided, demonstrating high agreement (k = 0.77 +/- 0.01) between the two techniques. These results validate the use of immobilized PPV targets and spot real-time RT-PCR as screening method for largescale analyses.

  1. Parental bonds and body dissatisfaction in a clinical sample: The mediating roles of attachment anxiety and media internalization.

    Science.gov (United States)

    Grenon, Renee; Tasca, Giorgio A; Maxwell, Hilary; Balfour, Louise; Proulx, Genevieve; Bissada, Hany

    2016-12-01

    We evaluated an attachment theory model in which mother and father care were hypothesized to be indirectly related to body dissatisfaction mediated by attachment anxiety and media internalization. Participants were 232 women diagnosed with an eating disorder who completed a retrospective measure of parental bonds, and measures of attachment anxiety, media internalization, and body image. Mother care was negatively associated with body dissatisfaction, suggesting that recollection of mothers as less caring was directly related to poorer body image. Lower father care, was indirectly associated with greater body dissatisfaction mediated by higher attachment anxiety and higher media internalization. That is, women with an eating disorder who recollected fathers as less caring had higher attachment anxiety, which was related to greater internalizing of media-related thin ideals, that in turn was associated with poorer body image. Mothers and fathers may impact body dissatisfaction by differing mechanisms in clinical samples. Copyright © 2016 Elsevier Ltd. All rights reserved.

  2. Influenza virus drug resistance: a time-sampled population genetics perspective.

    Directory of Open Access Journals (Sweden)

    Matthieu Foll

    2014-02-01

    Full Text Available The challenge of distinguishing genetic drift from selection remains a central focus of population genetics. Time-sampled data may provide a powerful tool for distinguishing these processes, and we here propose approximate Bayesian, maximum likelihood, and analytical methods for the inference of demography and selection from time course data. Utilizing these novel statistical and computational tools, we evaluate whole-genome datasets of an influenza A H1N1 strain in the presence and absence of oseltamivir (an inhibitor of neuraminidase collected at thirteen time points. Results reveal a striking consistency amongst the three estimation procedures developed, showing strongly increased selection pressure in the presence of drug treatment. Importantly, these approaches re-identify the known oseltamivir resistance site, successfully validating the approaches used. Enticingly, a number of previously unknown variants have also been identified as being positively selected. Results are interpreted in the light of Fisher's Geometric Model, allowing for a quantification of the increased distance to optimum exerted by the presence of drug, and theoretical predictions regarding the distribution of beneficial fitness effects of contending mutations are empirically tested. Further, given the fit to expectations of the Geometric Model, results suggest the ability to predict certain aspects of viral evolution in response to changing host environments and novel selective pressures.

  3. Rapid detection of cytomegalovirus in bronchoalveolar lavage fluid and serum samples by polymerase chain reaction: correlation of virus isolation and clinical outcome for patients with human immunodeficiency virus infection

    DEFF Research Database (Denmark)

    Hansen, K K; Vestbo, Jørgen; Benfield, T

    1997-01-01

    Bronchoalveolar lavage (BAL) fluids and serum samples from 153 patients with pulmonary symptoms who were infected with human immunodeficiency virus (HIV) and underwent BAL were examined for the presence of cytomegalovirus (CMV) by conventional culture and by polymerase chain reaction (PCR...

  4. Detection and Partial Characterization of Simian Immunodeficiency Virus SIVsm Strains from Bush Meat Samples from Rural Sierra Leone

    OpenAIRE

    Apetrei, Cristian; Metzger, Michael J.; Richardson, David; Ling, Binhua; Telfer, Paul T.; Reed, Patricia; Robertson, David L.; Marx, Preston A.

    2005-01-01

    Human immunodeficiency virus type 2 (HIV-2) originated from simian immunodeficiency viruses (SIVs) that naturally infect sooty mangabeys (SMs; Cercocebus atys). In order to further investigate the relationship between HIV-2 and SIVsm, the SIV specific to the SM, we characterized seven new SIVsm strains from SMs sold in Sierra Leone markets as bush meat. The gag, pol, and env sequences showed that, while the viruses of all seven SMs belonged to the SIVsm-HIV-2 lineage, they were highly diverge...

  5. Structural Features of the Seneca Valley Virus Internal Ribosome Entry Site (IRES) Element: a Picornavirus with a Pestivirus-Like IRES

    DEFF Research Database (Denmark)

    Willcocks, Margaret M.; Locker, Nicolas; Gomwalk, Zarmwa

    2011-01-01

    The RNA genome of Seneca Valley virus (SVV), a recently identified picornavirus, contains an internal ribosome entry site (IRES) element which has structural and functional similarity to that from classical swine fever virus (CSFV) and hepatitis C virus, members of the FLAVIVIRIDAE: The SVV IRES...... has an absolute requirement for the presence of a short region of virus-coding sequence to allow it to function either in cells or in rabbit reticulocyte lysate. The IRES activity does not require the translation initiation factor eIF4A or intact eIF4G. The predicted secondary structure indicates...... that the SVV IRES is more closely related to the CSFV IRES, including the presence of a bipartite IIId domain. Mutagenesis of the SVV IRES, coupled to functional assays, support the core elements of the IRES structure model, but surprisingly, deletion of the conserved IIId2 domain had no effect on IRES...

  6. Development of a two-step SYBR Green I based real time RT-PCR assay for detecting and quantifying peste des petits ruminants virus in clinical samples.

    Science.gov (United States)

    Abera, Tsegalem; Thangavelu, Ardhanary

    2014-12-01

    A two-step SYBR Green I based real time RT-PCR targeting the matrix (M) gene of Peste des petits ruminants virus (PPRV) was developed. The specificity of the assay was assessed against viral nucleic acid extracted from a range of animal viruses of clinical and structural similarities to PPRV including canine distemper virus, measles virus, bluetongue virus and Newcastle disease virus. But none of the viruses and no template control showed an amplification signal. Sensitivity of the same assay was assessed based on plasmid DNA copy number and with respect to infectivity titre. The lower detection limit achieved was 2.88 plasmid DNA copies/μl with corresponding Ct value of 35.93. Based on tissue culture infectivity titre the lower detection limits were 0.0001TCID50/ml and 1TCID50/ml for the SYBR green I based real time RT-PCR and conventional RT-PCR, respectively. The calculated coefficient of variations values for intra- and inter-assay variability were low, ranging from 0.21% to 1.83% and 0.44% to 1.97%, respectively. The performance of newly developed assay was evaluated on a total of 36 clinical samples suspected of PPR and compared with conventional RT-PCR. The SYBR Green I based real time RT-PCR assay detected PPRV in 32 (88.8%) of clinical samples compared to 19 (52.7%) by conventional RT-PCR. Thus, the two-step SYBR Green I based real time RT-PCR assay targeting the M gene of PPRV reported in this study was highly sensitive, specific and reproducible for detection and quantitation of PPRV nucleic acids. Copyright © 2014 Elsevier B.V. All rights reserved.

  7. Serum Neutralization Assay Can Efficiently Replace Plaque Reduction Neutralization Test for Detection and Quantitation of West Nile Virus Antibodies in Human and Animal Serum Samples

    Science.gov (United States)

    Di Gennaro, Annapia; Casaccia, Claudia; Conte, Annamaria; Monaco, Federica; Savini, Giovanni

    2014-01-01

    A serum neutralization assay (SN) was compared with the official plaque reduction neutralization test for the quantitation of West Nile virus antibodies. A total of 1,348 samples from equid sera and 38 from human sera were tested by these two methods. Statistically significant differences were not observed, thus supporting the use of SN for routine purposes. PMID:25100824

  8. Improvement of H5N1 influenza vaccine viruses: influence of internal gene segments of avian and human origin on production and hemagglutinin content.

    Science.gov (United States)

    Abt, Marion; de Jonge, Jørgen; Laue, Michael; Wolff, Thorsten

    2011-07-18

    The H5N1-clade 1 influenza vaccine strain NIBRG-14 produces exceptionally low amounts of antigen, a problem recently encountered also for initial pandemic H1N1-2009 vaccine seeds. Here, we report on a strategy that may contribute to overcome this obstacle. Influenza vaccine viruses usually consist of two segments coding for the antigenic HA and NA proteins of a wild-type strain and the six residual internal gene segments of the vaccine donor strain A/PR/8/34 (PR8). To enhance the antigen yield from H5N1 vaccine virus we generated by reverse genetics a set of PR8-based reassortant viruses expressing the HA and NA segments of the prototypic strain A/Vietnam/1203/2004 and additional replacements of the internal M or PB1 genes of PR8. The reassortants were compared to the parental PR8 and H5N1 viruses in terms of growth in embryonated chicken eggs and the amount of incorporated antigenic HA protein. Compared to NIBRG-14, three out of six viruses displayed an increased replication in embryonated chicken eggs and higher HA content that was also maintained after ether/detergent extraction of virions. Electron microscopic analysis showed that the reassortment hardly affected particle shape and size. Two selected H5N1 reassortant viruses were investigated concerning their pathogenicity in ferrets and found to behave as low pathogenic as the PR8 donor strain. In conclusion, this study shows that replication and antigen content of PR8-derived H5N1 influenza vaccine viruses can be improved by incorporation of heterologous internal gene segments without compromising their attenuated character. Copyright © 2011 Elsevier Ltd. All rights reserved.

  9. Internalized homophobia in a sample of HIV+ gay men, and its relationship to psychological distress, coping, and illness progression.

    Science.gov (United States)

    Wagner, G; Brondolo, E; Rabkin, J

    1996-01-01

    The purpose of this study was to determine whether internalized homophobia is related to psychological distress and coping style and whether these relationships are moderated by illness stage. A sample of gay men, most of whom were HIV+, Caucasian, and well educated, were administered assessments at both baseline and 2-year follow-up, which allowed for the assessment of change over time in the context of HIV illness progression and to determine whether internalized homophobia predicts psychological distress and coping over time. Greater internalized homophobia at baseline, specifically among those who were HIV+ asymptomatic, predicted higher levels of distress at follow-up. In contrast, internalized homophobia had, at best, a weak association with coping. No relationship was found between illness stage and internalized homophobia, psychological distress, or coping. Mental health professionals working with HIV+ gay men may be more effective in targeting resources and interventions aimed at improving mental health and quality of life if they address issues related to internalized homophobia.

  10. Revisiting the dimensionality of the Hospital Anxiety and Depression Scale in an international sample of patients with ischaemic heart disease.

    Science.gov (United States)

    Burns, Annette; Höfer, Stefan; Curry, Philip; Sexton, Eithne; Doyle, Frank

    2014-08-01

    Recently controversy has surrounded the dimensionality of the Hospital Anxiety and Depression Scale (HADS). We assessed the dimensionality of the HADS in a large international sample of patients with ischaemic heart disease (IHD) using confirmatory factor analysis (CFA). The analysis of an international sample enabled the current study to broaden knowledge gained from existing studies with small, regional samples. Data from the HeartQoL study of patients with IHD (n=6241, 22 countries speaking 15 languages) were analyzed using CFA. CFA indicated a hierarchical bifactor solution, with mostly strong item loadings on a general factor (explaining 73% of the variance), and weak to very weak loadings on orthogonal depression (16%) and anxiety (11%) subscales. The bifactor model fits the data significantly better than both the original bidimensional model and Dunbar's higher-order three-factor model. These results, from a large international sample of patients with IHD, suggest that the HADS scale is dominated by a single general distress factor. Although the best CFA model fit was a hierarchical bifactor solution, the subscales had weak item loadings, providing little psychometric evidence of the ability of the HADS to differentiate anxiety and depressive symptoms. It is argued that clinicians and researchers working with patients with IHD should abandon the HADS and use alternative measures of depression and anxiety. Copyright © 2014 Elsevier Inc. All rights reserved.

  11. Cloned cDNA of A/swine/Iowa/15/1930 internal genes as a candidate backbone for reverse genetics vaccine against influenza A viruses.

    Science.gov (United States)

    Lekcharoensuk, Porntippa; Wiriyarat, Witthawat; Petcharat, Nantawan; Lekcharoensuk, Chalermpol; Auewarakul, Prasert; Richt, Juergen A

    2012-02-14

    Reverse genetics viruses for influenza vaccine production usually utilize the internal genes of the egg-adapted A/Puerto Rico/8/34 (PR8) strain. This egg-adapted strain provides high production yield in embryonated eggs but does not necessarily give the best yield in mammalian cell culture. In order to generate a reverse genetics viral backbone that is well-adapted to high growth in mammalian cell culture, a swine influenza isolate A/swine/Iowa/15/30 (H1N1) (rg1930) that was shown to give high yield in Madin-Darby canine kidney (MDCK) cells was used as the internal gene donor for reverse genetics plasmids. In this report, the internal genes from rg1930 were used for construction of reverse genetics viruses carrying a cleavage site-modified hemagglutinin (HA) gene and neuraminidase (NA) gene from a highly pathogenic H5N1 virus. The resulting virus (rg1930H5N1) was low pathogenic in vivo. Inactivated rg1930H5N1 vaccine completely protected chickens from morbidity and mortality after challenge with highly pathogenic H5N1. Protective immunity was obtained when chickens were immunized with an inactivated vaccine consisting of at least 2(9) HA units of the rg1930H5N1 virus. In comparison to the PR8-based reverse genetics viruses carrying the same HA and NA genes from an H5N1 virus, rg1930 based viruses yielded higher viral titers in MDCK and Vero cells. In addition, the reverse genetics derived H3N2 and H5N2 viruses with the rg1930 backbone replicated in MDCK cells better than the cognate viruses with the rgPR8 backbone. It is concluded that this newly established reverse genetics backbone system could serve as a candidate for a master donor strain for development of inactivated influenza vaccines in cell-based systems. Copyright © 2011 Elsevier Ltd. All rights reserved.

  12. Analysis of Respiratory Syncytial Virus in Clinical Samples by Reverse Transcriptase-Polymerase Chain Reaction Restriction Mapping

    Directory of Open Access Journals (Sweden)

    Angel Valdivia

    1997-05-01

    Full Text Available The aim of this study was to develop a polymerase chain reaction (PCR for the detection of respiratory syncytial virus (RSV genomes. The primers were designed from published sequences and selected from conserved regions of the genome encoding for the N protein of subgroups A and B of RSV. PCR was applied to 20 specimens from children admitted to the respiratory ward of "William Soler" Pediatric Hospital in Havana City with a clinical diagnosis of bronchiolitis. The PCR was compared with viral isolation and with an indirect immunofluorescence technique that employs monoclonal antibodies of subgroups A and B. Of 20 nasopharyngeal exudates, 10 were found positive by the three assayed methods. In only two cases, samples that yielded positive RNA-PCR were found negative by indirect immunofluorescence and cell culture. Considering viral isolation as the "gold standard" technique, RNA-PCR had 100% sensitivity and 80% specificity. RNA-PCR is a specific and sensitive technique for the detection of the RSV genome. Technical advantages are discussed

  13. Analysis of respiratory syncytial virus in clinical samples by reverse transcriptase-polymerase chain reaction restriction mapping.

    Science.gov (United States)

    Valdivia, A; Savón, C; Chacón, D; Sarmiento, L; Morier, L; Otero, A; Soto, Y; Oropesa, S; Goyenechea, A

    1997-01-01

    The aim of this study was to develop a polymerase chain reaction (PCR) for the detection of respiratory syncytial virus (RSV) genomes. The primers were designed from published sequences and selected from conserved regions of the genome encoding for the N protein of subgroups A and B of RSV. PCR was applied to 20 specimens from children admitted to the respiratory ward of "William Soler" Pediatric Hospital in Havana City with a clinical diagnosis of bronchiolitis. The PCR was compared with viral isolation and with an indirect immunofluorescence technique that employs monoclonal antibodies of subgroups A and B. Of 20 nasopharyngeal exudates, 10 were found positive by the three assayed methods. In only two cases, samples that yielded positive RNA-PCR were found negative by indirect immunofluorescence and cell culture. Considering viral isolation as the "gold standard" technique, RNA-PCR had 100% sensitivity and 80% specificity. RNA-PCR is a specific and sensitive technique for the detection of the RSV genome. Technical advantages are discussed.

  14. Measurement invariance of internalizing and externalizing behavioral syndrome factors in a non-Western sample.

    Science.gov (United States)

    Yarnell, Lisa M; Sargeant, Marsha N; Prescott, Carol A; Tilley, Jacqueline L; Farver, Jo Ann M; Mednick, Sarnoff A; Venables, Peter H; Raine, Adrian; Luczak, Susan E

    2013-10-01

    This study examined the measurement structure of Child Behavior Checklist internalizing and externalizing syndrome scales in 1,146 eleven-year-old children from a birth cohort in Mauritius. We tested for measurement invariance at configural, metric, and scalar levels by gender and religioethnicity (Creole, Hindu, Muslim). A pared-down model representing five primary factors and two secondary factors met all three forms of invariance, supporting the validity of their use for group comparisons among Mauritian children. As rated by their parents, girls were higher than boys on Somatic Complaints and lower on Aggressive Behavior, Attention Problems, and Externalizing. Creoles were higher than Muslims and Hindus on all seven factors. Hindus were higher than Muslims on Somatic Complaints and lower on Aggressive Behavior. To our knowledge, this is the first study to demonstrate strict invariance of a Child Behavior Checklist-based internalizing and externalizing factor structure among subgroups within a society.

  15. [Immunogenicity of influenza virus H5N2 vaccine strain samples produced by roller cultivation in media with plant derived components].

    Science.gov (United States)

    Mazurkova, N A; Desheva, Iu A; Shishkina, L N; Stavskiĭ, E A; Rudenko, L G

    2011-01-01

    Study in CBA line mice of immunogenicity of cold adapted reassortant influenza virus H5N2 vaccine strain samples produced in rollers in MDCK and Vero cell cultures by using plant derived components. Antibody levels in blood sera and nasal swabs, lungs and small intestine of experimental vaccine strain sample immunized mice were evaluated by using HI reaction in accordance with WHO recommendations. Reassortant vaccine strain A/17/duck/Potsdam/86/92 (H5N2) produced in MDCK and Vero cells by using plant derived components (rice and soy flour hydrolyzate and plant protease based nutrient medium) after intranasal immunization of mice induced local and humoral antibodies, and the latter not only against homologous virus, but also against highly pathogenic avian influenza virus strains A/ Chicken/Suzdalka/Nov-11/2005 and A/Chicken/Kurgan/05/2005. Immunogenicity studies of reassortant influenza virus A/17/duck/Potsdam/86/92 (H5N2) vaccine strain samples cultivated in MDCK and Vero cells by using media with plant derived components in mice show high levels of humoral and secretory immunity.

  16. Influenza A viral loads in respiratory samples collected from patients infected with pandemic H1N1, seasonal H1N1 and H3N2 viruses

    Directory of Open Access Journals (Sweden)

    Chuchottaworn Charoen

    2010-04-01

    Full Text Available Abstract Background Nasopharyngeal aspirate (NPA, nasal swab (NS, and throat swab (TS are common specimens used for diagnosis of respiratory virus infections based on the detection of viral genomes, viral antigens and viral isolation. However, there is no documented data regarding the type of specimen that yields the best result of viral detection. In this study, quantitative real time RT-PCR specific for M gene was used to determine influenza A viral loads present in NS, NPA and TS samples collected from patients infected with the 2009 pandemic H1N1, seasonal H1N1 and H3N2 viruses. Various copy numbers of RNA transcripts derived from recombinant plasmids containing complete M gene insert of each virus strain were assayed by RT-PCR. A standard curve for viral RNA quantification was constructed by plotting each Ct value against the log quantity of each standard RNA copy number. Results Copy numbers of M gene were obtained through the extrapolation of Ct values of the test samples against the corresponding standard curve. Among a total of 29 patients with severe influenza enrolled in this study (12 cases of the 2009 pandemic influenza, 5 cases of seasonal H1N1 and 12 cases of seasonal H3N2 virus, NPA was found to contain significantly highest amount of viral loads and followed in order by NS and TS specimen. Viral loads among patients infected with those viruses were comparable regarding type of specimen analyzed. Conclusion Based on M gene copy numbers, we conclude that NPA is the best specimen for detection of influenza A viruses, and followed in order by NS and TS.

  17. Detection of foot-and-mouth disease virus RNA in pharyngeal epithelium biopsy samples obtained from infected cattle: Investigation of possible sites of virus replication and persistence

    DEFF Research Database (Denmark)

    Stenfeldt, Anna Carolina; Belsham, Graham

    2012-01-01

    Foot-and-mouth disease (FMD) is a highly contagious viral infection of significant financial importance to the export and trade of agricultural products. The occurrence of persistently infected ‘‘carriers’’ of FMD-virus (FMDV) in ruminant species adds further complications to disease control...

  18. Orthorexic eating behaviors related to exercise addiction and internal motivations in a sample of university students.

    Science.gov (United States)

    Oberle, Crystal D; Watkins, Ryan S; Burkot, Andrew J

    2017-12-20

    This research explored the exercise tendencies and motivations of individuals varying in orthorexia symptomatology. Participants were 411 university students, who completed the Eating Habits Questionnaire alongside measures of exercise activity and addiction in Study 1 (a modified version of the Leisure-Time Exercise Questionnaire, the Exercise Addiction Inventory, and the Compulsive Exercise Test) and various exercise motivations in Study 2 (the Behavioural Regulations in Exercise Questionnaire and the Exercise Motivations Inventory-2). Orthorexia symptomatology was positively correlated with aerobic and strength-training exercise levels; all measures of exercise addiction; all measures of internal exercise motivation; and nearly all measures of exercise motivation for the purposes of psychological, social, health, and body improvement. Symptomatology was not significantly related to either measure that specifically assessed external motivation to exercise. Individuals high in orthorexia symptomatology are internally driven to exercise for the purposes of improving their physical and mental health, but these strong motivations also lead to exercise addiction characterized by a compulsive need to follow a rigid schedule of intensive exercise even in the face of injury, illness, or other problems. Level V, descriptive cross-sectional study.

  19. Avian Influenza Virus Surveillance in South-Central Spain Using Fecal Samples of Aquatic Birds Foraging at Landfills

    Directory of Open Access Journals (Sweden)

    Andreia Bárbara

    2017-10-01

    Full Text Available Aquatic wild birds have been intensively studied to better understand their role in avian influenza virus (AIV maintenance and spread. To date, AIV surveillance has primarily focused on natural aquatic environments where different bird species aggregate and viral survival is enhanced. However, artificial habitats such as landfills are attracting substantial numbers of wild birds, AIV reservoir species included. The use of landfills as a predictable food source has significantly influenced population size, migratory traits, and feeding behavior of white storks (Ciconia ciconia and black-headed gulls (Chroicocephalus ridibundus among others. Considering the proximity of landfills to urban settlements and frequently poultry-farms, targeted monitoring of AIV in bird species that forage at landfills but are known to also frequent urban and agricultural habitats could be a useful means for monitoring of AIV, especially during periods of bird aggregation. During the wintering season 2014–2015, the prevalence of AIV in five avian species at two landfills in South-Central Spain was explored by rRT-PCR and species related temporal variation in AIV prevalence determined. We collected and tested 1,186 fresh fecal samples from white storks (N = 689, cattle egrets (Bubulcus ibis, N = 116 and mixed flocks of gulls (N = 381 as well as cloacal and oral swabs from five birds found dead. Seven samples contained AIV, five from gulls and one each from a stork and a cattle egret. Overall, AIV prevalence was 0.60%. No significant temporal variation was observed in AIV prevalence. Prevalence differed significantly among the sampled taxonomic groups, being highest in gulls (1.31%. H16N3 subtype was detected from a cattle egret and H11N9 subtype from a white stork, whereas gulls harbored both subtypes in addition to H11N3 subtype. H16 subtype detection in a cattle egret evidences its host range may not be restricted to gulls. Our results indicate that wild

  20. Identification of minimal sequences of the Rhopalosiphum padi virus 5' untranslated region required for internal initiation of protein synthesis in mammalian, plant and insect translation systems

    DEFF Research Database (Denmark)

    Groppelli, Elisabetta; Belsham, Graham; Roberts, Lisa O.

    2007-01-01

    Rhopalosiphum padi virus (RhPV) is a member of the family Dicistroviridae. The genomes of viruses in this family contain two open reading frames, each preceded by distinct internal ribosome entry site (IRES) elements. The RhPV 5' IRES is functional in mammalian, insect and plant translation systems...... (rabbit reticulocyte lysate), plant (wheatgerm extract) and insect (Sf21 cells) translation systems have now been defined. A fragment (nt 426–579) from the 3' portion of the 5' UTR can direct translation in each of these translation systems. In addition, a distinct region (nt 300–429) is also active. Thus...

  1. Identification of episomal human papillomavirus and other DNA viruses in cytological anal samples of HIV-uninfected men who have sex with men.

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    Maria Gabriella Donà

    Full Text Available To date, there have been only few studies that investigated integration of anal Human Papillomavirus (HPV. Most of them were conducted on HIV-infected individuals and mainly analyzed samples from high-grade lesions and invasive cancer. We aimed to investigate HPV physical status in HIV-negative men who have sex with men (MSM with a detectable anal HPV infection, irrespective of the presence of lesions. We also sought to explore the presence of other circular DNA viruses in the anal region. Study participants were attendees of an STI screening program, which were also screened for anal HPV infection and cytological abnormalities. HPV physical status was assessed using multiply-primed RCA. HPV16-positive samples were also analyzed using E2/E6 multiplex PCR, qRT-PCR and APOT assay. RCA and virus-specific PCR were employed to investigate the presence of other DNA viruses. Anal HPV infection was detected in 76.9% of the 230 MSM enrolled. The anal cytological reports were: 129 NILM, 37 ASC-US and 28 L-SIL (36 samples were inadequate for interpretation. HPV physical status was evaluated in the 109 anal specimens that harbored one or two different HPV genotypes. Integration was observed only in one HPV16-positive sample (0.9%, in which integrate-derived viral transcripts of type B were detected. Integration occurred in chromosome 14 q. In 22 of the 53 (41.5% mucosal HPV-negative samples, RCA restriction results would seem to indicate the presence of circular DNA viruses. Indeed, cutaneous HPV (4 samples, MCPyV (5 samples and TTV (4 samples were detected. In conclusion, anal HPV integration was rarely evidenced in HIV-uninfected MSM with no or mild anal cytological abnormalities, although the integration rate may have been underestimated because of the limitations of the employed assays. Other DNA viruses were detected in the anal samples of these individuals, although the significance of this occurrence needs to be assessed.

  2. Isolation and sequence analysis of hemagglutinin gene of Influenza A H1N1 virus from Iranian clinical samples during 2009 pandemic flu

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    Seyyedeh Fahimeh Mousavi

    2014-05-01

    Full Text Available Background: Influenza virus is a globally important respiratory pathogen causing high degree of morbidity and mortality annually. The novel Influenza virus (A/H1N1 which involved many populations of the world in 2009 is a sort of triple reassortment between swine, bird and human viruses. Given the important role of hemagglutinin in the infectivity of influenza virus, genome sequencing of this protein and investigation of its changes seems necessary. Material and Method: In this experimental study, the viral genome was extracted from clinical throat swab samples, in which the presence of swine influenza genome has been confirmed by Real-time PCR according to WHO protocol in Influenza Research Lab, Pasteur Institute of Iran. Full-length of HA genome was amplified using specific primers by one step-RT-PCR, cloned into pGEM-T Easy vector followed by identification with restriction enzyme analysis and sequencing. Results: Full genome of novel influenza A/H1N1 from clinical samples was amplified by PCR and the expected 1777 bp segment PCR product was visualized by electrophoresis, gel purified, cloned into pGEM-TEasy vector and then sequenced. Analysis of sequencing was accomplished by chromas software (version 1.45-Australia and the nucleotide sequence data was deposited in GenBank database under the accession number: “HQ419001.1”. Conclusion: The result of sequencing was well-matched with the recommended vaccine strain and other registered sequences in NCBI.

  3. Stability of Bovine viral diarrhea virus 1 nucleic acid in fetal bovine samples stored under different conditions

    Science.gov (United States)

    Infection of pregnant cattle with bovine viral diarrhea viruses can result in reproductive disease that includes fetal reabsorption, mummification, abortion, still births, congenital defects affecting structural, neural, reproductive and immune systems and the birth of calves persistently infected w...

  4. A sensitive one-step TaqMan amplification approach for detection of rubella virus clade I and II genotypes in clinical samples.

    Science.gov (United States)

    Claus, C; Bergs, S; Emmrich, N C; Hübschen, J M; Mankertz, A; Liebert, U G

    2017-02-01

    Although teratogenic rubella virus (RV) causes a vaccine-preventable disease, it is still endemic in several countries worldwide. Thus, there is a constant risk of RV importation into non-endemic areas. RV monitoring, especially during measles and Zika virus outbreaks, requires reliable diagnostic tools. For this study, a TaqMan-based one-step reverse transcription-quantitative PCR (RT-qPCR) assay, with the p90 gene as a novel and so far unexplored target for detection of clade I and II genotypes, was developed and evaluated. Automated nucleic acid extraction was carried out. Performance characteristics of the TaqMan RT-qPCR assay were determined for a RV plasmid standard and RNA extracted from virus-infected cell culture supernatants representing clade I and II genotypes. Diagnostic specificity and sensitivity were validated against other RNA and DNA viruses, relevant for RV diagnostic approaches and for RV-positive clinical samples, respectively. The assay is specific and highly sensitive with a limit of detection as low as five to one copies per reaction or 200 infectious virus particles per ml. The coefficients of variation (CV) were specified as intra- (within one run) and inter- (between different runs) assay variation, and calculated based on the standard deviations for the obtained Ct values of the respective samples. Intra- and inter-assay CV values were low, with a maximum of 3.4% and 2.4%, respectively. The assay was shown to be suitable and specific for the analysis of clinical samples. With p90 as a novel target, the highly sensitive and specific TaqMan assay outlined in this study is suitable for RV diagnosis worldwide.

  5. Postmortem detection of hepatitis B, C, and human immunodeficiency virus genomes in blood samples from drug-related deaths in Denmark*

    DEFF Research Database (Denmark)

    Eriksen, Mette Brandt; Jakobsen, Marianne Antonius; Kringsholm, Birgitte

    2009-01-01

    virus (HBV) DNA was detected in 20% (3/15) of anti-HBc-positive/anti-HBs-negative samples, HCV RNA was found in 64% (16/25) of anti-HCV-positive samples, and HIV RNA was detected in 40% (6/15) of anti-HIV-positive samples. The postmortem and antemortem prevalences of HBV DNA and HCV RNA were similar....... Postmortem HIV RNA testing was less sensitive than antemortem testing. Thus, postmortem PCR analysis for HBV and HBC infection is feasible and relevant for demonstrating ongoing infections at death or for transmission analysis during outbreaks....

  6. Monitoring porcine reproductive and respiratory syndrome virus infection status in swine herds based on analysis of antibodies in meat juice samples

    DEFF Research Database (Denmark)

    Mortensen, Sten; Strandbygaard, Bertel; Bøtner, Anette

    2001-01-01

    An indirect ELISA test was developed as a novel tool aimed at monitoring the herd infection status of swine herds. Meat juice samples from pig carcasses were analysed for the presence of antibodies against porcine reproductive and respiratory syndrome virus (PRRSV). A study of samples from herds...... was validated in 47 herds by collection of blood samples from the herds. Eighteen herds were classified as PRRS negative by both test systems. Twenty-nine herds were classified as PRRS seropositive by both test systems. Acceptable herd classification was achieved using this test....

  7. Quantitative assessment of serum NV-F virus DNA concentrations in samples from patients coinfected with hepatitis B or C virus.

    Science.gov (United States)

    Hsu, Chao-Wei; Cheng, Ju-Chien; Yeh, Chau-Ting

    2006-09-01

    A novel hepatotropic virus, named NV-F virus, was recently identified. The clinical information for this virus is still scarce. Using PCR assay, NV-F viral DNA (NV-F-DNA) was detected in 12 of 50 (24%) hepatitis C virus (HCV)-infected patients (HCV-coinfected [HCVCI] group), 34 of 250 (13.6%) hepatitis B virus (HBV)-infected patients (HBV-coinfected [HBVCI] group), and 28 of 100 (28%) non-A-to-E (NAE) hepatitis patients. Basic clinical parameters were not significantly different among the three groups. By use of a PCR-based quantitative assay, the NV-F-DNA concentration was found to be above the detection limit (1.2 x 10(5) copies/ml) in 12/12 (100%) HCVCI patients, 14/34 (41.2%) HBVCI patients, and 4/28 (14.3%) NAE patients. The median serum NV-F-DNA concentration was 9.3 x 10(5) copies/ml in HCVCI patients, but it was below the detection limit in HBVCI and NAE patients (P values were 0.0045 and 0.0001, respectively). Stepwise multiple regression analysis identified the presence of anti-HCV as an independent factor for NV-F-DNA concentrations (beta = 6.2 x 10(9); P = 0.0245). In HBVCI patients, the NV-F-DNA concentration was inversely correlated with the HBV DNA concentration. The median NV-F-DNA concentration was below the detection limit in patients with HBV DNA concentrations above 1.4 x 10(5) copies/ml, but it was 1.58 x 10(6) copies/ml in patients with HBV DNA concentrations below 1.4 x 10(5) copies/ml (P = 0.030). In conclusion, NV-F-DNA concentrations were higher in HCVCI patients. A reciprocal relationship was found between NV-F-DNA and HBV DNA concentrations in HBVCI patients, indicating the presence of viral interference between these two DNA viruses.

  8. Directionally Solidified Aluminum - 7 wt% Silicon Alloys: Comparison of Earth and International Space Station Processed Samples

    Science.gov (United States)

    Grugel, Richard N,; Tewari, Surendra; Rajamure, R. S.; Erdman, Robert; Poirier, David

    2012-01-01

    Primary dendrite arm spacings of Al-7 wt% Si alloy directionally solidified in low gravity environment of space (MICAST-6 and MICAST-7: Thermal gradient approx. 19 to 26 K/cm, Growth speeds varying from 5 to 50 microns/s show good agreement with the Hunt-Lu model. Primary dendrite trunk diameters of the ISS processed samples show a good fit with a simple analytical model based on Kirkwood s approach, proposed here. Natural convection, a) decreases primary dendrite arm spacing. b) appears to increase primary dendrite trunk diameter.

  9. Predicting social work students' interest in gerontology: results from an international sample.

    Science.gov (United States)

    Chonody, Jill M; Wang, Donna

    2014-01-01

    The need for social workers with a specialization in gerontology has become a global priority. The purpose of this study was to explore social work students' interest in gerontology. This cross-sectional survey was completed by 1,042 students from the United States, England, and Australia, and only 5.4% of the sample indicated an interest in gerontology. Results of the logistic regression found that personal aging beliefs and the frequency of time spent with an older adult were significant in explaining gerontological interest. The infusion of aging content may facilitate further advancement in the field, but additional strategies may also be needed.

  10. Detection and Isolation of Swine Influenza A Virus in Spiked Oral Fluid and Samples from Individually Housed, Experimentally Infected Pigs: Potential Role of Porcine Oral Fluid in Active Influenza A Virus Surveillance in Swine

    Science.gov (United States)

    Decorte, Inge; Steensels, Mieke; Lambrecht, Bénédicte

    2015-01-01

    Background The lack of seasonality of swine influenza A virus (swIAV) in combination with the capacity of swine to harbor a large number of co-circulating IAV lineages, resulting in the risk for the emergence of influenza viruses with pandemic potential, stress the importance of swIAV surveillance. To date, active surveillance of swIAV worldwide is barely done because of the short detection period in nasal swab samples. Therefore, more sensitive diagnostic methods to monitor circulating virus strains are requisite. Methods qRT-PCR and virus isolations were performed on oral fluid and nasal swabs collected from individually housed pigs that were infected sequentially with H1N1 and H3N2 swIAV strains. The same methods were also applied to oral fluid samples spiked with H1N1 to study the influence of conservation time and temperature on swIAV infectivity and detectability in porcine oral fluid. Results All swIAV infected animals were found qRT-PCR positive in both nasal swabs and oral fluid. However, swIAV could be detected for a longer period in oral fluid than in nasal swabs. Despite the high detectability of swIAV in oral fluid, virus isolation from oral fluid collected from infected pigs was rare. These results are supported by laboratory studies showing that the PCR detectability of swIAV remains unaltered during a 24 h incubation period in oral fluid, while swIAV infectivity drops dramatically immediately upon contact with oral fluid (3 log titer reduction) and gets lost after 24 h conservation in oral fluid at ambient temperature. Conclusions Our data indicate that porcine oral fluid has the potential to replace nasal swabs for molecular diagnostic purposes. The difficulty to isolate swIAV from oral fluid could pose a drawback for its use in active surveillance programs. PMID:26431039

  11. Developing and Validating a Computerized Adaptive Test to Measure Broad and Specific Factors of Internalizing in a Community Sample.

    Science.gov (United States)

    Sunderland, Matthew; Batterham, Philip; Carragher, Natacha; Calear, Alison; Slade, Tim

    2017-05-01

    Highly efficient assessments that better account for comorbidity between mood and anxiety disorders (internalizing) are required to identify individuals who are most at risk of psychopathology in the community. The current study examined the efficiency and validity associated with a multidimensional computerized adaptive test (CAT) to measure broad and specific levels of internalizing psychopathology. The sample comprised 3,175 respondents to an online survey. Items from five banks (generalized anxiety, depression, obsessive-compulsive disorder, panic disorder, social anxiety disorder) were jointly calibrated using a bifactor item response theory model. Simulations indicated that an adaptive algorithm could accurately ( rs ≥ 0.90) estimate general internalizing and specific disorder scores using on average 44 items in comparison with the full 133-item bank (67% reduction in items). Scores on the CAT demonstrate convergent and divergent validity with previously validated short severity scales and could significantly differentiate cases of DSM-5 disorder. As such, the CAT validly measures both broad and specific constructs of internalizing disorders in a manner similar to the full item bank and a static brief form but with greater gains in efficiency and, therefore, a reduced degree of respondent burden.

  12. Identification of Rhopalosiphum Padi Virus 5′ Untranslated Region Sequences Required for Cryptic Promoter Activity and Internal Ribosome Entry

    Directory of Open Access Journals (Sweden)

    Ming-Kun Liu

    2015-07-01

    Full Text Available The 579-nucleotide 5′ untranslated region (5′UTR of the Rhopalosiphum padi virus (RhPV possesses a cross-kingdom internal ribosome entry site (IRES activity that functions in insect, mammalian, and plant-derived in vitro translation systems, and six TAAG motifs within the DNA fragment encoding the RhPV 5′UTR were previously found to confer the RhPV 5′UTR with late promoter activity in baculovirus. In the present study, various truncated RhPV 5′UTR sequences were produced, and among them, a fragment of 110 bp ranging from nucleotides 309 to 418 was identified to be the shortest fragment responsible for the late promoter activity in baculovirus infected Sf21 cells. This 110 bp fragment contains a TAAG tandem repeat that retains more than 60% of the late promoter activity of the full length RhPV 5′UTR sequence. Further, IRES activity remained unchanged in all truncated RhPV 5′UTR constructs. Taken together, this novel 110 bp fragment having late promoter activity in baculovirus as well as IRES activity in mammalian cell, renders it a useful tool for the development of a “shuttle” bi-cistronic baculovirus gene expression and/or delivery vector.

  13. Identification of Rhopalosiphum Padi Virus 5′ Untranslated Region Sequences Required for Cryptic Promoter Activity and Internal Ribosome Entry

    Science.gov (United States)

    Liu, Ming-Kun; Lin, Jie-Zue; Jinn, Tzyy-Rong; Chan, Hong-Lin; Wu, Tzong-Yuan

    2015-01-01

    The 579-nucleotide 5′ untranslated region (5′UTR) of the Rhopalosiphum padi virus (RhPV) possesses a cross-kingdom internal ribosome entry site (IRES) activity that functions in insect, mammalian, and plant-derived in vitro translation systems, and six TAAG motifs within the DNA fragment encoding the RhPV 5′UTR were previously found to confer the RhPV 5′UTR with late promoter activity in baculovirus. In the present study, various truncated RhPV 5′UTR sequences were produced, and among them, a fragment of 110 bp ranging from nucleotides 309 to 418 was identified to be the shortest fragment responsible for the late promoter activity in baculovirus infected Sf21 cells. This 110 bp fragment contains a TAAG tandem repeat that retains more than 60% of the late promoter activity of the full length RhPV 5′UTR sequence. Further, IRES activity remained unchanged in all truncated RhPV 5′UTR constructs. Taken together, this novel 110 bp fragment having late promoter activity in baculovirus as well as IRES activity in mammalian cell, renders it a useful tool for the development of a “shuttle” bi-cistronic baculovirus gene expression and/or delivery vector. PMID:26184188

  14. Identification of Rhopalosiphum Padi Virus 5' Untranslated Region Sequences Required for Cryptic Promoter Activity and Internal Ribosome Entry.

    Science.gov (United States)

    Liu, Ming-Kun; Lin, Jie-Zue; Jinn, Tzyy-Rong; Chan, Hong-Lin; Wu, Tzong-Yuan

    2015-07-15

    The 579-nucleotide 5' untranslated region (5'UTR) of the Rhopalosiphum padi virus (RhPV) possesses a cross-kingdom internal ribosome entry site (IRES) activity that functions in insect, mammalian, and plant-derived in vitro translation systems, and six TAAG motifs within the DNA fragment encoding the RhPV 5'UTR were previously found to confer the RhPV 5'UTR with late promoter activity in baculovirus. In the present study, various truncated RhPV 5'UTR sequences were produced, and among them, a fragment of 110 bp ranging from nucleotides 309 to 418 was identified to be the shortest fragment responsible for the late promoter activity in baculovirus infected Sf21 cells. This 110 bp fragment contains a TAAG tandem repeat that retains more than 60% of the late promoter activity of the full length RhPV 5'UTR sequence. Further, IRES activity remained unchanged in all truncated RhPV 5'UTR constructs. Taken together, this novel 110 bp fragment having late promoter activity in baculovirus as well as IRES activity in mammalian cell, renders it a useful tool for the development of a "shuttle" bi-cistronic baculovirus gene expression and/or delivery vector.

  15. Water extract of Cinnamomum cassia Blume inhibited human respiratory syncytial virus by preventing viral attachment, internalization, and syncytium formation.

    Science.gov (United States)

    Yeh, Chia Feng; Chang, Jung San; Wang, Kuo Chih; Shieh, Den En; Chiang, Lien Chai

    2013-05-20

    Cinnamomum cassia Blume is a popular traditional Chinese herbal medicine that has been used to manage respiratory tract disease, including common cold and chronic bronchitis for thousand years. Human respiratory syncytial virus (HRSV) is one of the leading causes of severe lower respiratory tract illness worldwide. No effective therapeutic modality against HRSV infection has been proved. It is unknown whether Cinnamomum cassia is effective against HRSV. This study tested the hypothesis that Cinnamomum cassia can effectively decrease HRSV-induced plaque formation and syncytium formation in respiratory mucosal cell lines. Antiviral activity of the hot water extract of Cinnamomum cassia against HRSV was tested by plaque reduction assay in both human upper (HEp-2) and low (A549) respiratory tract cell lines. Its ability to inhibit the synthesis of viral fusion (F) protein was examined by Western blot assay. Cinnamomum cassia dose-dependently inhibited HRSV-induced plaque formation in both HEp-2 and A549 cell lines (pCinnamomum cassia was more effective when given before viral infection (pCinnamomum cassia could inhibit F protein production and syncytium formation to interfere with HRSV spreading. Cinnamomum cassia prevented airway epithelia from HRSV infection through inhibiting viral attachment, internalization and syncytium formation. Cinnamomum cassia could be a candidate to develop therapeutic modalities to manage HRSV infection in the future. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  16. Application of FTA technology for sampling, recovery and molecular characterization of viral pathogens and virus-derived transgenes from plant tissues

    Directory of Open Access Journals (Sweden)

    Aveling Terry

    2005-05-01

    Full Text Available Abstract Background Plant viral diseases present major constraints to crop production. Effective sampling of the viruses infecting plants is required to facilitate their molecular study and is essential for the development of crop protection and improvement programs. Retaining integrity of viral pathogens within sampled plant tissues is often a limiting factor in this process, most especially when sample sizes are large and when operating in developing counties and regions remote from laboratory facilities. FTA is a paper-based system designed to fix and store nucleic acids directly from fresh tissues pressed into the treated paper. We report here the use of FTA as an effective technology for sampling and retrieval of DNA and RNA viruses from plant tissues and their subsequent molecular analysis. Results DNA and RNA viruses were successfully recovered from leaf tissues of maize, cassava, tomato and tobacco pressed into FTA® Classic Cards. Viral nucleic acids eluted from FTA cards were found to be suitable for diagnostic molecular analysis by PCR-based techniques and restriction analysis, and for cloning and nucleotide sequencing in a manner equivalent to that offered by tradition isolation methods. Efficacy of the technology was demonstrated both from sampled greenhouse-grown plants and from leaf presses taken from crop plants growing in farmer's fields in East Africa. In addition, FTA technology was shown to be suitable for recovery of viral-derived transgene sequences integrated into the plant genome. Conclusion Results demonstrate that FTA is a practical, economical and sensitive method for sampling, storage and retrieval of viral pathogens and plant genomic sequences, when working under controlled conditions and in the field. Application of this technology has the potential to significantly increase ability to bring modern analytical techniques to bear on the viral pathogens infecting crop plants.

  17. Application of FTA technology for sampling, recovery and molecular characterization of viral pathogens and virus-derived transgenes from plant tissues.

    Science.gov (United States)

    Ndunguru, Joseph; Taylor, Nigel J; Yadav, Jitender; Aly, Haytham; Legg, James P; Aveling, Terry; Thompson, Graham; Fauquet, Claude M

    2005-05-18

    Plant viral diseases present major constraints to crop production. Effective sampling of the viruses infecting plants is required to facilitate their molecular study and is essential for the development of crop protection and improvement programs. Retaining integrity of viral pathogens within sampled plant tissues is often a limiting factor in this process, most especially when sample sizes are large and when operating in developing counties and regions remote from laboratory facilities. FTA is a paper-based system designed to fix and store nucleic acids directly from fresh tissues pressed into the treated paper. We report here the use of FTA as an effective technology for sampling and retrieval of DNA and RNA viruses from plant tissues and their subsequent molecular analysis. DNA and RNA viruses were successfully recovered from leaf tissues of maize, cassava, tomato and tobacco pressed into FTA Classic Cards. Viral nucleic acids eluted from FTA cards were found to be suitable for diagnostic molecular analysis by PCR-based techniques and restriction analysis, and for cloning and nucleotide sequencing in a manner equivalent to that offered by tradition isolation methods. Efficacy of the technology was demonstrated both from sampled greenhouse-grown plants and from leaf presses taken from crop plants growing in farmer's fields in East Africa. In addition, FTA technology was shown to be suitable for recovery of viral-derived transgene sequences integrated into the plant genome. Results demonstrate that FTA is a practical, economical and sensitive method for sampling, storage and retrieval of viral pathogens and plant genomic sequences, when working under controlled conditions and in the field. Application of this technology has the potential to significantly increase ability to bring modern analytical techniques to bear on the viral pathogens infecting crop plants.

  18. Characterization of Complex Fractionated Atrial Electrograms by Sample Entropy: An International Multi-Center Study

    Directory of Open Access Journals (Sweden)

    Eva Cirugeda–Roldán

    2015-10-01

    Full Text Available Atrial fibrillation (AF is the most commonly clinically-encountered arrhythmia. Catheter ablation of AF is mainly based on trigger elimination and modification of the AF substrate. Substrate mapping ablation of complex fractionated atrial electrograms (CFAEs has emerged to be a promising technique. To improve substrate mapping based on CFAE analysis, automatic detection algorithms need to be developed in order to simplify and accelerate the ablation procedures. According to the latest studies, the level of fractionation has been shown to be promisingly well estimated from CFAE measured during radio frequency (RF ablation of AF. The nature of CFAE is generally nonlinear and nonstationary, so the use of complexity measures is considered to be the appropriate technique for the analysis of AF records. This work proposes the use of sample entropy (SampEn, not only as a way to discern between non-fractionated and fractionated atrial electrograms (A-EGM, Entropy 2015, 17 7494 but also as a tool for characterizing the degree of A-EGM regularity, which is linked to changes in the AF substrate and to heart tissue damage. The use of SampEn combined with a blind parameter estimation optimization process enables the classification between CFAE and non-CFAE with statistical significance (p < 0:001, 0.89 area under the ROC, 86% specificity and 77% sensitivity over a mixed database of A-EGM combined from two independent CFAE signal databases, recorded during RF ablation of AF in two EU countries (542 signals in total. On the basis of the results obtained in this study, it can be suggested that the use of SampEn is suitable for real-time support during navigation of RF ablation of AF, as only 1.5 seconds of signal segments need to be analyzed.

  19. A magnesium-induced RNA conformational switch at the internal ribosome entry site of hepatitis C virus genome visualized by atomic force microscopy

    OpenAIRE

    García-Sacristán, Ana; Moreno Molina, Miguel; Ariza-Mateos, Ascensión; López-Camacho, Elena; Jáudenes, Rosa M.; Vázquez, Luis; Gómez, Jordi; Martín-Gago, José A.; Briones, Carlos

    2014-01-01

    The 5? untranslated region of hepatitis C virus (HCV) genomic RNA contains an internal ribosome entry site (IRES) element, composed of domains II?IV, which is required for cap-independent translation initiation. Little information on the 3D structure of the whole functional HCV IRES is still available. Here, we use atomic force microscopy to visualize the HCV IRES conformation in its natural sequence context, which includes the upstream domain I and the essential, downstream domains V and VI....

  20. Quality Control Assessment of Human Immunodeficiency Virus Type 2 (HIV-2) Viral Load Quantification Assays: Results from an International Collaboration on HIV-2 Infection in 2006▿

    Science.gov (United States)

    Damond, Florence; Benard, Antoine; Ruelle, Jean; Alabi, Abraham; Kupfer, Bernd; Gomes, Perpetua; Rodes, Berta; Albert, Jan; Böni, Jürg; Garson, Jeremy; Ferns, Bridget; Matheron, Sophie; Chene, Geneviève; Brun-Vezinet, Françoise

    2008-01-01

    Human immunodeficiency virus type 2 (HIV-2) RNA quantification assays used in nine laboratories of the ACHIEV2E (A Collaboration on HIV-2 Infection) study group were evaluated. In a blinded experimental design, laboratories quantified three series of aliquots of an HIV-2 subtype A strain, each at a different theoretical viral load. Quantification varied between laboratories, and international standardization of quantification assays is strongly needed. PMID:18434556

  1. Investigation of Total and Hexavalent Chromium in Filtered and Unfiltered Groundwater Samples at the Tucson International Airport Superfund Site.

    Science.gov (United States)

    Tillman, Fred D; McCleskey, R Blaine; Hermosillo, Edyth

    2016-10-01

    Potential health effects from hexavalent chromium in groundwater have recently become a concern to regulators at the Tucson International Airport Area Superfund site. In 2016, the U.S. Geological Survey sampled 46 wells in the area to characterize the nature and extent of chromium in groundwater, to understand what proportion of total chromium is in the hexavalent state, and to determine if substantial differences are present between filtered and unfiltered chromium concentrations. Results indicate detectable chromium concentrations in all wells, over 75 % of total chromium is in the hexavalent state in a majority of wells, and filtered and unfiltered results differ substantially in only a few high-turbidity total chromium samples.

  2. The application of statistical and/or non-statistical sampling techniques by internal audit functions in the South African banking industry

    Directory of Open Access Journals (Sweden)

    D.P. van der Nest

    2015-03-01

    Full Text Available This article explores the use by internal audit functions of audit sampling techniques in order to test the effectiveness of controls in the banking sector. The article focuses specifically on the use of statistical and/or non-statistical sampling techniques by internal auditors. The focus of the research for this article was internal audit functions in the banking sector of South Africa. The results discussed in the article indicate that audit sampling is still used frequently as an audit evidence-gathering technique. Non-statistical sampling techniques are used more frequently than statistical sampling techniques for the evaluation of the sample. In addition, both techniques are regarded as important for the determination of the sample size and the selection of the sample items

  3. Validation of the rapid fluorescent focus inhibition test for rabies virus-neutralizing antibodies in clinical samples

    NARCIS (Netherlands)

    Kostense, Stefan; Moore, Susan; Companjen, Arjen; Bakker, Alexander B. H.; Marissen, Wilfred E.; von Eyben, Rie; Weverling, Gerrit Jan; Hanlon, Cathleen; Goudsmit, Jaap

    2012-01-01

    Monoclonal antibodies are successful biologics in treating a variety of diseases, including the prevention or treatment of viral infections. CL184 is a 1:1 combination of two human monoclonal IgG1 antibodies (CR57 and CR4098) against rabies virus, produced in the PER.C6 human cell line. The two

  4. Human herpes virus-8 DNA in bronchoalveolar lavage samples from patients with AIDS-associated pulmonary Kaposi's sarcoma

    DEFF Research Database (Denmark)

    Benfield, T L; Dodt, K K; Lundgren, Jens Dilling

    1997-01-01

    Kaposi's sarcoma (KS) is the most frequent AIDS-associated neoplasm, and often disseminates to visceral organs, including the lungs. An ante-mortem diagnosis of pulmonary KS is difficult. Recently, DNA sequences resembling a new human herpes virus (HHV-8), have been identified in various forms...

  5. Impact of Internal RNA on Aggregation and Electrokinetics of Viruses: Comparison between MS2 Phage and Corresponding Virus-Like Particles ▿

    OpenAIRE

    Dika, C.; Duval, J.F.L.; Ly-Chatain, H. M.; C. Merlin; Gantzer, C.

    2011-01-01

    We compare for the first time the electrokinetic and aggregation properties of MS2 phage (pH 2.5 to 7, 1 to 100 mM NaNO3 electrolyte concentration) with those of the corresponding virus-like particles (VLPs), which lack entirely the inner viral RNA component. In line with our previous work (J. Langlet, F. Gaboriaud, C. Gantzer, and J. F. L. Duval, Biophys. J. 94:3293-3312, 2008), it is found that modifying the content of RNA within the virus leads to very distinct electrohydrodynamic and aggr...

  6. Optimizing Viable Leukocyte Sampling from the Female Genital Tract for Clinical Trials: An International Multi-Site Study

    Science.gov (United States)

    De Rosa, Stephen C.; Martinson, Jeffrey A.; Plants, Jill; Brady, Kirsten E.; Gumbi, Pamela P.; Adams, Devin J.; Vojtech, Lucia; Galloway, Christine G.; Fialkow, Michael; Lentz, Gretchen; Gao, Dayong; Shu, Zhiquan; Nyanga, Billy; Izulla, Preston; Kimani, Joshua; Kimwaki, Steve; Bere, Alfred; Moodie, Zoe; Landay, Alan L.; Passmore, Jo-Ann S.; Kaul, Rupert; Novak, Richard M.; McElrath, M. Juliana; Hladik, Florian

    2014-01-01

    Background Functional analysis of mononuclear leukocytes in the female genital mucosa is essential for understanding the immunologic effects of HIV vaccines and microbicides at the site of HIV exposure. However, the best female genital tract sampling technique is unclear. Methods and Findings We enrolled women from four sites in Africa and the US to compare three genital leukocyte sampling methods: cervicovaginal lavages (CVL), endocervical cytobrushes, and ectocervical biopsies. Absolute yields of mononuclear leukocyte subpopulations were determined by flow cytometric bead-based cell counting. Of the non-invasive sampling types, two combined sequential cytobrushes yielded significantly more viable mononuclear leukocytes than a CVL (pbiopsies. Sample yields were consistent between sites. In a subgroup analysis, we observed significant reproducibility between replicate same-day biopsies (r = 0.89, p = 0.0123). Visible red blood cells in cytobrushes increased leukocyte yields more than three-fold (p = 0.0078), but did not change their subpopulation profile, indicating that these leukocytes were still largely derived from the mucosa and not peripheral blood. We also confirmed that many CD4+ T cells in the female genital tract express the α4β7 integrin, an HIV envelope-binding mucosal homing receptor. Conclusions CVL sampling recovered the lowest number of viable mononuclear leukocytes. Two cervical cytobrushes yielded comparable total numbers of viable leukocytes to one biopsy, but cytobrushes and biopsies were biased toward macrophages and T lymphocytes, respectively. Our study also established the feasibility of obtaining consistent flow cytometric analyses of isolated genital cells from four study sites in the US and Africa. These data represent an important step towards implementing mucosal cell sampling in international clinical trials of HIV prevention. PMID:24454917

  7. A cross-sectional description of social capital in an international sample of persons living with HIV/AIDS (PLWH

    Directory of Open Access Journals (Sweden)

    Webel Allison

    2012-03-01

    Full Text Available Abstract Background Social capital refers to the resources linked to having a strong social network. This concept plays into health outcomes among People Living with HIV/AIDS because, globally, this is a highly marginalized population. Case studies show that modifying social capital can lead to improvements in HIV transmission and management; however, there remains a lack of description or definition of social capital in international settings. The purpose of our paper was to describe the degree of social capital in an international sample of adults living with HIV/AIDS. Methods We recruited PLWH at 16 sites from five countries including Canada, China, Namibia, Thailand, and the United States. Participants (n = 1,963 completed a cross-sectional survey and data were collected between August, 2009 and December, 2010. Data analyses included descriptive statistics, factor analysis, and correlational analysis. Results Participant's mean age was 45.2 years, most (69% identified as male, African American/Black (39.9%, and unemployed (69.5%. Total mean social capital was 2.68 points, a higher than average total social capital score. Moderate correlations were observed between self-reported physical (r = 0.25 and psychological condition (r = 0.36, social support (r = 0.31, and total social capital. No relationships between mental health factors, including substance use, and social capital were detected. Conclusions This is the first report to describe levels of total social capital in an international sample of PLWH and to describe its relationship to self-reported health in this population.

  8. Development, Characterisation and Application of Monoclonal Antibodies for the Detection and Quantification of Infectious Salmon Anaemia Virus in Plasma Samples Using Luminex Bead Array Technology.

    Directory of Open Access Journals (Sweden)

    R Hoare

    Full Text Available Infectious salmon anaemia virus (ISAV is an orthomyxovirus that has had a significant economic impact on Atlantic salmon farming in Europe, North America and Chile. Monoclonal antibodies (mAbs were developed against Segment 3 (encoding the viral nucleoprotein, NP of the virus. Six of the mAbs were shown to be specific to ISAV and recognised all isolates from Scotland, Norway and Canada. They reacted with ISAV in enzyme-linked immunosorbent assay (ELISA, indirect fluorescent antibody technique (IFAT and western blotting. They were also used to develop a novel detection method based on Luminex (Bio-Plex bead-based flow cytometric technology for the detection of ISAV in the plasma of Atlantic salmon (Salmo salar L. smolts experimentally infected with ISAV. Fish were challenged by intraperitoneal (i.p. injection of virus at 50% Tissue Culture Infective Dose (TCID50 = 2.8 x106 per animal. Virus present in plasma of infected fish, collected at 0, 4, 8, 12, 16, 21 and 28 days post infection using a non-lethal sampling method (n = 12 at each time point, was quantified using the optimised Bio-Plex assay. The results obtained with this assay were compared with absolute quantification of the virus by RT-qPCR using SYBR Green I and TaqMan chemistries. The Bio-Plex assay developed using the NP mAbs appears to be a rapid, sensitive method for detecting and quantifying ISAV in small volumes of fish plasma and has the potential to be multiplexed for the detection of other fish pathogens (e.g. during co-infections. To our knowledge this is the first report of the use of Luminex (Bio-Plex technology for the detection of a fish pathogen.

  9. Assessment of Epstein-Barr virus nucleic acids in gastric but not in breast cancer by next-generation sequencing of pooled Mexican samples

    Science.gov (United States)

    Fuentes-Pananá, Ezequiel M; Larios-Serrato, Violeta; Méndez-Tenorio, Alfonso; Morales-Sánchez, Abigail; Arias, Carlos F; Torres, Javier

    2016-01-01

    Gastric (GC) and breast (BrC) cancer are two of the most common and deadly tumours. Different lines of evidence suggest a possible causative role of viral infections for both GC and BrC. Wide genome sequencing (WGS) technologies allow searching for viral agents in tissues of patients with cancer. These technologies have already contributed to establish virus-cancer associations as well as to discovery new tumour viruses. The objective of this study was to document possible associations of viral infection with GC and BrC in Mexican patients. In order to gain idea about cost effective conditions of experimental sequencing, we first carried out an in silico simulation of WGS. The next-generation-platform IlluminaGallx was then used to sequence GC and BrC tumour samples. While we did not find viral sequences in tissues from BrC patients, multiple reads matching Epstein-Barr virus (EBV) sequences were found in GC tissues. An end-point polymerase chain reaction confirmed an enrichment of EBV sequences in one of the GC samples sequenced, validating the next-generation sequencing-bioinformatics pipeline. PMID:26910355

  10. Assessment of Epstein-Barr virus nucleic acids in gastric but not in breast cancer by next-generation sequencing of pooled Mexican samples

    Directory of Open Access Journals (Sweden)

    Ezequiel M Fuentes-Pananá

    2016-01-01

    Full Text Available Gastric (GC and breast (BrC cancer are two of the most common and deadly tumours. Different lines of evidence suggest a possible causative role of viral infections for both GC and BrC. Wide genome sequencing (WGS technologies allow searching for viral agents in tissues of patients with cancer. These technologies have already contributed to establish virus-cancer associations as well as to discovery new tumour viruses. The objective of this study was to document possible associations of viral infection with GC and BrC in Mexican patients. In order to gain idea about cost effective conditions of experimental sequencing, we first carried out an in silico simulation of WGS. The next-generation-platform IlluminaGallx was then used to sequence GC and BrC tumour samples. While we did not find viral sequences in tissues from BrC patients, multiple reads matching Epstein-Barr virus (EBV sequences were found in GC tissues. An end-point polymerase chain reaction confirmed an enrichment of EBV sequences in one of the GC samples sequenced, validating the next-generation sequencing-bioinformatics pipeline.

  11. Current Methods for Extraction and Concentration of Enteric Viruses from Fresh Fruit and Vegetables: Towards International Standards

    NARCIS (Netherlands)

    Croci, L.; Dubois, E.; Cook, N.; Medici, D.; Schultz, A.C.; China, B.; Rutjes, S.A.; Hoorfar, J.; Poel, van der W.H.M.

    2008-01-01

    Virus-contaminated soft fruits or vegetables are increasingly identified as causes of foodborne viral illness. Noroviruses and hepatitis A virus are the most common pathogens in viral infections transmitted by these kinds of foods. To improve microbiological detection and monitoring and to increase

  12. [Investigation of herpes group and hepatitis A virus nucleic acids in the atherome plaque samples of patients with coronary arterial disease].

    Science.gov (United States)

    Altun, Belgin; Rota, Seyyal; Demircin, Metin; Reşatoğlu, Adem; Yener, Ali; Bozdayi, Gülendam

    2007-10-01

    It is assumed that various infectious agents play direct or indirect roles in the pathogenesis of atherosclerosis which is accepted as a chronic inflammatory phenomenon. However, the data obtained from different studies are contradictory. The aim of this study was to investigate the roles of herpes virus group [Herpes simplex virus (HSV), Epstein-Barr virus (EBV), Cytomegalovirus (CMV)] and hepatitis A virus (HAV) which are debated in terms of their impact in the pathogenesis of coronary arterial diseases. For this purpose, atherome plaque samples collected from 28 patients (23 were male; age range: 43-74 years) with atherosclerotic heart disease and vein samples from 22 control patients (19 were male; age range: 37-85 years) who had vascular diseases other than atherosclerosis, were investigated by means of the presence of nucleic acids of the above mentioned viruses by real-time polymerase chain reaction (PCR). Besides, classical cardiovascular risk factors (hypertension, hyperlipidemia, hypercholestrolemia, diabetes mellitus, smoking habits, gender, age and familial background) were questioned in both patient and control groups. As a result, no positivity were detected for nucleic acids of HSV type 1 and 2, EBV and HAV, whereas CMV-DNA was found positive in three of 28 (10.7%) atheromateous plaques (viral loads were 21, 188 and 288 copies/mg). Amongst 22 vascular samples from controls, two (9.1%) yielded positive results for EBV-DNA (viral loads were 5 and 10 copies/mg), while the other samples were found negative for nucleic acids of HSV type 1 and 2, CMV and HAV. The evaluation of the known risk factors for atherosclerosis revealed that, the difference between the presence of hypertension and hyperlipidemia which are the major risk factors, was statistically important (p < 0.05) in patient group (64% and 50%, respectively) and control group (32% and 23%, respectively). In conclusion, the hypothesis concerning the possible relationship between these viral

  13. Comparison of the FilmArray RP, Verigene RV+, and Prodesse ProFLU+/FAST+ multiplex platforms for detection of influenza viruses in clinical samples from the 2011-2012 influenza season in Belgium.

    Science.gov (United States)

    Van Wesenbeeck, Liesbeth; Meeuws, Hanne; Van Immerseel, Andrea; Ispas, Gabriela; Schmidt, Kristiane; Houspie, Lieselot; Van Ranst, Marc; Stuyver, Lieven

    2013-09-01

    Respiratory tract infections (RTIs) are caused by a plethora of viral and bacterial pathogens. In particular, lower RTIs are a leading cause of hospitalization and mortality. Timely detection of the infecting respiratory pathogens is crucial to optimize treatment and care. In this study, three U.S. Food and Drug Administration-approved molecular multiplex platforms (Prodesse ProFLU+/FAST+, FilmArray RP, and Verigene RV+) were evaluated for influenza virus detection in 171 clinical samples collected during the Belgian 2011-2012 influenza season. Sampling was done using mid-turbinate flocked swabs, and the collected samples were stored in universal transport medium. The amount of viral RNA present in the swab samples ranged between 3.07 and 8.82 log10 copies/ml. Sixty samples were concordant influenza A virus positive, and 8 samples were found to be concordant influenza B virus positive. Other respiratory viruses that were detected included human rhinovirus/enterovirus, respiratory syncytial virus, parainfluenza virus type 1, human metapneumovirus, and coronavirus NL63. Twenty-five samples yielded discordant results across the various assays which required further characterization by sequencing. The FilmArray RP and Prodesse ProFLU+/FAST+ assays were convenient to perform with regard to sensitivity, ease of use, and low percentages of invalid results. Although the limit of sensitivity is of utmost importance, many other factors should be taken into account in selecting the most convenient molecular diagnostic assay for the detection of respiratory pathogens in clinical samples.

  14. Prevalence of xenotropic murine leukaemia virus-related virus in patients with chronic fatigue syndrome in the Netherlands: retrospective analysis of samples from an established cohort.

    Science.gov (United States)

    van Kuppeveld, Frank J M; de Jong, Arjan S; Lanke, Kjerstin H; Verhaegh, Gerald W; Melchers, Willem J G; Swanink, Caroline M A; Bleijenberg, Gijs; Netea, Mihai G; Galama, Jochem M D; van der Meer, Jos W M

    2010-02-25

    The presence of the retrovirus xenotropic murine leukaemia virus-related virus (XMRV) has been reported in peripheral blood mononuclear cells of patients with chronic fatigue syndrome. Considering the potentially great medical and social relevance of such a discovery, we investigated whether this finding could be confirmed in an independent European cohort of patients with chronic fatigue syndrome. Analysis of a well defined cohort of patients and matched neighbourhood controls by polymerase chain reaction. Certified (ISO 15189) laboratory of clinical virology in a university hospital in the Netherlands. Population Between December 1991 and April 1992, peripheral blood mononuclear cells were isolated from 76 patients and 69 matched neighbourhood controls. In this study we tested cells from 32 patients and 43 controls from whom original cryopreserved phials were still available. Detection of XMRV in peripheral blood mononuclear cells by real time polymerase chain reaction assay targeting the XMRV integrase gene and/or a nested polymerase chain reaction assay targeting the XMRV gag gene. We detected no XMRV sequences in any of the patients or controls in either of the assays, in which relevant positive and negative isolation controls and polymerase chain reaction controls were included. Spiking experiments showed that we were able to detect at least 10 copies of XMRV sequences per 10(5) peripheral blood mononuclear cells by real time as well as by nested polymerase chain reaction, demonstrating high sensitivity of both assays. This study failed to show the presence of XMRV in peripheral blood mononuclear cells of patients with chronic fatigue syndrome from a Dutch cohort. These data cast doubt on the claim that XMRV is associated with chronic fatigue syndrome in the majority of patients.

  15. Maintenance of influenza A viruses and antibody response in mallards (Anas platyrhynchos) sampled during the non-breeding season in Alaska

    Science.gov (United States)

    Spivey, Timothy; Lindberg, Mark S.; Meixell, Brandt W.; Smith, Kyle R.; Puryear, Wendy B.; Davis, Kimberly R.; Runstadler, Jonathan A.; Stallknecht, David E.; Ramey, Andy M.

    2017-01-01

    Prevalence of influenza A virus (IAV) infections in northern-breeding waterfowl has previously been reported to reach an annual peak during late summer or autumn; however, little is known about IAV infection dynamics in waterfowl populations persisting at high-latitude regions such as Alaska, during winter. We captured mallards (Anas platyrhynchos) throughout the non-breeding season (August–April) of 2012–2015 in Fairbanks and Anchorage, the two largest cities in Alaska, to assess patterns of IAV infection and antibody production using molecular methods and a standard serologic assay. In addition, we used virus isolation, genetic sequencing, and a virus microneutralization assay to characterize viral subtypes and to evaluate the immune response of mallards captured on multiple occasions through time. We captured 923 mallards during three successive sampling years: Fairbanks in 2012/13 and 2013/14, and Anchorage in 2014/15. Prevalence varied by age, season, and year/site with high and relatively stable estimates throughout the non-breeding season. Infected birds were detected in all locations/seasons except early-winter in Fairbanks during 2013/14. IAVs with 17 combinations of hemagglutinin (H1–5, H7–9, H11, H12) and neuraminidase (N1–6, N8, N9) subtypes were isolated. Antibodies to IAVs were detected throughout autumn and winter for all sampling locations and years, however, seroprevalence was higher among adults and varied among years. Mallards exhibited individual heterogeneity with regard to immune response, providing instances of both seroconversion and seroreversion to detected viral subtypes. The probability that an individual transitioned from one serostatus to another varied by age, with juvenile mallards having higher rates of seroconversion and seroreversion than adults. Our study provides evidence that a diversity of IAVs circulate in populations of mallards wintering at urban locations in Alaska, and we suggest waterfowl wintering at high

  16. Comparison of stomach contents of haddock (Melanogrammus aeglefinus) from the 1981 and 1991 North Sea International Stomach Sampling Projects

    Science.gov (United States)

    Adlerstein, S.A.; Temming, A.; Mergardt, N.

    2002-01-01

    This study analyses data from over 20 000 haddock stomachs collected during the 1981 and 1991 Stomach Sampling Projects of the North Sea. Sampling was within the framework of the Multispecies Virtual Population Analysis (MSVPA) for fisheries stock assessment. In 1981 stomachs were collected to calculate input feeding parameters from main predators. During 1991 the sampling exercise was repeated to test stability of the parameters in the region. We investigate stability of haddock stomach content weight between years accounting for ontogenic, spatial and temporal variations within the scope of the survey resolution. Analysis using generalized linear and additive models is performed for weight of the stomach content including and excluding empty stomachs and also for proportion of stomachs without food. Results indicate that haddock stomach contents varied significantly between years, quarters and North Sea roundfish areas. Content weights were overall higher in 1981 than in 1991. In 1981 levels were high from spring to fall and in 1991 mostly in spring. During both years levels were lowest in the central North Sea and in winter. Most of the deviance in modelling the stomach weight is explained by the length of the predator. Stomachs sampled in 1981 were most frequently empty in spring and those sampled in 1991 in winter. In both years, proportions decreased with fish length except in winter when levels increased. Proportion of empty stomachs was highest in the central region of the North Sea. Most of the proportion variation is explained by quarterly fluctuation. Variation of content weight can be related to prey composition found in the stomachs. High stomach contents are generally associated with high contribution of fish prey to the total stomach content, mainly sandeels. We propose that sandeels were more vulnerable to predation in 1981 than in 1991 due to colder temperatures. ?? 2002 International Council for the Exploration of the Sea. Published by Elsevier

  17. Post-Flight Microbial Analysis of Samples from the International Space Station Water Recovery System and Oxygen Generation System

    Science.gov (United States)

    Birmele, Michele N.

    2011-01-01

    The Regenerative, Environmental Control and Life Support System (ECLSS) on the International Space Station (ISS) includes the the Water Recovery System (WRS) and the Oxygen Generation System (OGS). The WRS consists of a Urine Processor Assembly (UPA) and Water Processor Assembly (WPA). This report describes microbial characterization of wastewater and surface samples collected from the WRS and OGS subsystems, returned to KSC, JSC, and MSFC on consecutive shuttle flights (STS-129 and STS-130) in 2009-10. STS-129 returned two filters that contained fluid samples from the WPA Waste Tank Orbital Recovery Unit (ORU), one from the waste tank and the other from the ISS humidity condensate. Direct count by microscopic enumeration revealed 8.38 x 104 cells per mL in the humidity condensate sample, but none of those cells were recoverable on solid agar media. In contrast, 3.32 x lOs cells per mL were measured from a surface swab of the WRS waste tank, including viable bacteria and fungi recovered after S12 days of incubation on solid agar media. Based on rDNA sequencing and phenotypic characterization, a fungus recovered from the filter was determined to be Lecythophora mutabilis. The bacterial isolate was identified by rDNA sequence data to be Methylobacterium radiotolerans. Additional UPA subsystem samples were returned on STS-130 for analysis. Both liquid and solid samples were collected from the Russian urine container (EDV), Distillation Assembly (DA) and Recycle Filter Tank Assembly (RFTA) for post-flight analysis. The bacterium Pseudomonas aeruginosa and fungus Chaetomium brasiliense were isolated from the EDV samples. No viable bacteria or fungi were recovered from RFTA brine samples (N= 6), but multiple samples (N = 11) from the DA and RFTA were found to contain fungal and bacterial cells. Many recovered cells have been identified to genus by rDNA sequencing and carbon source utilization profiling (BiOLOG Gen III). The presence of viable bacteria and fungi from WRS

  18. The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data

    Science.gov (United States)

    Clarke, Laura; Fairley, Susan; Zheng-Bradley, Xiangqun; Streeter, Ian; Perry, Emily; Lowy, Ernesto; Tassé, Anne-Marie; Flicek, Paul

    2017-01-01

    The International Genome Sample Resource (IGSR; http://www.internationalgenome.org) expands in data type and population diversity the resources from the 1000 Genomes Project. IGSR represents the largest open collection of human variation data and provides easy access to these resources. IGSR was established in 2015 to maintain and extend the 1000 Genomes Project data, which has been widely used as a reference set of human variation and by researchers developing analysis methods. IGSR has mapped all of the 1000 Genomes sequence to the newest human reference (GRCh38), and will release updated variant calls to ensure maximal usefulness of the existing data. IGSR is collecting new structural variation data on the 1000 Genomes samples from long read sequencing and other technologies, and will collect relevant functional data into a single comprehensive resource. IGSR is extending coverage with new populations sequenced by collaborating groups. Here, we present the new data and analysis that IGSR has made available. We have also introduced a new data portal that increases discoverability of our data—previously only browseable through our FTP site—by focusing on particular samples, populations or data sets of interest. PMID:27638885

  19. CHLORELLA VIRUSES

    Science.gov (United States)

    Yamada, Takashi; Onimatsu, Hideki; Van Etten, James L.

    2007-01-01

    Chlorella viruses or chloroviruses are large, icosahedral, plaque‐forming, double‐stranded‐DNA—containing viruses that replicate in certain strains of the unicellular green alga Chlorella. DNA sequence analysis of the 330‐kbp genome of Paramecium bursaria chlorella virus 1 (PBCV‐1), the prototype of this virus family (Phycodnaviridae), predict ∼366 protein‐encoding genes and 11 tRNA genes. The predicted gene products of ∼50% of these genes resemble proteins of known function, including many that are completely unexpected for a virus. In addition, the chlorella viruses have several features and encode many gene products that distinguish them from most viruses. These products include: (1) multiple DNA methyltransferases and DNA site‐specific endonucleases, (2) the enzymes required to glycosylate their proteins and synthesize polysaccharides such as hyaluronan and chitin, (3) a virus‐encoded K+ channel (called Kcv) located in the internal membrane of the virions, (4) a SET domain containing protein (referred to as vSET) that dimethylates Lys27 in histone 3, and (5) PBCV‐1 has three types of introns; a self‐splicing intron, a spliceosomal processed intron, and a small tRNA intron. Accumulating evidence indicates that the chlorella viruses have a very long evolutionary history. This review mainly deals with research on the virion structure, genome rearrangements, gene expression, cell wall degradation, polysaccharide synthesis, and evolution of PBCV‐1 as well as other related viruses. PMID:16877063

  20. Analysis of Respiratory Syncytial Virus in Clinical Samples by Reverse Transcriptase-Polymerase Chain Reaction Restriction Mapping

    OpenAIRE

    Valdivia, Angel; Savón, Clara; Chacón, Danay; Sarmiento, Luis; Morier, Luis; Otero, Anselmo; Soto, Yudira; Oropesa, Suset; Goyenechea, Angel

    1997-01-01

    The aim of this study was to develop a polymerase chain reaction (PCR) for the detection of respiratory syncytial virus (RSV) genomes. The primers were designed from published sequences and selected from conserved regions of the genome encoding for the N protein of subgroups A and B of RSV. PCR was applied to 20 specimens from children admitted to the respiratory ward of "William Soler" Pediatric Hospital in Havana City with a clinical diagnosis of bronchiolitis. The PCR was compared with vir...

  1. Bluetongue virus RNA detection by real-time rt-PCR in post-vaccination samples from cattle.

    Science.gov (United States)

    De Leeuw, I; Garigliany, M; Bertels, G; Willems, T; Desmecht, D; De Clercq, K

    2015-04-01

    Bluetongue virus serotype 8 (BTV-8) was responsible for a large outbreak among European ruminant populations in 2006-2009. In spring 2008, a massive vaccination campaign was undertaken, leading to the progressive disappearance of the virus. During surveillance programmes in Western Europe in 2010-2011, a low but significant number of animals were found weakly positive using BTV-specific real-time RT-PCR, raising questions about a possible low level of virus circulation. An interference of the BTV-8 inactivated vaccine on the result of the real-time RT-PCR was also hypothesized. Several studies specifically addressed the potential association between a recent vaccination and BTV-8 RNA detection in the blood of sheep. Results were contradictory and cattles were not investigated. To enlighten this point, a large study was performed to determine the risks of detection of bluetongue vaccine-associated RNA in the blood and spleen of cattle using real-time RT-PCR. Overall, the results presented clearly demonstrate that vaccine viral RNA can reach the blood circulation in sufficient amounts to be detected by real-time RT-PCR in cattle. This BTV-8 vaccine RNA carriage appears as short lasting. © 2013 Blackwell Verlag GmbH.

  2. International Retrovirology Association brings together scientists and clinicians to bridge discoveries about human T-lymphotropic viruses from the laboratory to clinical trials

    Directory of Open Access Journals (Sweden)

    Morgan Owen

    2005-03-01

    Full Text Available Abstract Human T-lymphotropic virus type 1 (HTLV-1 and HTLV-2 were among the first human retroviruses discovered in the early 1980's. The International Retrovirology Association is an organized effort that fostered the efforts of scientists and clinicians to form interdisciplinary groups to study this group of retroviruses and their related diseases. The Association promotes excellent science, patient education, and fosters the training of young scientists to promote "bench-to-bedside" research. The International Conference on Human Retrovirology: HTLV and Related Viruses sponsored by the Association supports clinicians and researchers in the exchange of research findings and stimulation of new research directions. This years conference will be held from June 22 to 25, in Montego Bay, Jamaica http://www.htlvconference.org.jm/. Since its inception in 1988, these conferences have provided a highly interactive forum for the global community of HTLV scientists. This is of particular importance as HTLV research enters its third decade and a new generation of scientists takes over this important work. Many of the scientists attending the meeting will be from developing countries where HTLV is endemic, consistent with the history of international collaborations that have characterized HTLV research. The International Conference on Human Retrovirology provides a unique opportunity for researchers of all disciplines interested in HTLV infections to meet their peers and to address the questions facing clinicians and scientists who study retroviruses, like HTLV.

  3. Current Methods for Extraction and Concentration of Enteric Viruses from Fresh Fruit and Vegetables: Towards International Standards

    DEFF Research Database (Denmark)

    Croci, L.; Dubois, E.; Cook, N.

    2008-01-01

    Virus-contaminated soft fruits or vegetables are increasingly identified as causes of foodborne viral illness. Noroviruses and hepatitis A virus are the most common pathogens in viral infections transmitted by these kinds of foods. To improve microbiological detection and monitoring and to increase...... insights into the contribution of fruits and vegetables to foodborne viral transmission, sensitive, reliable, and standardized methods are needed. More studies on virus detection methods for foods are being published, but validated consensus protocols are not yet available. In this paper, different...

  4. Impact of Sample Matrix on Accuracy of Peptide Quantification: Assessment of Calibrator and Internal Standard Selection and Method Validation.

    Science.gov (United States)

    Arnold, Samuel L; Stevison, Faith; Isoherranen, Nina

    2016-01-05

    Protein quantification based on peptides using LC-MS/MS has emerged as a promising method to measure biomarkers, protein drugs, and endogenous proteins. However, the best practices for selection, optimization, and validation of the quantification peptides are not well established, and the influence of different matrices on protein digestion, peptide stability, and MS detection has not been systematically addressed. The aim of this study was to determine how biological matrices affect digestion, detection, and stability of peptides. The microsomal retinol dehydrogenase (RDH11) and cytosolic soluble aldehyde dehydrogenases (ALDH1As) involved in the synthesis of retinoic acid (RA) were chosen as model proteins. Considerable differences in the digestion efficiency, sensitivity, and matrix effects between peptides were observed regardless of the target protein's subcellular localization. The precision and accuracy of the quantification of RDH11 and ALDH1A were affected by the choice of calibration and internal standards. The final method using recombinant protein calibrators and stable isotope labeled (SIL) peptide internal standards was validated for human liver. The results demonstrate that different sample matrices have peptide, time, and matrix specific effects on protein digestion and absolute quantification.

  5. Multiplex RT-PCR method for the simultaneous detection of nine grapevine viruses.

    Science.gov (United States)

    Gambino, Giorgio

    2015-01-01

    Viral diseases are a serious pathological problem for grapevines, and in recent years the need for increasingly specific and rapid diagnostic methods for the selection of propagation materials has grown. Arabis mosaic virus, Grapevine fanleaf virus, Grapevine virus A, Grapevine virus B, Grapevine rupestris stem pitting-associated virus, Grapevine fleck virus, and Grapevine leafroll-associated viruses 1, 2, and 3 are nine of the most widespread viruses that naturally infect grapevines. A multiplex RT-PCR was developed for simultaneous detection of these nine grapevine viruses, in combination with a plant RNA internal control used as an indicator of the effectiveness of the reaction. One to ten fragments specific for the viruses and an internal control were simultaneously amplified from infected samples and identified by their specific molecular sizes in agarose gel. The protocol reported is an update of previously published protocols for RNA extraction and multiplex diagnosis of viruses. After several years of use and hundreds of samples tested, and following validation in several laboratories, this multiplex RT-PCR provides a reliable and rapid method for detecting grapevine viruses from a large number of samples.

  6. Sample Stacking Provides Three Orders of Magnitude Sensitivity Enhancement in SDS Capillary Gel Electrophoresis of Adeno-Associated Virus Capsid Proteins.

    Science.gov (United States)

    Zhang, Chao-Xuan; Meagher, Michael M

    2017-03-21

    Size-based protein analysis utilizing only 25 ng of total proteins has been realized by sodium dodecyl sulfate capillary gel electrophoresis (SDS CGE) with head-column field-amplified sample stacking as an online sample preconcentration technique. This method has been used as a replacement of SDS-PAGE for purity analysis of adeno-associated virus (AAV) therapeutic products of different serotypes and transgenes. A limit of detection of 0.2 ng/mL (3.3 pM) capsid proteins was achieved with convenient UV absorbance detection at 214 nm, equivalent to 20 pg of protein (330 attomole) loaded in the autosampler vial. For purity analysis, only 25 ng of total AAV capsid proteins (4.3 femtomole virus particles) were loaded to the autosampler vial. The sensitivity is comparable to silver-stained SDS-PAGE. The RSD of purity measurement was 0.0-0.8%, comparable to conventional SDS CGE utilizing 0.1-0.5 mg proteins. The new method provided 3 orders of magnitude sensitivity enhancement as compared to conventional SDS CGE. It shares all the advantages of conventional SDS CGE (labor-saving, easy automation, and convenient quantitation) and also the high sensitivity of silver stained SDS-PAGE. The sample stacking SDS CGE technique can be adopted for size-based analysis of other types of proteins. It is especially useful when protein quantity or concentration is not sufficient for regular SDS CGE or SDS-PAGE assay.

  7. International Study to Evaluate PCR Methods for Detection of Trypanosoma cruzi DNA in Blood Samples from Chagas Disease Patients

    Science.gov (United States)

    Schijman, Alejandro G.; Bisio, Margarita; Orellana, Liliana; Sued, Mariela; Duffy, Tomás; Mejia Jaramillo, Ana M.; Cura, Carolina; Auter, Frederic; Veron, Vincent; Qvarnstrom, Yvonne; Deborggraeve, Stijn; Hijar, Gisely; Zulantay, Inés; Lucero, Raúl Horacio; Velazquez, Elsa; Tellez, Tatiana; Sanchez Leon, Zunilda; Galvão, Lucia; Nolder, Debbie; Monje Rumi, María; Levi, José E.; Ramirez, Juan D.; Zorrilla, Pilar; Flores, María; Jercic, Maria I.; Crisante, Gladys; Añez, Néstor; De Castro, Ana M.; Gonzalez, Clara I.; Acosta Viana, Karla; Yachelini, Pedro; Torrico, Faustino; Robello, Carlos; Diosque, Patricio; Triana Chavez, Omar; Aznar, Christine; Russomando, Graciela; Büscher, Philippe; Assal, Azzedine; Guhl, Felipe; Sosa Estani, Sergio; DaSilva, Alexandre; Britto, Constança; Luquetti, Alejandro; Ladzins, Janis

    2011-01-01

    Background A century after its discovery, Chagas disease still represents a major neglected tropical threat. Accurate diagnostics tools as well as surrogate markers of parasitological response to treatment are research priorities in the field. The purpose of this study was to evaluate the performance of PCR methods in detection of Trypanosoma cruzi DNA by an external quality evaluation. Methodology/Findings An international collaborative study was launched by expert PCR laboratories from 16 countries. Currently used strategies were challenged against serial dilutions of purified DNA from stocks representing T. cruzi discrete typing units (DTU) I, IV and VI (set A), human blood spiked with parasite cells (set B) and Guanidine Hidrochloride-EDTA blood samples from 32 seropositive and 10 seronegative patients from Southern Cone countries (set C). Forty eight PCR tests were reported for set A and 44 for sets B and C; 28 targeted minicircle DNA (kDNA), 13 satellite DNA (Sat-DNA) and the remainder low copy number sequences. In set A, commercial master mixes and Sat-DNA Real Time PCR showed better specificity, but kDNA-PCR was more sensitive to detect DTU I DNA. In set B, commercial DNA extraction kits presented better specificity than solvent extraction protocols. Sat-DNA PCR tests had higher specificity, with sensitivities of 0.05–0.5 parasites/mL whereas specific kDNA tests detected 5.10−3 par/mL. Sixteen specific and coherent methods had a Good Performance in both sets A and B (10 fg/µl of DNA from all stocks, 5 par/mL spiked blood). The median values of sensitivities, specificities and accuracies obtained in testing the Set C samples with the 16 tests determined to be good performing by analyzing Sets A and B samples varied considerably. Out of them, four methods depicted the best performing parameters in all three sets of samples, detecting at least 10 fg/µl for each DNA stock, 0.5 par/mL and a sensitivity between 83.3–94.4%, specificity of 85–95

  8. International study to evaluate PCR methods for detection of Trypanosoma cruzi DNA in blood samples from Chagas disease patients.

    Directory of Open Access Journals (Sweden)

    Alejandro G Schijman

    Full Text Available BACKGROUND: A century after its discovery, Chagas disease still represents a major neglected tropical threat. Accurate diagnostics tools as well as surrogate markers of parasitological response to treatment are research priorities in the field. The purpose of this study was to evaluate the performance of PCR methods in detection of Trypanosoma cruzi DNA by an external quality evaluation. METHODOLOGY/FINDINGS: An international collaborative study was launched by expert PCR laboratories from 16 countries. Currently used strategies were challenged against serial dilutions of purified DNA from stocks representing T. cruzi discrete typing units (DTU I, IV and VI (set A, human blood spiked with parasite cells (set B and Guanidine Hidrochloride-EDTA blood samples from 32 seropositive and 10 seronegative patients from Southern Cone countries (set C. Forty eight PCR tests were reported for set A and 44 for sets B and C; 28 targeted minicircle DNA (kDNA, 13 satellite DNA (Sat-DNA and the remainder low copy number sequences. In set A, commercial master mixes and Sat-DNA Real Time PCR showed better specificity, but kDNA-PCR was more sensitive to detect DTU I DNA. In set B, commercial DNA extraction kits presented better specificity than solvent extraction protocols. Sat-DNA PCR tests had higher specificity, with sensitivities of 0.05-0.5 parasites/mL whereas specific kDNA tests detected 5.10(-3 par/mL. Sixteen specific and coherent methods had a Good Performance in both sets A and B (10 fg/µl of DNA from all stocks, 5 par/mL spiked blood. The median values of sensitivities, specificities and accuracies obtained in testing the Set C samples with the 16 tests determined to be good performing by analyzing Sets A and B samples varied considerably. Out of them, four methods depicted the best performing parameters in all three sets of samples, detecting at least 10 fg/µl for each DNA stock, 0.5 par/mL and a sensitivity between 83.3-94.4%, specificity of 85

  9. Impact of internal RNA on aggregation and electrokinetics of viruses: comparison between MS2 phage and corresponding virus-like particles.

    Science.gov (United States)

    Dika, C; Duval, J F L; Ly-Chatain, H M; Merlin, C; Gantzer, C

    2011-07-01

    We compare for the first time the electrokinetic and aggregation properties of MS2 phage (pH 2.5 to 7, 1 to 100 mM NaNO(3) electrolyte concentration) with those of the corresponding virus-like particles (VLPs), which lack entirely the inner viral RNA component. In line with our previous work (J. Langlet, F. Gaboriaud, C. Gantzer, and J. F. L. Duval, Biophys. J. 94:3293-3312, 2008), it is found that modifying the content of RNA within the virus leads to very distinct electrohydrodynamic and aggregation profiles for MS2 and MS2 VLPs. Under the given pH and concentration conditions, MS2 VLPs exhibit electrophoretic mobility larger in magnitude than that of MS2, and both have similar isoelectric point (IEP) values (∼4). The electrokinetic results reflect a greater permeability of MS2 VLPs to electroosmotic flow, developed within/around these soft particles during their migration under the action of the applied electrical field. Results also support the presence of some remaining negatively charged component within the VLPs. In addition, MS2 phage systematically forms aggregates at pH values below the IEP, regardless of the magnitude of the solution ionic strength, whereas MS2 VLPs aggregate under the strict condition where the pH is relatively equal to the IEP at sufficiently low salt concentrations (electrokinetics of MS2 and corresponding VLPs conform to recently developed formalisms for the stability and electrohydrodynamics of soft multilayered particles. The differences between the surface properties of these two kinds of particles reported here suggest that VLPs may not be appropriate for predicting the behavior of pathogenic viruses in aqueous media.

  10. Impact of Internal RNA on Aggregation and Electrokinetics of Viruses: Comparison between MS2 Phage and Corresponding Virus-Like Particles ▿

    Science.gov (United States)

    Dika, C.; Duval, J. F. L.; Ly-Chatain, H. M.; Merlin, C.; Gantzer, C.

    2011-01-01

    We compare for the first time the electrokinetic and aggregation properties of MS2 phage (pH 2.5 to 7, 1 to 100 mM NaNO3 electrolyte concentration) with those of the corresponding virus-like particles (VLPs), which lack entirely the inner viral RNA component. In line with our previous work (J. Langlet, F. Gaboriaud, C. Gantzer, and J. F. L. Duval, Biophys. J. 94:3293-3312, 2008), it is found that modifying the content of RNA within the virus leads to very distinct electrohydrodynamic and aggregation profiles for MS2 and MS2 VLPs. Under the given pH and concentration conditions, MS2 VLPs exhibit electrophoretic mobility larger in magnitude than that of MS2, and both have similar isoelectric point (IEP) values (∼4). The electrokinetic results reflect a greater permeability of MS2 VLPs to electroosmotic flow, developed within/around these soft particles during their migration under the action of the applied electrical field. Results also support the presence of some remaining negatively charged component within the VLPs. In addition, MS2 phage systematically forms aggregates at pH values below the IEP, regardless of the magnitude of the solution ionic strength, whereas MS2 VLPs aggregate under the strict condition where the pH is relatively equal to the IEP at sufficiently low salt concentrations (electrokinetics of MS2 and corresponding VLPs conform to recently developed formalisms for the stability and electrohydrodynamics of soft multilayered particles. The differences between the surface properties of these two kinds of particles reported here suggest that VLPs may not be appropriate for predicting the behavior of pathogenic viruses in aqueous media. PMID:21622784

  11. Dimensionality and stages of severity of DSM-5 criteria in an international sample of alcohol-consuming individuals.

    Science.gov (United States)

    Preuss, U W; Watzke, S; Wurst, F M

    2014-11-01

    The DSM-5 alcohol use disorder (AUD) criteria proposal contains 11 criteria that include most of the DSM-IV abuse and dependence criteria plus craving. The aims of the current study in a large and international alcohol-consuming sample were to confirm the dimensionality of the DSM-5 AUD criteria and to differentiate grades of severity of DSM-5 AUD in subjects who pass the proposed DSM-5 diagnostic threshold of two criteria. We used the World Health Organization (WHO)/International Society on Biomedical Research on Alcoholism (ISBRA) Study on State and Trait Markers of Alcohol Use and Dependence dataset. Subjects included in the analyses were aged ≥ 18 years and were recruited in five countries: Australia, Brazil, Canada, Finland and Japan. Assessment of AUD and additional characteristics was conducted using an adapted version of the Alcohol Use Disorder and Associated Disabilities Interview Schedule (AUDADIS). Dimensionality of the DSM-5 criteria was evaluated using factor analysis and item response theory (IRT) models. The IRT results led to the classification of AUD patients into three severity groups. External validators were used to differentiate statistically across subgroups. A total of 1424 currently drinking individuals were included in the analyses. Factor and IRT analyses confirmed the dimensional structure of DSM-5 AUD criteria. More than 99% of the subjects could be allocated to one of the suggested severity subgroups. The magnitude of the external validators differed significantly across the severity groups. The results confirm the dimensional structure of the proposed DSM-5 AUD criteria. The suggested stages of severity (mild, moderate and severe) may be useful to clinicians by grouping individuals not only in the mild but also in the moderate to severe spectrum of DSM-5 AUD.

  12. Development and inter-laboratory validation study of an improved new real-time PCR assay with internal control for detection and laboratory diagnosis of African swine fever virus.

    Science.gov (United States)

    Tignon, Marylène; Gallardo, Carmina; Iscaro, Carmen; Hutet, Evelyne; Van der Stede, Yves; Kolbasov, Denis; De Mia, Gian Mario; Le Potier, Marie-Frédérique; Bishop, Richard P; Arias, Marisa; Koenen, Frank

    2011-12-01

    A real-time polymerase chain reaction (PCR) assay for the rapid detection of African swine fever virus (ASFV), multiplexed for simultaneous detection of swine beta-actin as an endogenous control, has been developed and validated by four National Reference Laboratories of the European Union for African swine fever (ASF) including the European Union Reference Laboratory. Primers and a TaqMan(®) probe specific for ASFV were selected from conserved regions of the p72 gene. The limit of detection of the new real-time PCR assay is 5.7-57 copies of the ASFV genome. High accuracy, reproducibility and robustness of the PCR assay (CV ranging from 0.7 to 5.4%) were demonstrated both within and between laboratories using different real-time PCR equipments. The specificity of virus detection was validated using a panel of 44 isolates collected over many years in various geographical locations in Europe, Africa and America, including recent isolates from the Caucasus region, Sardinia, East and West Africa. Compared to the OIE-prescribed conventional and real-time PCR assays, the sensitivity of the new assay with internal control was improved, as demonstrated by testing 281 field samples collected in recent outbreaks and surveillance areas in Europe and Africa (170 samples) together with samples obtained through experimental infections (111 samples). This is particularly evident in the early days following experimental infection and during the course of the disease in pigs sub-clinically infected with strains of low virulence (from 35 up to 70dpi). The specificity of the assay was also confirmed on 150 samples from uninfected pigs and wild boar from ASF-free areas. Measured on the total of 431 tested samples, the positive deviation of the new assay reaches 21% or 26% compared to PCR and real-time PCR methods recommended by OIE. This improved and rigorously validated real-time PCR assay with internal control will provide a rapid, sensitive and reliable molecular tool for ASFV

  13. Psychological capital: Internal and external validity of the Psychological Capital Questionnaire (PCQ-24 on a South African sample

    Directory of Open Access Journals (Sweden)

    Gina Görgens-Ekermans

    2013-03-01

    Full Text Available Orientation: Psychological capital (PsyCap is a relatively novel construct measured with the Psychological Capital Questionnaire 24 (PCQ-24. Only one published South African study on the instrument exists, providing inconsistent psychometric results, when compared with other United States of America (USA and non-USA studies.Research purpose: The objectives of this study were to investigate the internal validity (construct and discriminant validity, reliability and external validity (relationship with theoretically relevant variables, namely stress, burnout and work engagement of the PCQ-24.Motivation for the study: Multiple studies have underscored the value of PsyCap within the workplace. In order to harness the full potential of the construct in the South African environment, sound measurement thereof, evidenced by a psychometrically sound instrument, is needed.Research design, approach and method: A cross-sectional survey design was used. The sample consisted of employees at managerial and non-managerial levels, from a medium-sized construction company in the Western Cape, South Africa. In addition to PsyCap, perceived stress, work-related burnout and work engagement were measured.Main findings: The results provided preliminary evidence of construct and discriminant validity, reliability and significant relations with external theoretically relevant variables.Practical/managerial implications: Researchers may confidently use the PCQ-24 to measure the construct of PsyCap and investigate relations with workplace outcomes in the South African environment, informing human relations practices.Contribution/value-add: Preliminary evidence of the psychometric properties of the PCQ-24, which measures the construct of PsyCap (consisting of hope, self-efficacy, resilience and optimism on a South African sample, was provided in this study.

  14. Lifestyle factors, demographics and medications associated with depression risk in an international sample of people with multiple sclerosis.

    Science.gov (United States)

    Taylor, Keryn L; Hadgkiss, Emily J; Jelinek, George A; Weiland, Tracey J; Pereira, Naresh G; Marck, Claudia H; van der Meer, Dania M

    2014-12-03

    Depression is the most common co-morbidity for people with Multiple Sclerosis (MS); irrespective of disease severity, depression has the greatest impact on quality of life. An emerging paradigm in the treatment of depression is lifestyle medicine. There is significant potential to prevent and treat depression through modification of lifestyle risk factors for people with MS. This study sought to understand the association between lifestyle risk factors, medication and depression risk through the analysis of self-reported data from a large international sample of people with MS. This cross-sectional analysis recruited a total of 2459 participants via Web 2.0 platforms. Survey data included socio-demographics; a range of lifestyle risk factors; medication; disease variables and depression risk using the Patient Health Questionnaire-2 (PHQ-2). In total approximately one fifth (19.3%) of our sample screened positive for depression (PHQ-2 score ≥3). Several demographic factors were significantly associated with this depression risk in bivariate analysis. Regression analyses showed that poor diet, low levels of exercise, obesity, smoking, marked social isolation and taking interferon were associated with greater depression risk. Participants who supplemented with omega 3s, particularly flaxseed oil, had frequent fish consumption, supplemented with vitamin D, meditated, and had moderate alcohol consumption had significantly reduced depression risk. This study demonstrates a significant association between modifiable lifestyle factors and depression risk. Planned longitudinal follow up may clarify causality. Clinicians and people with MS should be aware of the wide range of modifiable lifestyle factors that may reduce depression risk as part of a comprehensive secondary and tertiary preventive medical approach to managing MS.

  15. Biopsies of cicatricial conjunctivitis cases reveal highly variable sampling practice among ophthalmologists: time for national and international standardisation.

    Science.gov (United States)

    Mudhar, Hardeep Singh

    2016-06-01

    There has been no in-depth study examining the preanalytical direct immunofluorescence (DIF) biopsy phase for patients with cicatricial conjunctivitis. 90 patients with cicatricial conjunctivitis had biopsies taken for DIF. The study examined the following biopsy and clinical parameters: Age and sex of patient, unilateral or bilateral involvement, unilateral or bilateral biopsy, site of biopsy, nature of biopsy site (normal or diseased), number of biopsies per eye, size of biopsy, medium in which biopsy sent, whether buccal mucosa biopsied, whether tissue biopsied for histology (fixed in formalin) DIF results for conjunctival and buccal biopsies and final clinicopathological diagnosis. Most cases had unilateral sampling despite many cases showing bilateral disease. 15/90 cases had buccal biopsies. The conjunctival site for biopsy was not consistent from case to case. The mean maximum biopsy size was 3.3 mm length, 1 mm depth. No case was inadequate for DIF. Biopsies were obtained from conjunctiva with varying disease activity. 80/90 cases were sent in an appropriate medium permitting DIF. DIF+ biopsy rates were not affected by biopsy site disease activity. Five cases of bilateral involvement and bilateral biopsies showed only unilateral DIF+. In five cases, the conjunctival biopsies were DIF+ and the buccal biopsy was DIF-. Five cases showed in situ and invasive carcinoma seen on the accompanying formalin-fixed biopsy. DIF biopsies for cicatricial conjunctivitis showed highly variable preanalytical phase sampling practice that requires national and international standardisation to facilitate prompt diagnosis, treatment, research and audit. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

  16. ICTV Virus Taxonomy Profile

    DEFF Research Database (Denmark)

    Simmonds, Peter; Becher, Paul; Bukh, Jens

    2017-01-01

    borne, and many are important human and veterinary pathogens (e.g. yellow fever virus, dengue virus). This is a summary of the current International Committee on Taxonomy of Viruses (ICTV) report on the taxonomy of the Flaviviridae, which is available at www.ictv.global/report/flaviviridae....

  17. Internal Structure and Measurement Invariance of the Dutch Eating Behavior Questionnaire (DEBQ) in a (Nearly) Representative Dutch Community Sample.

    Science.gov (United States)

    Barrada, Juan Ramón; van Strien, Tatjana; Cebolla, Ausiàs

    2016-11-01

    The Dutch Eating Behavior Questionnaire is a widely used instrument for assessment of emotional, external and restrained eating. The aim of the present study is to (i) analyse its internal structure using exploratory structural equation modelling; (ii) to assess its measurement invariance with respect to sex, BMI, age and level of education; and (iii) to evaluate the relations of the factors with these variables. Except that women were slightly over-represented, the sample (n = 2173) closely followed the sociodemographic characteristics of the overall Dutch population. The three theoretical factors that emerged from the analysis were in close correspondence with the three scales for emotional, external and restrained eating. Only two items (item 3 - 'desire to eat when nothing to do…' and item 21 - 'resist delicious food...') presented problematic loadings. The questionnaire showed satisfactory measurement invariance, and expected patterns of mean differences and relations were found. All in all, the results highlight the adequate psychometric properties of the Dutch Eating Behavior Questionnaire. Copyright © 2016 John Wiley & Sons, Ltd and Eating Disorders Association. Copyright © 2016 John Wiley & Sons, Ltd and Eating Disorders Association.

  18. [Investigation of BK and JC virus DNA positivities by real-time polymerase chain reaction in the clinical samples of patients with high risk].

    Science.gov (United States)

    Rota, Seyyal; Fidan, Kibriya; Bozdayı, Gülendam; Dalgıç, Aydın; Fidan, Işıl; Sucak, Gülsan; Müderris, Tuba

    2011-04-01

    Human polyomaviruses, namely BK (BKV) and JC (JCV) viruses are small DNA viruses that cause latent infections worldwide. Primary infections are usually acquired in the early periods of life and are generally asymptomatic. However BKV/JCV infections may cause severe clinical conditions in immunosuppressive patients such as bone marrow and solid organ transplantation or cancer patients. The aim of this retrospective study was to investigate the presence of BKV and JCV nucleic acids by real-time polymerase chain reaction (RT-PCR) in the clinical samples of patients with high risk. A total of 268 (62 blood, 206 urine) samples obtained from 115 immunocompromised patients hospitalized in Gazi University Hospital between July 2007 to January 2009, were included to the study. Viral nucleic acids were extracted from the samples with High Pure PCR Template Preparation Kit (Roche, Germany). By using amplification mix (TIB Molbiol GmbH, Germany) that included primers targeting 174 (JCV) and 219 (BKV) base pair fragments of the small t antigen, and hybridization probes (Roche, Germany), nucleic acids were amplified with LightCycler (Roche Applied Science, Germany) system. As a result, total polyomavirus DNA positivity rate was found as 33.2% (89/268). When BKV and JCV DNA positivities were evaluated according to the samples, 25.2% (53/206) of urine samples yielded positive results for BKV, 14.5% (30/206) for JCV and 2.4% (5/206) for both BKV and JCV. Only one of the blood samples (1/62; 1.6%) were found positive by means of BKV DNA, while none of the blood samples were positive for JCV DNA. The distribution of BKV and JCV DNA positivity rates according to the inpatient clinics were as follows, respectively; 24.3% and 9.5% for pediatric nephrology, 9.6% and 8.2% for renal transplantation unit, 13.5% and 18.9% for adult nephrology, 30.8% and 15.4% for bone marrow transplantation unit, 22.9% and 8.6% for pediatric clinics. In samples from pediatric hematology patients, BKV

  19. Clinically significant fatigue: prevalence and associated factors in an international sample of adults with multiple sclerosis recruited via the internet.

    Directory of Open Access Journals (Sweden)

    Tracey J Weiland

    Full Text Available Fatigue contributes a significant burden of disease for people with multiple sclerosis (PwMS. Modifiable lifestyle factors have been recognized as having a role in a range of morbidity outcomes in PwMS. There is significant potential to prevent and treat fatigue in PwMS by addressing modifiable risk factors.To explore the associations between clinically significant fatigue and demographic factors, clinical factors (health-related quality of life, disability and relapse rate and modifiable lifestyle, disease-modifying drugs (DMD and supplement use in a large international sample of PwMS.PwMS were recruited to the study via Web 2.0 platforms and completed a comprehensive survey measuring demographic, lifestyle and clinical characteristics, including health-related quality of life, disability, and relapse rate.Of 2469 participants with confirmed MS, 2138 (86.6% completed a validated measure of clinically significant fatigue, the Fatigue Severity Scale. Participants were predominantly female from English speaking countries, with relatively high levels of education, and due to recruitment methods may have been highly pro-active about engaging in lifestyle management and self-help. Approximately two thirds of our sample (1402/2138; 65.6% (95% CI 63.7-67.7 screened positive for clinically significant fatigue. Bivariate associations were present between clinically significant fatigue and several demographic, clinical, lifestyle, and medication variables. After controlling for level of disability and a range of stable socio-demographic variables, we found increased odds of fatigue associated with obesity, DMD use, poor diet, and reduced odds of fatigue with exercise, fish consumption, moderate alcohol use, and supplementation with vitamin D and flaxseed oil.This study supports strong and significant associations between clinically significant fatigue and modifiable lifestyle factors. Longitudinal follow-up of this sample may help clarify the contribution

  20. The internal initiation of translation in bovine viral diarrhea virus RNA depends on the presence of an RNA pseudoknot upstream of the initiation codon

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    Moes Lorin

    2007-11-01

    Full Text Available Abstract Background Bovine viral diarrhea virus (BVDV is the prototype representative of the pestivirus genus in the Flaviviridae family. It has been shown that the initiation of translation of BVDV RNA occurs by an internal ribosome entry mechanism mediated by the 5' untranslated region of the viral RNA 1. The 5' and 3' boundaries of the IRES of the cytopathic BVDV NADL have been mapped and it has been suggested that the IRES extends into the coding of the BVDV polyprotein 2. A putative pseudoknot structure has been recognized in the BVDV 5'UTR in close proximity to the AUG start codon. A pseudoknot structure is characteristic for flavivirus IRESes and in the case of the closely related classical swine fever virus (CSFV and the more distantly related Hepatitis C virus (HCV pseudoknot function in translation has been demonstrated. Results To characterize the BVDV IRESes in detail, we studied the BVDV translational initiation by transfection of dicistronic expression plasmids into mammalian cells. A region coding for the amino terminus of the BVDV SD-1 polyprotein contributes considerably to efficient initiation of translation. The translation efficiency mediated by the IRES of BVDV strains NADL and SD-1 approximates the poliovirus type I IRES directed translation in BHK cells. Compared to the poliovirus IRES increased expression levels are mediated by the BVDV IRES of strain SD-1 in murine cell lines, while lower levels are observed in human cell lines. Site directed mutagenesis revealed that a RNA pseudoknot upstream of the initiator AUG is an important structural element for IRES function. Mutants with impaired ability to base pair in stem I or II lost their translational activity. In mutants with repaired base pairing either in stem 1 or in stem 2 full translational activity was restored. Thus, the BVDV IRES translation is dependent on the pseudoknot integrity. These features of the pestivirus IRES are reminiscent of those of the classical

  1. A sensitive one-step real-time PCR for detection of avian influenza viruses using a MGB probe and an internal positive control

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    Delogu Mauro

    2006-05-01

    Full Text Available Abstract Background Avian influenza viruses (AIVs are endemic in wild birds and their introduction and conversion to highly pathogenic avian influenza virus in domestic poultry is a cause of serious economic losses as well as a risk for potential transmission to humans. The ability to rapidly recognise AIVs in biological specimens is critical for limiting further spread of the disease in poultry. The advent of molecular methods such as real time polymerase chain reaction has allowed improvement of detection methods currently used in laboratories, although not all of these methods include an Internal Positive Control (IPC to monitor for false negative results. Therefore we developed a one-step reverse transcription real time PCR (RRT-PCR with a Minor Groove Binder (MGB probe for the detection of different subtypes of AIVs. This technique also includes an IPC. Methods RRT-PCR was developed using an improved TaqMan technology with a MGB probe to detect AI from reference viruses. Primers and probe were designed based on the matrix gene sequences from most animal and human A influenza virus subtypes. The specificity of RRT-PCR was assessed by detecting influenza A virus isolates belonging to subtypes from H1–H13 isolated in avian, human, swine and equine hosts. The analytical sensitivity of the RRT-PCR assay was determined using serial dilutions of in vitro transcribed matrix gene RNA. The use of a rodent RNA as an IPC in order not to reduce the efficiency of the assay was adopted. Results The RRT-PCR assay is capable to detect all tested influenza A viruses. The detection limit of the assay was shown to be between 5 and 50 RNA copies per reaction and the standard curve demonstrated a linear range from 5 to 5 × 108 copies as well as excellent reproducibility. The analytical sensitivity of the assay is 10–100 times higher than conventional RT-PCR. Conclusion The high sensitivity, rapidity, reproducibility and specificity of the AIV RRT-PCR with

  2. Multiplex RT-PCR detection of four aphid-borne strawberry viruses in Fragaria spp. in combination with a plant mRNA specific internal control

    NARCIS (Netherlands)

    Thompson, J.R.; Wetzel, S.; Klerks, M.M.; Vasková, D.; Schoen, C.D.; Spak, J.; Jelkmann, W.

    2003-01-01

    The principal aphid-borne viruses infecting Strawberry (Fragaria spp.) Strawberry crinkle virus (SCV), Strawberry mild yellow edge virus (SMYEV), Strawberry mottle virus (SMoV) and Strawberry vein banding virus (SVBV) can cause serious crop losses. In this paper, a multiplex reverse transcriptase

  3. Epstein-Barr virus-associated lymphoproliferative disease in non-immunocompromised hosts: a status report and summary of an international meeting, 8-9 September 2008.

    Science.gov (United States)

    Cohen, J I; Kimura, H; Nakamura, S; Ko, Y-H; Jaffe, E S

    2009-09-01

    Recently novel Epstein-Barr virus (EBV) lymphoproliferative diseases (LPDs) have been identified in non-immunocompromised hosts, both in Asia and Western countries. These include aggressive T-cell and NK-cell LPDs often subsumed under the heading of chronic active Epstein-Barr virus (CAEBV) infection and EBV-driven B-cell LPDs mainly affecting the elderly. To better define the pathogenesis, classification, and treatment of these disorders, participants from Asia, The Americas, Europe, and Australia presented clinical and experimental data at an international meeting. The term systemic EBV-positive T-cell LPD, as adopted by the WHO classification, is preferred as a pathological classification over CAEBV (the favored clinical term) for those cases that are clonal. The disease has an aggressive clinical course, but may arise in the background of CAEBV. Hydroa vacciniforme (HV) and HV-like lymphoma represent a spectrum of clonal EBV-positive T-cell LPDs, which have a more protracted clinical course; spontaneous regression may occur in adult life. Severe mosquito bite allergy is a related syndrome usually of NK cell origin. Immune senescence in the elderly is associated with both reactive and neoplastic EBV-driven LPDs, including EBV-positive diffuse large B-cell lymphomas. The participants proposed an international consortium to facilitate further clinical and biological studies of novel EBV-driven LPDs.

  4. Epstein–Barr virus-associated lymphoproliferative disease in non-immunocompromised hosts: a status report and summary of an international meeting, 8–9 September 2008

    Science.gov (United States)

    Cohen, J. I.; Kimura, H.; Nakamura, S.; Ko, Y.-H.; Jaffe, E. S.

    2009-01-01

    Background: Recently novel Epstein–Barr virus (EBV) lymphoproliferative diseases (LPDs) have been identified in non-immunocompromised hosts, both in Asia and Western countries. These include aggressive T-cell and NK-cell LPDs often subsumed under the heading of chronic active Epstein–Barr virus (CAEBV) infection and EBV-driven B-cell LPDs mainly affecting the elderly. Design: To better define the pathogenesis, classification, and treatment of these disorders, participants from Asia, The Americas, Europe, and Australia presented clinical and experimental data at an international meeting. Results: The term systemic EBV-positive T-cell LPD, as adopted by the WHO classification, is preferred as a pathological classification over CAEBV (the favored clinical term) for those cases that are clonal. The disease has an aggressive clinical course, but may arise in the background of CAEBV. Hydroa vacciniforme (HV) and HV-like lymphoma represent a spectrum of clonal EBV-positive T-cell LPDs, which have a more protracted clinical course; spontaneous regression may occur in adult life. Severe mosquito bite allergy is a related syndrome usually of NK cell origin. Immune senescence in the elderly is associated with both reactive and neoplastic EBV-driven LPDs, including EBV-positive diffuse large B-cell lymphomas. Conclusion: The participants proposed an international consortium to facilitate further clinical and biological studies of novel EBV-driven LPDs. PMID:19515747

  5. Heparin removal by ecteola-cellulose pre-treatment enables the use of plasma samples for accurate measurement of anti-Yellow fever virus neutralizing antibodies.

    Science.gov (United States)

    Campi-Azevedo, Ana Carolina; Peruhype-Magalhães, Vanessa; Coelho-Dos-Reis, Jordana Grazziela; Costa-Pereira, Christiane; Yamamura, Anna Yoshida; Lima, Sheila Maria Barbosa de; Simões, Marisol; Campos, Fernanda Magalhães Freire; de Castro Zacche Tonini, Aline; Lemos, Elenice Moreira; Brum, Ricardo Cristiano; de Noronha, Tatiana Guimarães; Freire, Marcos Silva; Maia, Maria de Lourdes Sousa; Camacho, Luiz Antônio Bastos; Rios, Maria; Chancey, Caren; Romano, Alessandro; Domingues, Carla Magda; Teixeira-Carvalho, Andréa; Martins-Filho, Olindo Assis

    2017-09-01

    Technological innovations in vaccinology have recently contributed to bring about novel insights for the vaccine-induced immune response. While the current protocols that use peripheral blood samples may provide abundant data, a range of distinct components of whole blood samples are required and the different anticoagulant systems employed may impair some properties of the biological sample and interfere with functional assays. Although the interference of heparin in functional assays for viral neutralizing antibodies such as the functional plaque-reduction neutralization test (PRNT), considered the gold-standard method to assess and monitor the protective immunity induced by the Yellow fever virus (YFV) vaccine, has been well characterized, the development of pre-analytical treatments is still required for the establishment of optimized protocols. The present study intended to optimize and evaluate the performance of pre-analytical treatment of heparin-collected blood samples with ecteola-cellulose (ECT) to provide accurate measurement of anti-YFV neutralizing antibodies, by PRNT. The study was designed in three steps, including: I. Problem statement; II. Pre-analytical steps; III. Analytical steps. Data confirmed the interference of heparin on PRNT reactivity in a dose-responsive fashion. Distinct sets of conditions for ECT pre-treatment were tested to optimize the heparin removal. The optimized protocol was pre-validated to determine the effectiveness of heparin plasma:ECT treatment to restore the PRNT titers as compared to serum samples. The validation and comparative performance was carried out by using a large range of serum vs heparin plasma:ECT 1:2 paired samples obtained from unvaccinated and 17DD-YFV primary vaccinated subjects. Altogether, the findings support the use of heparin plasma:ECT samples for accurate measurement of anti-YFV neutralizing antibodies. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. The comparative utility of oral swabs and probang samples for detection of foot-and-mouth disease virus infection in cattle and pigs.

    Science.gov (United States)

    Stenfeldt, Carolina; Lohse, Louise; Belsham, Graham J

    2013-03-23

    Foot-and-mouth disease virus (FMDV) RNA was measured using quantitative reverse transcription-PCR (qRT-PCR) assays in oral swab and probang samples collected from cattle and pigs during experimental infections with serotype O FMDV. During acute infection, FMDV RNA was measurable in oral swabs as well as in probang samples from both species. FMDV RNA could be detected in oral swabs and probang samples from a time point corresponding to the onset of viremia in directly inoculated animals, whereas animals which were infected through contact exposure had low levels of FMDV RNA in oral swabs before viral RNA could be measured in serum. Analysis of samples collected from cattle persistently infected with FMDV showed that it was not possible to detect FMDV RNA in oral swabs harvested beyond 10 days post infection (dpi), despite the presence of FMDV RNA in probang samples that had been collected as late as 35 dpi. An interesting feature of the persistent infection in the cattle was the apparent decline in the level of FMDV RNA in probang samples after the acute phase of infection, which was followed by a marked rise again (in all the carrier animals) by 28 dpi. Results from this study indicate that qRT-PCR analysis of oral swabs is a useful approach in order to achieve a time efficient and reliable initial diagnosis of acute FMD in cattle and pigs, whereas probang sampling is essential for the detection of cattle that are persistently infected "carriers" of FMDV. Copyright © 2012 Elsevier B.V. All rights reserved.

  7. Polymerase chain reaction genotyping of Epstein-Barr virus in scraping samples of the tongue lateral border in HIV-1 seropositive patients

    Directory of Open Access Journals (Sweden)

    TF Robaina

    2008-06-01

    Full Text Available The Epstein-Barr virus (EBV is the etiological agent of oral hairy leukoplakia (OHL, an oral lesion with important diagnostic and prognostic value in acquired immunodeficiency disease syndrome. The two EBV genotypes, EBV-1 and EBV-2, can be distinguished by divergent gene sequences encoding the EBNA-2, 3A, 3B, and 3C proteins. The purpose of this study was to identify the EBV genotype prevalent in 53 samples of scrapings from the lateral border of the tongue of HIV-1 seropositive patients, with and without OHL, and to correlate the genotypes with presence of clinical or subclinical OHL with the clinic data collected. EBV-1 and EBV-2 were identified through PCR and Nested-PCR based on sequence differences of the EBNA-2 gene. EBV-1 was identified in the 31 samples (15 without OHL, 7 with clinical OHL and 9 with subclinical OHL, EBV-2 in 12 samples (10 without OHL, 1 with clinical and 1 subclinical OHL, and a mixed infection in 10 samples (2 without OHL, 3 with clinical and 5 with subclinical OHL. The presence of EBV-1 was higher in women, but a significant statistical result relating one the EBV genotypes to the development of OHL was not found. We conclude that the oral epithelium in HIV-1 seropositive patients can be infected by EBV-1, EBV-2 or by a mixed viral population.

  8. SELDI-TOF-MS determination of hepcidin in clinical samples using stable isotope labelled hepcidin as an internal standard

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    Johnson Philip J

    2008-10-01

    Full Text Available Abstract Background Hepcidin is a 25-residue peptide hormone crucial to iron homeostasis. It is essential to measure the concentration of hepcidin in cells, tissues and body fluids to understand its mechanisms and roles in physiology and pathophysiology. With a mass of 2791 Da hepcidin is readily detectable by mass spectrometry and LC-ESI, MALDI and SELDI have been used to estimate systemic hepcidin concentrations by analysing serum or urine. However, peak heights in mass spectra may not always reflect concentrations in samples due to competition during binding steps and variations in ionisation efficiency. Thus the purpose of this study was to develop a robust assay for measuring hepcidin using a stable isotope labelled hepcidin spiking approach in conjunction with SELDI-TOF-MS. Results We synthesised and re-folded hepcidin labelled with 13C/15N phenylalanine at position 9 to generate an internal standard for mass spectrometry experiments. This labelled hepcidin is 10 Daltons heavier than the endogenous peptides and does not overlap with the isotopic envelope of the endogenous hepcidin or other common peaks in human serum or urine mass spectra and can be distinguished in low resolution mass spectrometers. We report the validation of adding labelled hepcidin into serum followed by SELDI analysis to generate an improved assay for hepcidin. Conclusion We demonstrate that without utilising a spiking approach the hepcidin peak height in SELDI spectra gives a good indication of hepcidin concentration. However, a stable isotope labelled hepcidin spiking approach provides a more robust assay, measures the absolute concentration of hepcidin and should facilitate inter-laboratory hepcidin comparisons.

  9. International Atomic Energy Agency. Supporting member states to combat Zika virus outbreaks through its human health programme

    Energy Technology Data Exchange (ETDEWEB)

    Becic, Taric; Paez, Diana; Abdel-Wahab, May [International Atomic Energy Agency, Vienna (Austria). Div. of Human Health

    2016-10-15

    Zika virus, discovered in late 1940s in Uganda, has rapidly spread into other parts of Africa and Asia. Since 2007, outbreaks have been documented in a great number of countries and territories, with Latin America and Caribbean region carrying the highest burden. The IAEA has therefore undertaken immediate actions to support members states as part of the global effort led by WHO. Due to its well-established know-how in the use of molecular diagnostic techniques, the IAEA organised a training course for detection of Zika virus in coordination with WHO-PAHO and provided equipment and reagents to some member states in Central America and the Caribbean as well as Pacific islands. In addition, the IAEA's support also comprises SIT as part of integrated vector management control.

  10. Evaluation of the suitability of six host genes as internal control in real-time RT-PCR assays in chicken embryo cell cultures infected with infectious bursal disease virus

    DEFF Research Database (Denmark)

    Li, Yiping; Bang, Dang Duong; Handberg, Kurt

    2005-01-01

    -time RT-PCR is needed to a suitable internal control. We thus investigated the expression pattern of six chicken genes, including P-actin, 28S rRNA, 18S rRNA, glyceral dehyde-3-phosphate dehydrogenase (GAPDH), TATA box-binding protein (TBP) and beta-2-microglobulin, in chicken embryo (CE) cell cultures...... and GAPDH had a lower expression level in CE cell cultures. Also, beta-actin showed no significant variation in both normalized and non-normalized assays and virus dose-independent of inoculation, while other genes did. beta-Actin was further successfully used as an internal control to quantitate Bursine-2...... virus-specific RNA load in CE cell cultures. Thus, beta-actin was suggested as a suitable internal control in studying gene expression as well as virus-specific RNA load in CE cell after IBDV infection....

  11. Hepatitis B Virus DNA in Blood Samples Positive for Antibodies to Core Antigen and Negative for Surface Antigen

    Science.gov (United States)

    Gutiérrez, C.; León, G.; Loureiro, C. L.; Uzcátegui, N.; Liprandi, F.; Pujol, F. H.

    1999-01-01

    Anti-hepatitis B core antigen (HBcAg)-positive hepatitis B surface antigen (HBsAg)-negative plasma samples from blood donors were tested by nested PCR. DNA positivity was more significantly associated with high levels of anti-HBcAg than with low levels of anti-HBsAg antibodies. Analysis of a dilution of anti-HBcAg antibodies might result in a more rational exclusion of anti-HBcAg-positive HBsAg-negative samples, reducing the number of donations discarded and enabling more countries to incorporate anti-HBcAg testing. PMID:10473534

  12. Exosomes Derived from Epstein-Barr Virus-Infected Cells Are Internalized via Caveola-Dependent Endocytosis and Promote Phenotypic Modulation in Target Cells

    Science.gov (United States)

    Kawanishi, Eri; Yoshida, Ryuji; Yoshiyama, Hironori

    2013-01-01

    Epstein-Barr virus (EBV), a human gammaherpesvirus, establishes a lifelong latent infection in B lymphocytes and epithelial cells following primary infection. Several lines of evidence suggest that exosomes derived from EBV-infected cells are internalized and transfer viral factors, including EBV-encoded latent membrane protein and microRNAs, to the recipient cells. However, the detailed mechanism by which exosomes are internalized and their physiological impact on the recipient cells are still poorly understood. In this study, we visualized the internalization of fluorescently labeled exosomes derived from EBV-uninfected and EBV-infected B cells of type I and type III latency into EBV-negative epithelial cells. In this way, we demonstrated that exosomes derived from all three cell types were internalized into the target cells in a similar fashion. Internalization of exosomes was significantly suppressed by treatment with an inhibitor of dynamin and also by the knockdown of caveolin-1. Labeled exosomes were colocalized with caveolae and subsequently trafficked through endocytic pathways. Moreover, we observed that exosomes derived from type III latency cells upregulated proliferation and expression of intercellular adhesion molecule 1 (ICAM-1) in the recipient cells more significantly than did those derived from EBV-negative and type I latency cells. We also identified the EBV latent membrane protein 1 (LMP1) gene as responsible for induction of ICAM-1 expression. Taken together, our data indicate that exosomes released from EBV-infected B cells are internalized via caveola-dependent endocytosis, which, in turn, contributes to phenotypic changes in the recipient cells through transferring one or more viral factors. PMID:23864627

  13. Detection of hepatitis C virus RNA in saliva samples from patients with seric anti-HCV antibodies

    Directory of Open Access Journals (Sweden)

    Patrícia L. Gonçalves

    Full Text Available We examined the frequency of HCV-RNA in saliva samples from anti-HCV positive patients. Both plasma and saliva samples from 39 HCV patients (13 with normal liver enzymes, 19 with abnormal liver enzymes and 13 with cirrhosis were investigated. Stimulated saliva and fresh plasma were centrifuged (900 x g,10 min and stored at -70ºC, after the addition of guanidine isothiocyanate RNA extraction buffer. HCV-RNA was detected by RT- nested-PCR (amplification of HCV-cDNA for two rounds, using HCV primers 939/209 and 940/211. HCV genotyping was carried out by RFLP (using Mva I and Hinf 1 or Hae III and Rsa I restriction enzymes. Thirty-two out of 39 (82%; 95% CI=70-94% anti-HCV-positive patients had HCV-RNA in plasma samples. Eight out of 39 (20.5%; 95% CI=6.6-34.4% had HCV-RNA in the saliva. The HCV genotype in saliva samples from these patients matched the genotype found for plasma HCV-RNA. No significant correlation between the presence of HCV and either age, gender, HCV genotype or any risk factor for HCV infection was found. The observed prevalence (20.5% of anti HCV positive patients or 25% of the patients with HCV-RNA in plasma was lower than that previously reported from other countries. The low frequency of HCV-RNA in saliva samples observed in our study may be due to the use of cell-free saliva. Other authors reporting higher frequencies of HCV-RNA in saliva used whole saliva, without centrifugation.

  14. An internal ribosomal entry signal in the rat VL30 region of the Harvey murine sarcoma virus leader and its use in dicistronic retroviral vectors.

    Science.gov (United States)

    Berlioz, C; Torrent, C; Darlix, J L

    1995-10-01

    The genetic organization of the 5' genomic RNA domain of the highly oncogenic Harvey murine sarcoma virus appears to be unusual in that a multifunctional untranslated leader precedes the v-ras oncogene. This 5' leader is 1,076 nucleotides in length and is formed of independent regions involved in key steps of the viral life cycle: (i) the Moloney murine leukemia virus 5' repeat, untranslated 5' region, and primer binding site sequences necessary for the first steps of proviral DNA synthesis, (ii) the virus-like 30S (VL30)-derived sequence containing a functional dimerization-packaging signal (E/DLS) directing viral RNA dimerization and packaging into MLV virions, and (iii) an Alu-like sequence preceding the 5' untranslated sequence of v-rasH which contains the initiation codon of the p21ras oncoprotein. These functional features, the unusual length of this leader (1,076 nucleotides), and the presence of stable secondary structures between the cap and the v-ras initiation codon might well cause a premature stop of the scanning ribosomes and thus inhibit v-ras translation. In order to understand how Harvey murine sarcoma virus achieves a high level of expression of the ras oncogene, we asked whether the rat VL30 sequence, 5' to v-ras, could contribute to an efficient synthesis of the ras oncoprotein. The implications of the VL30 sequence in the translation initiation of Ha-ras were investigated in the rabbit reticulocyte lysate system and in murine cells. Results show that the rat VL30 sequence allows a cap-independent translation of a downstream reporter gene both in vitro and in murine cells. Additional experiments performed with dicistronic neo.VL30.lacZ mRNAs indicate that the 5' VL30 sequence (positions 380 to 794) contains an internal ribosomal entry signal. This finding led us to construct a new dicistronic retroviral vector with which the rat VL30 sequence was able to direct the efficient expression of a 3' cistron and packaging of recombinant dicistronic RNA

  15. Quantitative detection of epstein-barr virus DNA in cerebrospinal fluid and blood samples of patients with relapsing-remitting multiple sclerosis.

    Directory of Open Access Journals (Sweden)

    Clementina E Cocuzza

    Full Text Available The presence of Epstein-Barr Virus (EBV DNA in cerebrospinal fluid (CSF and peripheral blood (PB samples collected from 55 patients with clinical and radiologically-active relapsing-remitting MS (RRMS and 51 subjects with other neurological diseases was determined using standardized commercially available kits for viral nucleic acid extraction and quantitative EBV DNA detection. Both cell-free and cell-associated CSF and PB fractions were analyzed, to distinguish latent from lytic EBV infection. EBV DNA was detected in 5.5% and 18.2% of cell-free and cell-associated CSF fractions of patients with RRMS as compared to 7.8% and 7.8% of controls; plasma and peripheral blood mononuclear cells (PBMC positivity rates were 7.3% and 47.3% versus 5.8% and 31.4%, respectively. No significant difference in median EBV viral loads of positive samples was found between RRMS and control patients in all tested samples. Absence of statistically significant differences in EBV positivity rates between RRMS and control patients, despite the use of highly sensitive standardized methods, points to the lack of association between EBV and MS disease activity.

  16. Retrospective Species Identification of Microsporidian Spores in Diarrheic Fecal Samples from Human Immunodeficiency Virus/AIDS Patients by Multiplexed Fluorescence In Situ Hybridization▿

    Science.gov (United States)

    Graczyk, Thaddeus K.; Johansson, Michael A.; Tamang, Leena; Visvesvara, Govinda S.; Moura, Laci S.; DaSilva, Alexandre J.; Girouard, Autumn S.; Matos, Olga

    2007-01-01

    In order to assess the applicability of multiplexed fluorescence in situ hybridization (FISH) assay for the clinical setting, we conducted retrospective analysis of 110 formalin-stored diarrheic stool samples from human immunodeficiency virus (HIV)/AIDS patients with intestinal microsporidiosis collected between 1992 and 2003. The multiplexed FISH assay identified microsporidian spores in 94 of 110 (85.5%) samples: 49 (52.1%) were positive for Enterocytozoon bieneusi, 43 (45.8%) were positive for Encephalitozoon intestinalis, 2 (2.1%) were positive for Encephalitozoon hellem, and 9 samples (9.6%) contained both E. bieneusi and E. intestinalis spores. Quantitative spore counts per ml of stool yielded concentration values from 3.5 × 103 to 4.4 × 105 for E. bieneusi (mean, 8.8 × 104/ml), 2.3 × 102 to 7.8 × 104 (mean, 1.5 × 104/ml) for E. intestinalis, and 1.8 × 102 to 3.6 × 102 for E. hellem (mean, 2.7 × 102/ml). Identification of microsporidian spores by multiplex FISH assay was more sensitive than both Chromotrope-2R and CalcoFluor White M2R stains; 85.5% versus 72.7 and 70.9%, respectively. The study demonstrated that microsporidian coinfection in HIV/AIDS patients with intestinal microsporidiosis is not uncommon and that formalin-stored fecal samples older than 10 years may not be suitable for retrospective analysis by techniques targeting rRNA. Multiplexed FISH assay is a reliable, quantitative fluorescence microscopy method for the simultaneous identification of E. bieneusi, E. intestinalis, and E. hellem, as well as Encephalitozoon cuniculi, spores in fecal samples and is a useful tool for assessing spore shedding intensity in intestinal microsporidiosis. The method can be used for epidemiological investigations and applied in clinical settings. PMID:17287331

  17. Physical activity, screen time and obesity status in a nationally representative sample of Maltese youth with international comparisons.

    Science.gov (United States)

    Decelis, Andrew; Jago, Russell; Fox, Kenneth R

    2014-06-28

    There is some evidence that physical activity (PA), sedentary time and screen time (ST) are associated with childhood obesity, but research is inconclusive and studies are mainly based on self-reported data. The literature is dominated by data from North American countries and there is a shortage of objective data from Malta which has one of the highest prevalences of childhood obesity in the world. The aims of this study were to assess the PA levels and ST patterns of Maltese boys and girls and how they compared with children in other countries while also examining differences in PA and ST by weight status. A nationally representative sample of 1126 Maltese boys and girls aged 10-11 years, of which 811 provided complete data. Physical activity was assessed using accelerometry, and ST by questionnaire. Body mass index (BMI) was computed from measured height and weight. Only 39% of boys and 10% of girls met the recommendation of one hour of daily MVPA. Comparison with international data indicated that mean MVPA (58.1 min for boys; 41.7 min for girls) was higher than in North America and Australia, but lower than in England. Girls were less active than boys at all measured times and spent less time in ST. A quarter of the children exceeded guidelines of two hours of TV on weekends, and double the amount on weekdays. Obese children were less active than normal weight children on weekdays and on weekends, reaching significance during the period after school, and they spent more time in ST than their normal weight counterparts. A low percentage of Maltese 10-11 year olds, particularly girls, reached the recommended levels of daily MVPA and spent large amounts of time engaged in screen time. Obese children were less active than non-obese children. As children spend most of their waking time at school and that activity during this time is less than one third of the daily requirements, aiming to increase MVPA at school for all Maltese children is likely to be an important

  18. Titan : A new facility for ultraclean sampling of trace elements and isotopes in the deep oceans in the international Geotraces program

    NARCIS (Netherlands)

    de Baar, H.J.W.; Timmermans, K.R; Laan, P.; De Porto, H.H.; Ober, S.; Blom, J.J.; Bakker, M.C.; Schilling, J; Sarthou, G.; Smit, M. G.; Klunder, M

    2008-01-01

    Towards more rapid ultraclean sampling of deep ocean waters for trace elements, a novel rectangular frame was constructed of titanium, holding two rows of 12 samplers, as well as various sensors. The frame is deployed to deep ocean waters by an 8000 m length Kevlar wire with internal power and

  19. The BD Onclarity HPV assay on SurePath collected samples meets the International Guidelines for Human Papillomavirus Test Requirements for Cervical Screening

    DEFF Research Database (Denmark)

    Ejegod, Ditte; Bottari, Fabio; Pedersen, Helle

    2016-01-01

    This study describes a validation of the BD Onclarity HPV (Onclarity) assay using the international guidelines for HPV test requirements for cervical cancer screening of women 30 years and above using Danish SurePath screening samples. The clinical specificity (0.90, 95% CI: 0.......93). The inter laboratory agreement was 97% with lower confidence bound of 95% (kappa value: 0.92). The BD Onclarity HPV assay fulfills all the international guidelines for a new HPV test to be used in primarily screening. This is the first clinical validation of a new HPV assay using SurePath screening samples...... and thus the Onclarity HPV assay is the first HPV assay to hold an international validation for both SurePath and ThinPrep....

  20. The measurement properties of the spence children's anxiety scale-parent version in a large international pooled sample of young people with autism spectrum disorder.

    Science.gov (United States)

    Magiati, Iliana; Lerh, Jian Wei; Hollocks, Matthew J; Uljarevic, Mirko; Rodgers, Jacqui; McConachie, Helen; Ozsivadjian, Ann; South, Mikle; Van Hecke, Amy; Hardan, Antonio; Libove, Robin; Leekam, Susan; Simonoff, Emily

    2017-10-01

    Anxiety-related difficulties are common in ASD, but measuring anxiety reliably and validly is challenging. Despite an increasing number of studies, there is no clear agreement on which existing anxiety measure is more psychometrically sound and what is the factor structure of anxiety in ASD. The present study examined the internal consistency, convergent, divergent, and discriminant validity, as well as the factor structure of the Spence Children's Anxiety Scale-Parent Version (SCAS-P), in a large international pooled sample of 870 caregivers of youth with ASD from 12 studies in the United Kingdom, United States, and Singapore who completed the SCAS-P. Most were community recruited, while the majority had at least one measure of ASD symptomatology and either cognitive or adaptive functioning measures completed. Existing SCAS-P total scale and subscales had excellent internal consistency and good convergent, divergent and discriminant validity similar to or better than SCAS-P properties reported in typically developing children, except for the poorer internal consistency of the physical injury subscale. Confirmatory Factor Analysis (CFA) of the existing SCAS-P six-correlated factor structure was a poor fit for this pooled database. Principal component analysis using half of the pooled sample identified a 30-item five correlated factor structure, but a CFA of this PCA-derived structure in the second half of this pooled sample revealed a poor fit, although the PCA-derived SCAS-P scale and subscales had stronger validity and better internal consistency than the original SCAS-P. The study's limitations, the use of the SCAS-P to screen for DSM-derived anxiety problems in ASD and future research directions are discussed. Autism Res 2017, 10: 1629-1652. © 2017 International Society for Autism Research, Wiley Periodicals, Inc. © 2017 International Society for Autism Research, Wiley Periodicals, Inc.

  1. Strategies for the inclusion of an internal amplification control in conventional and real time PCR detection of Campylobacter spp. in chicken fecal samples

    DEFF Research Database (Denmark)

    Lund, Marianne; Madsen, Mogens

    2006-01-01

    To illustrate important issues in optimization of a PCR assay with an internal control four different primer combinations for conventional PCR, two non-competitive and two competitive set-ups for real time PCR were used for detection of Campylobacter spp. in chicken faecal samples....... In the conventional PCR assays the internal control was genomic DNA from Yersinia ruckeri, which is not found in chicken faeces. This internal control was also used in one of the set LIPS in real time PCR. In the three other set-ups different DNA fragments of 109 bp length prepared from two oligos of each 66 bp...... against faecal inhibitors to ensure that the internal control and the target PCR had the same sensitivity towards inhibitors....

  2. Development and laboratory validation of a lateral flow device for the detection of serotype SAT 2 foot-and-mouth disease viruses in clinical samples.

    Science.gov (United States)

    Ferris, Nigel P; Nordengrahn, Ann; Hutchings, Geoffrey H; Paton, David J; Kristersson, Therese; Brocchi, Emiliana; Grazioli, Santina; Merza, Malik

    2010-02-01

    A lateral flow device (LFD) for the detection of foot-and-mouth disease virus (FMDV) of the SAT 2 serotype was developed using a monoclonal antibody (Mab 2H6). The performance of the LFD was evaluated in the laboratory on suspensions of vesicular epithelia: 305 positive for FMDV type SAT 2 from suspected cases of vesicular disease collected from 30 countries and 1002 samples shown to be negative for FMDV type SAT 2 collected from 67 countries between 1968 and 2008. The diagnostic sensitivity of the LFD for FMDV type SAT 2 was higher at 88% compared to 79% obtained by the reference method of antigen ELISA, and the diagnostic specificity of the LFD was approximately 99% compared to 100% for the ELISA. The device recognized FMDV strains of wide diversity within the FMDV SAT 2 serotype and gave a superior performance for their detection compared to the 1F10 LFD which had been developed previously and shown to perform less well for the detection of FMDVs of this particular serotype. Reactions in the SAT 2 2H6 LFD with the viruses of other FMDV serotypes and swine vesicular disease (which produces a clinically indistinguishable syndrome in pigs), did not occur. These data illustrate the potential for the LFD to be employed to complement the 1F10 device next to the animal in the pen-side diagnosis of FMD, for providing rapid and objective support to veterinarians in their clinical judgment of the disease and for specific confirmation of a FMDV type SAT 2 infection. 2009 Elsevier B.V. All rights reserved.

  3. Evaluation of Two Lyophilized Molecular Assays to Rapidly Detect Foot-and-Mouth Disease Virus Directly from Clinical Samples in Field Settings.

    Science.gov (United States)

    Howson, E L A; Armson, B; Madi, M; Kasanga, C J; Kandusi, S; Sallu, R; Chepkwony, E; Siddle, A; Martin, P; Wood, J; Mioulet, V; King, D P; Lembo, T; Cleaveland, S; Fowler, V L

    2017-06-01

    Accurate, timely diagnosis is essential for the control, monitoring and eradication of foot-and-mouth disease (FMD). Clinical samples from suspect cases are normally tested at reference laboratories. However, transport of samples to these centralized facilities can be a lengthy process that can impose delays on critical decision making. These concerns have motivated work to evaluate simple-to-use technologies, including molecular-based diagnostic platforms, that can be deployed closer to suspect cases of FMD. In this context, FMD virus (FMDV)-specific reverse transcription loop-mediated isothermal amplification (RT-LAMP) and real-time RT-PCR (rRT-PCR) assays, compatible with simple sample preparation methods and in situ visualization, have been developed which share equivalent analytical sensitivity with laboratory-based rRT-PCR. However, the lack of robust 'ready-to-use kits' that utilize stabilized reagents limits the deployment of these tests into field settings. To address this gap, this study describes the performance of lyophilized rRT-PCR and RT-LAMP assays to detect FMDV. Both of these assays are compatible with the use of fluorescence to monitor amplification in real-time, and for the RT-LAMP assays end point detection could also be achieved using molecular lateral flow devices. Lyophilization of reagents did not adversely affect the performance of the assays. Importantly, when these assays were deployed into challenging laboratory and field settings within East Africa they proved to be reliable in their ability to detect FMDV in a range of clinical samples from acutely infected as well as convalescent cattle. These data support the use of highly sensitive molecular assays into field settings for simple and rapid detection of FMDV. © 2015 The Authors. Transboundary and Emerging Diseases Published by Blackwell Verlag GmbH.

  4. Ghosts of infections past: using archival samples to understand a century of monkeypox virus prevalence among host communities across space and time

    Science.gov (United States)

    Harrigan, Ryan J.; Thomassen, Henri A.; Smith, Thomas B.

    2018-01-01

    Infectious diseases that originate from multiple wildlife hosts can be complex and problematic to manage. A full understanding is further limited by large temporal and spatial gaps in sampling. However, these limitations can be overcome, in part, by using historical samples, such as those derived from museum collections. Here, we screened over 1000 museum specimens collected over the past 120 years to examine the historical distribution and prevalence of monkeypox virus (MPXV) in five species of African rope squirrel (Funisciurus sp.) collected across Central Africa. We found evidence of MPXV infections in host species as early as 1899, half a century earlier than the first recognized case of MPXV in 1958, supporting the suggestion that historic pox-like outbreaks in humans and non-human primates may have been caused by MPXV rather than smallpox as originally thought. MPX viral DNA was found in 93 of 1038 (9.0%) specimens from five Funisciurus species (F. anerythrus, F. carruthersi, F. congicus, F. lemniscatus and F. pyrropus), of which F. carruthersi and pyrropus had not previously been identified as potential MPXV hosts. We additionally documented relative prevalence rates of infection in museum specimens of Funisciurus and examined the spatial and temporal distribution of MPXV in these potential host species across nearly a hundred years (1899–1993). PMID:29410823

  5. Psychosocial stressors and alcohol use, severity, and treatment receipt across human immunodeficiency virus (HIV) status in a nationally representative sample of US residents.

    Science.gov (United States)

    Williams, Emily C; Joo, Young Sun; Lipira, Lauren; Glass, Joseph E

    2017-01-01

    Human immunodeficiency virus (HIV) is stigmatized and disproportionately impacts vulnerable populations. Thus, people living with HIV (PLWH) may have greater exposure to psychosocial stressors than those without HIV. Exposure to psychosocial stressors may increase alcohol use and serve as barriers to alcohol treatment receipt. The authors evaluate whether psychosocial stressors and alcohol use, symptom severity, and treatment receipt vary across HIV status in a general population sample of US residents and assess whether psychosocial stressors mediate identified associations. Data from Wave 2 of the National Epidemiologic Survey on Alcohol and Related Conditions (NESARC) were used to assess associations between HIV status and psychosocial stressors (perceived stress, alcohol-related stigma, and perceived discrimination based on race/ethnicity, sexual orientation, or sex) and alcohol-related outcomes (any use, heavy drinking, symptom severity, and treatment receipt). For each outcome, regression models were fit and iteratively adjusted for sociodemographic characteristics and comorbidities. Indirect effects of HIV on alcohol-related outcomes through stressors were estimated to assess mediation when main effects were significant. Among 34,653 NESARC Wave 2 respondents, 161 were PLWH. PLWH were more likely than those without HIV to experience discrimination and had higher levels of perceived stress than those without HIV (P values stressors and alcohol use, severity, and treatment receipt across HIV status further highlight PLWH as a population that is particularly vulnerable to experiences of psychosocial stress and certain adverse alcohol-related outcomes. Future longitudinal research is needed in a larger sample of PLWH to identify intervention targets.

  6. TaqMan based real-time duplex PCR for simultaneous detection and quantitation of capripox and orf virus genomes in clinical samples.

    Science.gov (United States)

    Venkatesan, G; Balamurugan, V; Bhanuprakash, V

    2014-06-01

    A rapid and sensitive TaqMan based real-time duplex PCR (drt-PCR) assay for simultaneous detection, differentiation and quantitation of Capripoxvirus (CaPV) and Orf virus (ORFV) DNA, was optimized targeting the highly conserved DNA polymerase genes of these virus genomes. Two pairs of oligonucleotide primers and two hybridization probes labeled with Cy5/BHQ1 and Hex/BHQ1 for CaPV and ORFV, respectively, were used in the drt-PCR assay. The assay was found to be specific only to targeted viruses and did not react with buffalopox virus (BPXV), camelpox virus (CMLV) (Orthopoxviruses) and cDNA of Peste des petits ruminants virus and bluetongue virus, the other common viruses of sheep and goats. The detection limit of the assay was 20 copies for each of the standard plasmid and 35fg of viral genomic DNA for CaPV and ORFV, respectively, in a single and mixed virus population. Both intra-(0.49-4.6% and 0.7-3.7%) and inter-(0.6-2.35% and 0.27-2.1%) assay variations of drt-PCR for CaPV and ORFV DNA were within the acceptable limits, implying high reproducibility and repeatability of the assay. Further, the diagnostic specificity and the sensitivity of the assay was assessed using known virus isolates of sheeppox virus (SPPV), goatpox virus (GTPV) and ORFV and the clinical specimens from sheep and goats. The developed drt-PCR assay was able to detect, differentiate, quantify simultaneously and also to identity mixed infections of CaPV and ORFV in sheep and goats. Copyright © 2014 Elsevier B.V. All rights reserved.

  7. Internal structure and measurement invariance of the Dutch Eating Behavior Questionnaire (DEBQ) in a (nearly) representative Dutch community sample

    NARCIS (Netherlands)

    Barrada, J.R.; Strien, T. van; Cebolla, A.

    2016-01-01

    The Dutch Eating Behavior Questionnaire is a widely used instrument for assessment of emotional, external and restrained eating. The aim of the present study is to (i) analyse its internal structure using exploratory structural equation modelling; (ii) to assess its measurement invariance with

  8. Detection and genetic characterization of tick-borne encephalitis virus (TBEV) derived from ticks removed from red foxes (Vulpes vulpes) and isolated from spleen samples of red deer (Cervus elaphus) in Croatia.

    Science.gov (United States)

    Jemeršić, Lorena; Dežđek, Danko; Brnić, Dragan; Prpić, Jelena; Janicki, Zdravko; Keros, Tomislav; Roić, Besi; Slavica, Alen; Terzić, Svjetlana; Konjević, Dean; Beck, Relja

    2014-02-01

    Tick-borne encephalitis (TBE) is a growing public health concern in central and northern European countries. Even though TBE is a notifiable disease in Croatia, there is a significant lack of information in regard to vector tick identification, distribution as well as TBE virus prevalence in ticks or animals. The aim of our study was to identify and to investigate the viral prevalence of TBE virus in ticks removed from red fox (Vulpes vulpes) carcasses hunted in endemic areas in northern Croatia and to gain a better insight in the role of wild ungulates, especially red deer (Cervus elaphus) in the maintenance of the TBE virus in the natural cycle. We identified 5 tick species (Ixodes ricinus, Ixodes hexagonus, Haemaphysalis punctata, Dermacentor reticulatus, Rhipicephalus sanguineus) removed from 40 red foxes. However, TBE virus was isolated only from adult I. ricinus and I. hexagonus ticks showing a viral prevalence (1.6%) similar to or higher than reported in endemic areas of other European countries. Furthermore, 2 positive spleen samples from 182 red deer (1.1%) were found. Croatian TBE virus isolates were genetically analyzed, and they were shown to be closely related, all belonging to the European TBE virus subgroup. However, on the basis of nucleotide and amino acid sequence analysis, 2 clusters were identified. Our results show that further investigation is needed to understand the clustering of isolates and to identify the most common TBE virus reservoir hosts in Croatia. Sentinel surveys based on wild animal species would give a better insight in defining TBE virus-endemic and possible risk areas in Croatia. Copyright © 2013. Published by Elsevier GmbH.

  9. Development of a reverse transcription-quantitative PCR system for detection and genotyping of aichi viruses in clinical and environmental samples.

    Science.gov (United States)

    Kitajima, Masaaki; Hata, Akihiko; Yamashita, Teruo; Haramoto, Eiji; Minagawa, Hiroko; Katayama, Hiroyuki

    2013-07-01

    Aichi viruses (AiVs) have been proposed as a causative agent of human gastroenteritis potentially transmitted by fecal-oral routes through contaminated food or water. In the present study, we developed a TaqMan minor groove binder (MGB)-based reverse transcription-quantitative PCR (RT-qPCR) system that is able to quantify AiVs and differentiate between genotypes A and B. This system consists of two assays, an AiV universal assay utilizing a universal primer pair and a universal probe and a duplex genotype-specific assay utilizing the same primer pair and two genotype-specific probes. The primers and probes were designed based on multiple alignments of the 21 available AiV genome sequences containing the capsid gene. Using a 10-fold dilution of plasmid DNA containing the target sequences, it was confirmed that both assays allow detection and quantification of AiVs with a quantitative range of 1.0 × 10(1) to 1.0 × 10(7) copies/reaction, and the genotype-specific assay reacts specifically to each genotype. To validate the newly developed assays, 30 clinical stool specimens were subsequently examined with the assays, and the AiV RNA loads were determined to be 1.4 × 10(4) to 6.6 × 10(9) copies/g stool. We also examined 12 influent and 12 effluent wastewater samples collected monthly for a 1-year period to validate the applicability of the assays for detection of AiVs in environmental samples. The AiV RNA concentrations in influent and effluent wastewater were determined to be up to 2.2 × 10(7) and 1.8 × 10(4) copies/liter, respectively. Our RT-qPCR system is useful for routine diagnosis of AiVs in clinical stool specimens and environmental samples.

  10. Human virus and microbial indicator occurrence in public-supply groundwater systems: meta-analysis of 12 international studies

    Science.gov (United States)

    Groundwater quality is often evaluated using microbial indicators. This study examines data from 12 international groundwater studies (conducted 1992–2013). Sites were chosen from 718 public drinking-water systems with a range of hydrogeological conditions. Focus was on testing the value of indicato...

  11. Collaborative study to establish World Health Organization international reference reagents for dengue virus Types 1 to 4 RNA for use in nucleic acid testing.

    Science.gov (United States)

    Añez, Germán; Volkova, Evgeniya; Jiang, Zhen; Heisey, Daniel A R; Chancey, Caren; Fares, Rafaelle C G; Rios, Maria

    2017-08-01

    Dengue is the most important reemerging mosquito-borne viral disease worldwide. Caused by dengue virus (DENV), a member of the genus Flavivirus in the Flaviviridae family, dengue can be asymptomatic (approx. 80% of cases) or symptomatic, ranging from a flu-like illness known as dengue fever, to a life-threatening form called severe dengue. DENV is primarily transmitted from human to human through the bite of mosquitoes of the genus Aedes; however, it is also transmissible by transfusion of blood and blood components and by solid organ transplant. Nucleic acid test (NAT) assays are considered the most appropriate approach for blood donor screening for recent DENV infections, but there is no Food and Drug Administration-approved assay for the screening of blood for DENV. An international collaborative study was conducted to assess the suitability of reference reagent (RR) candidates for DENV Types 1 to 4 RNA for use in NAT-based assays. Two sets of RR candidates were prepared for each DENV type, one liquid frozen (Set 1) and one lyophilized (Set 2). A total of 28 laboratories from 20 countries agreed to participate in the study, of which 21 submitted the results for qualitative and/or quantitative assessments. The World Health Organization has established the lyophilized materials as international RRs for DENV RNA with a unitage of 13,500, 69,200, 23,400, and 33,900 units/mL for DENV-1 to -4, respectively. © 2017 AABB.

  12. Genome sequences of seven foot-and-mouth disease virus isolates collected from serial samples from one persistently infected carrier cow in Vietnam

    Science.gov (United States)

    Several FMDV carrier cattle were identified in Vietnam by recovery of infectious virus from oropharyngeal fluid. This report contains the first near-complete genome sequences of seven viruses isolated from a single carrier animal over the course of one year. Understanding within-host viral evolution...

  13. Development and validation of an indirect Enzyme-linked Immunosorbent Assay for the detection of antibodies against Schmallenberg virus in blood samples from ruminants

    NARCIS (Netherlands)

    Heijden, van der H.M.J.F.; Bouwstra, R.J.; Mars, M.H.; Poel, van der W.H.M.; Wellenberg, G.J.; Maanen, van C.

    2013-01-01

    To detect Schmallenberg virus (SBV) infections in ruminants and to perform SBV epidemiological studies a cost-effective serological test is required. For these purposes an indirect whole virus Enzyme-linked Immunosorbent Assay (ELISA) for detection of SBV specific antibodies in ruminant blood

  14. Variation in Bluetongue virus real-time reverse transcription polymerase chain reaction assay results in blood samples of sheep, cattle, and alpaca.

    Science.gov (United States)

    Brito, Barbara P; Gardner, Ian A; Hietala, Sharon K; Crossley, Beate M

    2011-07-01

    Bluetongue is a vector-borne viral disease that affects domestic and wild ruminants. The epidemiology of this disease has recently changed, with occurrence in new geographic areas. Various real-time quantitative reverse transcription polymerase chain reaction (real-time qRT-PCR) assays are used to detect Bluetongue virus (BTV); however, the impact of biologic differences between New World camelids and domestic ruminant samples on PCR efficiency, for which the BTV real-time qRT-PCR was initially validated are unknown. New world camelids are known to have important biologic differences in whole blood composition, including hemoglobin concentration, which can alter PCR performance. In the present study, sheep, cattle, and alpaca blood were spiked with BTV serotypes 10, 11, 13, and 17 and analyzed in 10-fold dilutions by real-time qRT-PCR to determine if species affected nucleic acid recovery and assay performance. A separate experiment was performed using spiked alpaca blood subsequently diluted in 10-fold series in sheep blood to assess the influence of alpaca blood on performance efficiency of the BTV real-time qRT-PCR assay. Results showed that BTV-specific nucleic acid detection from alpaca blood was consistently 1-2 logs lower than from sheep and cattle blood, and results were similar for each of the 4 BTV serotypes analyzed.

  15. Three-way Interaction of Neuroticism, Extraversion, and Conscientiousness in the Internalizing Disorders: Evidence of Disorder Specificity in a Psychiatric Sample.

    Science.gov (United States)

    Naragon-Gainey, Kristin; Simms, Leonard J

    2017-10-01

    It is well-established that neuroticism, extraversion, and conscientiousness are individually associated with internalizing disorders, but research suggests that these main effects may be qualified by a three-way interaction when predicting depression. The current study was the first to examine this three-way interaction in a psychiatric sample (N=463) with a range of internalizing symptoms as the outcomes. Using two omnibus personality inventories and a diagnostic interview, the expected three-way interaction emerged most consistently for symptoms of major depression, and there was also evidence of synergistic effects for post-traumatic stress disorder and generalized anxiety disorder. Findings indicate that, even in a clinically-distressed and currently-disordered sample, high levels of extraversion and conscientiousness protect against distress disorders for those with high levels of neuroticism.

  16. Simple technique for in field samples collection in the cases of skin rash illness and subsequent PCR detection of orthopoxviruses and varicella zoster virus.

    Science.gov (United States)

    Dumont, Catherine; Irenge, Leonid M; Magazani, Edmond K; Garin, Daniel; Muyembe, Jean-Jacques T; Bentahir, Mostafa; Gala, Jean-Luc

    2014-01-01

    In case of outbreak of rash illness in remote areas, clinically discriminating monkeypox (MPX) from severe form of chickenpox and from smallpox remains a concern for first responders. The goal of the study was therefore to use MPX and chickenpox outbreaks in Democratic Republic of Congo (DRC) as a test case for establishing a rapid and specific diagnosis in affected remote areas. In 2008 and 2009, successive outbreaks of presumed MPX skin rash were reported in Bena Tshiadi, Yangala and Ndesha healthcare districts of the West Kasai province (DRC). Specimens consisting of liquid vesicle dried on filter papers or crusted scabs from healing patients were sampled by first responders. A field analytical facility was deployed nearby in order to carry out a real-time PCR (qPCR) assay using genus consensus primers, consensus orthopoxvirus (OPV) and smallpox-specific probes spanning over the 14 kD fusion protein encoding gene. A PCR-restriction fragment length polymorphism was used on-site as backup method to confirm the presence of monkeypox virus (MPXV) in samples. To complete the differential diagnosis of skin rash, chickenpox was tested in parallel using a commercial qPCR assay. In a post-deployment step, a MPXV-specific pyrosequencing was carried out on all biotinylated amplicons generated on-site in order to confirm the on-site results. Whereas MPXV proved to be the agent causing the rash illness outbreak in the Bena Tshiadi, VZV was the causative agent of the disease in Yangala and Ndesha districts. In addition, each on-site result was later confirmed by MPXV-specific pyrosequencing analysis without any discrepancy. This experience of rapid on-site dual use DNA-based differential diagnosis of rash illnesses demonstrates the potential of combining tests specifically identifying bioterrorism agents and agents causing natural outbreaks. This opens the way to rapid on-site DNA-based identification of a broad spectrum of causative agents in remote areas.

  17. Innovative method for carbon dioxide determination in human postmortem cardiac gas samples using headspace-gas chromatography-mass spectrometry and stable labeled isotope as internal standard.

    Science.gov (United States)

    Varlet, V; Smith, F; de Froidmont, S; Dominguez, A; Rinaldi, A; Augsburger, M; Mangin, P; Grabherr, S

    2013-06-19

    A novel approach to measure carbon dioxide (CO2) in gaseous samples, based on a precise and accurate quantification by (13)CO2 internal standard generated in situ is presented. The main goal of this study was to provide an innovative headspace-gas chromatography-mass spectrometry (HS-GC-MS) method applicable in the routine determination of CO2. The main drawback of the GC methods discussed in the literature for CO2 measurement is the lack of a specific internal standard necessary to perform quantification. CO2 measurement is still quantified by external calibration without taking into account analytical problems which can often occur considering gaseous samples. To avoid the manipulation of a stable isotope-labeled gas, we have chosen to generate in situ an internal labeled standard gas ((13)CO2) on the basis of the stoichiometric formation of CO2 by the reaction of hydrochloric acid (HCl) with sodium hydrogen carbonate (NaH(13)CO3). This method allows a precise measurement of CO2 concentration and was validated on various human postmortem gas samples in order to study its efficiency. Copyright © 2013 Elsevier B.V. All rights reserved.

  18. Ebola Virus and Marburg Virus

    Science.gov (United States)

    Ebola virus and Marburg virus Overview Ebola virus and Marburg virus are related viruses that cause hemorrhagic fevers — illnesses marked by severe bleeding (hemorrhage), organ failure and, in many ...

  19. The association between serum biomarkers and disease outcome in influenza A(H1N1pdm09 virus infection: results of two international observational cohort studies.

    Directory of Open Access Journals (Sweden)

    Richard T Davey

    Full Text Available Prospective studies establishing the temporal relationship between the degree of inflammation and human influenza disease progression are scarce. To assess predictors of disease progression among patients with influenza A(H1N1pdm09 infection, 25 inflammatory biomarkers measured at enrollment were analyzed in two international observational cohort studies.Among patients with RT-PCR-confirmed influenza A(H1N1pdm09 virus infection, odds ratios (ORs estimated by logistic regression were used to summarize the associations of biomarkers measured at enrollment with worsened disease outcome or death after 14 days of follow-up for those seeking outpatient care (FLU 002 or after 60 days for those hospitalized with influenza complications (FLU 003. Biomarkers that were significantly associated with progression in both studies (p<0.05 or only in one (p<0.002 after Bonferroni correction were identified.In FLU 002 28/528 (5.3% outpatients had influenza A(H1N1pdm09 virus infection that progressed to a study endpoint of complications, hospitalization or death, whereas in FLU 003 28/170 (16.5% inpatients enrolled from the general ward and 21/39 (53.8% inpatients enrolled directly from the ICU experienced disease progression. Higher levels of 12 of the 25 markers were significantly associated with subsequent disease progression. Of these, 7 markers (IL-6, CD163, IL-10, LBP, IL-2, MCP-1, and IP-10, all with ORs for the 3(rd versus 1(st tertile of 2.5 or greater, were significant (p<0.05 in both outpatients and inpatients. In contrast, five markers (sICAM-1, IL-8, TNF-α, D-dimer, and sVCAM-1, all with ORs for the 3(rd versus 1(st tertile greater than 3.2, were significantly (p≤.002 associated with disease progression among hospitalized patients only.In patients presenting with varying severities of influenza A(H1N1pdm09 virus infection, a baseline elevation in several biomarkers associated with inflammation, coagulation, or immune function strongly predicted a

  20. Research on computer virus database management system

    Science.gov (United States)

    Qi, Guoquan

    2011-12-01

    The growing proliferation of computer viruses becomes the lethal threat and research focus of the security of network information. While new virus is emerging, the number of viruses is growing, virus classification increasing complex. Virus naming because of agencies' capture time differences can not be unified. Although each agency has its own virus database, the communication between each other lacks, or virus information is incomplete, or a small number of sample information. This paper introduces the current construction status of the virus database at home and abroad, analyzes how to standardize and complete description of virus characteristics, and then gives the information integrity, storage security and manageable computer virus database design scheme.

  1. Background review for diagnostic test development for Zika virus infection.

    Science.gov (United States)

    Charrel, Rémi N; Leparc-Goffart, Isabelle; Pas, Suzan; de Lamballerie, Xavier; Koopmans, Marion; Reusken, Chantal

    2016-08-01

    To review the state of knowledge about diagnostic testing for Zika virus infection and identify areas of research needed to address the current gaps in knowledge. We made a non-systematic review of the published literature about Zika virus and supplemented this with information from commercial diagnostic test kits and personal communications with researchers in European preparedness networks. The review covered current knowledge about the geographical spread, pathogen characteristics, life cycle and infection kinetics of the virus. The available molecular and serological tests and biosafety issues are described and discussed in the context of the current outbreak strain. We identified the following areas of research to address current knowledge gaps: (i) an urgent assessment of the laboratory capacity and capability of countries to detect Zika virus; (ii) rapid and extensive field validation of the available molecular and serological tests in areas with and without Zika virus transmission, with a focus on pregnant women; (iii) monitoring the genomic diversity of circulating Zika virus strains; (iv) prospective studies into the virus infection kinetics, focusing on diagnostic sampling (specimen types, combinations and timings); and (v) developing external quality assessments for molecular and serological testing, including differential diagnosis for similar viruses and symptom clusters. The availability of reagents for diagnostic development (virus strains and antigens, quantified viral ribonucleic acid) needs to be facilitated. An international laboratory response is needed, including preparation of protocols for prospective studies to address the most pressing information needs.

  2. DIAGNOSTICS OF VIRUS PHYTOPATHOGENS FRUIT TREE PLUM POX VIRUS, PRUNUS NECROTIC RINGSPOT VIRUS AND PRUNUS DWARF VIRUS BY BIOLOGICAL AND MOLECULAR DIAGNOSTICS

    Directory of Open Access Journals (Sweden)

    Július Rozák

    2013-02-01

    Full Text Available The aim of this study was to determine the incidence of viral phytopathogen Plum pox virus, Prunus necrotic ringspot virus and Prunus dwarf virus in selected localities of Slovakia and diagnose them using a molecular and biological methods. Forty samples of fruit trees of the genus Prunus, twenty samples from intensive plantings and twenty samples from wild subject were analysed. Biological diagnostic by using biological indicators Prunus persica cv. GF 305, Prunus serrulata cv. Schirofugen and molecular diagnostic by mRT-PCR were applied. Five samples with Plum pox virus were infected. The two samples positive for Prunus necrotic ringspot virus and one sample for Prunus dwarf virus were confirmed. The two samples were found to be infected with two viruses Prunus necrotic ringspot virus and Prunus dwarf virus. This work focuses on two techniques, their application to the diagnosis of stone fruit viruses and their routinely used for sanitary and certification programmes.

  3. Blue Tongue Virus

    African Journals Online (AJOL)

    Anupama

    bluetongue virus (BTV) infection cycle is initiated when the virus core is delivered into the cytoplasm of ... products available for the consumer market; therefore, .... BTV life cycle. BTV interacts with the target cell surface via VP2 timers which is then internalized in endosomes via a clathrin- dependent endocytosis pathway ...

  4. Successful Validation of Sample Processing and Quantitative Real-Time PCR Capabilities on the International Space Station

    Science.gov (United States)

    Parra, Macarena; Jung, Jimmy; Almeida, Eduardo; Boone, Travis; Schonfeld, Julie; Tran, Luan

    2016-01-01

    The WetLab-2 system was developed by NASA Ames Research Center to offer new capabilities to researchers. The system can lyse cells and extract RNA (Ribonucleic Acid) on-orbit from different sample types ranging from microbial cultures to animal tissues. The purified RNA can then either be stabilized for return to Earth or can be used to conduct on-orbit quantitative Reverse Transcriptase PCR (Polymerase Chain Reaction) (qRT-PCR) analysis without the need for sample return. The qRT-PCR results can be downlinked to the ground a few hours after the completion of the run. The validation flight of the WetLab-2 system launched on SpaceX-8 on April 8, 2016. On orbit operations started on April 15th with system setup and was followed by three quantitative PCR runs using an E. coli genomic DNA template pre-loaded at three different concentrations. These runs were designed to discern if quantitative PCR functions correctly in microgravity and if the data is comparable to that from the ground control runs. The flight data showed no significant differences compared to the ground data though there was more variability in the values, this was likely due to the numerous small bubbles observed. The capability of the system to process samples and purify RNA was then validated using frozen samples prepared on the ground. The flight data for both E. coli and mouse liver clearly shows that RNA was successfully purified by our system. The E. coli qRT-PCR run showed successful singleplex, duplex and triplex capability. Data showed high variability in the resulting Cts (Cycle Thresholds [for the PCR]) likely due to bubble formation and insufficient mixing during the procedure run. The mouse liver qRT-PCR run had successful singleplex and duplex reactions and the variability was slightly better as the mixing operation was improved. The ability to purify and stabilize RNA and to conduct qRT-PCR on-orbit is an important step towards utilizing the ISS as a National Laboratory facility. The

  5. Detection of influenza A virus from live-bird market poultry swab samples in China by a pan-IAV, one-step reverse-transcription FRET-PCR.

    Science.gov (United States)

    Luan, Lu; Sun, Zhihao; Kaltenboeck, Bernhard; Huang, Ke; Li, Min; Peng, Daxin; Xu, Xiulong; Ye, Jianqiang; Li, Jing; Guo, Weina; Wang, Chengming

    2016-07-22

    The persistent public health threat of animal to human transmission of influenza A virus (IAV) has stimulated interest in rapid and accurate detection of all IAV subtypes in clinical specimens of animal origin. In this study, a new set of primers and probes was designed for one-step pan-IAV reverse-transcription fluorescence resonance energy transfer (FRET)-PCR. The detection limit of one-step pan-IAV RT FRET-PCR was 10 copies of the matrix gene per reaction, and proved to be equivalent or superior to virus isolation in detecting nine IAV subtypes. Application of the pan-IAV RT FRET-PCR to oral-pharyngeal and cloacal swab specimens collected from healthy poultry in 34 live bird markets in 24 provinces of China revealed that 9.2% of the animals (169/1,839) or 6.3% of their oral-pharyngeal or cloacal swabs (233/3,678) were positive for IAV, and 56.8% of IAV-positive samples were of the H9N2 subtype. Paralleling detection of IAV in H9N2-infected SPF chickens and chickens from LBM showed that pan-IAV FRET-PCR had a higher detection limit than virus isolation in eggs while the results by FRET-PCR and virus isolation overall matched. It is expected that this strategy can be useful for facile surveillance for IAV in clinical samples from a variety of sources.

  6. Self-reported mental health problems among adolescents in developing countries: results from an international pilot sample.

    Science.gov (United States)

    Atilola, Olayinka; Singh Balhara, Yatan Pal; Stevanovic, Dejan; Avicenna, Mohamad; Kandemir, Hasan

    2013-02-01

    To evaluate the prevalence, pattern, and sociodemographic correlates of self-reported mental health problems among a pilot sample of adolescents from 5 developing countries and to speculate the methodology and design of a larger scale study. The sociodemographic questionnaire was developed based on extant literature on the sociodemographic correlates of mental health problems among adolescents. Additional information about the socioeconomic status of parents/caregivers of the participants was obtained using the Family Affluence Scale (FAS). Mental health problems were evaluated using the Strength and Difficulty Questionnaire (SDQ). Logistic regression analysis was done to determine independent sociodemographic correlates of mental health problems. A total of 1894 adolescents sampled from 5 countries completed the study. The prevalence of self-reported mental health problems was 10.5% (range, 5.8-15) with conduct and emotional problems being the most prevalent. When the raw total-SDQ scores were adjusted for age, gender, and FAS scores, there was a statistically significant difference in the mean scores among the adolescents from different countries (F = 17.23, p mental health problems. Study has added to the currently limited data on prevalence of mental health problems among adolescents in developing countries. It further established that socioeconomic and family factors still play a major role in the mental health of children irrespective of region of the world. Significant but surmountable methodological issues for a larger scale study were raised.

  7. Frequency-tuned contactless conductivity detector for the electrophoretic separation of clinical samples in capillaries with very small internal dimensions.

    Science.gov (United States)

    Tůma, Petr

    2017-02-01

    An axial design of a capacitively coupled contactless conductivity detector was tested in combination with fused-silica capillaries with internal diameters of 10, 15, and 25 μm, which are used for high-efficiency electrophoretic separation. The transmission of the signal in the detection probe dependent on the specific conductivity of the solution in the capillary in the range 0-278 mS.m-1 has a complex character and a minimum appears on the curve at very low conductivities. The position of the minimum of the calibration dependence gradually shifts with decreasing frequency of the exciting signal from 1.0 to 0.25 MHz toward lower specific conductivity values. The presence of a minimum on the calibration curves is a natural property of the axial design of contactless conductivity detector, demonstrated by solution of the equivalent electrical circuit of the detection probe, and is specifically caused by the use of shielding foil. The behavior of contactless conductivity detector in the vicinity of the minimum was documented for practical separations of amino acids in solutions of 3.2 M acetic acid with addition of 0-50% v/v methanol. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Hepatitis C virus internal ribosome entry site RNA contains a tertiary structural element in a functional domain of stem–loop II

    Science.gov (United States)

    Lyons, Alita J.; Lytle, J. Robin; Gomez, Jordi; Robertson, Hugh D.

    2001-01-01

    The internal ribosome entry site (IRES) of hepatitis C virus (HCV) RNA contains >300 bases of highly conserved 5′-terminal sequence, most of it in the uncapped 5′-untranslated region (5′-UTR) upstream from the single AUG initiator triplet at which translation of the HCV polyprotein begins. Although progress has been made in defining singularities like the RNA pseudoknot near this AUG, the sequence and structural features of the HCV IRES which stimulate accurate and efficient initiation of protein synthesis are only partially defined. Here we report that a region further upstream from the AUG, stem–loop II of the HCV IRES, also contains an element of local tertiary structure which we have detected using RNase H cleavage and have mapped using the singular ability of two bases therein to undergo covalent intra-chain crosslinking stimulated by UV light. This pre-existing element maps to two non-contiguous stretches of the HCV IRES sequence, residues 53–68 and 103–117. Several earlier studies have shown that the correct sequence between bases 45 and 70 of the HCV IRES stem–loop II domain is required for initiation of protein synthesis. Because features of local tertiary structure like the one we report here are often associated with protein binding, we propose that the HCV stem–loop II element is directly involved in IRES action. PMID:11410661

  9. Use of the International Classification of Diseases, 9th revision, coding in identifying chronic hepatitis B virus infection in health system data: implications for national surveillance.

    Science.gov (United States)

    Mahajan, Reena; Moorman, Anne C; Liu, Stephen J; Rupp, Loralee; Klevens, R Monina

    2013-05-01

    With increasing use electronic health records (EHR) in the USA, we looked at the predictive values of the International Classification of Diseases, 9th revision (ICD-9) coding system for surveillance of chronic hepatitis B virus (HBV) infection. The chronic HBV cohort from the Chronic Hepatitis Cohort Study was created based on electronic health records (EHR) of adult patients who accessed services from 2006 to 2008 from four healthcare systems in the USA. Using the gold standard of abstractor review to confirm HBV cases, we calculated the sensitivity, specificity, positive and negative predictive values using one qualifying ICD-9 code versus using two qualifying ICD-9 codes separated by 6 months or greater. Of 1 652 055 adult patients, 2202 (0.1%) were confirmed as having chronic HBV. Use of one ICD-9 code had a sensitivity of 83.9%, positive predictive value of 61.0%, and specificity and negative predictive values greater than 99%. Use of two hepatitis B-specific ICD-9 codes resulted in a sensitivity of 58.4% and a positive predictive value of 89.9%. Use of one or two hepatitis B ICD-9 codes can identify cases with chronic HBV infection with varying sensitivity and positive predictive values. As the USA increases the use of EHR, surveillance using ICD-9 codes may be reliable to determine the burden of chronic HBV infection and would be useful to improve reporting by state and local health departments.

  10. [Zika virus infection during pregnancy].

    Science.gov (United States)

    Picone, O; Vauloup-Fellous, C; D'Ortenzio, E; Huissoud, C; Carles, G; Benachi, A; Faye, A; Luton, D; Paty, M-C; Ayoubi, J-M; Yazdanpanah, Y; Mandelbrot, L; Matheron, S

    2016-05-01

    A Zika virus epidemic is currently ongoing in the Americas. This virus is linked to congenital infections with potential severe neurodevelopmental dysfunction. However, incidence of fetal infection and whether this virus is responsible of other fetal complications are still unknown. National and international public health authorities recommend caution and several prevention measures. Declaration of Zika virus infection is now mandatory in France. Given the available knowledge on Zika virus, we suggest here a review of the current recommendations for management of pregnancy in case of suspicious or infection by Zika virus in a pregnant woman. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  11. Molecular Characterization of Fasciola Samples Using Sequences of Second Internal Transcribed Spacer-rDNA in Different Geographical Localities of Sistan and Balouchestan Province, Iran

    Directory of Open Access Journals (Sweden)

    Mahsa Shahbakhsh

    2016-02-01

    Full Text Available Background: The Fasciola trematodes are the most common liver flukes, living in a range of animals with global distribution and resulting in profound economic loss and public health challenges. Previous studies have indicated that the sequences of the second internal transcribed spacer (ITS-2 of ribosomal DNA (rDNA provide reliable genetic markers for molecular systemic studies of Fasciola. Objectives: The objective of the present study was to characterize Fasciola samples from different geographical regions of Sistan and Balouchestan province using sequences of second internal transcribed spacer (ITS-2 of ribosomal DNA (rDNA. Materials and Methods: Twenty adult trematodes were collected from the livers of slaughtered infected cattle. Total genomic DNA was extracted and ITS-2 rDNA targets were amplified by polymerase chain reaction (PCR. All samples were sequenced and investigated using the ClustalW2 sequence alignment tool and MEGA software. The sequences of some Iranian and non-Iranian isolates were used for comparison, in order to evaluate the variation in sequence homology between geographically different trematode populations. Results: The results of comparing the ITS-2 sequences with the BLAST GenBank database showed one type of sequence for F. hepatica and three different types of sequences for F. gigantica in the specimens. Conclusions: The present study demonstrated that Fasciola samples from cattle in two geographical locations in Sistan and Balouchestan province represented no genetic diversity in F. hepatica and high genetic variation in F. gigantica.

  12. Simple technique for in field samples collection in the cases of skin rash illness and subsequent PCR detection of orthopoxviruses and varicella zoster virus.

    Directory of Open Access Journals (Sweden)

    Catherine Dumont

    Full Text Available BACKGROUND: In case of outbreak of rash illness in remote areas, clinically discriminating monkeypox (MPX from severe form of chickenpox and from smallpox remains a concern for first responders. OBJECTIVE: The goal of the study was therefore to use MPX and chickenpox outbreaks in Democratic Republic of Congo (DRC as a test case for establishing a rapid and specific diagnosis in affected remote areas. METHODS: In 2008 and 2009, successive outbreaks of presumed MPX skin rash were reported in Bena Tshiadi, Yangala and Ndesha healthcare districts of the West Kasai province (DRC. Specimens consisting of liquid vesicle dried on filter papers or crusted scabs from healing patients were sampled by first responders. A field analytical facility was deployed nearby in order to carry out a real-time PCR (qPCR assay using genus consensus primers, consensus orthopoxvirus (OPV and smallpox-specific probes spanning over the 14 kD fusion protein encoding gene. A PCR-restriction fragment length polymorphism was used on-site as backup method to confirm the presence of monkeypox virus (MPXV in samples. To complete the differential diagnosis of skin rash, chickenpox was tested in parallel using a commercial qPCR assay. In a post-deployment step, a MPXV-specific pyrosequencing was carried out on all biotinylated amplicons generated on-site in order to confirm the on-site results. RESULTS: Whereas MPXV proved to be the agent causing the rash illness outbreak in the Bena Tshiadi, VZV was the causative agent of the disease in Yangala and Ndesha districts. In addition, each on-site result was later confirmed by MPXV-specific pyrosequencing analysis without any discrepancy. CONCLUSION: This experience of rapid on-site dual use DNA-based differential diagnosis of rash illnesses demonstrates the potential of combining tests specifically identifying bioterrorism agents and agents causing natural outbreaks. This opens the way to rapid on-site DNA-based identification of a

  13. Performance of HBsAg quantification assays for detection of Hepatitis B virus genotypes and diagnostic escape-variants in clinical samples.

    Science.gov (United States)

    Thibault, Vincent; Servant-Delmas, Annabelle; Ly, Thoai Duong; Roque-Afonso, Anne-Marie; Laperche, Syria

    2017-04-01

    The impact of hepatitis B virus (HBV) genomic variability on the measurement of HBsAg level has been poorly evaluated. This study was designed to compare the performance of all the available assays measuring HBsAg level in this setting. A large selection of wild type HBV genotypes (n=184) and HBsAg strains harboring mutations in the S gene (n=81) from clinical samples was studied with three HBsAg quantification assays: Architect HBsAg (Abbott), LiaisonXL Murex HBsAg Quant (DiaSorin) and the Elecsys HBsAgII (Roche). The overall percentage of positive results was 99.2% for Abbott, 98.9% for DiaSorin and 98.1% for Roche. Abbott and Roche assays provided an excellent concordance in HBsAg quantification (global mean bias of -0.006 logIU/mL). By contrast, DiaSorin underestimated HBsAg level with values 0.112 logIU/ml and 0.103 logIU/ml lower than Abbott and Roche, respectively. By contrast, DiaSorin slightly over quantified gtC (2.5% over the expected value) while Abbott provided values 6.2% lower than expected and 16.2% lower than what observed for the other genotypes. HBsAg quantitative assays were influenced by HBs protein substitutions irrespective to the genotype but no specific protein pattern that would particularly impair the quantification by one technique has been identified. However, Roche seemed to be particularly impacted by substitutions at 145 residue: 75% of under quantified samples carried a substituted 145 residue. This head-to-head comparison indicates a good correlation between all current systems used to quantify HBsAg but clearly shows an influence of both the genotype and the presence of "a" determinant variants in the absolute quantification of HBsAg. While these discrepancies may not translate into major clinical consequence, they may explain an absence of detection of weak concentration of HBsAg on some systems. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Development and Progress of Ireland's Biobank Network: Ethical, Legal, and Social Implications (ELSI), Standardized Documentation, Sample and Data Release, and International Perspective

    LENUS (Irish Health Repository)

    Mee, Blanaid

    2013-02-19

    Biobank Ireland Trust (BIT) was established in 2004 to promote and develop an Irish biobank network to benefit patients, researchers, industry, and the economy. The network commenced in 2008 with two hospital biobanks and currently consists of biobanks in the four main cancer hospitals in Ireland. The St. James\\'s Hospital (SJH) Biobank coordinates the network. Procedures, based on ISBER and NCI guidelines, are standardized across the network. Policies and documents—Patient Consent Policy, Patient Information Sheet, Biobank Consent Form, Sample and Data Access Policy (SAP), and Sample Application Form have been agreed upon (after robust discussion) for use in each hospital. An optimum sequence for document preparation and submission for review is outlined. Once consensus is reached among the participating biobanks, the SJH biobank liaises with the Research and Ethics Committees, the Office of the Data Protection Commissioner, The National Cancer Registry (NCR), patient advocate groups, researchers, and other stakeholders. The NCR provides de-identified data from its database for researchers via unique biobank codes. ELSI issues discussed include the introduction of prospective consent across the network and the return of significant research results to patients. Only 4 of 363 patients opted to be re-contacted and re-consented on each occasion that their samples are included in a new project. It was decided, after multidisciplinary discussion, that results will not be returned to patients. The SAP is modeled on those of several international networks. Biobank Ireland is affiliated with international biobanking groups—Marble Arch International Working Group, ISBER, and ESBB. The Irish government continues to deliberate on how to fund and implement biobanking nationally. Meanwhile BIT uses every opportunity to promote awareness of the benefits of biobanking in events and in the media.

  15. International veterinary epilepsy task force recommendations for systematic sampling and processing of brains from epileptic dogs and cats.

    Science.gov (United States)

    Matiasek, Kaspar; Pumarola I Batlle, Martí; Rosati, Marco; Fernández-Flores, Francisco; Fischer, Andrea; Wagner, Eva; Berendt, Mette; Bhatti, Sofie F M; De Risio, Luisa; Farquhar, Robyn G; Long, Sam; Muñana, Karen; Patterson, Edward E; Pakozdy, Akos; Penderis, Jacques; Platt, Simon; Podell, Michael; Potschka, Heidrun; Rusbridge, Clare; Stein, Veronika M; Tipold, Andrea; Volk, Holger A

    2015-08-28

    Traditionally, histological investigations of the epileptic brain are required to identify epileptogenic brain lesions, to evaluate the impact of seizure activity, to search for mechanisms of drug-resistance and to look for comorbidities. For many instances, however, neuropathological studies fail to add substantial data on patients with complete clinical work-up. This may be due to sparse training in epilepsy pathology and or due to lack of neuropathological guidelines for companion animals.The protocols introduced herein shall facilitate systematic sampling and processing of epileptic brains and therefore increase the efficacy, reliability and reproducibility of morphological studies in animals suffering from seizures.Brain dissection protocols of two neuropathological centres with research focus in epilepsy have been optimised with regards to their diagnostic yield and accuracy, their practicability and their feasibility concerning clinical research requirements.The recommended guidelines allow for easy, standardised and ubiquitous collection of brain regions, relevant for seizure generation. Tissues harvested the prescribed way will increase the diagnostic efficacy and provide reliable material for scientific investigations.

  16. Are children like werewolves? Full moon and its association with sleep and activity behaviors in an international sample of children

    Directory of Open Access Journals (Sweden)

    Jean-Philippe eChaput

    2016-03-01

    Full Text Available In order to verify if the full moon is associated with sleep and activity behaviors, we used a 12-country study providing 33710 24-hour accelerometer recordings of sleep and activity. The present observational, cross-sectional study included 5812 children ages 9-11 years from study sites that represented all inhabited continents and wide ranges of human development (Australia, Brazil, Canada, China, Colombia, Finland, India, Kenya, Portugal, South Africa, United Kingdom and United States. Three moon phases were used in this analysis: full moon (±4 days; reference, half moon (±5-9 days and new moon (±10-14 days from nearest full moon. Nocturnal sleep duration, moderate-to-vigorous physical activity (MVPA, light-intensity physical activity (LPA and total sedentary time (SED were monitored over 7 consecutive days using a waist-worn accelerometer worn 24 hours a day. Only sleep duration was found to significantly differ between moon phases (~5 min per night shorter during full moon compared to new moon. Differences in MVPA, LPA and SED between moon phases were negligible and non-significant (<2 min per day difference. There was no difference in the associations between study sites. In conclusion, sleep duration was 1% shorter at full moon compared to new moon while activity behaviors were not significantly associated with the lunar cycle in this global sample of children. Whether this seemingly minimal difference is clinically meaningful is questionable.

  17. Internal jugular vein: Peripheral vein adrenocorticotropic hormone ratio in patients with adrenocorticotropic hormone-dependent Cushing′s syndrome: Ratio calculated from one adrenocorticotropic hormone sample each from right and left internal jugular vein during corticotrophin releasing hormone stimulation test

    Directory of Open Access Journals (Sweden)

    Sachin Chittawar

    2013-01-01

    Full Text Available Background: Demonstration of central: Peripheral adrenocorticotropic hormone (ACTH gradient is important for diagnosis of Cushing′s disease. Aim: The aim was to assess the utility of internal jugular vein (IJV: Peripheral vein ACTH ratio for diagnosis of Cushing′s disease. Materials and Methods: Patients with ACTH-dependent Cushing′s syndrome (CS patients were the subjects for this study. One blood sample each was collected from right and left IJV following intravenous hCRH at 3 and 5 min, respectively. A simultaneous peripheral vein sample was also collected with each IJV sample for calculation of IJV: Peripheral vein ACTH ratio. IJV sample collection was done under ultrasound guidance. ACTH was assayed using electrochemiluminescence immunoassay (ECLIA. Results: Thirty-two patients participated in this study. The IJV: Peripheral vein ACTH ratio ranged from 1.07 to 6.99 ( n = 32. It was more than 1.6 in 23 patients. Cushing′s disease could be confirmed in 20 of the 23 cases with IJV: Peripheral vein ratio more than 1.6. Four patients with Cushing′s disease and 2 patients with ectopic ACTH syndrome had IJV: Peripheral vein ACTH ratio less than 1.6. Six cases with unknown ACTH source were excluded for calculation of sensitivity and specificity of the test. Conclusion: IJV: Peripheral vein ACTH ratio calculated from a single sample from each IJV obtained after hCRH had 83% sensitivity and 100% specificity for diagnosis of CD.

  18. The influence of samples incubation on detection of PLRV and the effect of some extraction buffer’s additives on the detection of potato viruses Y, A, X and by ELISA technique

    Directory of Open Access Journals (Sweden)

    Krisztina PETRUSCA

    2009-11-01

    Full Text Available The goal of this research was to examine and evaluate the effects of several modifications of ELISA (enzyme linked immunosorbent assay technique on the detection of potato viruses Y, A, X, S and potato leafroll virus by this technique. These modifications consisted on: modification of the incubation modality of conjugate (IgG-AP, the use of several additives in extraction buffer, replacement of grinding buffer with McIlvain buffer. The results show a better identification of PLRV in leaves and sprouting tubers using the co-incubation sample and IgG-AP conjugate. Compared with the classical method, the test safety and sensitivity increased. Testing leaves, the average values of OD at 405 nm was 5-6,6 times higher than those obtained by standard DAS ELISA method and using sap from sprouting tubers (dilution 1/10 this average was 1,5 times higher. The detection of potato viruses Y and A by enzyme–linked immunosorbent assay (ELISA can be improved using extraction buffers with new composition. Using McIlvain’s phosphate-citric acid buffer (0,18M; pH 7, the absorbance values (A405nm increased significantly for PVY and PVA detection comparing with the classic extraction buffer. Sodium diethyldithiocarbamate (0.01M in phosphate-buffered saline plus Tween 20 (PBS-T used instead of the polyvinylpyrrolidone increased the sensitivity of potato virus Y but this additives decrease the absorbance values in case of PLRV identification. The same decrease was observed when we used sodium thioglicolat (0.01M and sodium diethyldithiocarbamate (0.01M in PBS-T. The co-incubation sample and conjugate and the use of McIlvain’s buffer could save time and costs of potato viruses diagnostic tests.

  19. Hepatitis-C-virus-like internal ribosome entry sites displace eIF3 to gain access to the 40S subunit

    Science.gov (United States)

    Hashem, Yaser; Des Georges, Amedee; Dhote, Vidya; Langlois, Robert; Liao, Hstau Y.; Grassucci, Robert A.; Pestova, Tatyana V.; Hellen, Christopher U. T.; Frank, Joachim

    2013-11-01

    Hepatitis C virus (HCV) and classical swine fever virus (CSFV) messenger RNAs contain related (HCV-like) internal ribosome entry sites (IRESs) that promote 5'-end independent initiation of translation, requiring only a subset of the eukaryotic initiation factors (eIFs) needed for canonical initiation on cellular mRNAs. Initiation on HCV-like IRESs relies on their specific interaction with the 40S subunit, which places the initiation codon into the P site, where it directly base-pairs with eIF2-bound initiator methionyl transfer RNA to form a 48S initiation complex. However, all HCV-like IRESs also specifically interact with eIF3 (refs 2, 5, 6, 7, 9, 10, 11, 12), but the role of this interaction in IRES-mediated initiation has remained unknown. During canonical initiation, eIF3 binds to the 40S subunit as a component of the 43S pre-initiation complex, and comparison of the ribosomal positions of eIF3 and the HCV IRES revealed that they overlap, so that their rearrangement would be required for formation of ribosomal complexes containing both components. Here we present a cryo-electron microscopy reconstruction of a 40S ribosomal complex containing eIF3 and the CSFV IRES. Remarkably, although the position and interactions of the CSFV IRES with the 40S subunit in this complex are similar to those of the HCV IRES in the 40S-IRES binary complex, eIF3 is completely displaced from its ribosomal position in the 43S complex, and instead interacts through its ribosome-binding surface exclusively with the apical region of domain III of the IRES. Our results suggest a role for the specific interaction of HCV-like IRESs with eIF3 in preventing ribosomal association of eIF3, which could serve two purposes: relieving the competition between the IRES and eIF3 for a common binding site on the 40S subunit, and reducing formation of 43S complexes, thereby favouring translation of viral mRNAs.

  20. Towards an international standard for PCR-based detection of foodborne thermotolerant campylobacters: interaction of enrichment media and pre-PCR treatment on carcass rinse samples

    DEFF Research Database (Denmark)

    Josefsen, Mathilde Hartmann; Lübeck, Peter Stephensen; Hansen, F.

    2004-01-01

    As part of a large EU project for standardisation of polymerase chain reaction (PCR), a systematic evaluation of the interaction of enrichment media, type of DNA polymerase and pre-PCR sample treatment for a PCR detecting thermotolerant campylobacters was carried out. The growth-supporting capacity...... and PCR compatibility of enrichment in Preston, Mueller-Hinton and Bolton broth (blood-containing and blood-free) were evaluated. The effect of resin-based DNA extraction and DNA extraction by boiling on the final PCR assay was investigated. The time-course studies indicated that a 20-h sample enrichment...... in blood-containing Bolton broth, followed by a simple resin-based extraction of DNA and a PCR amplification using Tth polymerase, resulted in strong and clear PCR amplicons for target (287 bp) and internal amplification control (IAC, 124 bp). The enrichment PCR-based method, tested on 68 presumably...

  1. Mathematics beliefs and achievement of a national sample of Native American students: results from the Trends in International Mathematics and Science Study (TIMSS) 2003 United States assessment.

    Science.gov (United States)

    House, J Daniel

    2009-04-01

    Recent mathematics assessment findings indicate that Native American students tend to score below students of the ethnic majority. Findings suggest that students' beliefs about mathematics are significantly related to achievement outcomes. This study examined relations between self-beliefs and mathematics achievement for a national sample of 130 Grade 8 Native American students from the Trends in International Mathematics and Science Study (TIMSS) 2003 United States sample of (M age = 14.2 yr., SD = 0.5). Multiple regression indicated several significant relations of mathematics beliefs with achievement and accounted for 26.7% of the variance in test scores. Students who earned high test scores tended to hold more positive beliefs about their ability to learn mathematics quickly, while students who earned low scores expressed negative beliefs about their ability to learn new mathematics topics.

  2. Production and use of mycotoxins uniformly enriched with stable isotopes for their dosage in biological samples: (3) Tools for pharmacokinetics and as internal standards

    Energy Technology Data Exchange (ETDEWEB)

    Bravin, F.; Delaforge, M.; Duca, R.C. [CNRS, URA 2096, F-91191 Gif Sur Yvette (France); Bravin, F.; Delaforge, M.; Duca, R.C. [CEA Saclay, DSV, DBJC, SBFM, F-91191 Gif Sur Yvette (France); Pean, M. [CEA Cadarache, DEVM, GRAP, St Paul Les Durance (France); Puel, O. [INRA, Lab Pharmacol Toxicol, UR 66, Toulouse (France)

    2007-07-01

    Pharmacological studies of exogenous compounds often encounter problems: these compounds are in such infinitesimal amount in their biological matrices, that they require particular detection method. We have implemented an alternative method to the usual radioactivity, based on incorporation of stable isotopes, through the example of biosynthesis of uniformly {sup 13}C enriched mycotoxins. The isotopic cluster obtained from a 10% {sup 13}C enrichment of several mycotoxins (and their metabolites) can be easily recovered from biological tissue samples by mass spectrometry allowing an easy discrimination from natural non-enriched compounds. We illustrate such pharmacological approaches by in vitro zearalenone metabolism. Such enriched compound can also be used as internal standard with high reliability in order to quantify mycotoxins in contaminated food samples. (authors)

  3. Statistical coherence of primary schooling in IPUMS-International integrated population samples for China, India, Vietnam, and ten other Asia-Pacific countries.

    Science.gov (United States)

    McCaa, Robert; Cleveland, Lara; Kelly-Hall, Patricia; Ruggles, Steven; Sobek, Matthew

    2015-09-01

    IPUMS-International www.ipums.org/international disseminates harmonized census microdata for more than 80 countries at no cost, although access is restricted to bona-fide researchers and students who agree to the stringent conditions of use license. Currently over 270 samples are available, totalling more than 600 million person records. Each year 15-20 additional samples are released, as more countries cooperate with the IPUMS initiative and the integration of 2010 round census samples is completed. With so much microdata so readily available, questions of data quality naturally arise. This paper focusses on the concept of statistical coherence over time for a single concept, primary schooling completed. From an analysis of the percentage completing primary schooling by birth year for pairs of samples for thirteen Asia-Pacific countries, we find outstanding coherence for four-China, Mongolia, Vietnam, and Indonesia-with mean differences of less than 0.5 percentage points, regression coefficient (b) ranging from 0.93 to 1.07 and R(2) =.99. For the thirteen countries as a group there is considerable variation overall with mean absolute difference as high as 16 percentage points, b ranging from 0.62-1.44 and R(2)=.65-.99. As a whole, statistical coherence of primary schooling is outstanding. Nonetheless, to make expert use of the harmonized microdata, researchers are cautioned to carefully study the IPUMS integrated metadata as well as the original source documentation. National Statistical Offices not currently cooperating or that have not yet entrusted 2010 round census microdata are invited to do so.

  4. Sample environment for neutron scattering measurements of internal stresses in engineering materials in the temperature range of 6 K to 300 K.

    Science.gov (United States)

    Kirichek, O; Timms, J D; Kelleher, J F; Down, R B E; Offer, C D; Kabra, S; Zhang, S Y

    2017-02-01

    Internal stresses in materials have a considerable effect on material properties including strength, fracture toughness, and fatigue resistance. The ENGIN-X beamline is an engineering science facility at ISIS optimized for the measurement of strain and stress using the atomic lattice planes as a strain gauge. Nowadays, the rapidly rising interest in the mechanical properties of engineering materials at low temperatures has been stimulated by the dynamic development of the cryogenic industry and the advanced applications of the superconductor technology. Here we present the design and discuss the test results of a new cryogenic sample environment system for neutron scattering measurements of internal stresses in engineering materials under a load of up to 100 kN and in the temperature range of 6 K to 300 K. Complete cooling of the system starting from the room temperature down to the base temperature takes around 90 min. Understanding of internal stresses in engineering materials at cryogenic temperatures is vital for the modelling and designing of cutting-edge superconducting magnets and other superconductor based applications.

  5. Internal correction of hafnium oxide spectral interferences and mass bias in the determination of platinum in environmental samples using isotope dilution analysis.

    Science.gov (United States)

    Rodríguez-Castrillón, José Angel; Moldovan, Mariella; García Alonso, J Ignacio

    2009-05-01

    A method has been developed for the accurate determination of platinum by isotope dilution analysis, using enriched (194)Pt, in environmental samples containing comparatively high levels of hafnium without any chemical separation. The method is based on the computation of the contribution of hafnium oxide as an independent factor in the observed isotope pattern of platinum in the spiked sample. Under these conditions, the ratio of molar fractions between natural abundance and isotopically enriched platinum was independent of the amount of hafnium present in the sample. Additionally, mass bias was corrected by an internal procedure in which the regression variance was minimised. This was possible as the mass bias factor for hafnium oxide was very close to that of platinum. The final procedure required the measurement of three platinum isotope ratios (192/194, 195/194 and 196/194) to calculate the concentration of platinum in the sample. The methodology has been validated using the reference material "BCR-723 road dust" and has been applied to different environmental matrices (road dust, air particles, bulk wet deposition and epiphytic lichens) collected in the Aspe Valley (Pyrenees Mountains). A full uncertainty budget, using Kragten's spreadsheet method, showed that the total uncertainty was limited only by the uncertainty in the measured isotope ratios and not by the uncertainties of the isotopic composition of platinum and hafnium.

  6. High-internal-phase-emulsion polymeric monolith coupled with liquid chromatography-electrospray tandem mass spectrometry for enrichment and sensitive detection of trace cytokinins in plant samples.

    Science.gov (United States)

    Du, Fuyou; Sun, Lin; Zhen, Xian; Nie, Honggang; Zheng, Yanjie; Ruan, Guihua; Li, Jianping

    2015-08-01

    High-internal-phase-emulsion polymers (polyHIPEs) show great promise as solid-phase-extraction (SPE) materials because of the tremendous porosity and highly interconnected framework afforded by the high-internal-phase-emulsion (HIPE) technique. In this work, polyHIPE monolithic columns as novel SPE materials were prepared and applied to trace enrichment of cytokinins (CKs) from complex plant samples. The polyHIPE monoliths were synthesized via the in-situ polymerization of the continuous phase of a HIPE containing styrene (STY) and divinylbenzene (DVB) in a stainless column, and revealed highly efficient and selective enrichment ability for aromatic compounds. Under the optimized experimental conditions, a method using a monolithic polyHIPE column combined with liquid chromatography-electrospray tandem mass spectrometry (LC-MS-MS) was developed for the simultaneous extraction and sensitive determination of trans-zeatin (tZ), meta-topolin (mT), kinetin (K), and kinetin riboside (KR). The proposed method had good linearity, with correlation coefficients (R (2)) from 0.9957 to 0.9984, and low detection limits (LODs, S/N = 3) in the range 2.4-47 pg mL(-1) for the four CKs. The method was successfully applied to the determination of CKs in real plant samples, and obtained good recoveries ranging from 68.8 % to 103.0 % and relative standard deviations (RSDs) lower than 16 %.

  7. Internal Consistency, Test–Retest Reliability and Measurement Error of the Self-Report Version of the Social Skills Rating System in a Sample of Australian Adolescents

    Science.gov (United States)

    Vaz, Sharmila; Parsons, Richard; Passmore, Anne Elizabeth; Andreou, Pantelis; Falkmer, Torbjörn

    2013-01-01

    The social skills rating system (SSRS) is used to assess social skills and competence in children and adolescents. While its characteristics based on United States samples (US) are published, corresponding Australian figures are unavailable. Using a 4-week retest design, we examined the internal consistency, retest reliability and measurement error (ME) of the SSRS secondary student form (SSF) in a sample of Year 7 students (N = 187), from five randomly selected public schools in Perth, western Australia. Internal consistency (IC) of the total scale and most subscale scores (except empathy) on the frequency rating scale was adequate to permit independent use. On the importance rating scale, most IC estimates for girls fell below the benchmark. Test–retest estimates of the total scale and subscales were insufficient to permit reliable use. ME of the total scale score (frequency rating) for boys was equivalent to the US estimate, while that for girls was lower than the US error. ME of the total scale score (importance rating) was larger than the error using the frequency rating scale. The study finding supports the idea of using multiple informants (e.g. teacher and parent reports), not just student as recommended in the manual. Future research needs to substantiate the clinical meaningfulness of the MEs calculated in this study by corroborating them against the respective Minimum Clinically Important Difference (MCID). PMID:24040116

  8. Internal consistency, test-retest reliability and measurement error of the self-report version of the social skills rating system in a sample of Australian adolescents.

    Directory of Open Access Journals (Sweden)

    Sharmila Vaz

    Full Text Available The social skills rating system (SSRS is used to assess social skills and competence in children and adolescents. While its characteristics based on United States samples (US are published, corresponding Australian figures are unavailable. Using a 4-week retest design, we examined the internal consistency, retest reliability and measurement error (ME of the SSRS secondary student form (SSF in a sample of Year 7 students (N = 187, from five randomly selected public schools in Perth, western Australia. Internal consistency (IC of the total scale and most subscale scores (except empathy on the frequency rating scale was adequate to permit independent use. On the importance rating scale, most IC estimates for girls fell below the benchmark. Test-retest estimates of the total scale and subscales were insufficient to permit reliable use. ME of the total scale score (frequency rating for boys was equivalent to the US estimate, while that for girls was lower than the US error. ME of the total scale score (importance rating was larger than the error using the frequency rating scale. The study finding supports the idea of using multiple informants (e.g. teacher and parent reports, not just student as recommended in the manual. Future research needs to substantiate the clinical meaningfulness of the MEs calculated in this study by corroborating them against the respective Minimum Clinically Important Difference (MCID.

  9. Development of high-yield influenza B virus vaccine viruses.

    Science.gov (United States)

    Ping, Jihui; Lopes, Tiago J S; Neumann, Gabriele; Kawaoka, Yoshihiro

    2016-12-20

    The burden of human infections with influenza A and B viruses is substantial, and the impact of influenza B virus infections can exceed that of influenza A virus infections in some seasons. Over the past few decades, viruses of two influenza B virus lineages (Victoria and Yamagata) have circulated in humans, and both lineages are now represented in influenza vaccines, as recommended by the World Health Organization. Influenza B virus vaccines for humans have been available for more than half a century, yet no systematic efforts have been undertaken to develop high-yield candidates. Therefore, we screened virus libraries possessing random mutations in the six "internal" influenza B viral RNA segments [i.e., those not encoding the major viral antigens, hemagglutinin (HA) and neuraminidase NA)] for mutants that confer efficient replication. Candidate viruses that supported high yield in cell culture were tested with the HA and NA genes of eight different viruses of the Victoria and Yamagata lineages. We identified combinations of mutations that increased the titers of candidate vaccine viruses in mammalian cells used for human influenza vaccine virus propagation and in embryonated chicken eggs, the most common propagation system for influenza viruses. These influenza B virus vaccine backbones can be used for improved vaccine virus production.

  10. The comparative utility of oral swabs and probang samples for detection of foot-and-mouth disease virus infection in cattle and pigs

    DEFF Research Database (Denmark)

    Stenfeldt, Anna Carolina; Lohse, Louise; Belsham, Graham

    2013-01-01

    Foot-and-mouth disease virus (FMDV) RNA was measured using quantitative reverse transcription-PCR (qRT-PCR) assays in oralswab and probangsamples collected from cattle and pigs during experimental infections with serotype O FMDV. During acute infection, FMDV RNA was measurable in oralswabs as wel...

  11. Prevalence of gastrointestinal symptoms in patients with influenza, clinical significance, and pathophysiology of human influenza viruses in faecal samples: what do we know?

    Science.gov (United States)

    Minodier, Laetitia; Charrel, Remi N; Ceccaldi, Pierre-Emmanuel; van der Werf, Sylvie; Blanchon, Thierry; Hanslik, Thomas; Falchi, Alessandra

    2015-12-12

    This review provides for the first time an assessment of the current understanding about the occurrence and the clinical significance of gastrointestinal (GI) symptoms in influenza patients, and their correlation with the presence of human influenza viruses in stools of patients with confirmed influenza virus infection. Studies exploring how human influenza viruses spread to the patient's GI tract after a primary respiratory infection have been summarized. We conducted a systematic search of published peer-reviewed literature up to June 2015 with regard to the above-mentioned aspects, focusing on human influenza viruses (A(H1N1), A(H1N1)pdm09, A(H3N2), and B). Forty-four studies were included in this systematic review and meta-analysis. The pooled prevalence of any digestive symptoms ranged from 30.9% (95% CI, 9.8 to 57.5; I(2) = 97.5%) for A(H1N1)pdm09 to 2.8% (95% CI, 0.6 to 6.5; I(2) = 75.4%) for A(H1N1). The pooled prevalence of influenza viruses in stool was 20.6% (95% CI, 8.9 to 35.5; I(2) = 96.8%), but their correlation with GI symptoms has rarely been explored. The presence of viral RNA in stools because of haematogenous dissemination to organs via infected lymphocytes is likely, but the potential to cause direct intestinal infection and faecal-oral transmission warrants further investigation. This review highlights the gaps in our knowledge, and the high degree of uncertainty about the prevalence and significance of GI symptoms in patients with influenza and their correlation with viral RNA positivity in stool because of the high level of heterogeneity among studies.

  12. Self-rated psychopathic traits in a sample of treatment-seeking adolescent girls with internalizing and externalizing disorders: comparisons to girls in the community.

    Science.gov (United States)

    Oshukova, Svetlana; Kaltiala-Heino, Riittakerttu; Miettunen, Jouko; Marttila, Riikka; Aronen, Eeva T; Marttunen, Mauri; Kaivosoja, Matti; Lindberg, Nina

    2017-04-01

    Psychopathy research has thus far focused mostly on child, male, and delinquent samples, but the results are most likely non-generalizable to adolescent girls with mental health disorders. The present study aimed to compare self-rated psychopathic traits between female psychiatric outpatients and girls in the community, and to investigate how psychopathic traits relate to psychiatric disorders. The outpatient sample comprised 163 girls aged 15-17-years recruited from municipal mental health services. Psychiatric diagnoses were assessed based on the ICD-10 classification. The community sample comprised 355 girls from secondary, vocational, and high schools. The Youth Psychopathic trait Inventory (YPI) served as a self-assessment tool. Treatment-seeking girls exhibit a more impulsive and irresponsible lifestyle than do girls in the community. Girls with externalizing psychopathology, unlike those with an internalizing disorder, exhibit more deficient affective experience than do girls in the community. Psychopathic traits associate with having a psychiatric disorder, a depressive disorder, ADHD, and a conduct disorder. The psychiatric examination of treatment-seeking adolescent girls would likely benefit from screening for psychopathy and its underlying components.

  13. More than 150 novel variants of HLA class I genes detected in German Stem Cell Donor Registry and UCLA International Cell Exchange samples.

    Science.gov (United States)

    Balz, V; Krause, S; Fischer, J; Enczmann, J

    2018-01-08

    High throughput analysis using amplicon-based next-generation sequencing (NGS) of HLA class I genes in samples of registered stem cell donors of the German Stem Cell Donor Registry Düsseldorf revealed 151 novel variants. In addition, four new variants were identified in well-defined samples obtained from the UCLA International Cell Exchange program. New alleles included 37 HLA-A, 57 HLA-B, and 61 HLA-C variant alleles. All variants were confirmed by NGS of HLA-A, HLA-B, and HLA-C genes including the respective 5' and 3' untranslated regions as well as Sanger sequence analysis. Mainly, the variants encompass single nucleotide changes in intronic as well as exonic parts of the genes. We identified intronic variations in 114 new alleles, nonsynonymous nucleotide changes in 25 alleles, synonymous nucleotide changes in nine alleles, and three hybrid alleles. Four alleles carry exonic deletions or insertions resulting in frameshift of peptide translation. Two novel alleles of HLA-C were shown to result in splicing defects of the transcript. Two alleles showed exonic as well as intronic changes. Thirty-four of the new alleles were found in multiple samples. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  14. Development and evaluation of a reverse transcription-insulated isothermal polymerase chain reaction (RT-iiPCR) assay for detection of equine arteritis virus in equine semen and tissue samples using the POCKIT™ system.

    Science.gov (United States)

    Carossino, Mariano; Lee, Pei-Yu A; Nam, Bora; Skillman, Ashley; Shuck, Kathleen M; Timoney, Peter J; Tsai, Yun-Long; Ma, Li-Juan; Chang, Hsiao-Fen G; Wang, Hwa-Tang T; Balasuriya, Udeni B R

    2016-08-01

    Equine arteritis virus (EAV) is the causative agent of equine viral arteritis (EVA), a respiratory and reproductive disease of horses. Most importantly, EAV induces abortion in pregnant mares and can establish persistent infection in up to 10-70% of the infected stallions, which will continue to shed the virus in their semen. The objective of this study was to develop and evaluate a reverse transcription insulated isothermal polymerase chain reaction (RT-iiPCR) for the detection of EAV in semen and tissue samples. The newly developed assay had a limit of detection of 10 RNA copies and a 10-fold higher sensitivity than a previously described real-time RT-PCR (RT-qPCR). Evaluation of 125 semen samples revealed a sensitivity and specificity of 98.46% and 100.00%, respectively for the RT-qPCR assay, and 100.00% and 98.33%, respectively for the RT-iiPCR assay. Both assays had the same accuracy (99.2%, k=0.98) compared to virus isolation. Corresponding values derived from testing various tissue samples (n=122) collected from aborted fetuses, foals, and EAV carrier stallions are as follows: relative sensitivity, specificity, and accuracy of 88.14%, 96.83%, and 92.62% (k=0.85), respectively for the RT-qPCR assay, and 98.31%, 92.06%, and 95.08% (k=0.90), respectively for the RT-iiPCR assay. These results indicate that RT-iiPCR is a sensitive, specific, and a robust test enabling detection of EAV in semen and tissue samples with very considerable accuracy. Even though the RT-qPCR assay showed a sensitivity and specificity equal to virus isolation for semen samples, its diagnostic performance was somewhat limited for tissue samples. Thus, this new RT-iiPCR could be considered as an alternative tool in the implementation of EAV control and prevention strategies. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. Heterogeneity of the Epstein-Barr Virus (EBV) Major Internal Repeat Reveals Evolutionary Mechanisms of EBV and a Functional Defect in the Prototype EBV Strain B95-8.

    Science.gov (United States)

    Ba Abdullah, Mohammed M; Palermo, Richard D; Palser, Anne L; Grayson, Nicholas E; Kellam, Paul; Correia, Samantha; Szymula, Agnieszka; White, Robert E

    2017-12-01

    Epstein-Barr virus (EBV) is a ubiquitous pathogen of humans that can cause several types of lymphoma and carcinoma. Like other herpesviruses, EBV has diversified through both coevolution with its host and genetic exchange between virus strains. Sequence analysis of the EBV genome is unusually challenging because of the large number and lengths of repeat regions within the virus. Here we describe the sequence assembly and analysis of the large internal repeat 1 of EBV (IR1; also known as the BamW repeats) for more than 70 strains. The diversity of the latency protein EBV nuclear antigen leader protein (EBNA-LP) resides predominantly within the exons downstream of IR1. The integrity of the putative BWRF1 open reading frame (ORF) is retained in over 80% of strains, and deletions truncating IR1 always spare BWRF1. Conserved regions include the IR1 latency promoter (Wp) and one zone upstream of and two within BWRF1. IR1 is heterogeneous in 70% of strains, and this heterogeneity arises from sequence exchange between strains as well as from spontaneous mutation, with interstrain recombination being more common in tumor-derived viruses. This genetic exchange often incorporates regions of Epstein-Barr virus (EBV) infects the majority of the world population but causes illness in only a small minority of people. Nevertheless, over 1% of cancers worldwide are attributable to EBV. Recent sequencing projects investigating virus diversity to see if different strains have different disease impacts have excluded regions of repeating sequence, as they are more technically challenging. Here we analyze the sequence of the largest repeat in EBV (IR1). We first characterized the variations in protein sequences encoded across IR1. In studying variations within the repeat of each strain, we identified a mutation in the main laboratory strain of EBV that impairs virus function, and we suggest that tumor-associated viruses may be more likely to contain DNA mixed from two strains. The

  16. Evaluation of the effects of long-term storage of bovine ear notch samples on the ability of 2 diagnostic assays to identify calves persistently infected with bovine viral diarrhoea virus

    Directory of Open Access Journals (Sweden)

    F. Khan

    2011-04-01

    Full Text Available Research aimed at optimising diagnostic laboratory procedures is central to the development of effective bovine viral diarrhoea virus (BVDV control programmes. BVDV is a singlestranded RNA virus that crosses the placenta to infect foetuses, resulting in reproductive losses due to foetal death or persistently infected calves that die early in life. Persistently infected animals are widely accepted to be the primary reservoir of BVDV and the largest source of infection. This poses important challenges to overall animal/herd health and can cause major losses to the cattle industry. Long-term storage of bovine ear notch samples from calves persistently infected with BVDV may adversely affect the ability of diagnostic assays to detect the virus efficiently. In order to test this hypothesis, ear notch samples from 7 animals were divided into 2 groups. One set was subjected to prompt formalin fixation and the other set stored either as fresh samples without preservatives at –2 °C, or soaked overnight in phosphate buffered saline followed by freezing of the supernatant fluid at –2 °C. Frozen ear notches and ear notch supernatant yielded positive results with an antigen- capture, enzyme linked immunosorbent assay (AC-ELISA for the duration of the study (6 months and optical density (OD values remained significantly within range. There was no significant difference between storing fresh ear notch samples or PBS at –2 °C. However, positive immunohistochemistry (IHC staining on formalin fixed ear notches started to fade between Day 17 and Day 29 when stored at room temperature. It was concluded that fresh ear notches could safely be stored at –2 °C for a period of 6 months prior to testing for BVD viral antigens.

  17. Evaluation of the effects of long-term storage of bovine ear notch samples on the ability of 2 diagnostic assays to identify calves persistently infected with bovine viral diarrhoea virus.

    Science.gov (United States)

    Khan, F; Vorster, J H; van Vuuren, M; Mapham, P

    2011-03-01

    Research aimed at optimising diagnostic laboratory procedures is central to the development of effective bovine viral diarrhoea virus (BVDV) control programmes. BVDV is a single-stranded RNA virus that crosses the placenta to infect foetuses, resulting in reproductive losses due to foetal death or persistently infected calves that die early in life. Persistently infected animals are widely accepted to be the primary reservoir of BVDV and the largest source of infection. This poses important challenges to overall animal/herd health and can cause major losses to the cattle industry. Long-term storage of bovine ear notch samples from calves persistently infected with BVDV may adversely affect the ability of diagnostic assays to detect the virus efficiently. In order to test this hypothesis, ear notch samples from 7 animals were divided into 2 groups. One set was subjected to prompt formalin fixation and the other set stored either as fresh samples without preservatives at -2 degrees C, or soaked overnight in phosphate buffered saline followed by freezing of the supernatant fluid at -2 degrees C. Frozen ear notches and ear notch supernatant yielded positive results with an antigen-capture, enzyme linked immunosorbent assay (AC-ELISA) for the duration of the study (6 months) and optical density (OD) values remained significantly within range. There was no significant difference between storing fresh ear notch samples or PBS at -2 degrees C. However, positive immunohistochemistry (IHC) staining on formalin fixed ear notches started to fade between Day 17 and Day 29 when stored at room temperature. It was concluded that fresh ear notches could safely be stored at -2 degrees C for a period of 6 months prior to testing for BVD viral antigens.

  18. Acid-base properties of electrolytic manganese dioxide in aqueous electrolyte solution 3. International common sample number 1-RNO sub 3 (R :Li ,K ) solution system

    Energy Technology Data Exchange (ETDEWEB)

    Tari, Isao; Tokin, Yasushi; Nakahara, Takashi; Hirai, Taketsugu (Okayama Univ., Faculty of Engineering, Okayama, Japan Osaka City Univ., Faculty of Engineering Osaka (Japan))

    1989-07-05

    Behavior of electrolytic manganese dioxide as acid and base in the electrolyte solution of lithium and pottasium nitrates international common sample was studied. Regarding electrolytic manganese dioxide, special treatment was applied for removing Na , treatment method for it was explained. Experiment was conducted by potentiometric titration, continuously and intermittently, Concentration of each ion was measured by atomic absorption to obtain adsorbed quantity of it by electrolytic manganese dioxide. As the result of experiment, those were obtained that, in case pH was higher than 3, electrolytic manganese dioxide acted as acid by releasing H , and at the same time, equivalent amount of Li or K was adsorbed, the quantity of which depended on pH value. As the consideration on experimental result, it was concluded that Li or K was adsorbed at different location. 11 refs., 6 figs.

  19. Single Assay Detection of Acute Bee Paralysis Virus, Kashmir Bee Virus and Israeli Acute Paralysis Virus

    DEFF Research Database (Denmark)

    Francis, Roy Mathew; Kryger, Per

    2012-01-01

    A new RT-PCR primer pair designed to identify Acute Bee Paralysis Virus (ABPV), Kashmir Bee Virus (KBV) or Israeli Acute Bee Paralysis Virus (IAPV) of honey bees (Apis mellifera L.) in a single assay is described. These primers are used to screen samples for ABPV, KBV, or IAPV in a single RT...

  20. Constructing computer virus phylogenies

    Energy Technology Data Exchange (ETDEWEB)

    Goldberg, L.A. [Warwick Univ., Coventry (United Kingdom) Dept. of Computer Science; Goldberg, P.W. [Aston Univ., Birmingham (United Kingdom) Dept. of Applied Mathematics; Phillips, C.A. [Sandia National Labs., Albuquerque, NM (United States); Sorkin, G.B. [International Business Machines Corp., Yorktown Heights, NY (United States). Thomas J. Watson Research Center

    1996-03-01

    There has been much recent algorithmic work on the problem of reconstructing the evolutionary history of biological species. Computer virus specialists are interested in finding the evolutionary history of computer viruses--a virus is often written using code fragments from one or more other viruses, which are its immediate ancestors. A phylogeny for a collection of computer viruses is a directed acyclic graph whose nodes are the viruses and whose edges map ancestors to descendants and satisfy the property that each code fragment is ``invented`` only once. To provide a simple explanation for the data, we consider the problem of constructing such a phylogeny with a minimal number of edges. In general, this optimization problem cannot be solved in quasi-polynomial time unless NQP=QP; we present positive and negative results for associated approximated problems. When tree solutions exist, they can be constructed and randomly sampled in polynomial time.

  1. Concentration and trend of 1,4-dioxane in wells sampled during 2002–2017 in the vicinity of the Tucson International Airport Area Superfund Site, Arizona

    Science.gov (United States)

    Tillman, Fred D

    2017-09-25

    Industrial activities causing extensive groundwater contamination led to the listing of the Tucson International Airport Area (TIAA) as a Superfund Site in 1983. Early groundwater investigations identified volatile organic compounds (VOCs), including the chlorinated solvents trichloroethylene (TCE) and perchloroethylene (PCE), in wells in the area. Several responsible parties were identified and cleanup activities began in the late 1980s. In 2002, the compound 1,4-dioxane was discovered in wells in the area and has since been detected in measurable concentrations throughout the site. The U.S. Environmental Protection Agency (USEPA) classifies 1,4-dioxane as a likely human carcinogen.The purpose of this map is to present 1,4-dioxane concentrations in wells sampled from 2002 through mid-2017 in the TIAA Superfund Site area to indicate both the current status and trends in 1,4-dioxane groundwater contamination. This map includes data from wells in the commercial and residential community in the TIAA and does not include data from wells in suspected or confirmed source areas, such as Air Force Plant 44 and Tucson International Airport, or from wells within treatment facilities.

  2. Internalized Homophobia and Perceived Stigma: A Validation Study of Stigma Measures in a Sample of Young Men who Have Sex with Men.

    Science.gov (United States)

    Puckett, Jae A; Newcomb, Michael E; Ryan, Daniel T; Swann, Greg; Garofalo, Robert; Mustanski, Brian

    2017-03-01

    Young men who have sex with men (YMSM) experience minority stressors that impact their mental health, substance use, and sexual risk behaviors. Internalized homophobia (IH) and perceived stigma represent two of these minority stressors, and there has been limited research empirically validating measures of these constructs. We validated measures of IH and perceived stigma with a sample of 450 YMSM (mean age=18.9) and a sample of 370 YMSM (mean age=22.9). Results from exploratory and confirmatory factor analyses supported modifications to the IH and perceived stigma scales, ultimately revealing a three factor and one factor structure, respectively. Convergent and discriminant validity were examined utilizing correlations between IH, perceived stigma, and other variables related to minority stress (e.g., victimization). We evaluated predictive validity by examining relations with mental health, substance use, and risky sexual behaviors measured 12-months from baseline. There were mixed findings for IH, with subscales varying in their relations to mental health, drinking, and sexual risk variables. Perceived stigma was not related to mental health or substance use, but was associated with greater prevalence of STIs. Findings supported the use of these modified scales with YMSM and highlight the need for further measurement studies.

  3. Development and evaluation of specific PCR primers targeting the ribosomal DNA-internal transcribed spacer (ITS) region of peritrich ciliates in environmental samples

    Science.gov (United States)

    Su, Lei; Zhang, Qianqian; Gong, Jun

    2017-07-01

    Peritrich ciliates are highly diverse and can be important bacterial grazers in aquatic ecosystems. Morphological identifications of peritrich species and assemblages in the environment are time-consuming and expertise-demanding. In this study, two peritrich-specific PCR primers were newly designed to amplify a fragment including the internal transcribed spacer (ITS) region of ribosomal rDNA from environmental samples. The primers showed high specificity in silico, and in tests with peritrich isolates and environmental DNA. Application of these primers in clone library construction and sequencing yielded exclusively sequences of peritrichs for water and sediment samples. We also found the ITS1, ITS2, ITS, D1 region of 28S rDNA, and ITS+D1 region co-varied with, and generally more variable than, the V9 region of 18S rDNA in peritrichs. The newly designed specific primers thus provide additional tools to study the molecular diversity, community composition, and phylogeography of these ecologically important protists in different systems.

  4. A new StaRT-PCR approach to detect and quantify fish Viral Hemorrhagic Septicemia virus (VHSv): enhanced quality control with internal standards.

    Science.gov (United States)

    Pierce, Lindsey R; Willey, James C; Crawford, Erin L; Palsule, Vrushalee V; Leaman, Douglas W; Faisal, Mohamed; Kim, Robert K; Shepherd, Brian S; Stanoszek, Lauren M; Stepien, Carol A

    2013-04-01

    Viral Hemorrhagic Septicemia virus (VHSv) causes one of the world's most important finfish diseases, killing >80 species across Eurasia and North America. A new and especially virulent strain (IVb) emerged in the North American Great Lakes in 2003, threatening fisheries, baitfish, and aquaculture industries. Weeks-long and costly cell culture is the OIE and USDA-APHIS approved diagnostic. A new Standardized Reverse Transcriptase Polymerase Chain Reaction (StaRT-PCR) assay that uniquely incorporates internal standards to improve accuracy and prevent false negatives was developed and evaluated for its ability to detect and quantify VHSv. Results from StaRT-PCR, SYBR(®) green real time qRT-PCR, and cell culture were compared, as well as the effects of potential PCR inhibitors (EDTA and high RNA). Findings show that StaRT-PCR is sensitive, detecting a single molecule, with 100% accuracy at six molecules, and had no false negatives. In comparison, false negatives ranged from 14 to 47% in SYBR(®) green real time qRT-PCR tests, and 47-70% with cell culture. StaRT-PCR uniquely controlled for EDTA and RNA interference. Range of VHSv quantitation by StaRT-PCR was 1.0×10(0)-1.2×10(5) VHSv/10(6)actb1 molecules in wild caught fishes and 1.0×10(0)-8.4×10(5) molecules in laboratory challenged specimens. In the latter experiments, muskellunge with skin lesions had significantly more viral molecules (mean=1.9×10(4)) than those without (1.1×10(3)) (p<0.04). VHSv infection was detected earlier in injection than in immersion challenged yellow perch (two versus three days), with molecule numbers in both being comparable and relatively consistent over the remaining course of the experiment. Our results show that the StaRT-PCR test accurately and reliably detects and quantifies VHSv. Copyright © 2013 Elsevier B.V. All rights reserved.

  5. ECHO virus

    Science.gov (United States)

    ... page: //medlineplus.gov/ency/article/001340.htm ECHO virus To use the sharing features on this page, please enable JavaScript. Enteric cytopathic human orphan (ECHO) viruses are a group of viruses that can lead ...

  6. Effects of achievement differences for internal/external frame of reference model investigations: A test of robustness of findings over diverse student samples.

    Science.gov (United States)

    Schmidt, Isabelle; Brunner, Martin; Preckel, Franzis

    2017-11-12

    Achievement in math and achievement in verbal school subjects are more strongly correlated than the respective academic self-concepts. The internal/external frame of reference model (I/E model; Marsh, 1986, Am. Educ. Res. J., 23, 129) explains this finding by social and dimensional comparison processes. We investigated a key assumption of the model that dimensional comparisons mainly depend on the difference in achievement between subjects. We compared correlations between subject-specific self-concepts of groups of elementary and secondary school students with or without achievement differences in the respective subjects. The main goals were (1) to show that effects of dimensional comparisons depend to a large degree on the existence of achievement differences between subjects, (2) to demonstrate the generalizability of findings over different grade levels and self-concept scales, and (3) to test a rarely used correlation comparison approach (CCA) for the investigation of I/E model assumptions. We analysed eight German elementary and secondary school student samples (grades 3-8) from three independent studies (Ns 326-878). Correlations between math and German self-concepts of students with identical grades in the respective subjects were compared with the correlation of self-concepts of students having different grades using Fisher's Z test for independent samples. In all samples, correlations between math self-concept and German self-concept were higher for students having identical grades than for students having different grades. Differences in median correlations had small effect sizes for elementary school students and moderate effect sizes for secondary school students. Findings generalized over grades and indicated a developmental aspect in self-concept formation. The CCA complements investigations within I/E-research. © 2017 The British Psychological Society.

  7. Molecular and antigenic characterization of reassortant H3N2 viruses from turkeys with a unique constellation of pandemic H1N1 internal genes.

    Directory of Open Access Journals (Sweden)

    Yohannes Berhane

    Full Text Available Triple reassortant (TR H3N2 influenza viruses cause varying degrees of loss in egg production in breeder turkeys. In this study we characterized TR H3N2 viruses isolated from three breeder turkey farms diagnosed with a drop in egg production. The eight gene segments of the virus isolated from the first case submission (FAV-003 were all of TR H3N2 lineage. However, viruses from the two subsequent case submissions (FAV-009 and FAV-010 were unique reassortants with PB2, PA, nucleoprotein (NP and matrix (M gene segments from 2009 pandemic H1N1 and the remaining gene segments from TR H3N2. Phylogenetic analysis of the HA and NA genes placed the 3 virus isolates in 2 separate clades within cluster IV of TR H3N2 viruses. Birds from the latter two affected farms had been vaccinated with a H3N4 oil emulsion vaccine prior to the outbreak. The HAl subunit of the H3N4 vaccine strain had only a predicted amino acid identity of 79% with the isolate from FAV-003 and 80% for the isolates from FAV-009 and FAV-0010. By comparison, the predicted amino acid sequence identity between a prototype TR H3N2 cluster IV virus A/Sw/ON/33853/2005 and the three turkey isolates from this study was 95% while the identity between FAV-003 and FAV-009/10 isolates was 91%. When the previously identified antigenic sites A, B, C, D and E of HA1 were examined, isolates from FAV-003 and FAV-009/10 had a total of 19 and 16 amino acid substitutions respectively when compared with the H3N4 vaccine strain. These changes corresponded with the failure of the sera collected from turkeys that received this vaccine to neutralize any of the above three isolates in vitro.

  8. [Ebola virus disease].

    Science.gov (United States)

    Nazimek, Katarzyna; Bociaga-Jasik, Monika; Bryniarski, Krzysztof; Gałas, Aleksander; Garlicki, Aleksander; Gawda, Anna; Gawlik, Grzegorz; Gil, Krzysztof; Kosz-Vnenchak, Magdalena; Mrozek-Budzyn, Dorota; Olszanecki, Rafał; Piatek, Anna; Zawilińska, Barbara; Marcinkiewicz, Janusz

    2014-01-01

    Ebola is one of the most virulent zoonotic RNA viruses causing in humans haemorrhagic fever with fatality ratio reaching 90%. During the outbreak of 2014 the number of deaths exceeded 8.000. The "imported" cases reported in Western Europe and USA highlighted the extreme risk of Ebola virus spreading outside the African countries. Thus, haemorrhagic fever outbreak is an international epidemiological problem, also due to the lack of approved prevention and therapeutic strategies. The editorial review article briefly summarizes current knowledge on Ebola virus disease epidemiology, etiology, pathogenesis, clinical presentation, diagnosis as well as possible prevention and treatment.

  9. ICTV Virus Taxonomy Profile: Corticoviridae.

    Science.gov (United States)

    Oksanen, Hanna M; Ictv Report Consortium

    2017-05-01

    The Corticoviridae is a family of icosahedral, internal-membrane-containing viruses with double-stranded circular DNA genomes of approximately 10 kb. Only one species, Pseudoalteromonas virus PM2, has been recognized. Pseudoalteromonas virus PM2 infects Gram-negative bacteria and was isolated from seawater in 1968. Pseudoalteromonas virus PM2 is the first bacterial virus in which the presence of lipids in the virion has been demonstrated. Viral lipids are acquired selectively during virion assembly from the host cytoplasmic membrane. The outer protein capsid is an icosahedron with a pseudo T=21 symmetry. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Corticoviridae, which is available at www.ictv.global/report/corticoviridae.

  10. Reassortant Pandemic (H1N1) 2009 Virus in Pigs, United Kingdom

    Science.gov (United States)

    Howard, Wendy A.; Essen, Steve C.; Strugnell, Benjamin W.; Russell, Christine; Barrass, Laura; Reid, Scott M.

    2011-01-01

    Surveillance for influenza virus in pigs in the United Kingdom during spring 2010 detected a novel reassortant influenza virus. This virus had genes encoding internal proteins from pandemic (H1N1) 2009 virus and hemagglutinin and neuraminidase genes from swine influenza virus (H1N2). Our results demonstrate processes contributing to influenza virus heterogeneity. PMID:21749767

  11. Molecular diagnosis of Papaya meleira virus (PMeV) from leaf samples of Carica papaya L. using conventional and real-time RT-PCR.

    Science.gov (United States)

    Abreu, Paolla M V; Piccin, João G; Rodrigues, Silas P; Buss, David S; Ventura, José A; Fernandes, Patricia M B

    2012-03-01

    Papaya meleira virus (PMeV) is the causal agent of papaya sticky disease. This study describes two methods for molecular diagnosis of PMeV using conventional and real-time PCR. These methods were shown to be more efficient than current methods of viral detection using extraction of PMeV dsRNA and observation of symptoms in the field. The methods described here were used to evaluate the effect of inoculation of papaya plants with purified PMeV dsRNA on the progress of PMeV infection. A single inoculation with PMeV dsRNA was observed to delay the progress of the virus infection by several weeks. The possibility of vertical transmission of PMeV was also investigated. No evidence was found for PMeV transmission through seeds collected from diseased fruit. The implications of these results for the epidemiology of PMeV and the management of papaya sticky disease are discussed. Copyright © 2011 Elsevier B.V. All rights reserved.

  12. [The impact of conservative and hypervariable immunodominant epitopes in internal proteins of the influenza A virus on cytotoxic T-cell immune responses].

    Science.gov (United States)

    Naikhin, A N; Losev, I V

    2015-01-01

    The cytotoxic T-cell immune response plays an important role in the prevention of influenza infection and reducing of the illness severity. The knowledge about mechanisms of the virus-specific CD8+ T-cell induction in humans is necessary for better understanding of influenza epidemiology and vaccine development. Due to application of new immunological and genetic methods in last years, considerable amount of.data became available in the literature about CD8+ T-cell immune responses to different influenza A viruses. This review summarizes these data. The main attention is paid to (i) heterosubtypic CTL responses to conservative immunodominant sites; (ii) mechanisms of viral escape from the virus-specific CTLs by means of evolutional escape-mutations; (iii) influence of the HLA haplotype on CD8+ T-cell immune responses. The importance of these data for immunology and vaccinology is discussed.

  13. Health-related quality of life in Kazakh heart failure patients evaluated by the Minnesota living with heart failure questionnaire and comparison with a published large international sample.

    Science.gov (United States)

    Kozhekenova, L G; Lanzoni, M; Rakhypbekov, T K; Mussakhanova, A K; Zurikanov, K S; Castaldi, S

    2014-01-01

    To assess health-related quality of life (HRQL) in Kazakh patients (n=285) treated in Cardiology Department of the Emergency Hospital of Semey during 2012 with acute myocardial infarction and to compare results with HRQL measured in 21 countries (n=3,847). Telephone interviews survey was conducted in February 2014 with the Russian translation of Minnesota Living with Heart Failure Questionnaire (MLHFQ). Descriptive statistics were used to characterize the sample according to each single item of MLHFQ and grouping them in three subset concerning physical, emotional, and social environment dimensions of patients' life. The distribution of scores was evaluated in terms of floor and ceiling effects; Cronbach's alpha coefficient was calculated for the different dimensions to assess internal consistency. Mean age of sample is 60.8 years, most of patients are male (71.6%) and retired (43.5%). The total MLHFQ score was generally low at a moderate degree (mean 34.7, range 0-105). Physical dimension score (mean 14.92) shows mild to moderate impairment in HRQL and a better perception than the average of the control countries (14.9 vs 16.6); emotional status (mean 4.8) is moderately adequate and better than the controls (4.8 vs 7.2); social environment (9.82) showed significant impairment of HRQL and a worse evaluation (9.82 vs 7.8). Kazakh patients reported better emotional and physical HRQL as consequence of the social structure where family environment promotes emotional support and improves self-care, social environment affects the total MLHFQ score that is low and related to the requested availability of free medicines.

  14. Tensegrity applied to modelling the motion of viruses

    Science.gov (United States)

    Simona-Mariana, Cretu; Gabriela-Catalina, Brinzan

    2011-02-01

    A considerable number of viruses' structures have been discovered and more are expected to be identified. Different viruses' symmetries can be observed at the nanoscale level. The mechanical models of some viruses realised by scientists are described in this paper, none of which has taken into consideration the internal deformation of subsystems. The authors' models for some viruses' elements are introduced, with rigid and flexible links, which reproduce the movements of viruses including internal deformations of the subunits.

  15. Development of duplex dual-gene and DIVA real-time RT-PCR assays and use of feathers as a non-invasive sampling method for diagnosis of Turkey Meningoencephalitis Virus.

    Science.gov (United States)

    Davidson, Irit; Raibstein, Israel; Altory-Natour, Amira; Simanov, Michael; Khinich, Yevgeny

    2017-06-01

    The avian flavivirus Turkey Meningoencephalitis Virus (TMEV) causes a neuroparalytic disease of commercial turkeys, expressed in paresis, incoordination, drooping wings and mortality that is controlled by vaccination. The molecular diagnosis using brain tissue RNA has now been upgraded by the development of a diagnostic dual-gene multiplex real-time PCR targeting the envelope and the non-structural NS5 gene, increasing the sensitivity by 10-100-fold compared to the previously existing assays. Based on the recent complete sequences of five TMEV isolates we have now developed a Differentiating Infected from Vaccinated Animals (DIVA) assay, to distinguish between wild-type TMEV strains and the vaccine virus. The DIVA assay was evaluated on commercial vaccines produced by two manufacturers, on RNA purified from brains of experimentally infected turkeys with TMEV strains, and on clinical samples collected between the years 2009 and 2015. We also investigated turkey feather pulps for their suitability to serve for TMEV detection, to avoid invasive sampling and bird killing. The parallel TMEV diagnosis in brain and feather-pulp RNA were similarly useful for diagnosis, at least in experimentally infected turkeys and in three cases of disease encountered in commercial flocks.

  16. Diagnostic criteria for bipolarity based on an international sample of 5,635 patients with DSM-IV major depressive episodes.

    Science.gov (United States)

    Angst, J; Gamma, A; Bowden, C L; Azorin, J M; Perugi, G; Vieta, E; Young, A H

    2012-02-01

    To assess the clinical validity of individual DSM-IV criteria for hypomania. In an international sample of 5,635 patients with major depressive episodes (Bridge Study), DSM-IV criteria for hypomania (stem questions, number and quality of symptoms, duration and exclusion criteria) were systematically assessed and their validity analysed on the basis of clinical data including family history, course, and other clinical characteristics. Three stem questions for hypomania, irritability, elevated mood and the added question of increased activity, showed comparable validity. The results support the current DSM-IV requirement for a higher symptom threshold (4 of 7 hypomanic symptoms) in cases of irritable mood. Longer durations of hypomanic episodes were associated with higher scores on all validators. The results did not support the DSM-IV durational requirements for hypomanic episodes (4 days) and manic episodes (7 days). Brief hypomanic episodes of 1, 2 or 3 days were valid and would meet validity criteria for inclusion. The three exclusion criteria in DSM-IV (hypomania due to the use of antidepressants or of other substances, or to other medical conditions) were found to exclude patients with bipolar depression and should therefore not be retained. These results support several revisions of the DSM-IV concept of hypomanic episodes: specifically, the inclusion of increased activity as a gate question, the inclusion of 1 or 2 to 3-day episodes and the elimination of all exclusion criteria.

  17. Understanding the Potential Content and Structure of an International Convention on the Human Rights of People with Disabilities: Sample Treaty Provisions Drawn from Existing International Instruments. A Reference Tool.

    Science.gov (United States)

    Lord, Janet E.

    This document is designed to prepare advocates in the international disability community for productive participation in the development of international conventions on the human rights of people with disabilities. Knowledge of the standard categories of international law provisions will help participants address issues related to the structure of…

  18. Low prevalence of hepatitis B virus, hepatitis D virus and hepatitis C virus among patients with human immunodeficiency virus or acquired immunodeficiency syndrome in the Brazilian Amazon basin

    OpenAIRE

    Braga,Wornei Silva Miranda; Castilho,Márcia da Costa; Santos,Isabelle Cristina Vale dos; Moura,Marco Antônio Sabóia; Segurado,Aluisio Cotrim

    2006-01-01

    Comorbidities in human immunodeficiency virus infection are of great interest due to their association with unfavorable outcomes and failure of antiretroviral therapy. This study evaluated the prevalence of coinfection by human immunodeficiency virus and viral hepatitis in an endemic area for hepatitis B in the Western Amazon basin. Serological markers for hepatitis B virus, hepatitis C virus and hepatitis D virus were tested in a consecutive sample of all patients referred for treatment of h...

  19. Genomic characterization of influenza A (H7N9) viruses isolated in Shenzhen, Southern China, during the second epidemic wave.

    Science.gov (United States)

    Fang, Shisong; Wang, Xin; Dong, Fangyuan; Jin, Tao; Liu, Guang; Lu, Xing; Peng, Bo; Wu, Weihua; Liu, Hui; Kong, Dongfeng; Tang, Xiujuan; Qin, Yanmin; Mei, Shujiang; Xie, Xu; He, Jianfan; Ma, Hanwu; Zhang, Renli; Cheng, Jinquan

    2016-08-01

    There were three epidemic waves of human infection with avian influenza A (H7N9) virus in 2013-2014. While many analyses of the genomic origin, evolution, and molecular characteristics of the influenza A (H7N9) virus have been performed using sequences from the first epidemic wave, genomic characterization of the virus from the second epidemic wave has been comparatively less reported. In this study, an in-depth analysis was performed with respect to the genomic characteristics of 11 H7N9 virus strains isolated from confirmed cases and four H7N9 virus strains isolated from environmental samples in Shenzhen during the second epidemic wave. Phylogenetic analysis demonstrated that six internal segments of the influenza A (H7N9) virus isolated from confirmed cases and environmental samples in Shenzhen were clustered into two different clades and that the origin of the influenza A (H7N9) virus isolated from confirmed cases in Shenzhen was different from that of viruses isolated during the first wave. In addition, H9N2 viruses, which were prevalent in southern China, played an important role in the reassortment of the influenza A (H7N9) virus isolated in Shenzhen. HA-R47K and -T122A, PB2-V139I, PB1-I397M, and NS1-T216P were the signature amino acids of the influenza A (H7N9) virus isolated from confirmed cases in Shenzhen. We found that the HA, NA, M, and PA genes of the A(H7N9) viruses underwent positive selection in the human population. Therefore, enhanced surveillance should be carried out to determine the origin and mode of transmission of the novel influenza A (H7N9) virus and to facilitate the formulation of effective policies for prevention and containment of a human infection epidemics.

  20. Coping with Computer Viruses: General Discussion and Review of Symantec Anti-Virus for the Macintosh.

    Science.gov (United States)

    Primich, Tracy

    1992-01-01

    Discusses computer viruses that attack the Macintosh and describes Symantec AntiVirus for Macintosh (SAM), a commercial program designed to detect and eliminate viruses; sample screen displays are included. SAM is recommended for use in library settings as well as two public domain virus protection programs. (four references) (MES)

  1. Molecular detection and characterization of Influenza 'C' viruses from western India.

    Science.gov (United States)

    Potdar, V A; Hinge, D D; Dakhave, M R; Manchanda, A; Jadhav, N; Kulkarni, P B; Chadha, M S

    2017-10-01

    Since 2003, India has had a well-established influenza surveillance network, though Influenza C virus was not the focus of study. We therefore retrospectively analyzed clinical samples from Pune, western India collected during January 2009 to August 2015, by real-time RT-PCR. Three of 2530 samples of patients with influenza-like illness (ILI) or severe acute respiratory illness (SARI) showed positivity for Influenza C virus infection, while 105 and 31 samples were positive for Influenza A and B viruses respectively. Influenza C viruses were successfully isolated using the embryonated egg system and whole genomes were sequenced and analyzed phylogenetically. HE gene-based phylogeny showed that two viruses C/India/P119564/2011 and C/India P121719/2012 clustered with the C/Sao Paulo/378/82 (SP82) lineage, whereas C/India/P135047/2013 clustered with the C/Kanagawa/1/76 (KA76) lineage. The internal gene of these viruses grouped in two lineages. The PB1, PB2, M and NS genes of the study viruses grouped with C/Yamagata/26/81 (YA81), while the P3 (PA) and NP genes grouped with C/Mississippi/80 (MS80). Bayesian clock studies conclude that the Indian strains may have emerged through multiple reassortment events. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Background review for diagnostic test development for Zika virus infection

    Science.gov (United States)

    Charrel, Rémi N; Leparc-Goffart, Isabelle; Pas, Suzan; de Lamballerie, Xavier; Koopmans, Marion; Reusken, Chantal

    2016-01-01

    Abstract Objective To review the state of knowledge about diagnostic testing for Zika virus infection and identify areas of research needed to address the current gaps in knowledge. Methods We made a non-systematic review of the published literature about Zika virus and supplemented this with information from commercial diagnostic test kits and personal communications with researchers in European preparedness networks. The review covered current knowledge about the geographical spread, pathogen characteristics, life cycle and infection kinetics of the virus. The available molecular and serological tests and biosafety issues are described and discussed in the context of the current outbreak strain. Findings We identified the following areas of research to address current knowledge gaps: (i) an urgent assessment of the laboratory capacity and capability of countries to detect Zika virus; (ii) rapid and extensive field validation of the available molecular and serological tests in areas with and without Zika virus transmission, with a focus on pregnant women; (iii) monitoring the genomic diversity of circulating Zika virus strains; (iv) prospective studies into the virus infection kinetics, focusing on diagnostic sampling (specimen types, combinations and timings); and (v) developing external quality assessments for molecular and serological testing, including differential diagnosis for similar viruses and symptom clusters. The availability of reagents for diagnostic development (virus strains and antigens, quantified viral ribonucleic acid) needs to be facilitated. Conclusion An international laboratory response is needed, including preparation of protocols for prospective studies to address the most pressing information needs. PMID:27516635

  3. The association of alcohol consumption and smoking with quality of life, disability and disease activity in an international sample of people with multiple sclerosis.

    Science.gov (United States)

    Weiland, Tracey J; Hadgkiss, Emily J; Jelinek, George A; Pereira, Naresh G; Marck, Claudia H; van der Meer, Dania M

    2014-01-15

    Modifiable lifestyle factors represent important targets for preventive intervention in multiple sclerosis (MS). We aimed to explore the association of cigarette smoking and alcohol consumption with major MS morbidity outcomes. We surveyed a large, international sample of people with MS recruited via Web 2.0 platforms about type of MS, relapse rates, disability, disease activity, health-related quality of life (HRQOL), alcohol use and smoking. Of 2469 respondents with confirmed MS, 11.7% were current and 40.3% former smokers. Most (61.5%) consumed less than 15 g alcohol weekly; few (0.8%) drank large amounts. Moderate alcohol consumption was associated with increased HRQOL; and after controlling for age and gender, was associated with lower odds of significant disability (41% decrease). After controlling for age, gender and alcohol use, smokers had an increased likelihood of major mobility requirements by 90% compared to never smokers. There was no association between alcohol or smoking and relapse rate or disease activity after controlling for age and gender, however among former smokers, a longer duration of smoking cessation was associated with reduced disease activity. Smokers had significantly lower HRQOL than never smokers and former smokers; heavier smoking was associated with greater decreases in HRQOL. This cross-sectional study supports previous research showing a link between morbidity indicators in MS and alcohol use and smoking. While people with MS should be advised of the potential risks of smoking, any risks and benefits of alcohol consumption require validation using a prospective cohort of people with MS. © 2013.

  4. Coplanar electrowetting-induced stirring as a tool to manipulate biological samples in lubricated digital microfluidics. Impact of ambient phase on drop internal flow pattern.

    Science.gov (United States)

    Davoust, Laurent; Fouillet, Yves; Malk, Rachid; Theisen, Johannes

    2013-01-01

    Oscillating electrowetting on dielectrics (EWOD) with coplanar electrodes is investigated in this paper as a way to provide efficient stirring within a drop with biological content. A supporting model inspired from Ko et al. [Appl. Phys. Lett. 94, 194102 (2009)] is proposed allowing to interpret oscillating EWOD-induced drop internal flow as the result of a current streaming along the drop surface deformed by capillary waves. Current streaming behaves essentially as a surface flow generator and the momentum it sustains within the (viscous) drop is even more significant as the surface to volume ratio is small. With the circular electrode pair considered in this paper, oscillating EWOD sustains toroidal vortical flows when the experiments are conducted with aqueous drops in air as ambient phase. But when oil is used as ambient phase, it is demonstrated that the presence of an electrode gap is responsible for a change in drop shape: a pinch-off at the electrode gap yields a peanut-shaped drop and a symmetry break-up of the EWOD-induced flow pattern. Viscosity of oil is also responsible for promoting an efficient damping of the capillary waves which populate the surface of the actuated drop. As a result, the capillary network switches from one standing wave to two superimposed traveling waves of different mechanical energy, provided that actuation frequency is large enough, for instance, as large as the one commonly used in electrowetting applications (f ∼ 500 Hz and beyond). Special emphasis is put on stirring of biological samples. As a typical application, it is demonstrated how beads or cell clusters can be focused under flow either at mid-height of the drop or near the wetting plane, depending on how the nature of the capillary waves is (standing or traveling), and therefore, depending on the actuation frequency (150 Hz-1 KHz).

  5. International challenge to predict the impact of radioxenon releases from medical isotope production on a comprehensive nuclear test ban treaty sampling station.

    Science.gov (United States)

    Eslinger, Paul W; Bowyer, Ted W; Achim, Pascal; Chai, Tianfeng; Deconninck, Benoit; Freeman, Katie; Generoso, Sylvia; Hayes, Philip; Heidmann, Verena; Hoffman, Ian; Kijima, Yuichi; Krysta, Monika; Malo, Alain; Maurer, Christian; Ngan, Fantine; Robins, Peter; Ross, J Ole; Saunier, Olivier; Schlosser, Clemens; Schöppner, Michael; Schrom, Brian T; Seibert, Petra; Stein, Ariel F; Ungar, Kurt; Yi, Jing

    2016-06-01

    The International Monitoring System (IMS) is part of the verification regime for the Comprehensive Nuclear-Test-Ban-Treaty Organization (CTBTO). At entry-into-force, half of the 80 radionuclide stations will be able to measure concentrations of several radioactive xenon isotopes produced in nuclear explosions, and then the full network may be populated with xenon monitoring afterward. An understanding of natural and man-made radionuclide backgrounds can be used in accordance with the provisions of the treaty (such as event screening criteria in Annex 2 to the Protocol of the Treaty) for the effective implementation of the verification regime. Fission-based production of (99)Mo for medical purposes also generates nuisance radioxenon isotopes that are usually vented to the atmosphere. One of the ways to account for the effect emissions from medical isotope production has on radionuclide samples from the IMS is to use stack monitoring data, if they are available, and atmospheric transport modeling. Recently, individuals from seven nations participated in a challenge exercise that used atmospheric transport modeling to predict the time-history of (133)Xe concentration measurements at the IMS radionuclide station in Germany using stack monitoring data from a medical isotope production facility in Belgium. Participants received only stack monitoring data and used the atmospheric transport model and meteorological data of their choice. Some of the models predicted the highest measured concentrations quite well. A model comparison rank and ensemble analysis suggests that combining multiple models may provide more accurate predicted concentrations than any single model. None of the submissions based only on the stack monitoring data predicted the small measured concentrations very well. Modeling of sources by other nuclear facilities with smaller releases than medical isotope production facilities may be important in understanding how to discriminate those releases from

  6. Comparison of the Outcomes of Individuals With Medically Attended Influenza A and B Virus Infections Enrolled in 2 International Cohort Studies Over a 6-Year Period

    DEFF Research Database (Denmark)

    Dwyer, Dominic E; Lynfield, Ruth; Losso, Marcelo H

    2017-01-01

    infections were compared in 2 prospective cohorts enrolled globally from 2009 through 2015. Logistic regression was used to compare outcomes among influenza virus type/subtypes. Results: Of 3952 outpatients, 1290 (32.6%) had A(H1N1)pdm09 virus infection, 1857 (47.0%) had A(H3N2), and 805 (20.4%) had...... enrolled from intensive care units (ICUs) than those with A(H3N2) (11.3%) or B (9.8%; P ... (P = .30) among influenza types/subtypes. These findings were consistent after covariate adjustment, in sensitivity analyses, and for subgroups defined by age, enrollment location, and comorbidities. Conclusions: Outpatients infected with influenza A(H1N1)pdm09 or influenza B were more likely...

  7. The International development of PROQOL-HCV: An instrument to assess the health-related quality of life of patients treated for Hepatitis C virus

    OpenAIRE

    Armstrong, Andrew Richard; Herrmann, Susan Elizabeth; Chassany, Olivier; Lalanne, Christophe; Da Silva, Mariliza Henrique; Galano,Eliana; Carrieri, Patrizia M.; Estellon, Vincent; Sogni, Philippe; Duracinsky, Martin

    2016-01-01

    Background Hepatitis C virus (HCV) compromises Health-related Quality of Life (HRQL) with detriments to Physical, Mental and Social health domains. Treatment with interferon and ribavirin is associated with side effects which further impair HRQL. New treatments appear potent, effective and tolerable. However, Patient Reported Outcomes instruments that capture the impact on HRQL for people with hepatitis C are largely non-specific and will be needed in the new treatment era. Therefore, we deve...

  8. The Trajectories of Child's Internalizing and Externalizing Problems, Social Competence and Adolescent Self-Reported Problems in a Finnish Normal Population Sample

    Science.gov (United States)

    Korhonen, Marie; Luoma, Ilona; Salmelin, Raili K.; Helminen, Mika; Kaltiala-Heino, Riittakerttu; Tamminen, Tuula

    2014-01-01

    Group-based modeling techniques are increasingly used in developmental studies to explore the patterns and co-occurrence of internalizing and externalizing problems. Social competence has been found to reciprocally influence internalizing and externalizing problems, but studies on its associations with different patterns of these problems are…

  9. Deliberate Self-Harm within an International Community Sample of Young People: Comparative Findings from the Child & Adolescent Self-Harm in Europe (CASE) Study

    Science.gov (United States)

    Madge, Nicola; Hewitt, Anthea; Hawton, Keith; de Wilde, Erik Jan; Corcoran, Paul; Fekete, Sandor; van Heeringen, Kees; De Leo, Diego; Ystgaard, Mette

    2008-01-01

    Background: Deliberate self-harm among young people is an important focus of policy and practice internationally. Nonetheless, there is little reliable comparative international information on its extent or characteristics. We have conducted a seven-country comparative community study of deliberate self-harm among young people. Method: Over 30,000…

  10. Incidence of respiratory viruses among travelers with a febrile syndrome returning from tropical and subtropical areas.

    Science.gov (United States)

    Camps, M; Vilella, A; Marcos, M A; Letang, E; Muñoz, J; Salvadó, E; González, A; Gascón, J; Jiménez de Anta, M T; Pumarola, T

    2008-04-01

    Fifty million people are estimated to travel from industrial countries to the tropics annually. In spite of exhaustive studies and widely different diagnosis among returned patients, some cases of febrile illnesses remain without an etiological diagnosis, suggesting that these cases could be due to viral respiratory tract infections. From August 2005 to October 2006, 118 febrile patients without a specific diagnosis in their first visit at the Center for International Health of the Hospital Clínic of Barcelona were included. In all of them, in order to study respiratory viruses, a nasopharyngeal swab was collected. Clinical and radiological features and epidemiological data, as well as other samples for microbiologic studies, were also collected during consultation. Based on the physician's judgment at the time of consultation, patients were classified into four groups: respiratory symptoms (62%), febrile syndrome with nonspecific symptoms (24%), digestive symptoms (10%), and patients presenting both respiratory and digestive symptoms (4%). A pathogen microorganism was detected in 61 patients (52%). Respiratory viruses were detected in 44 out of 118 (37%) travelers included in the study, representing 56% of the patients with respiratory symptoms. The most frequently viruses detected were influenza virus (38%), rhinovirus (23%), adenovirus (9%), and respiratory syncytial virus (9%). Respiratory viruses have been shown to play an important role in imported fever. In light of the fact that international tourism is an increasing phenomenon, new strategies to prevent the spread of respiratory viruses should be considered, specially for influenza when a vaccine is available.

  11. Internalizing symptoms and polyvictimization in a clinical sample of adolescents: The roles of social support and non-productive coping strategies.

    Science.gov (United States)

    Guerra, Cristóbal; Pereda, Noemí; Guilera, Georgina; Abad, Judit

    2016-04-01

    Given the high prevalence of internalizing disorders during adolescence, it is necessary to determine the factors influencing their development and evolution. The aim of this study was to evaluate the role of polyvictimization in developing internalizing symptoms while considering the possible effect of non-productive coping and the availability of social support. The participants were 144 adolescents (M=14.31, SD=1.48) cared for in child and adolescent mental health services. The results of multiple regression analysis indicated that polyvictimization, non-productive coping and social support were good predictors of internalizing symptoms. In addition, non-productive coping acted as a mediator in the relationship between polyvictimization and internalizing symptoms. The results of the study emphasized the importance of the studied factors to understanding the process of development internalizing symptoms and to preventing or treating adolescents who suffer from these types of disorders. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. Screening for Viral Hemorrhagic Septicemia Virus in Marine Fish along the Norwegian Coastal Line

    DEFF Research Database (Denmark)

    Sandlund, Nina; Gjerset, Britt; Bergh, Øivind

    2014-01-01

    Viral hemorrhagic septicemia virus (VHSV) infects a wide range of marine fish species. To study the occurrence of VHSV in wild marine fish populations in Norwegian coastal waters and fjord systems a total of 1927 fish from 39 different species were sampled through 5 research cruises conducted...... pout also tested positive in internal organs. Successful virus isolation in cell culture was only obtained from one pooled Atlantic herring sample which shows that today's PCR methodology have a much higher sensitivity than cell culture for detection of VHSV. Sequencing revealed that the positive...

  13. National survey of foodborne viruses in Australian oysters at production.

    Science.gov (United States)

    Torok, Valeria; Hodgson, Kate; McLeod, Catherine; Tan, Jessica; Malhi, Navreet; Turnbull, Alison

    2018-02-01

    Internationally human enteric viruses, such as norovirus (NoV) and hepatitis A virus (HAV), are frequently associated with shellfish related foodborne disease outbreaks, and it has been suggested that acceptable NoV limits based on end-point testing be established for this high risk food group. Currently, shellfish safety is generally managed through the use of indicators of faecal contamination. Between July 2014 and August 2015, a national prevalence survey for NoV and HAV was done in Australian oysters suitable for harvest. Two sampling rounds were undertaken to determine baseline levels of these viruses. Commercial Australian growing areas, represented by 33 oyster production regions in New South Wales, South Australia, Tasmania and Queensland, were included in the survey. A total of 149 and 148 samples were collected during round one and two of sampling, respectively, and tested for NoV and HAV by quantitative RT-PCR. NoV and HAV were not detected in oysters collected in either sampling round, indicating an estimated prevalence for these viruses in Australian oysters of oysters was consistent with epidemiological evidence, with no oyster-related foodborne viral illness reported during the survey period. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. A Lab on a chip device for rapid identification of Avian Influenza virus by on-chip sample preparation and solid phase PCR

    DEFF Research Database (Denmark)

    Yi, Sun; Dhumpa, Raghuram; Bang, Dang Duong

    2009-01-01

    In this paper, we describe a novel lab-on-a-chip device for fast AIV screening by integrating DNA microarray-based solid phase PCR on microchip. The device can handle viral samples in an automatic way. Moreover, multiplex PCR and sequence detection are done in one-step, which greatly simplifies...

  15. Subpopulations of bovine T lymphocytes collected during foot-and-mouth disease virus infection are affected by freezing, but are subsequently stable in frozen samples

    Science.gov (United States)

    Immunophenotyping of peripheral-blood lymphocytes by flow cytometry is an important tool for infectious disease research. In many live-animal experiments and other longitudinal studies, the processing, prompt staining, and analysis of fresh samples is a logistical challenge and daily variation can c...

  16. Analysis of the temporal relationship between human immunodeficiency virus type 1 quasispecies in sequential blood samples and various organs obtained at autopsy

    NARCIS (Netherlands)

    van't Wout, A. B.; Ran, L. J.; Kuiken, C. L.; Kootstra, N. A.; Pals, S. T.; Schuitemaker, H.

    1998-01-01

    We studied the temporal relationship between human immunodeficiency type 1 (HIV-1) quasispecies in tissues and in peripheral blood mononuclear cells (PBMC) of infected individuals. Sequential PBMC and tissue samples from various organs obtained at autopsy from three patients who died of AIDS-related

  17. Chikungunya virus

    Science.gov (United States)

    Chikungunya virus infection; Chikungunya ... Where Chikungunya is Found Before 2013, the virus was found in Africa, Asia, Europe, and the Indian and Pacific oceans. In late 2013, outbreaks occurred for the first time in the ...

  18. Zika Virus

    Science.gov (United States)

    ... through blood transfusions. There have been outbreaks of Zika virus in the United States, Africa, Southeast Asia, the ... not travel to areas where there is a Zika virus outbreak. If you do decide to travel, first ...

  19. Chikungunya Virus

    Science.gov (United States)

    ... Gaines, PhD, MPH, MA, CHES Differentiating Chikungunya From Dengue: A Clinical Challenge For Travelers CDC Travelers' Health Chikungunya Virus Home Prevention Transmission Symptoms & Treatment Geographic Distribution Chikungunya virus in the United States ...

  20. Zika Virus

    Science.gov (United States)

    ... Funding CDC Activities For Healthcare Providers Clinical Evaluation & Disease Sexual Transmission HIV Infection & Zika Virus Testing for Zika Test Specimens – At Time of Birth Diagnostic Tests Understanding Zika Virus Test Results ...

  1. Prevalence of Comorbidities, Overweight and Obesity in an International Sample of People with Multiple Sclerosis and Associations with Modifiable Lifestyle Factors

    Science.gov (United States)

    Marck, Claudia Helena; Neate, Sandra Leanne; Taylor, Keryn Louise; Weiland, Tracey Joy; Jelinek, George Alexander

    2016-01-01

    Multiple sclerosis (MS) is a chronic neurological disorder, often affecting young people. Comorbid disorders such as depression, anxiety and hypertension are common and can affect disease course, treatment, and quality of life (QOL) of people with MS (PwMS). The associations between comorbidities, body mass index (BMI) and health outcomes are not well studied in MS, although research shows most PwMS are overweight. Most data on the prevalence of comorbidities and obesity in PwMS comes from North American populations. This study describes the prevalence of comorbidities, overweight and obesity and associations with modifiable factors in an international sample of PwMS recruited online through social media, MS societies and websites. The online survey consisted of validated and researcher-devised instruments to assess self-reported health outcomes and lifestyle behaviors. Of the 2399 respondents, 22.5% were overweight, 19.4% were obese and 67.2% reported at least one comorbidity, with back pain (36.2%), depression (31.7%), anxiety (29.1%) and arthritis (13.7%) most prevalent and most limiting in daily activities. Obesity and most comorbid disorders were significantly more prevalent in North America. Obese participants were more likely to have comorbidities, especially diabetes (OR 4.8) and high blood pressure (OR 4.5) but also depression (OR 2.2). Being overweight, obese, or a former, or current smoker was associated with an increase in the number of comorbidities; while healthy diet, physical activity (borderline significant) and moderate alcohol consumption were associated with decreased number of comorbidities. Increasing number of comorbidities was related to worse QOL, increased odds of disability and prior relapse. Obese PwMS had higher odds of disability and lower QOL. The associations between BMI, comorbidities and health outcomes are likely to be bi-directional and associated with lifestyle behaviors. Preventing and treating comorbid disorders and obesity in

  2. Prevalence of Comorbidities, Overweight and Obesity in an International Sample of People with Multiple Sclerosis and Associations with Modifiable Lifestyle Factors.

    Science.gov (United States)

    Marck, Claudia Helena; Neate, Sandra Leanne; Taylor, Keryn Louise; Weiland, Tracey Joy; Jelinek, George Alexander

    2016-01-01

    Multiple sclerosis (MS) is a chronic neurological disorder, often affecting young people. Comorbid disorders such as depression, anxiety and hypertension are common and can affect disease course, treatment, and quality of life (QOL) of people with MS (PwMS). The associations between comorbidities, body mass index (BMI) and health outcomes are not well studied in MS, although research shows most PwMS are overweight. Most data on the prevalence of comorbidities and obesity in PwMS comes from North American populations. This study describes the prevalence of comorbidities, overweight and obesity and associations with modifiable factors in an international sample of PwMS recruited online through social media, MS societies and websites. The online survey consisted of validated and researcher-devised instruments to assess self-reported health outcomes and lifestyle behaviors. Of the 2399 respondents, 22.5% were overweight, 19.4% were obese and 67.2% reported at least one comorbidity, with back pain (36.2%), depression (31.7%), anxiety (29.1%) and arthritis (13.7%) most prevalent and most limiting in daily activities. Obesity and most comorbid disorders were significantly more prevalent in North America. Obese participants were more likely to have comorbidities, especially diabetes (OR 4.8) and high blood pressure (OR 4.5) but also depression (OR 2.2). Being overweight, obese, or a former, or current smoker was associated with an increase in the number of comorbidities; while healthy diet, physical activity (borderline significant) and moderate alcohol consumption were associated with decreased number of comorbidities. Increasing number of comorbidities was related to worse QOL, increased odds of disability and prior relapse. Obese PwMS had higher odds of disability and lower QOL. The associations between BMI, comorbidities and health outcomes are likely to be bi-directional and associated with lifestyle behaviors. Preventing and treating comorbid disorders and obesity in

  3. Prevalence of Comorbidities, Overweight and Obesity in an International Sample of People with Multiple Sclerosis and Associations with Modifiable Lifestyle Factors.

    Directory of Open Access Journals (Sweden)

    Claudia Helena Marck

    Full Text Available Multiple sclerosis (MS is a chronic neurological disorder, often affecting young people. Comorbid disorders such as depression, anxiety and hypertension are common and can affect disease course, treatment, and quality of life (QOL of people with MS (PwMS. The associations between comorbidities, body mass index (BMI and health outcomes are not well studied in MS, although research shows most PwMS are overweight. Most data on the prevalence of comorbidities and obesity in PwMS comes from North American populations. This study describes the prevalence of comorbidities, overweight and obesity and associations with modifiable factors in an international sample of PwMS recruited online through social media, MS societies and websites. The online survey consisted of validated and researcher-devised instruments to assess self-reported health outcomes and lifestyle behaviors. Of the 2399 respondents, 22.5% were overweight, 19.4% were obese and 67.2% reported at least one comorbidity, with back pain (36.2%, depression (31.7%, anxiety (29.1% and arthritis (13.7% most prevalent and most limiting in daily activities. Obesity and most comorbid disorders were significantly more prevalent in North America. Obese participants were more likely to have comorbidities, especially diabetes (OR 4.8 and high blood pressure (OR 4.5 but also depression (OR 2.2. Being overweight, obese, or a former, or current smoker was associated with an increase in the number of comorbidities; while healthy diet, physical activity (borderline significant and moderate alcohol consumption were associated with decreased number of comorbidities. Increasing number of comorbidities was related to worse QOL, increased odds of disability and prior relapse. Obese PwMS had higher odds of disability and lower QOL. The associations between BMI, comorbidities and health outcomes are likely to be bi-directional and associated with lifestyle behaviors. Preventing and treating comorbid disorders and

  4. Monitoring virus entry into living cells using DiD-labeled dengue virus particles

    NARCIS (Netherlands)

    Ayala Nunez, Vanesa; Wilschut, Jan; Smit, Jolanda M.

    2011-01-01

    A variety of approaches can be applied to investigate the multiple steps and interactions that occur during virus entry into the host cell. Single-virus tracking is a powerful real-time imaging technique that offers the possibility to monitor virus-cell binding, internalization, intracellular

  5. Taxonomy of prokaryotic viruses : 2016 update from the ICTV bacterial and archaeal viruses subcommittee

    NARCIS (Netherlands)

    Adriaenssens, Evelien M.; Krupovic, Mart; Knezevic, Petar; Ackermann, Hans Wolfgang; Barylski, Jakub; Brister, J. Rodney; Clokie, Martha R C; Duffy, Siobain; Dutilh, Bas E.|info:eu-repo/dai/nl/304546313; Edwards, Robert A; Enault, Francois; Jang, Ho Bin; Klumpp, Jochen; Kropinski, Andrew M.; Lavigne, Rob; Poranen, Minna M.; Prangishvili, David; Rumnieks, Janis; Sullivan, Matthew B.; Wittmann, Johannes; Oksanen, Hanna M.; Gillis, Annika; Kuhn, Jens H.

    The prokaryotic virus community is represented at the International Committee on Taxonomy of Viruses (ICTV) by the Bacterial and Archaeal Viruses Subcommittee. Since our last report [8], the committee composition has changed, and a large number of taxonomic proposals (TaxoProps) were submitted to

  6. Controlled Directional Solidification of Aluminum - 7 wt Percent Silicon Alloys: Comparison Between Samples Processed on Earth and in the Microgravity Environment Aboard the International Space Station

    Science.gov (United States)

    Grugel, Richard N.; Tewari, Surendra N.; Erdman, Robert G.; Poirier, David R.

    2012-01-01

    An overview of the international "MIcrostructure Formation in CASTing of Technical Alloys" (MICAST) program is given. Directional solidification processing of metals and alloys is described, and why experiments conducted in the microgravity environment aboard the International Space Station (ISS) are expected to promote our understanding of this commercially relevant practice. Microstructural differences observed when comparing the aluminum - 7 wt% silicon alloys directionally solidified on Earth to those aboard the ISS are presented and discussed.

  7. [Detection of human papilloma virus (HPV) in liquid-based cervical samples. Correlation with protein p16INK4a expression].

    Science.gov (United States)

    Toro de Méndez, Morelva; Ferrández Izquierdo, Antonio

    2011-03-01

    The liquid-based cervical cytology improves the quality of the sample and the residual sample could be used efficiently to carry out complementary tests, such as the detection of HPV DNA and the immunocytochemical biomarkers study. The purpose of this study was to correlate the presence of HPV and immunoexpression of p16INK4a in liquid-based cervical samples to examine the utility of these new tools in the detection of cervical cancer. The included patients (n = 67) presented an abnormal cytology or previous cervical pathology. The HPV detection and genotyping were carried out with PCR-SPF10/LiPA (INNOLiPA Extra Amp) and for p16INK4a immunodetection was used antibody clone E6H4. The conventional cytology provided the same cytologic interpretations that those of liquid-based cytology. The overall HPV prevalence was 43.3% (29/67). HPV16 was the most frequent viral type (31.03%) and 48.3% of the cases were infected with multiple HPV types. p16INK4a immunoexpression was observed in 35.8% of liquid-based cytological samples and this was significantly (p HPV presence. These results support the evidence that the implementation of new technologies in the daily routine of the laboratory, contribute significantly in the early detection of cervical cancer and provide important data to help in the patient's efficient management. The combined use of HPV detection and p16INK4a expression could be used for evaluation of patients with more risk to develop significant cervical lesions.

  8. Inactivation of rabies virus.

    Science.gov (United States)

    Wu, Guanghui; Selden, David; Fooks, Anthony R; Banyard, Ashley

    2017-05-01

    Rabies virus is a notifiable pathogen that must be handled in high containment facilities where national and international guidelines apply. For the effective inactivation of rabies virus, a number of reagents were tested. Virkon S (1%) solution caused more than 4log reduction of rabies virus in culture medium supplemented with 10% foetal calf serum within 1min. Isopropyl alcohol (70%) treatment resulted in >3log reduction of rabies virus within 20s when applied at a ratio of 19:1, making it a suitable agent for surface decontamination whereas 70% ethanol was ineffective. Rabies virus (from 102.33 to 103ffu/ml) was also inactivated when cell cultures were fixed with 3% or 4% paraformaldehyde for 30min. Regardless of inactivation procedure, when taking inactivated virus preparations out of a biological containment envelope, proof of inocuity must be demonstrated to cover any possible error/deviation from procedure. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

  9. Solanum americanum: reservoir for Potato virus Y and Cucumber mosaic virus in sweet pepper crops

    National Research Council Canada - National Science Library

    Moura, Monika Fecury; Soman, Marcelo; Mituti, Tatiana; Pavan, Marcelo Agenor; Krause-Sakate, Renate

    2014-01-01

    Weeds can act as important reservoirs for viruses. Solanum americanum (Black nightshade) is a common weed in Brazil and samples showing mosaic were collected from sweet pepper crops to verify the presence of viruses...

  10. [ZIKA--VIRUS INFECTION].

    Science.gov (United States)

    Velev, V

    2016-01-01

    This review summarizes the knowledge of the scientific community for Zika-virus infection. It became popular because of severe congenital damage causes of CNS in newborns whose mothers are infected during pregnancy, as well as the risk of pandemic distribution. Discusses the peculiarities of the biology and ecology of vectors--blood-sucking mosquitoes Aedes; stages in the spread of infection and practical problems which caused during pregnancy. Attention is paid to the recommendations that allow leading national and international medical organizations to deal with the threat Zika-virus infection.

  11. Update on Zika Virus

    Science.gov (United States)

    Toresdahl, Brett G.; Asif, Irfan M.

    2016-01-01

    As public health experts work to contain the outbreak of Zika virus in South America and minimize the devastating prenatal complications, the international sports community prepares for the 2016 Summer Olympic and Paralympic Games in Rio de Janeiro, Brazil. Athletes have publicly expressed concern regarding the health risks of competition in Zika-endemic areas.33 Ensuring the safety of the athletes during training and competition is the primary role of the team physician. Special consideration is needed for sports teams preparing for travel to areas affected by Zika virus. PMID:27436751

  12. Zika virus en seksuele transmissie.

    NARCIS (Netherlands)

    Duijster, J W; Brandwagt, D A H; Timen, A; van der Eijk, A A; Vennema, H; Te Wierik, M J M

    2017-01-01

    - More evidence has become available concerning the sexual transmission of Zika virus and viral shedding in semen, which has led to the expansion of international guidelines for prevention of sexual transmission; Dutch guidelines have not been altered.- Internationally, the use of condoms during sex

  13. Presence and Distribution of Tobacco Viruses in Serbia

    Directory of Open Access Journals (Sweden)

    Nataša Duduk

    2006-01-01

    Full Text Available Infection with a large number of plant viruses could imperil tobacco yield and quality. Tobacco is a natural host for more than 20 viruses, among which the most important and economically harmful are tobacco mosaic virus (TMV, tomato spotted wilt virus (TSWV, cucumber mosaic virus (CMV, potato virus Y (PVY, alfalfa mosaic virus (AMV, tobacco ringspot virus (TRSV, tobacco each virus (TEV and tobacco vein mottling virus (TVMV.The occurence and distribution of tobacco viruses were investigated for 4 years (2002-2005. During this period many different tobacco growing localities in Vojvodina and central Serbia were monitored and samples showing virus symptoms were collected. The collected samples were tested by DAS ELISA using polyclonal antisera, specific for the detection of PVY, TSWV, TMV, CMV, AMV and TRSV.The results obtained for the tobacco virus distribution during these four years of investigation proved the presence of four economically important viruses in our country, whose frequencies varied from year to year. In 2002, 2003 and 2004, the most frequent was TSWV(86.84%; 79% and 49.56%, respectively, while in 2005 PVY was prevalent (56.16%. All viruses detected in the samples tested were present in single or mixed infections. A corellation was established between the field symptoms on tobacco and the virus causal agents.The results obtained showed that TSWV and PVY were the most important tobacco viruses in our country, so that further research of tobacco virus diseases should be directed towards their more detailed characterization.

  14. Ebola Virus Persistence in Semen Ex Vivo.

    Science.gov (United States)

    Fischer, Robert J; Judson, Seth; Miazgowicz, Kerri; Bushmaker, Trent; Munster, Vincent J

    2016-02-01

    On March 20, 2015, a case of Ebola virus disease was identified in Liberia that most likely was transmitted through sexual contact. We assessed the efficiency of detecting Ebola virus in semen samples by molecular diagnostics and the stability of Ebola virus in ex vivo semen under simulated tropical conditions.

  15. Development and validation of a short-time cell culture and multiplex reverse transcriptase polymerase chain reaction assay for infectious pancreatic necrosis virus in Mexican farm-sampled rainbow trout.

    Science.gov (United States)

    Barrera-Mejía, Magda; Simón-Martínez, J; Salgado-Miranda, Celene; Vega, Fernando; Ortega, César; Aragón, Andrés

    2009-09-01

    The infectious pancreatic necrosis virus (IPNV) affects several species of freshwater and marine fish. In Mexico, IPNV has an important impact on farming of rainbow trout Oncorhynchus mykiss; however, IPNV distribution in Mexico is unclear. The diagnosis of IPNV is laborious; usually it is based on isolation tests in cell culture followed by immunological identification using techniques of serum neutralization, immunofluorescence, or enzyme-linked immunosorbent assay. It has recently been demonstrated that reverse transcriptase polymerase chain reaction (RT-PCR) is an adequate method for the detection of aquatic birnaviruses. However, its diagnostic use is still limited because very low titers of viable virus cannot be easily detected. In this study, a combination of short-time cell culture and multiplex RT-PCR was established for the diagnosis of IPNV in rainbow trout obtained from farms in the state of Mexico. Three primer sets were used in a single reaction in the multiplex RT-PCR to increase the probability of identifying all serotypes of IPNV serogroup A as well as to help prevent a false-negative result. This approach was able to identify samples with an IPNV concentration of just 0.01 tissue culture infective dose with 50% endpoint (TCID50)/mL, and it identified more infected fish than RT-PCR alone or first-passage cell culture alone. Moreover, this technique made the same identifications as second-passage cell culture but in approximately 30% of the time needed for second-passage cell culture. Consequently, the time and cost efficiency of IPNV diagnosis were greatly reduced.

  16. Identification of Genotype 3 Hepatitis E Virus (HEV) in Serum and Fecal Samples from Pigs in Thailand and Mexico, Where Genotype 1 and 2 HEV Strains Are Prevalent in the Respective Human Populations

    Science.gov (United States)

    Cooper, K.; Huang, F. F.; Batista, L.; Rayo, C. D.; Bezanilla, J. C.; Toth, T. E.; Meng, X. J.

    2005-01-01

    Hepatitis E virus (HEV), the causative agent of hepatitis E, is an important public health concern in many developing countries. Increasing evidence indicates that hepatitis E is a zoonotic disease. There exist four major genotypes of HEV, and HEV isolates identified in samples from pigs belong to either genotype 3 or 4. Genotype 1 and 2 HEVs are found exclusively in humans. To determine whether genotype 1 and 2 HEVs also exist in pigs, a universal reverse transcription-PCR assay that is capable of detecting all four HEV genotypes was used to test for the presence of HEV RNA in serum and/or fecal samples from pigs in Thailand, where genotype 1 human HEV is prevalent, and from pigs in Mexico, where genotype 2 human HEV was epidemic. In Thailand, swine HEV RNA was detected in sera from 10/26 pigs of 2 to 4 months of age but not in sera from 50 pigs of other ages. In Mexico, swine HEV RNA was detected in 8/125 sera and 28/92 fecal samples from 2- to 4-month-old pigs. Antibodies to swine HEV were also detected in about 81% of the Mexican pigs. A total of 44 swine HEV isolates were sequenced for the open reading frame 2 gene region. Sequence analyses revealed that all swine HEV isolates identified in samples from pigs in Thailand and Mexico belong to genotype 3. Phylogenetic analyses revealed that minor branches associated with geographic origin exist among the swine HEV isolates. The results indicated that genotype 1 or 2 swine HEV does not exist in pigs from countries where the respective human HEV genotype 1 or 2 is prevalent. It is likely that only genotype 3 and 4 HEV strains have zoonotic potential. PMID:15814985

  17. Evaluation of the Biofire FilmArray BioThreat-E Test (v2.5) for Rapid Identification of Ebola Virus Disease in Heat-Treated Blood Samples Obtained in Sierra Leone and the United Kingdom.

    Science.gov (United States)

    Weller, Simon A; Bailey, Daniel; Matthews, Steven; Lumley, Sarah; Sweed, Angela; Ready, Derren; Eltringham, Gary; Richards, Jade; Vipond, Richard; Lukaszewski, Roman; Payne, Phillippa M; Aarons, Emma; Simpson, Andrew J; Hutley, Emma J; Brooks, Tim

    2016-01-01

    Rapid Ebola virus (EBOV) detection is crucial for appropriate patient management and care. The performance of the FilmArray BioThreat-E test (v2.5) using whole-blood samples was evaluated in Sierra Leone and the United Kingdom and was compared with results generated by a real-time Ebola Zaire PCR reference method. Samples were tested in diagnostic laboratories upon availability, included successive samples from individual patients, and were heat treated to facilitate EBOV inactivation prior to PCR. The BioThreat-E test had a sensitivity of 84% (confidence interval [CI], 64% to 95%) and a specificity of 89% (CI, 73% to 97%) in Sierra Leone (n = 60; 44 patients) and a sensitivity of 75% (CI, 19% to 99%) and a specificity of 100% (CI, 97% to 100%) in the United Kingdom (n = 108; 70 patients) compared to the reference real-time PCR. Statistical analysis (Fisher's exact test) indicated there was no significant difference between the methods at the 99% confidence level in either country. In 9 discrepant results (5 real-time PCR positives and BioThreat-E test negatives and 4 real-time PCR negatives and BioThreat-E test positives), the majority (n = 8) were obtained from samples with an observed or probable low viral load. The FilmArray BioThreat-E test (v2.5) therefore provides an attractive option for laboratories (either in austere field settings or in countries with an advanced technological infrastructure) which do not routinely offer an EBOV diagnostic capability. © Crown copyright 2015.

  18. Prevalence, Risk Behaviors, and Virological Characteristics of Hepatitis B Virus Infection in a Group of Men Who Have Sex with Men in Brazil: Results from a Respondent-Driven Sampling Survey.

    Directory of Open Access Journals (Sweden)

    Marina P Oliveira

    Full Text Available Men who have sex with men (MSM are at increased risk of exposure to hepatitis B virus (HBV compared with the general population. This study aims to assess the epidemiological and virological characteristics of HBV infection in a sample of MSM in Brazil, where data are scarce.A cross-sectional study was conducted among MSM in the City of Goiânia, Central Brazil, from March to November 2014, using Respondent-Driven Sampling (RDS. After signing the consent form, participants were interviewed and a blood sample collected. All samples were tested for HBV serological markers and HBV DNA. HBV nucleotide sequence analysis was also performed.A total of 522 MSM were recruited in the study. The prevalence of HBV infection (current or past [presence of anti-HBc marker] was 15.4% (95% CI: 8.7-25.8 and the rate of HBsAg carriers was 0.6% (95% CI: 0.2-1.6. About 40% (95% CI: 32.3-48.8 of the participants had serological evidence of previous HBV vaccination (reactive for isolated anti-HBs. In addition, 44.3% (95% CI: 36.1-52.9 were seronegative for all HBV markers. Age over 25 years old, receptive anal intercourse, previous sex with women, and history of sexually transmitted infections (STIs were factors associated with HBV infection. HBV DNA was detected only in HBsAg-positive individuals. HBV isolates were classified into genotype A (subgenotypes A1 and A2, and some mutations were identified throughout the genome. Therefore, occult HBV infection was not observed in the study population.Public health strategies should be improved for the MSM population in order to prevent HBV and other STIs, as well as to provide appropriate management of patients with active infections.

  19. Neuraminidase as an enzymatic marker for detecting airborne Influenza virus and other viruses.

    Science.gov (United States)

    Turgeon, Nathalie; Toulouse, Marie-Josée; Ho, Jim; Li, Dongqing; Duchaine, Caroline

    2017-02-01

    Little information is available regarding the effectiveness of air samplers to collect viruses and regarding the effects of sampling processes on viral integrity. The neuraminidase enzyme is present on the surface of viruses that are of agricultural and medical importance. It has been demonstrated that viruses carrying this enzyme can be detected using commercial substrates without having to process the sample by methods such as RNA extraction. This project aims at evaluating the effects of 3 aerosol-sampling devices on the neuraminidase enzyme activity of airborne viruses. The purified neuraminidase enzymes from Clostridium perfringens, a strain of Influenza A (H1N1) virus, the FluMist influenza vaccine, and the Newcastle disease virus were used as models. The neuraminidase models were aerosolized in aerosol chambers and sampled with 3 different air samplers (SKC BioSampler, 3-piece cassettes with polycarbonate filters, and Coriolis μ) to assess the effect on neuraminidase enzyme activity. Our results demonstrated that Influenza virus and Newcastle disease virus neuraminidase enzymes are resistant to aerosolization and sampling with all air samplers tested. Moreover, we demonstrated that the enzymatic neuraminidase assay is as sensitive as RT-qPCR for detecting low concentrations of Influenza virus and Newcastle disease virus. Therefore, given the sensitivity of the assay and its compatibility with air sampling methods, viruses carrying the neuraminidase enzyme can be rapidly detected from air samples using neuraminidase activity assay without having to preprocess the samples.

  20. High-Sensitivity LC-MS/MS Quantification of Peptides and Proteins in Complex Biological Samples : The Impact of Enzymatic Digestion and Internal Standard Selection on Method Performance

    NARCIS (Netherlands)

    Bronsema, Kees J.; Bischoff, Rainer; van de Merbel, Nico C.

    2013-01-01

    Two important aspects of peptide and protein quantification by LC-MS/MS, the enzymatic digestion step and the internal standardization approach, were systematically investigated with a small protein, salmon calcitonin, which could be analyzed both without and with digestion. Quantification of

  1. Serum Samples From Middle-aged Adults Vaccinated Annually with Seasonal Influenza Vaccines Cross-neutralize Some Potential Pandemic Influenza Viruses.

    Science.gov (United States)

    Wang, Wei; Alvarado-Facundo, Esmeralda; Chen, Qiong; Anderson, Christine M; Scott, Dorothy; Vassell, Russell; Weiss, Carol D

    2016-02-01

    We examined serum samples from adults ages 48-64 who received multiple seasonal influenza vaccines from 2004 to 2009 for cross-neutralizing antibodies to potential pandemic strains. Using pseudoviruses bearing various hemagglutinins (HA-pseudoviruses), we found serum neutralization titers (≥160) in 100% against A/Japan/305/1957 (H2N2), 53% against A/Hong Kong/1073/99 (H9N2), 56% against the H3N2 variant A/Indiana/08/11 (H3N2v), 11% against A/Hong Kong/G9/97 (H9N2), and 36% A/chicken/Hong Kong/SF4/01 (H6N1). None had titers >160 to A/Shanghai/2/13 (H7N9) or A/Netherlands/219/03 (H7N7). Thirty-six percent to 0% had neutralization titers to various H5N1 strains. Titers to H9, H6, and H5 HA-pseudoviruses correlated with each other, but not with H3N2v, suggesting group-specific cross-neutralization. Published by Oxford University Press for the Infectious Diseases Society of America 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US.

  2. A case report demonstrating the utility of next generation sequencing in analyzing serial samples from the lung following an infection with influenza A (H7N9) virus.

    Science.gov (United States)

    Hu, Yongfeng; Zhang, Yan; Ren, Xianwen; Liu, Yingmei; Xiao, Yan; Li, Li; Yang, Fan; Su, Haoxiang; Liu, Feng; Liu, Haiying; Cao, Bin; Jin, Qi

    2016-03-01

    Bacterial pneumonia is a well-recognized sequela of patient suffering from influenza, and a key factor, with cytokine dysregulation, that contribute to severe disease and mortality. To obtain a comprehensive assessment of lung microbial community dynamics in a fatal influenza H7N9 case during the whole clinical course, we undertook a longitudinal study. Serial bronchoalveolar lavage fluid samples were collected from a H7N9 patient after illness onset, and the microbiome was characterized by using next-generation sequencing and microbiological approaches. Furthermore, the kinetics of circulating cytokine storms related to viral and secondary bacterial infection were analyzed. Within complex and dynamic communities, the lung microbiome with H7N9 infection were dominated by gram-negative bacteria, Acinetobacter baumannii after the viral invasion and during the whole clinical course. Sputum and blood culture confirmed the secondary bacterial infection with multidrug-resistant A. baumannii 9 days later. The dynamics of the bacterial infection with carbapenem-resistant A. baumannii correlated with antibiotic therapy. Our observations also indicated that sustained high levels of host inflammatory factors, consisting of a set of distinct cytokines associated with disease stage, may contribute to disease progression and death. This study demonstrates an initial attempt to explore the dynamic microbiome involved inH7N9 infection and its response to antimicrobial therapy, as well as host cytokine response to infection by using next-generation sequencing. These type of investigations with longitudinal follow-up to understand dynamics of microbial community and cytokines involved in lung infection may provide opportunities for development and optimization of targeted antimicrobial therapy and even new therapeutic strategies. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. HPV vaginal self-sampling among women non-adherent to Papanicolaou screening in Chile Autotoma vaginal para detección de virus del papiloma humano en mujeres no adherentes a tamizaje con Papanicolaou en Chile

    Directory of Open Access Journals (Sweden)

    Javiera Léniz

    2013-04-01

    Full Text Available OBJECTIVE: To evaluate acceptance, preference and compliance with referral of vaginal self-sampling for the detection of Human papillomavirus (HPV among women non-adherent to Papanicolaou (Pap screening in Santiago, Chile. MATERIALS AND METHODS: Using multistage sampling we identified women aged 30-64 years who reported not receiving a Pap test in the previous three years and offered them Pap testing at the health center or vaginal self-sampling for HPV testing at home. Self-collected samples were analyzed with hybrid capture. All HPV+ women were referred for colposcopy, biopsy and treatment when needed. RESULTS: 1 254 eligible women were contacted; 86.5% performed self-sampling and 8.1% refused; 124 women were HPV+ (11.4%: 95%CI 9.6-13.5 of whom 85.5% attended colposcopy; 12 had CIN2+ (1.1%: 95 %CI 0.5-1.7. CONCLUSION: HPV vaginal self-sampling can be easily implemented in Chile and could improve coverage, successfully reaching women who drop out of the screening program.OBJETIVO: Evaluar la aceptación, preferencia y adherencia a seguimiento de la autotoma vaginal para detección del virus del papiloma humano (VPH en mujeres inasistentes a Papanicolaou (Pap en Santiago, Chile. MATERIAL Y MÉTODOS: Mediante un muestreo polietápico se identificaron mujeres entre 30 y 64 años inasistentes a Pap por < 3 años, invitándolas a realizarse un Pap en su centro de salud o una autotoma vaginal a domicilio. Las muestras fueron analizadas con captura de híbridos. Las mujeres VPH+ fueron referidas a colposcopía, biopsia y tratamiento en caso necesario. RESULTADOS: 1 254 mujeres elegibles fueron contactadas; 86.5% aceptó la autotoma vaginal y 8.1% la rechazó; 124 mujeres resultaron VPH+ (11.4%: IC95% 9.6-13.5 de las que 85.5% asistió a colposcopía; 12 tenían CIN2+ (1.1%: IC95% 0.5-1.7. CONCLUSIÓN: La autotoma vaginal para detección de VPH es implementable en Chile y su utilización podría mejorar la cobertura del programa rescatando a mujeres

  4. A Schistosoma haematobium-specific real-time PCR for diagnosis of urogenital schistosomiasis in serum samples of international travelers and migrants.

    Directory of Open Access Journals (Sweden)

    Lieselotte Cnops

    Full Text Available BACKGROUND: Diagnosis of urogenital schistosomiasis by microscopy and serological tests may be elusive in travelers due to low egg load and the absence of seroconversion upon arrival. There is need for a more sensitive diagnostic test. Therefore, we developed a real-time PCR targeting the Schistosoma haematobium-specific Dra1 sequence. METHODOLOGY/PRINCIPAL FINDINGS: The PCR was evaluated on urine (n = 111, stool (n = 84 and serum samples (n = 135, and one biopsy from travelers and migrants with confirmed or suspected schistosomiasis. PCR revealed a positive result in 7/7 urine samples, 11/11 stool samples and 1/1 biopsy containing S. haematobium eggs as demonstrated by microscopy and in 22/23 serum samples from patients with a parasitological confirmed S. haematobium infection. S. haematobium DNA was additionally detected by PCR in 7 urine, 3 stool and 5 serum samples of patients suspected of having schistosomiasis without egg excretion in urine and feces. None of these suspected patients demonstrated other parasitic infections except one with Blastocystis hominis and Entamoeba cyst in a fecal sample. The PCR was negative in all stool samples containing S. mansoni eggs (n = 21 and in all serum samples of patients with a microscopically confirmed S. mansoni (n = 22, Ascaris lumbricoides (n = 1, Ancylostomidae (n = 1, Strongyloides stercoralis (n = 1 or Trichuris trichuria infection (n = 1. The PCR demonstrated a high specificity, reproducibility and analytical sensitivity (0.5 eggs per gram of feces. CONCLUSION/SIGNIFICANCE: The real-time PCR targeting the Dra1 sequence for S. haematobium-specific detection in urine, feces, and particularly serum, is a promising tool to confirm the diagnosis, also during the acute phase of urogenital schistosomiasis.

  5. Prevalence of Human Immunodeficiency Virus and Sexually Transmitted Infections Among Cisgender and Transgender Women Sex Workers in Greater Kuala Lumpur, Malaysia: Results From a Respondent-Driven Sampling Study.

    Science.gov (United States)

    Wickersham, Jeffrey A; Gibson, Britton A; Bazazi, Alexander R; Pillai, Veena; Pedersen, Courtney J; Meyer, Jaimie P; El-Bassel, Nabila; Mayer, Kenneth H; Kamarulzaman, Adeeba; Altice, Frederick L

    2017-11-01

    Sex workers face a disproportionate burden of human immunodeficiency virus (HIV) and sexually transmitted infections (STI) worldwide. For cisgender women sex workers (CWSW), global HIV prevalence is over 10%, whereas transgender women sex workers (TWSW) face an HIV burden of 19% to 27%. We used respondent-driven sampling to recruit 492 sex workers, including CWSW (n = 299) and TWSW (n = 193) in Greater Kuala Lumpur, Malaysia. Participants completed an in-depth survey and were screened for HIV, syphilis, Chlamydia trachomatis, and Neisseria gonorrhoeae. Sample characteristics stratified by gender identity and interview site are presented. Bivariate analyses comparing CWSW and TWSW were conducted using independent samples t tests for continuous variables and χ tests for categorical variables. Pooled HIV prevalence was high (11.7%; 95% confidence interval [CI], 8.8-14.5), and was similar for CWSW (11.1%) and TWSW (12.4%). Rates of syphilis 25.5% (95% CI, 21.6-29.5), C. trachomatis (14.8%; 95% CI, 11.6-18.0) and N. gonorrhoeae (5.8%; 95% CI, 3.7-7.9) were also concerning. Both groups reported lifetime HIV testing (62.4%), but CWSW were less likely to have ever been HIV tested (54.5%) than TWSW (74.6%). Median time since last HIV test was 24 months. Previous screening for STI was low. Inconsistent condom use and drug use during sex work were not uncommon. High HIV and STI prevalence, coupled with infrequent HIV and STI screening, inconsistent condom use, and occupational drug use, underscore the need for expanded HIV and STI prevention, screening, and treatment efforts among CWSW and TWSW in Malaysia.

  6. Interpretation of mercury content in national samples of sailfish (Istiophorus platypterus and marlin (Makaira spp . Or Tetrapturus spp. from international toxicological parameters

    Directory of Open Access Journals (Sweden)

    Carlos E. Callega

    2014-06-01

    Full Text Available Total mercury results in eleven samples of sail fish and eleven samples of marlin from national market places (where they are called with those names, from a study by the Costarican Fishing Federation, are presented. Sail fish samples vary between 0,85 and 1,30 mg of mercury/kg of fish, with an average of (1,07±0,17 mg of mercury/kg of fish, and marlin samples varied between 0,41 and 1,18 mg of mercury/kg of fish with an average of (0,83±0,27 mg of mercury/kg of fish. Both cases showed mercury concentrations close to the maximum recommended value of the World Health Organization (WHO of 1 mg of mercury/kg of fish for predatory species. At least 64% of the samples were equal to or above the toxicological threshold of WHO, defined as the provisional tolerable weekly intake, PTWI, calculated for portion sizes between 100 g and 150 g. Results show the presence of mercury in these samples, and are used to interpret mercury content compared to WHO values and propose recommendations for Costa Rica. These results are consistent with mercury accumulation in the ocean and in predatory fish observed worldwide, documented with a large number of references.

  7. Outer packet sets and feature prediction of computer virus

    Science.gov (United States)

    Zhang, Ling

    2014-10-01

    The packet sets model was proposed by Prof. Shi in 2008. A packet sets is a set pair composed of internal and outer packet sets, and it has dynamic characteristic. Using packet sets theory, this paper gives the feature prediction of computer virus based on outer packet sets. The concept of virus screening-filtering is given, furthermore, the virus screening-filtering order theorem, composite virus screening-filtering theorem and virus screening-filtering rule are presented. A prediction method of computer virus feature is given based on the results. The outer packet sets is a new tool in the research of the prediction of dynamic virus feature.

  8. A 2014 nationwide survey of the distribution of Soybean mosaic virus (SMV), Soybean yellow mottle mosaic virus (SYMMV) and Soybean yellow common mosaic virus (SYCMV) major viruses in South Korean soybean fields, and changes

    Science.gov (United States)

    In 2014 symptomatic soybean samples were collected throughout Korea, and were tested for the most important soybean viruses found in Korea, namely Soybean mosaic virus (SMV), Soybean yellow common mosaic virus (SYCMV), and Soybean yellow mottle mosaic virus (SYMMV). SYMMV was most commonly detected,...

  9. Virus Crystallography

    Science.gov (United States)

    Fry, Elizabeth; Logan, Derek; Stuart, David

    Crystallography provides a means of visualizing intact virus particles as well as their isolated constituent proteins and enzymes (1-3) at near-atomic resolution, and is thus an extraordinarily powerful tool in the pursuit of a fuller understanding of the functioning of these simple biological systems. We have already expanded our knowledge of virus evolution, assembly, antigenic variation, and host-cell interactions; further studies will no doubt reveal much more. Although the rewards are enormous, an intact virus structure determination is not a trivial undertaking and entails a significant scaling up in terms of time and resources through all stages of data collection and processing compared to a traditional protein crystallographic structure determination. It is the methodology required for such studies that will be the focus of this chapter. The computational requirements were satisfied in the late 1970s, and when combined with the introduction of phase improvement techniques utilizing the virus symmetry (4,5), the application of crystallography to these massive macromolecular assemblies became feasible. This led to the determination of the first virus structure (the small RNA plant virus, tomato bushy stunt virus), by Harrison and coworkers in 1978 (6). The structures of two other plant viruses followed rapidly (7,8). In the 1980s, a major focus of attention was a family of animal RNA viruses; the Picornaviridae.

  10. Comparative evaluation of novel African swine fever virus (ASF) antibody detection techniques derived from specific ASF viral genotypes with the OIE internationally prescribed serological tests.

    Science.gov (United States)

    Gallardo, C; Soler, A; Nieto, R; Carrascosa, A L; De Mia, G M; Bishop, R P; Martins, C; Fasina, F O; Couacy-Hymman, E; Heath, L; Pelayo, V; Martín, E; Simón, A; Martín, R; Okurut, A R; Lekolol, I; Okoth, E; Arias, M

    2013-02-22

    The presence of antibodies against African swine fever (ASF), a complex fatal notifiable OIE disease of swine, is always indicative of previous infection, since there is no vaccine that is currently used in the field. The early appearance and subsequent long-term persistence of antibodies combined with cost-effectiveness make antibody detection techniques essential in control programmes. Recent reports appear to indicate that the serological tests recommended by the OIE for ASF monitoring are much less effective in East and Southern Africa where viral genetic and antigenic diversity is the greatest. We report herein an extensive analysis including more than 1000 field and experimental infection sera, in which the OIE recommended tests are compared with antigen-specific ELISAs and immuno-peroxidase staining of cells (IPT). The antibody detection results generated using new antigen-specific tests, developed in this study, which are based on production of antigen fractions generated by infection and virus purification from COS-1 cells, showed strong concordance with the OIE tests. We therefore conclude that the lack of success is not attributable to antigenic polymorphism and may be related to the specific characteristics of the local breeds African pigs. Copyright © 2012 Elsevier B.V. All rights reserved.

  11. Non-structural proteins P17 and P33 are involved in the assembly of the internal membrane-containing virus PRD1

    Energy Technology Data Exchange (ETDEWEB)

    Karttunen, Jenni; Mäntynen, Sari [Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä (Finland); Ihalainen, Teemu O. [Stem Cells in Neurological Applications Group, BioMediTech, University of Tampere, Tampere (Finland); Bamford, Jaana K.H. [Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä (Finland); Oksanen, Hanna M., E-mail: hanna.oksanen@helsinki.fi [Institute of Biotechnology and Department of Biosciences, University of Helsinki, Biocenter 2, P.O. Box 56 (Viikinkaari 5), FIN-00014 Helsinki (Finland)

    2015-08-15

    Bacteriophage PRD1, which has been studied intensively at the structural and functional levels, still has some gene products with unknown functions and certain aspects of the PRD1 assembly process have remained unsolved. In this study, we demonstrate that the phage-encoded non-structural proteins P17 and P33, either individually or together, complement the defect in a temperature-sensitive GroES mutant of Escherichia coli for host growth and PRD1 propagation. Confocal microscopy of fluorescent fusion proteins revealed co-localisation between P33 and P17 as well as between P33 and the host chaperonin GroEL. A fluorescence recovery after photobleaching assay demonstrated that the diffusion of the P33 fluorescent fusion protein was substantially slower in E. coli than theoretically calculated, presumably resulting from intermolecular interactions. Our results indicate that P33 and P17 function in procapsid assembly, possibly in association with the host chaperonin complex GroEL/GroES. - Highlights: • Two non-structural proteins of PRD1 are involved in the virus assembly. • P17 and P33 complement the defect in GroES of Escherichia coli. • P33 co-localises with GroEL and P17 in the bacterium. • Slow motion of P33 in the bacterium suggests association with cellular components.

  12. Viraemia and Ebola virus secretion in survivors of Ebola virus disease in Sierra Leone: a cross-sectional cohort study.

    Science.gov (United States)

    Green, Edward; Hunt, Luke; Ross, J C Gareth; Nissen, Nina Marie; Curran, Tanya; Badhan, Anjna; Sutherland, Katherine A; Richards, Jade; Lee, James S; Allen, Samuel H; Laird, Steven; Blackman, Mandy; Collacott, Ian; Parker, Paul A; Walbridge, Andrew; Phillips, Rebecca; Sellu, Sia Jammie; Dama, Agnes; Sheriff, Alpha Karim; Zombo, Joseph; Ngegba, Doris; Wurie, Alieh H; Checchi, Francesco; Brooks, Timothy J

    2016-09-01

    In survivors of Ebola virus disease, clinical sequelae including uveitis, arthralgia, and fatigue are common and necessitate systematic follow-up. However, the infection risk to health-care providers is poorly defined. Here we report Ebola virus RT-PCR data for body site and fluid samples from a large cohort of Ebola virus survivors at clinic follow-up. In this cross-sectional cohort study, consecutive survivors of Ebola virus disease attending Kerry Town survivor clinic (Freetown, Sierra Leone), who had been discharged from the Kerry Town Ebola treatment unit, were invited to participate. We collected and tested axillary, blood, conjunctival, forehead, mouth, rectal, semen, urine, and vaginal specimens for presence of Ebola virus using RT-PCR. We regarded samples to be positive for Ebola virus disease if the cycle threshold was 40 or lower. We collected demographic data from survivors of their age, sex, time since discharge from the treatment unit, and length of acute admission in the Ebola treatment unit using anonymised standard forms. Between April 2, and June 16, 2015, of 151 survivors of Ebola virus disease invited to participate, 112 (74%) provided consent. The median age of participants was 21·5 years (IQR 14-31·5) with 34 (30%) participants younger than 16 years. 50 (45%) of 112 participants were male. We tested a total of 555 specimens: 103 from the axilla, 93 from blood, 92 from conjunctiva, 54 from forehead, 105 from mouth, 17 from the rectum, one from semen, 69 from urine, and 21 from the vagina. The median time from Ebola treatment unit discharge to specimen collection was 142 days (IQR 127-159). 15 participants had a total of 74 swabs taken less than 100 days from discharge. The semen sample from one participant tested positive for Ebola virus at 114 days after discharge from the treatment unit; specimens taken from the axilla, blood, conjunctiva, forehead, mouth, rectum, and urine of the same participant tested negative. All specimens from the

  13. Influenza A Virus in Backyard Pigs and Poultry in Rural Cambodia.

    Science.gov (United States)

    Osbjer, K; Berg, M; Sokerya, S; Chheng, K; San, S; Davun, H; Magnusson, U; Olsen, B; Zohari, S

    2017-10-01

    Surveillance of influenza virus in humans and livestock is critical, given the worldwide public health threats and livestock production losses. Livestock farming involving close proximity between humans, pigs and poultry is often practised by smallholders in low-income countries and is considered an important driver of influenza virus evolution. This study determined the prevalence and genetic characteristics of influenza A virus (IAV) in backyard pigs and poultry in Cambodia. A total of 751 animals were tested by matrix gene-based rRT-PCR, and influenza virus was detected in 1.5% of sampled pigs, 1.4% of chickens and 1.0% of ducks, but not in pigeons. Full-length genome sequencing confirmed triple reassortant H3N2 in all IAV-positive pigs and various low pathogenic avian influenza subtypes in poultry. Phylogenetic analysis of the swine influenza viruses revealed that these had haemagglutinin and neuraminidase genes originating from human H3N2 viruses previously isolated in South-East Asia. Phylogenetic analysis also revealed that several of the avian influenza subtypes detected were closely related to internal viral genes from highly pathogenic H5N1 and H9N2 formerly sequenced in the region. High sequence homology was likewise found with influenza A viruses circulating in pigs, poultry and wild birds in China and Vietnam, suggesting transboundary introduction and cocirculation of the various influenza subtypes. In conclusion, highly pathogenic subtypes of influenza virus seem rare in backyard poultry, but virus reassortment, involving potentially zoonotic and pandemic subtypes, appears to occur frequently in smallholder pigs and poultry. Increased targeted surveillance and monitoring of influenza circulation on smallholdings would further improve understanding of the transmission dynamics and evolution of influenza viruses in humans, pigs and poultry in the Mekong subregion and could contribute to limit the influenza burden. © 2016 Blackwell Verlag GmbH.

  14. BWR Vessel and Internals Project Removal and Analysis of Material Samples from Core Shroud and Top Guide at Susquehanna Unit 2

    Energy Technology Data Exchange (ETDEWEB)

    Howell, D; Haertel, T; Lindberg, J; Oliver, B; Greenwood, L

    2005-04-15

    Fast and thermal fluence were determined by a laboratory analysis of the samples. Fluence in the upper regions of the shroud (between the H1 and H2 welds) was substantially lower than that in the belt line region (near the H4 weld). Fluence in the top guide was significantly higher than fluence on the core shroud. As expected, helium concentrations were highest in regions where fluence was highest. Estimates of the initial boron concentration were similar to measurements made on materials removed from other reactors. A technical justification evaluated the acceptability of the sampling process with respect to structural consequences of material removal and to increased cracking susceptibility due to the as-left condition. It was determined that the sampling process was acceptable on both counts.

  15. Insights into intercontinental spread of Zika virus.

    Science.gov (United States)

    Liang, Dachao; Leung, Ross Ka Kit; Lee, Shui Shan; Kam, Kai Man

    2017-01-01

    The epidemic of Zika virus (ZIKV) infection in South America has led to World Health Organization's declaration of a Public Health Emergency of International Concern. To further inform effective public health policy, an understanding of ZIKV's transmission mechanisms is crucial. To characterize the intercontinental transmission of ZIKV, we compiled and analyzed more than 250 gene sequences together with their sequence-related geographic and temporal information, sampled across 27 countries spanning from 1947 to 2016. After filtering and selecting appropriate sequences, extensive phylogenetic analyses were performed. Although phylogeographic reconstruction supported the transmission route of the virus in Africa, South-eastern Asia, Oceania and Latin America, we discovered that the Eastern Africa origin of ZIKV was disputable. On a molecular level, purifying selection was found to be largely responsible for the evolution of non-structural protein 5 and envelope protein E. Our dataset and ancestral sequences reconstruction analysis captured previously unidentified amino acid changes during evolution. Finally, based on the estimation of the time to the most recent common ancestors for the non-structural protein 5 gene, we hypothesized potential specific historic events that occurred in the 1940s and might have facilitated the spread of Zika virus from Africa to South-eastern Asia. Our findings provide new insights into the transmission characteristics of ZIKV, while further genetic and serologic studies are warranted to support the design of tailored prevention strategies.

  16. Insights into intercontinental spread of Zika virus.

    Directory of Open Access Journals (Sweden)

    Dachao Liang

    Full Text Available The epidemic of Zika virus (ZIKV infection in South America has led to World Health Organization's declaration of a Public Health Emergency of International Concern. To further inform effective public health policy, an understanding of ZIKV's transmission mechanisms is crucial. To characterize the intercontinental transmission of ZIKV, we compiled and analyzed more than 250 gene sequences together with their sequence-related geographic and temporal information, sampled across 27 countries spanning from 1947 to 2016. After filtering and selecting appropriate sequences, extensive phylogenetic analyses were performed. Although phylogeographic reconstruction supported the transmission route of the virus in Africa, South-eastern Asia, Oceania and Latin America, we discovered that the Eastern Africa origin of ZIKV was disputable. On a molecular level, purifying selection was found to be largely responsible for the evolution of non-structural protein 5 and envelope protein E. Our dataset and ancestral sequences reconstruction analysis captured previously unidentified amino acid changes during evolution. Finally, based on the estimation of the time to the most recent common ancestors for the non-structural protein 5 gene, we hypothesized potential specific historic events that occurred in the 1940s and might have facilitated the spread of Zika virus from Africa to South-eastern Asia. Our findings provide new insights into the transmission characteristics of ZIKV, while further genetic and serologic studies are warranted to support the design of tailored prevention strategies.

  17. Total internal reflectance fluorescence (TIRF) biosensor for environmental monitoring of testosterone with commercially available immunochemistry: antibody characterization, assay development and real sample measurements.

    Science.gov (United States)

    Tschmelak, Jens; Kumpf, Michael; Käppel, Nina; Proll, Guenther; Gauglitz, Guenter

    2006-04-15

    Nowadays, little technology exists that can monitor various water sources quickly and at a reasonable cost. The ultra-sensitive, fully automated and robust biosensor River Analyser (RIANA) is capable of detecting multiple organic targets rapidly and simultaneously at a heterogeneous assay format (solid phase: bulk optical glass transducers). Commercialization of such a biosensor requires the availability of commercial high-affinity recognition elements (e.g. antibodies) and suitable commercial haptens (modified target molecules) for surface chemistry. Therfore, testosterone was chosen as model analyte, which is also a task of common analytical methods like gas chromatography-mass spectrometry (GC-MS), because they have to struggle with detecting sub-nanogram per liter levels in environmental samples. The reflectometric interference spectroscopy (RIfS) was used to characterize the commercially available immunochemistry resulting in a high-affinity constant of 2.6+/-0.3 x 10(9)mol(-1) for the unlabeled antibody. After the labeling procedure, necessary for the TIRF-based biosensor, a mean affinity constant of 1.2 x 10(9)mol(-1) was calculated out of RIfS (1.4+/-0.4 x 10(9)mol(-1)) and TIRF (1.0+/-0.3 x 10(9)mol(-1)) measurements. Thereafter, the TIRF-based biosensor setup was used to determine the steroidal hormone testosterone at real world samples without sample pre-treatment or sample pre-concentration. Results are shown for rapid and ultra-sensitive analyses of testosterone in aqueous samples with at a remarkable limit of detection (LOD) of 0.2 ng L(-1). All real world samples, even those containing testosterone in the sub-nanogram per liter range (e.g. 0.9 ng L(-1)), could be determined with recovery rates between 70 and 120%. Therefore, the sensor system is perfectly suited to serve as a low-cost system for surveillance and early warning in environmental analysis in addition to the common analytical methods. For the first time, commercially available

  18. Spatial structure peculiarities of influenza A virus matrix M1 protein in an acidic solution that simulates the internal lysosomal medium.

    Science.gov (United States)

    Shishkov, Alexander; Bogacheva, Elena; Fedorova, Natalia; Ksenofontov, Alexander; Badun, Gennadii; Radyukhin, Victor; Lukashina, Elena; Serebryakova, Marina; Dolgov, Alexey; Chulichkov, Alexey; Dobrov, Evgeny; Baratova, Lyudmila

    2011-12-01

    The structure of the C-terminal domain of the influenza virus A matrix M1 protein, for which X-ray diffraction data were still missing, was studied in acidic solution. Matrix M1 protein was bombarded with thermally-activated tritium atoms, and the resulting intramolecular distribution of the tritium label was analyzed to assess the steric accessibility of the amino acid residues in this protein. This technique revealed that interdomain loops and the C-terminal domain of the protein are the most accessible to labeling with tritium atoms. A model of the spatial arrangement of the C-terminal domain of matrix M1 protein was generated using rosetta software adjusted to the data obtained by tritium planigraphy experiments. This model suggests that the C-terminal domain is an almost flat layer with a three-α-helical structure. To explain the high level of tritium label incorporation into the C-terminal domain of the M1 protein in an acidic solution, we also used independent experimental approaches (CD spectroscopy, limited proteolysis and MALDI-TOF MS analysis of the proteolysis products, dynamic light scattering and analytical ultracentrifugation), as well as multiple computational algorithms, to analyse the intrinsic protein disorder. Taken together, the results obtained in the present study indicate that the C-terminal domain is weakly structured. We hypothesize that the specific 3D structural peculiarities of the M1 protein revealed in acidic pH solution allow the protein greater structural flexibility and enable it to interact effectively with the components of the host cell. © 2011 The Authors Journal compilation © 2011 FEBS.

  19. The International development of PROQOL-HCV: An instrument to assess the health-related quality of life of patients treated for Hepatitis C virus.

    Science.gov (United States)

    Armstrong, Andrew Richard; Herrmann, Susan Elizabeth; Chassany, Olivier; Lalanne, Christophe; Da Silva, Mariliza Henrique; Galano, Eliana; Carrieri, Patrizia M; Estellon, Vincent; Sogni, Philippe; Duracinsky, Martin

    2016-08-23

    Hepatitis C virus (HCV) compromises Health-related Quality of Life (HRQL) with detriments to Physical, Mental and Social health domains. Treatment with interferon and ribavirin is associated with side effects which further impair HRQL. New treatments appear potent, effective and tolerable. However, Patient Reported Outcomes instruments that capture the impact on HRQL for people with hepatitis C are largely non-specific and will be needed in the new treatment era. Therefore, we developed a conceptually valid multidimensional model of HCV-specific quality of life and pilot survey instrument, the Patient Reported Outcome Quality of Life survey for HCV (PROQOL-HCV). HCV patients from France (n = 30), Brazil (n = 20) and Australia (n = 20) were interviewed to investigate HCV-HRQL issues raised in the scientific literature and by treatment specialists. Interviews were recorded, transcribed and translated into English and French. Fifteen content dimensions were derived from the qualitative analysis, refined and fitted to four domains: (1) Physical Health included: fatigue, pain, sleep, sexual impairment and physical activity; (2) Mental Health: psychological distress, psychosocial impact, and cognition; (3) Social Health: support, stigma, social activity, substance use; (4) TREATMENT: management, side effects, and fear of treatment failure. The impact of some dimensions extended beyond their primary domain including: physical activity, cognition, sleep, sexual impairment, and the three treatment dimensions. A bank of 300 items was constructed to reflect patient reports and, following expert review, reduced to a 72-item pilot questionnaire. We present a conceptually valid multidimensional model of HCV-specific quality of life and the pilot survey instrument, PROQOL-HCV. The model is widely inclusive of the experience of hepatitis C and the first to include the treatment dimension.

  20. Preliminary Validation of Direct Detection of Foot-And-Mouth Disease Virus within Clinical Samples Using Reverse Transcription Loop-Mediated Isothermal Amplification Coupled with a Simple Lateral Flow Device for Detection

    Science.gov (United States)

    Waters, Ryan A.; Fowler, Veronica L.; Armson, Bryony; Nelson, Noel; Gloster, John; Paton, David J.; King, Donald P.

    2014-01-01

    Rapid, field-based diagnostic assays are desirable tools for the control of foot-and-mouth disease (FMD). Current approaches involve either; 1) Detection of FMD virus (FMDV) with immuochromatographic antigen lateral flow devices (LFD), which have relatively low analytical sensitivity, or 2) portable RT-qPCR that has high analytical sensitivity but is expensive. Loop-mediated isothermal amplification (LAMP) may provide a platform upon which to develop field based assays without these drawbacks. The objective of this study was to modify an FMDV-specific reverse transcription–LAMP (RT-LAMP) assay to enable detection of dual-labelled LAMP products with an LFD, and to evaluate simple sample processing protocols without nucleic acid extraction. The limit of detection of this assay was demonstrated to be equivalent to that of a laboratory based real-time RT-qPCR assay and to have a 10,000 fold higher analytical sensitivity than the FMDV-specific antigen LFD currently used in the field. Importantly, this study demonstrated that FMDV RNA could be detected from epithelial suspensions without the need for prior RNA extraction, utilising a rudimentary heat source for amplification. Once optimised, this RT-LAMP-LFD protocol was able to detect multiple serotypes from field epithelial samples, in addition to detecting FMDV in the air surrounding infected cattle, pigs and sheep, including pre-clinical detection. This study describes the development and evaluation of an assay format, which may be used as a future basis for rapid and low cost detection of FMDV. In addition it provides providing “proof of concept” for the future use of LAMP assays to tackle other challenging diagnostic scenarios encompassing veterinary and human health. PMID:25165973

  1. Preliminary validation of direct detection of foot-and-mouth disease virus within clinical samples using reverse transcription loop-mediated isothermal amplification coupled with a simple lateral flow device for detection.

    Directory of Open Access Journals (Sweden)

    Ryan A Waters

    Full Text Available Rapid, field-based diagnostic assays are desirable tools for the control of foot-and-mouth disease (FMD. Current approaches involve either; 1 Detection of FMD virus (FMDV with immuochromatographic antigen lateral flow devices (LFD, which have relatively low analytical sensitivity, or 2 portable RT-qPCR that has high analytical sensitivity but is expensive. Loop-mediated isothermal amplification (LAMP may provide a platform upon which to develop field based assays without these drawbacks. The objective of this study was to modify an FMDV-specific reverse transcription-LAMP (RT-LAMP assay to enable detection of dual-labelled LAMP products with an LFD, and to evaluate simple sample processing protocols without nucleic acid extraction. The limit of detection of this assay was demonstrated to be equivalent to that of a laboratory based real-time RT-qPCR assay and to have a 10,000 fold higher analytical sensitivity than the FMDV-specific antigen LFD currently used in the field. Importantly, this study demonstrated that FMDV RNA could be detected from epithelial suspensions without the need for prior RNA extraction, utilising a rudimentary heat source for amplification. Once optimised, this RT-LAMP-LFD protocol was able to detect multiple serotypes from field epithelial samples, in addition to detecting FMDV in the air surrounding infected cattle, pigs and sheep, including pre-clinical detection. This study describes the development and evaluation of an assay format, which may be used as a future basis for rapid and low cost detection of FMDV. In addition it provides providing "proof of concept" for the future use of LAMP assays to tackle other challenging diagnostic scenarios encompassing veterinary and human health.

  2. CHANDIPURA VIRUS

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. CHANDIPURA VIRUS. First isolated from a village called Chandipura near Nagpur in 1965 in India. Belongs to rhabdoviridae family. Used as a Model System to study RNA virus multiplication in the infected cell at molecular level. Notes:

  3. Multiplex Real Time PCR For Detection of Wheat Streak Mosaic Virus and Triticum Mosaic Virus

    Science.gov (United States)

    Wheat streak mosaic virus (WSMV) and Triticum mosaic virus (TRIMV) are widespread throughout the southwestern Great Plains states. Using conventional diagnostics such as Enzyme-Linked Immunosorbent Assays (ELISA), these two viruses are commonly found together in infected wheat samples. Methods for m...

  4. Gastroenteritis and the novel picornaviruses aichi virus, cosavirus, saffold virus, and salivirus in young children.

    Science.gov (United States)

    Nielsen, Alex Christian Yde; Gyhrs, Mette Louise; Nielsen, Lars Peter; Pedersen, Court; Böttiger, Blenda

    2013-07-01

    During the last few years many new human picornaviruses have been discovered due to advances in metagenomics and other molecular biological approaches. The clinical significance and the occurrence are only sparsely described. To determine the epidemiology and clinical significance of infections with the novel human picornaviruses, aichi virus, cosavirus, salivirus, and saffold virus in infants in Denmark. We tested 1393 stool samples from a birth cohort of 454 children for these viruses. Samples were collected at ages 6, 10 and 15 months, and at episodes of gastroenteritis. Samples were tested by real-time reverse-transcriptase polymerase chain reaction assays. Each study participant had a diary, where the parents reported episodes of disease, including gastroenteritis. Aichi virus, salivirus and saffold virus were detected in 6, 9 and 38 of the children, respectively, but cosavirus was not detected in any of the children. There was a clear seasonal variation with most infections occurring in autumn and winter. A statistically significant association between the findings of salivirus and gastrointestinal disease was demonstrated. There was no association between gastrointestinal disease and the presence of aichi virus or saffold virus. The newly discovered human picornaviruses aichi virus, saffold virus, and salivirus are circulating in Danish children, with the most common being saffold virus. Saffold virus was seen almost exclusively in the autumn and winter period. Salivirus was the only virus, which was significantly associated with gastroenteritis, although the number of positive samples was rather low. Copyright © 2013 Elsevier B.V. All rights reserved.

  5. First detection of Grapevine rupestris stem pitting-associated virus and Grapevine rupestris vein feathering virus, and new phylogenetic groups for Grapevine fleck virus and Hop stunt viroid isolates, revealed from grapevine field surveys in Spain

    OpenAIRE

    Fiore, Nicola; Alan ZAMORANO; Nicolás SÁNCHEZ-DIANA; González, Ximena; Pallás, Vicente; Sánchez-Navarro, Jesús

    2016-01-01

    [EN] Evaluation of the prevalence of virus and viroid infections was conducted in a grapevine field collection in Valencia, Spain. Samples of autochthonous and traditional grapevine cultivars were collected during November 2011 and tested for the presence of fourteen viruses and five viroids, using RT-PCR. The prevalent viruses were Grapevine rupestris stem pitting-associated virus (GRSPaV: 49% infected samples) and Grapevine leafroll-associated virus 2 (GLRaV-2: 15% of samples). GLRaV-1, GLR...

  6. Collaborative study of the International Office of Cocoa, Chocolate and Sugar Confectionery on Salmonella detection from cocoa and chocolate processing environmental samples.

    Science.gov (United States)

    De Smedt, J M; Chartron, S; Cordier, J L; Graff, E; Hoekstra, H; Lecoupeau, J P; Lindblom, M; Milas, J; Morgan, R M; Nowacki, R

    1991-08-01

    A comparative collaborative study was performed in 13 laboratories to evaluate the use of motility enrichment on Modified Semisolid Rappaport-Vassiliadis medium for rapid Salmonella detection from food-processing environmental samples. Artificially contaminated chocolate scrapings and naturally contaminated cocoa bean dust samples were used in the study. Pre-enrichment was performed in buffered peptone water with added casein and malachite green oxalate. Motility enrichment was compared with a conventional cultural procedure using Rappaport-Vassiliadis broth and selenite cystine broth as selective enrichment. The productivity of motility enrichment was 93.5% compared to a productivity of the cultural procedure of 92%. Statistical analysis showed that there was no significant difference between the two procedures. Modified Semisolid Rappaport-Vassiliadis medium is a sensitive and simple diagnostic tool for the microbiological safety evaluation of food-processing environments.

  7. Concentration of 1,4-Dioxane in Wells Sampled During 2002-2009 in the Vicinity of the Tucson International Airport Area Superfund Site, Arizona

    Science.gov (United States)

    Tillman, Fred D

    2010-01-01

    Extensive groundwater contamination resulting from industrial activities led to the listing of the Tucson International Airport Area as a Superfund Site in 1983. Early investigations revealed elevated levels of volatile organic compounds (VOCs) including the chlorinated solvents trichloroethylene (TCE) and perchloroethylene (PCE) in wells in the area. Several responsible parties were identified and cleanup activities were begun in the late 1980s using technology designed for removal of VOCs. In 2002, the compound 1,4-dioxane was discovered in wells in the Tucson Airport Remediation Project (TARP) area. Since then, 1,4-dioxane has been detected throughout the TARP area, in some cases exceeding the U.S. Environmental Protection Agency (USEPA) drinking water advisory level of 3 ?g/L.

  8. Bovine parainfluenza-3 virus.

    Science.gov (United States)

    Ellis, John A

    2010-11-01

    Bovine parainfluenza-3 virus (bPI(3)V) is a long-recognized, currently underappreciated, endemic infection in cattle populations. Clinical disease is most common in calves with poor passive transfer or decayed maternal antibodies. It is usually mild, consisting of fever, nasal discharge, and dry cough. Caused at least partly by local immunosuppressive effects, bPI(3)V infection is often complicated by coinfection with other respiratory viruses and bacteria, and is therefore an important component of enzootic pneumonia in calves and bovine respiratory disease complex in feedlot cattle. Active infection can be diagnosed by virus isolation from nasal swabs, or IF testing on smears made from nasal swabs. Timing of sampling is critical in obtaining definitive diagnostic test results. Parenteral and intranasal modified live vaccine combination vaccines are available. Priming early in calfhood with intranasal vaccine, followed by boosting with parenteral vaccine, may be the best immunoprophylactic approach. Copyright © 2010 Elsevier Inc. All rights reserved.

  9. Environmental Stress Testing of the Single Sample Cylinder: A Proven Consensus Standard for Internal Gas Analysis (IGA) or Residual Gas Analysis (RGA)

    Science.gov (United States)

    Schuessler, Philipp WH

    2010-01-01

    In August 2008, Schuessler Consulting was contracted by NASA GSFC in support of the NASA Electronic Parts and Packaging (NEPP) program to perform two separate studies on moisture laden air in a stainless steel cylinder that had been designed to become a consensus standard for Test Method 1018. This Test Method was originally released for hybrids under Mil. Std. 883 but was quickly utilized on other microelectronic devices under the auspice of Mil. Std. 750. The cylinder had subsequently been fabricated for the 750 community. It was back-filled with moist air and subsequently analyzed over a period of time under a previous NASA contract. It had been shown that moisture in the 4000 - 5000 ppm range could be analyzed rather precisely with a mass spectrometer, commonly referred to as a Residual Gas Analyzer (RGA). The scope of this study was to ascertain if the composition and precision varied as a function of thermal shock at sub-zero temperatures and whether there was consensus when the standard was submitted to other RGA units. It was demonstrated and published that the consensus standard would yield precise RGA data for moisture within +/- 1% when optimized for a given RGA unit. It has been subsequently shown in this study at Oneida Research Services, that sub-zero storage did not affect that precision when a well-defined protocol for the analysis was followed. The consensus standard was taken to a second facility for analysis where it was found that moisture adsorption on the transfer lines caused precision to drop to +/- 12%. The Single Sample Cylinder (SSC) is a one liter stainless steel cylinder with associated sampling valves and has considerable weight and volume. But this considerable size allows for approximately 300 gas samples of the same composition to be delivered to any RGA unit. Lastly, a smaller cylinder, approximately 75 cc, of a second consensus standard was fabricated and tested with a different mix of fixed gases where moisture was kept in the

  10. Effects of fluid-rock interactions on faulting within active fault zones - evidence from fault rock samples retrieved from international drilling projects

    Science.gov (United States)

    Janssen, C.; Wirth, R.; Kienast, M.; Yabe, Y.; Sulem, J.; Dresen, G. H.

    2015-12-01

    Chemical and mechanical effects of fluids influence the fault mechanical behavior. We analyzed fresh fault rocks from several scientific drilling projects to study the effects of fluids on fault strength. For example, in drill core samples on a rupture plane of an Mw 2.2 earthquake in a deep gold mine in South Africa the main shock occurred on a preexisting plane of weakness that was formed by fluid-rock interaction (magnesiohornblende was intensively altered to chlinochlore). The plane acted as conduit for hydrothermal fluids at some time in the past. The chemical influence of fluids on mineralogical alteration and geomechanical processes in fault core samples from SAFOD (San Andreas Fault Observatory at Depth) is visible in pronounced dissolution-precipitation processes (stylolites, solution seams) as well as in the formation of new phases. Detrital quartz and feldspar grains are partially dissolved and replaced by authigenic illite-smectite (I-S) mixed-layer clay minerals. Transmission Electron Microscopy (TEM) imaging of these grains reveals that the alteration processes and healing were initiated within pores and small intra-grain fissures. Newly formed phyllosilicates growing into open pore spaces likely reduced the fluid permeability. The mechanical influence of fluids is indicated by TEM observations, which document open pores that formed in-situ in the gouge material during or after deformation. Pores were possibly filled with formation water and/or hydrothermal fluids suggesting elevated fluid pressure preventing pore collapse. Fluid-driven healing of fractures in samples from SAFOD and the DGLab Gulf of Corinth project is visible in cementation. Cathodoluminescence microscopy (CL) reveals different generations of calcite veins. Differences in CL-colors suggest repeated infiltration of fluids with different chemical composition from varying sources (formation and meteoric water).

  11. A new looming of Zika virus

    Directory of Open Access Journals (Sweden)

    Nirav R. Soni

    2016-05-01

    Full Text Available Zika virus (ZIKV is a member of the virus family Flaviviridae and the genus Flavivirus, transmitted by daytime-active Aedes mosquitoes, such as A. aegypti. ZIKV will continue to spread and it will be difficult to determine how the virus will spread over time. Sign and symptoms of ZIKAVD (Zika virus disease were conjunctivitis (red eyes, back pain, birth defect-abnormal brain development known as microcephaly and it is diagnosed through PCR (polymerase chain reaction and virus isolation from blood samples.

  12. The efficiency of concentration methods used to detect enteric viruses in anaerobically digested sludge

    Directory of Open Access Journals (Sweden)

    Tatiana Prado

    2013-02-01

    Full Text Available The presence of enteric viruses in biosolids can be underestimated due to the inefficient methods (mainly molecular methods used to recover the viruses from these matrices. Therefore, the goal of this study was to evaluate the different methods used to recover adenoviruses (AdV, rotavirus species A (RVA, norovirus genogroup II (NoV GII and the hepatitis A virus (HAV from biosolid samples at a large urban wastewater treatment plant in Brazil after they had been treated by mesophilic anaerobic digestion. Quantitative polymerase chain reaction (PCR was used for spiking experiments to compare the detection limits of feasible methods, such as beef extract elution and ultracentrifugation. Tests were performed to detect the inhibition levels and the bacteriophage PP7 was used as an internal control. The results showed that the inhibitors affected the efficiency of the PCR reaction and that beef extract elution is a suitable method for detecting enteric viruses, mainly AdV from biosolid samples. All of the viral groups were detected in the biosolid samples: AdV (90%, RVA, NoV GII (45% and HAV (18%, indicating the viruses' resistance to the anaerobic treatment process. This is the first study in Brazil to detect the presence of RVA, AdV, NoV GII and HAV in anaerobically digested sludge, highlighting the importance of adequate waste management.

  13. Computer viruses

    Science.gov (United States)

    Denning, Peter J.

    1988-01-01

    The worm, Trojan horse, bacterium, and virus are destructive programs that attack information stored in a computer's memory. Virus programs, which propagate by incorporating copies of themselves into other programs, are a growing menace in the late-1980s world of unprotected, networked workstations and personal computers. Limited immunity is offered by memory protection hardware, digitally authenticated object programs,and antibody programs that kill specific viruses. Additional immunity can be gained from the practice of digital hygiene, primarily the refusal to use software from untrusted sources. Full immunity requires attention in a social dimension, the accountability of programmers.

  14. Sequence characteristics of potato virus Y recombinants

    National Research Council Canada - National Science Library

    Hu, Xiaojun; Karasev, Alexander V; Brown, Celeste J; Lorenzen, Jim H

    2009-01-01

    ... Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA 4 International Institute of Tropical Agriculture, Kampala, Uganda Correspondence Alexander V. Karasev akarasev{at}uidaho.edu Potato virus Y (PVY...

  15. [Immunochip for differentiation of IgG to tick-borne encephalitis and West Nile fever viruses].

    Science.gov (United States)

    Pomelova, V G; Bychenkova, T A; Bekman, N I; Osin, N S

    2010-01-01

    To demonstrate the possibility of development of test based on phosphorescent analysis (PHOSPHAN) for simultaneous identification and differentiation of specific IgG to tick-borne encephalitis (TBE) and West Nile fever (WNF) viruses. Twenty six serum samples from patients with TBE, twenty five from WNF, and sixty six fromclinically healthy donors were used for the study. Immunologic analysis was performed in plate wells with active microzones "printed" on the wells' bottom and corresponding the complex of virus-specific antigens with immobilized monoclonal antibodies; internal control of specificity was included in each well. Species specificity of antibodies was determined on the basis of not less than 2-fold elevation of value of positivity coefficient (P/N) of sample studied with homologous antigen compared to heterologous one. PHOSPHAN provides simultaneous detection of IgG in human serum to two related flaviviruses: TBE and WNF viruses. Usage of P/N criterion assessed with homologous and heterologous antigen allowed correct determination of species specificity of antibodies in 90% of serum samples from patients with TBE and WNF CONCLUSION: PHOSPHAN allows to detect and differentiate IgG to TBE and WNF viruses during testing of one serum sample in one plate well without decrease of sensitivity compared to enzyme immunoassay with separated testing of samples on two viruses. This provides savings of biomaterial, which is an advantage compared to enzyme immunoassay.

  16. Serofrequency of feline immunodeficiency virus and feline leukemia virus in cats of Araçatuba, São Paulo

    OpenAIRE

    Sobrinho, Ludmila Silva Vicente [UNESP; Vides, Juliana Peloi [UNESP; Braga, Eveline Tozzi [UNESP; Gomes, Amélia Ana Domingues; Rossi,Claudio Nazaretian; Marcondes, Mary

    2011-01-01

    Feline immunodeficiency virus and feline leukemia represent important infectious diseases caused by retroviruses. This study aimed to investigate the prevalence of infection by feline immunodeficiency virus (FIV) and feline leukemia virus (FeLV) in cats from the municipality of Araçatuba, São Paulo. Blood samples from 302 cats were collected and tested for the presence of antibodies against feline immunodeficiency virus and antigen of feline leukemia virus by ELISA ® Snap- Combo FIV-FeLV (IDE...

  17. Minnesota Multiphasic Personality Inventory-2-Restructured Form (MMPI-2-RF) scores generated from the MMPI-2 and MMPI-2-RF test booklets: internal structure comparability in a sample of criminal defendants.

    Science.gov (United States)

    Tarescavage, Anthony M; Alosco, Michael L; Ben-Porath, Yossef S; Wood, Arcangela; Luna-Jones, Lynn

    2015-04-01

    We investigated the internal structure comparability of Minnesota Multiphasic Personality Inventory-2-Restructured Form (MMPI-2-RF) scores derived from the MMPI-2 and MMPI-2-RF booklets in a sample of 320 criminal defendants (229 males and 54 females). After exclusion of invalid protocols, the final sample consisted of 96 defendants who were administered the MMPI-2-RF booklet and 83 who completed the MMPI-2. No statistically significant differences in MMPI-2-RF invalidity rates were observed between the two forms. Individuals in the final sample who completed the MMPI-2-RF did not statistically differ on demographics or referral question from those who were administered the MMPI-2 booklet. Independent t tests showed no statistically significant differences between MMPI-2-RF scores generated with the MMPI-2 and MMPI-2-RF booklets on the test's substantive scales. Statistically significant small differences were observed on the revised Variable Response Inconsistency (VRIN-r) and True Response Inconsistency (TRIN-r) scales. Cronbach's alpha and standard errors of measurement were approximately equal between the booklets for all MMPI-2-RF scales. Finally, MMPI-2-RF intercorrelations produced from the two forms yielded mostly small and a few medium differences, indicating that discriminant validity and test structure are maintained. Overall, our findings reflect the internal structure comparability of MMPI-2-RF scale scores generated from MMPI-2 and MMPI-2-RF booklets. Implications of these results and limitations of these findings are discussed. © The Author(s) 2014.

  18. European interlaboratory comparison of Schmallenberg virus (SBV) real-time RT-PCR detection in experimental and field samples: The method of extraction is critical for SBV RNA detection in semen.

    Science.gov (United States)

    Schulz, Claudia; van der Poel, Wim H M; Ponsart, Claire; Cay, Ann Brigitte; Steinbach, Falko; Zientara, Stéphan; Beer, Martin; Hoffmann, Bernd

    2015-07-01

    Molecular methods for the detection of Schmallenberg virus (SBV) RNA were rapidly developed after the emergence of this novel orthobunyavirus in Europe. The SBV epizootic wave has declined, but infectious SBV in SBV RNA-positive semen remains a possible risk for the distribution of SBV. However, the abilities of SBV molecular detection methods used at European laboratories have not yet been assessed, to our knowledge. The performances of extraction and real-time reverse transcription polymerase chain reaction (RT-qPCR) methods used at 27 German and 17 other European laboratories for SBV RNA detection in the matrices of whole blood, serum, tissue homogenate, RNA eluates, and bovine semen were evaluated in 2 interlaboratory trials with special emphasis on semen extraction methods. For reliable detection of viral genome in bovine semen samples, highly effective extraction methods are essential to cope with the potential inhibitory effects of semen components on PCR results. All methods used by the 44 laboratories were sufficiently robust to detect SBV RNA with high diagnostic sensitivity (100%) and specificity (95.8%) in all matrices, except semen. The trials demonstrated that the published recommended semen extraction methods (Hoffmann et al. 2013) and a combination of TRIzol LS with an alternative extraction kit have a considerably higher diagnostic sensitivity to detect SBV RNA in semen up to a detection limit of Cq ≤35 compared to other extraction methods used. A thorough validation of extraction methods with standardized semen batches is essential before their use for SBV RNA detection in bovine semen. © 2015 The Author(s).

  19. Failed detection of Bovine viral diarrhea virus 2 subgenotype a (BVDV-2a) by direct fluorescent antibody test on tissue samples due to reduced reactivity of field isolates to raw anti-BVDV antibody.

    Science.gov (United States)

    Yan, Lifang; Pace, Lanny W; Baughman, Brittany; Wilson, Floyd D; Zhang, Shuping; Zhang, Michael Z

    2016-03-01

    Bovine viral diarrhea virus 1 (BVDV-1) is associated with mild or subclinical infections, whereas BVDV-2 is frequently implicated in outbreaks of severe thrombocytopenia and acute fatal disease. In the present study, the carcass of a beef breed cow and tissue samples of a beef calf were received for laboratory diagnosis. Both animals exhibited severe clinical signs compatible with thrombocytopenia or hemorrhagic syndrome. Direct fluorescent antibody test (DFAT) failed to detect BVDV antigen in the tissue specimens of both cases. However, immunohistochemistry (IHC) revealed the presence of BVDV antigen in oral and esophageal mucosa and Peyer patches of the beef breed cow. Real-time reverse transcription polymerase chain reaction (real-time RT-PCR) detected BVDV-2 in selected tissues of both animals. Subsequently, BVDV was isolated from both cases and subjected to genetic and serologic characterizations. Mutations in the 5'-untranslated genomic region (5'-UTR) primer and probe binding sites and the E2 gene were associated with reduced efficiency of an established real-time RT-PCR assay and amino acid alterations in the E2 glycoprotein, respectively. Both viral isolates were classified by real-time RT-PCR and phylogenetic analysis as BVDV-2 subgenotype a. Unlike BVDV reference strains Singer and 125c, the isolates cross-reacted with anti-BVDV-1 and anti-BVDV-2 reference sera, indicating antigenic variations in field isolates. The isolates also showed reduced reactivity to porcine anti-BVDV antiserum (the raw serum used to produce BVDV DFA conjugate). In summary, data from the present investigation indicated that genetic and antigenic variations affected the performance of detection assays, especially DFAT, highlighting the need for regular evaluation and modification of BVDV tests. © 2016 The Author(s).

  20. Risk behaviors, prevalence of HIV and hepatitis C virus infection and population size of current injection drug users in a China-Myanmar border city: results from a Respondent-Driven Sampling Survey in 2012.

    Science.gov (United States)

    Li, Lei; Assanangkornchai, Sawitri; Duo, Lin; McNeil, Edward; Li, Jianhua

    2014-01-01

    Injection drug use has been the major cause of HIV/AIDS in China in the past two decades. We measured the prevalences of HIV and hepatitis C virus (HCV) prevalence and their associated risk factors among current injection drug users (IDUs) in Ruili city, a border region connecting China with Myanmar that has been undergoing serious drug use and HIV spread problems. An estimate of the number of current IDUs is also presented. In 2012, Chinese IDUs who had injected within the past six months and aged ≥ 18 years were recruited using a respondent-driven sampling (RDS) technique. Participants underwent interviews and serological testing for HIV, HBV, HCV and syphilis. Logistic regression indentified factors associated with HIV and HCV infections. Multiplier method was used to obtain an estimate of the size of the current IDU population via combining available service data and findings from our survey. Among 370 IDUs recruited, the prevalence of HIV and HCV was 18.3% and 41.5%, respectively. 27.1% of participants had shared a needle/syringe in their lifetime. Consistent condom use rates were low among both regular (6.8%) and non-regular (30.4%) partners. Factors independently associated with being HIV positive included HCV infection, having a longer history of injection drug use and experience of needle/syringe sharing. Participants with HCV infection were more likely to be HIV positive, have injected more types of drugs, have shared other injection equipments and have unprotected sex with regular sex partners. The estimated number of current IDUs in Ruili city was 2,714 (95% CI: 1,617-5,846). IDUs may continue to be a critical subpopulation for transmission of HIV and other infections in this region because of the increasing population and persistent high risk of injection and sexual behaviours. Developing innovative strategies that can improve accessibility of current harm reduction services and incorporate more comprehensive contents is urgently needed.

  1. Novel approach for detection of enteric viruses to enable syndrome surveillance of acute viral gastroenteritis.

    Science.gov (United States)

    Svraka, Sanela; van der Veer, Bas; Duizer, Erwin; Dekkers, Jojanneke; Koopmans, Marion; Vennema, Harry

    2009-06-01

    Acute gastroenteritis is one of the most common diseases worldwide, with viruses, particularly noroviruses, being the leading cause in developed countries. In The Netherlands, systematic surveillance of gastroenteritis outbreaks of suspected viral etiology was established by the National Institute for Public Health and the Environment in 1994. Since 2002, the total number of outbreaks reported has been increasing, and with that comes the need for sensitive assays that can be performed quickly. In addition, the diagnostic demand changed so that now the proportion of samples from hospitals is higher and there is a need for patient-based test results. In order to target the diagnosis of acute gastroenteritis, we reviewed our data on outbreaks of gastroenteritis and the prevalence of individual viruses to provide a priority list of viruses for which samples should be evaluated. Random primers were used to replace the separate specific primers for each virus used in the reverse transcription steps. The individual PCR assays were replaced by multiplex PCR assays. We employed a two-step method in which in the first step we screened for the most common causes of viral gastroenteritis, noroviruses of genogroup II and rotaviruses of group A, with equine arteritis virus used as the internal control. Subsequently, in the second step, two parallel PCR assays were developed for the detection of noroviruses of genogroup I and equine arteritis virus in one run and adenoviruses, sapoviruses, and astroviruses in the other run. The specificities of the assays were calculated to be 92.5% for the assay for noroviruses of genogroup I and 100% for the assays for all other viruses, the detection limits were equal for all viruses, and the turnaround time was reduced to 1 day compared to the at least 3 days required for the methods used previously. This approach allows the targeted, rapid, and cost-effective elucidation of the causes of acute gastroenteritis outbreaks.

  2. Viruses in the Oceanic Basement.

    Science.gov (United States)

    Nigro, Olivia D; Jungbluth, Sean P; Lin, Huei-Ting; Hsieh, Chih-Chiang; Miranda, Jaclyn A; Schvarcz, Christopher R; Rappé, Michael S; Steward, Grieg F

    2017-03-07

    Microbial life has been detected well into the igneous crust of the seafloor (i.e., the oceanic basement), but there have been no reports confirming the presence of viruses in this habitat. To detect and characterize an ocean basement virome, geothermally heated fluid samples (ca. 60 to 65°C) were collected from 117 to 292 m deep into the ocean basement using seafloor observatories installed in two boreholes (Integrated Ocean Drilling Program [IODP] U1362A and U1362B) drilled in the eastern sediment-covered flank of the Juan de Fuca Ridge. Concentrations of virus-like particles in the fluid samples were on the order of 0.2 × 10 5 to 2 × 10 5  ml -1 ( n = 8), higher than prokaryote-like cells in the same samples by a factor of 9 on average (range, 1.5 to 27). Electron microscopy revealed diverse viral morphotypes similar to those of viruses known to infect bacteria and thermophilic archaea. An analysis of virus-like sequences in basement microbial metagenomes suggests that those from archaeon-infecting viruses were the most common (63 to 80%). Complete genomes of a putative archaeon-infecting virus and a prophage within an archaeal scaffold were identified among the assembled sequences, and sequence analysis suggests that they represent lineages divergent from known thermophilic viruses. Of the clustered regularly interspaced short palindromic repeat (CRISPR)-containing scaffolds in the metagenomes for which a taxonomy could be inferred (163 out of 737), 51 to 55% appeared to be archaeal and 45 to 49% appeared to be bacterial. These results imply that the warmed, highly altered fluids in deeply buried ocean basement harbor a distinct assemblage of novel viruses, including many that infect archaea, and that these viruses are active participants in the ecology of the basement microbiome. IMPORTANCE The hydrothermally active ocean basement is voluminous and likely provided conditions critical to the origins of life, but the microbiology of this vast habitat is not

  3. Extraterrestrial Viruses?

    OpenAIRE

    Jurado Hernández, Daniel José

    2017-01-01

    Fundamentals of Life - Origin and Fundamentals of Living Things. Evaluation rubric to evaluate the debate and presentation about the point of view regarding the possibility of viruses from the outer space.

  4. Limits in virus filtration capability? Impact of virus quality and spike level on virus removal with xenotropic murine leukemia virus.

    Science.gov (United States)

    Roush, David J; Myrold, Adam; Burnham, Michael S; And, Joseph V; Hughes, Joseph V

    2015-01-01

    Virus filtration (VF) is a key step in an overall viral clearance process since it has been demonstrated to effectively clear a wide range of mammalian viruses with a log reduction value (LRV) > 4. The potential to achieve higher LRV from virus retentive filters has historically been examined using bacteriophage surrogates, which commonly demonstrated a potential of > 9 LRV when using high titer spikes (e.g. 10(10) PFU/mL). However, as the filter loading increases, one typically experiences significant decreases in performance and LRV. The 9 LRV value is markedly higher than the current expected range of 4-5 LRV when utilizing mammalian retroviruses on virus removal filters (Miesegaes et al., Dev Biol (Basel) 2010;133:3-101). Recent values have been reported in the literature (Stuckey et al., Biotech Progr 2014;30:79-85) of LRV in excess of 6 for PPV and XMuLV although this result appears to be atypical. LRV for VF with therapeutic proteins could be limited by several factors including process limits (flux decay, load matrix), virus spike level and the analytical methods used for virus detection (i.e. the Limits of Quantitation), as well as the virus spike quality. Research was conducted using the Xenotropic-Murine Leukemia Virus (XMuLV) for its direct relevance to the most commonly cited document, the International Conference of Harmonization (ICH) Q5A (International Conference on Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use, Geneva, Switzerland, 1999) for viral safety evaluations. A unique aspect of this work is the independent evaluation of the impact of retrovirus quality and virus spike level on VF performance and LRV. The VF studies used XMuLV preparations purified by either ultracentrifugation (Ultra 1) or by chromatographic processes that yielded a more highly purified virus stock (Ultra 2). Two monoclonal antibodies (Mabs) with markedly different filtration characteristics and with similar levels of

  5. Evaluating the role of wild songbirds or rodents in spreading avian influenza virus across an agricultural landscape

    Directory of Open Access Journals (Sweden)

    Derek D. Houston

    2017-12-01

    Full Text Available Background Avian influenza virus (AIV infections occur naturally in wild bird populations and can cross the wildlife-domestic animal interface, often with devastating impacts on commercial poultry. Migratory waterfowl and shorebirds are natural AIV reservoirs and can carry the virus along migratory pathways, often without exhibiting clinical signs. However, these species rarely inhabit poultry farms, so transmission into domestic birds likely occurs through other means. In many cases, human activities are thought to spread the virus into domestic populations. Consequently, biosecurity measures have been implemented to limit human-facilitated outbreaks. The 2015 avian influenza outbreak in the United States, which occurred among poultry operations with strict biosecurity controls, suggests that alternative routes of virus infiltration may exist, including bridge hosts: wild animals that transfer virus from areas of high waterfowl and shorebird densities. Methods Here, we examined small, wild birds (songbirds, woodpeckers, etc. and mammals in Iowa, one of the regions hit hardest by the 2015 avian influenza epizootic, to determine whether these animals carry AIV. To assess whether influenza A virus was present in other species in Iowa during our sampling period, we also present results from surveillance of waterfowl by the Iowa Department of Natural Resources and Unites Stated Department of Agriculture. Results Capturing animals at wetlands and near poultry facilities, we swabbed 449 individuals, internally and externally, for the presence of influenza A virus and no samples tested positive by qPCR. Similarly, serology from 402 animals showed no antibodies against influenza A. Although several species were captured at both wetland and poultry sites, the overall community structure of wild species differed significantly between these types of sites. In contrast, 83 out of 527 sampled waterfowl tested positive for influenza A via qPCR. Discussion

  6. Universal influenza virus vaccines and therapeutic antibodies.

    Science.gov (United States)

    Nachbagauer, R; Krammer, F

    2017-04-01

    Current influenza virus vaccines are effective when well matched to the circulating strains. Unfortunately, antigenic drift and the high diversity of potential emerging zoonotic and pandemic viruses make it difficult to select the right strains for vaccine production. This problem causes vaccine mismatches, which lead to sharp drops in vaccine effectiveness and long response times to manufacture matched vaccines in case of novel pandemic viruses. To provide an overview of universal influenza virus vaccines and therapeutic antibodies in preclinical and clinical development. PubMed and clinicaltrials.gov were used as sources for this review. Universal influenza virus vaccines that target conserved regions of the influenza virus including the haemagglutinin stalk domain, the ectodomain of the M2 ion channel or the internal matrix and nucleoproteins are in late preclinical and clinical development. These vaccines could confer broad protection against all influenza A and B viruses including drift variants and thereby abolish the need for annual re-formulation and re-administration of influenza virus vaccines. In addition, these novel vaccines would enhance preparedness against emerging influenza virus pandemics. Finally, novel therapeutic antibodies against the same conserved targets are in clinical development and could become valuable tools in the fight against influenza virus infection. Both universal influenza virus vaccines and therapeutic antibodies are potential future options for the control of human influenza infections. Copyright © 2017 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

  7. International challenge to predict the impact of radioxenon releases from medical isotope production on a comprehensive nuclear test ban treaty sampling station

    Energy Technology Data Exchange (ETDEWEB)

    Eslinger, Paul W.; Bowyer, Ted W.; Achim, Pascal; Chai, Tianfeng; Deconninck, Benoit; Freeman, Katie; Generoso, Sylvia; Hayes, Philip; Heidmann, Verena; Hoffman, Ian; Kijima, Yuichi; Krysta, Monika; Malo, Alain; Maurer, Christian; Ngan, Fantine; Robins, Peter; Ross, J. Ole; Saunier, Olivier; Schlosser, Clemens; Schöppner, Michael; Schrom, Brian T.; Seibert, Petra; Stein, Ariel F.; Ungar, Kurt; Yi, Jing

    2016-06-01

    Abstract The International Monitoring System (IMS) is part of the verification regime for the Comprehensive Nuclear-Test-Ban-Treaty Organization (CTBTO). At entry-into-force, half of the 80 radionuclide stations will be able to measure concentrations of several radioactive xenon isotopes produced in nuclear explosions, and then the full network may be populated with xenon monitoring afterward (Bowyer et al., 2013). Fission-based production of 99Mo for medical purposes also releases radioxenon isotopes to the atmosphere (Saey, 2009). One of the ways to mitigate the effect of emissions from medical isotope production is the use of stack monitoring data, if it were available, so that the effect of radioactive xenon emissions could be subtracted from the effect from a presumed nuclear explosion, when detected at an IMS station location. To date, no studies have addressed the impacts the time resolution or data accuracy of stack monitoring data have on predicted concentrations at an IMS station location. Recently, participants from seven nations used atmospheric transport modeling to predict the time-history of 133Xe concentration measurements at an IMS station in Germany using stack monitoring data from a medical isotope production facility in Belgium. Participants received only stack monitoring data and used the atmospheric transport model and meteorological data of their choice. Some of the models predicted the highest measured concentrations quite well (a high composite statistical model comparison rank or a small mean square error with the measured values). The results suggest release data on a 15 min time spacing is best. The model comparison rank and ensemble analysis suggests that combining multiple models may provide more accurate predicted concentrations than any single model. Further research is needed to identify optimal methods for selecting ensemble members and those methods may depend on the specific transport problem. None of the submissions based only

  8. Zika Virus

    OpenAIRE

    Musso, Didier; Gubler, Duane J.

    2016-01-01

    Zika virus (ZIKV) is an arthropod-borne virus (arbovirus) in the genus Flavivirus and the family Flaviviridae. ZIKV was first isolated from a nonhuman primate in 1947 and from mosquitoes in 1948 in Africa, and ZIKV infections in humans were sporadic for half a century before emerging in the Pacific and the Americas. ZIKV is usually transmitted by the bite of infected mosquitoes. The clinical presentation of Zika fever is nonspecific and can be misdiagnosed as other infectious diseases, especi...

  9. Radiotoxicological analyses of {sup 239+240}Pu and {sup 241}Am in biological samples by anion-exchange and extraction chromatography: a preliminary study for internal contamination evaluations

    Energy Technology Data Exchange (ETDEWEB)

    Ridone, S.; Arginelli, D.; Bortoluzzi, S.; Canuto, G.; Montalto, M.; Nocente, M.; Vegro, M. [Italian National Agency for New Technologies, Energy and the Environment (ENEA), Research Centre of Saluggia, Radiation Protection Institute, Saluggia, VC (Italy)

    2006-07-01

    Many biological samples (urines and faeces) have been analysed by means of chromatographic extraction columns, utilising two different resins (AG 1-X2 resin chloride and T.R.U.), in order to detect the possible internal contamination of {sup 239{sup +}}{sup 240}Pu and {sup 241}Am, for some workers of a reprocessing nuclear plant in the decommissioning phase. The results obtained show on one hand the great suitability of the first resin for the determination of plutonium, and on the other the great selectivity of the second one for the determination of americium.

  10. Validez del Cuestionario International Personality Disorder Examination (IPDE en una muestra de población penitenciaria Validity of the International Personality Disorder Examination (IPDE questionnaire in a sample of prison inmates

    Directory of Open Access Journals (Sweden)

    E. Álvaro-Brun

    2008-10-01

    Full Text Available Objetivo: Conocer los índices validez y establecer el punto de corte más adecuado cuando se utiliza el cuestionario IPDE en una muestra de población penitenciaria. Material y método: Estudio transversal realizado con una muestra de 100 penados de dos centros penitenciarios de Madrid seleccionados de forma correlativa. Instrumentos de evaluación, cuestionario de datos demográficos, penitenciarios y toxicológicos; y entrevista completa y cuestionario de evaluación IPDE versión DSM-IV. Estudio de sensibilidad y especificidad del cuestionario IPDE con distintos puntos de corte utilizando como "patrón oro" la entrevista IPDE. Resultados: Utilizando el punto de corte 3 o más respuestas no coincidentes con la esperadas, se encuentra baja especificidad (2,5% para la presencia de uno o más trastornos de la personalidad, y baja sensibilidad para los trastornos antisocial (56,7% y límite (58,8% de la personalidad. Discusión: El cuestionario IPDE tiene escasa utilidad en la población penitenciaria estudiada cuando se aplica con los estándares de referencia habituales, pues el número de falsos positivos que produce es muy elevado. Los mejores índices de validez para identificar uno o más trastornos de la personalidad se obtienen con el punto de corte probable igual a 4 o más respuestas no coincidentes con las esperadas. En cualquier caso el uso del cuestionario IPDE en los reclusos evaluados no aporta beneficios ya que, incluso con el punto de corte habitual de 3 o más respuestas no coincidentes, para los trastornos de personalidad más frecuentes en la muestra estudiada, el antisocial y el límite, se observa que la sensibilidad es baja.Objective: To discover the validity indices and establish the most adequate cut off point when using the IPDE questionnaire on a sample of prison inmates. Materials and Methods: A transversal study was carried out on a correlatively selected sample of 100 inmates at two prisons in Madrid. Evaluation

  11. A human-like H1N2 influenza virus detected during an outbreak of acute respiratory disease in swine in Brazil.

    Science.gov (United States)

    Schaefer, Rejane; Rech, Raquel Rubia; Gava, Danielle; Cantão, Mauricio Egídio; da Silva, Marcia Cristina; Silveira, Simone; Zanella, Janice Reis Ciacci

    2015-01-01

    Passive monitoring for detection of influenza A viruses (IAVs) in pigs has been carried out in Brazil since 2009, detecting mostly the A(H1N1)pdm09 influenza virus. Since then, outbreaks of acute respiratory disease suggestive of influenza A virus infection have been observed frequently in Brazilian pig herds. During a 2010-2011 influenza monitoring, a novel H1N2 influenza virus was detected in nursery pigs showing respiratory signs. The pathologic changes were cranioventral acute necrotizing bronchiolitis to subacute proliferative and purulent bronchointerstitial pneumonia. Lung tissue samples were positive for both influenza A virus and A(H1N1)pdm09 influenza virus based on RT-qPCR of the matrix gene. Two IAVs were isolated in SPF chicken eggs. HI analysis of both swine H1N2 influenza viruses showed reactivity to the H1δ cluster. DNA sequencing was performed for all eight viral gene segments of two virus isolates. According to the phylogenetic analysis, the HA and NA genes clustered with influenza viruses of the human lineage (H1-δ cluster, N2), whereas the six internal gene segments clustered with the A(H1N1)pdm09 group. This is the first report of a reassortant human-like H1N2 influenza virus derived from pandemic H1N1 virus causing an outbreak of respiratory disease in pigs in Brazil. The emergence of a reassortant IAV demands the close monitoring of pigs through the full-genome sequencing of virus isolates in order to enhance genetic information about IAVs circulating in pigs.

  12. Genetically Diverse Low Pathogenicity Avian Influenza A Virus Subtypes Co-Circulate among Poultry in Bangladesh.

    Science.gov (United States)

    Gerloff, Nancy A; Khan, Salah Uddin; Zanders, Natosha; Balish, Amanda; Haider, Najmul; Islam, Ausraful; Chowdhury, Sukanta; Rahman, Mahmudur Ziaur; Haque, Ainul; Hosseini, Parviez; Gurley, Emily S; Luby, Stephen P; Wentworth, David E; Donis, Ruben O; Sturm-Ramirez, Katharine; Davis, C Todd

    2016-01-01

    Influenza virus surveillance, poultry outbreak investigations and genomic sequencing were assessed to understand the ecology and evolution of low pathogenicity avian influenza (LPAI) A viruses in Bangladesh from 2007 to 2013. We analyzed 506 avian specimens collected from poultry in live bird markets and backyard flocks to identify influenza A viruses. Virus isolation-positive specimens (n = 50) were subtyped and their coding-complete genomes were sequenced. The most frequently identified subtypes among LPAI isolates were H9N2, H11N3, H4N6, and H1N1. Less frequently detected subtypes included H1N3, H2N4, H3N2, H3N6, H3N8, H4N2, H5N2, H6N1, H6N7, and H7N9. Gene sequences were compared to publicly available sequences using phylogenetic inference approaches. Among the 14 subtypes identified, the majority of viral gene segments were most closely related to poultry or wild bird viruses commonly found in Southeast Asia, Europe, and/or northern Africa. LPAI subtypes were distributed over several geographic locations in Bangladesh, and surface and internal protein gene segments clustered phylogenetically with a diverse number of viral subtypes suggesting extensive reassortment among these LPAI viruses. H9N2 subtype viruses differed from other LPAI subtypes because genes from these viruses consistently clustered together, indicating this subtype is enzootic in Bangladesh. The H9N2 strains identified in Bangladesh were phylogenetically and antigenically related to previous human-derived H9N2 viruses detected in Bangladesh representing a potential source for human infection. In contrast, the circulating LPAI H5N2 and H7N9 viruses were both phylogenetically and antigenically unrelated to H5 viruses identified previously in humans in Bangladesh and H7N9 strains isolated from humans in China. In Bangladesh, domestic poultry sold in live bird markets carried a wide range of LPAI virus subtypes and a high diversity of genotypes. These findings, combined with the seven year

  13. Development of a duplex real-time TaqMan PCR assay with an internal control for the detection of Mycoplasma gallisepticum and Mycoplasma synoviae in clinical samples from commercial and backyard poultry.

    Science.gov (United States)

    Sprygin, A V; Andreychuk, D B; Kolotilov, A N; Volkov, M S; Runina, I A; Mudrak, N S; Borisov, A V; Irza, V N; Drygin, V V; Perevozchikova, N A

    2010-04-01

    In this study, we report the development and validation of a duplex real-time polymerase chain reaction (PCR) assay with an internal control using TaqMan-labelled probes for the detection of Mycoplasma gallisepticum and Mycoplasma synoviae (duplex MGMS PCR). The MGMS PCR was highly specific with a sensitivity of 7 and 1 colony-forming units/ml for M. gallisepticum and M. synoviae, respectively, using dilution of pure culture that corresponds to 34 and 29 DNA copies per reaction. Validation of the assay was completed with 260 and 27 pooled samples (tracheal swabs) from commercial chickens and turkeys, respectively, with potential M. gallisepticum and M. synoviae involvement and 42 samples (palatine cleft swabs) from backyard geese and ducks. Using isolation as the gold standard, the MGMS PCR was more sensitive than isolation and the analytical sensitivity was 0.944 and 0.958 for M. gallisepticum and M. synoviae, respectively. In comparison with a gapA-based assay (gapA PCR) and a 16S rRNA-based assay (16S PCR) for M. gallisepticum and M. synoviae, respectively, the results agreed for 94.5% and 96.6%, respectively. The use of the internal control allowed monitoring of proper extraction and inhibition of amplification that was detected in 12 samples. The duplex MGMS PCR was shown to be superior to the presently reported real-time PCR assays in terms of combination of sensitivity, specificity and capacity of detection of more than one target in a single tube. In conclusion, the duplex MGMS PCR was highly specific, sensitive, and reproducible and could be used on clinical samples from commercial chickens, turkeys and backyard poultry including ducks and geese.

  14. Newcastle Disease Virus (PDQ)

    Science.gov (United States)

    ... to Ask about Your Treatment Research Newcastle Disease Virus (PDQ®)–Patient Version Overview Go to Health Professional ... Question 8 ). Questions and Answers About Newcastle Disease Virus What is Newcastle disease virus? Newcastle disease virus ( ...

  15. Droplet Microfluidics for Virus Discovery

    Science.gov (United States)

    Rotem, Assaf; Cockrell, Shelley; Guo, Mira; Pipas, James; Weitz, David

    2012-02-01

    The ability to detect, isolate, and characterize an infectious agent is important for diagnosing and curing infectious diseases. Detecting new viral diseases is a challenge because the number of virus particles is often low and/or localized to a small subset of cells. Even if a new virus is detected, it is difficult