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Sample records for astroviruses seadornaviruses cytorhabdoviruses

  1. Candidates in Astroviruses, Seadornaviruses, Cytorhabdoviruses and Coronaviruses for +1 frame overlapping genes accessed by leaky scanning

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    Atkins John F

    2010-01-01

    Full Text Available Abstract Background Overlapping genes are common in RNA viruses where they serve as a mechanism to optimize the coding potential of compact genomes. However, annotation of overlapping genes can be difficult using conventional gene-finding software. Recently we have been using a number of complementary approaches to systematically identify previously undetected overlapping genes in RNA virus genomes. In this article we gather together a number of promising candidate new overlapping genes that may be of interest to the community. Results Overlapping gene predictions are presented for the astroviruses, seadornaviruses, cytorhabdoviruses and coronaviruses (families Astroviridae, Reoviridae, Rhabdoviridae and Coronaviridae, respectively.

  2. Novel human astroviruses: Novel human diseases?

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    Vu, Diem-Lan; Cordey, Samuel; Brito, Francisco; Kaiser, Laurent

    2016-09-01

    Astroviruses are small, non-enveloped, single-stranded positive RNA viruses that belong to the Astroviridae family. While classical human astroviruses (HAstV) are a well-recognized cause of acute non-bacterial diarrhea among young children worldwide, novel astroviruses, named HAstV-MLB and HAstV-VA/HMO, have been identified recently in humans by molecular assays. They are phylogenetically more related to animal astroviruses than to classical human astroviruses, thus suggesting cross-species transmission. Serological studies demonstrated a surprisingly high seroprevalence in certain populations and highlighted a high infection rate in the early years of life. Although their pathogenic role has not yet been clearly determined, novel astrovirus RNA sequences have been identified in different biological specimens of symptomatic patients, including the feces, plasma, cerebrospinal fluid, and brain biopsies. Thus, there is evidence that they could contribute not only to digestive tract infection, but also to unexpected clinical syndromes, notably encephalitis and meningitis. Severe infections affect mainly immunocompromised patients. These findings indicate that novel astroviruses should be considered in the differential diagnosis of immunocompromised patients with meningitis or encephalitis of unknown origin. PMID:27434149

  3. Complete genome sequence of Colocasia bobone disease-associated virus, a putative cytorhabdovirus infecting taro.

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    Higgins, Colleen M; Bejerman, Nicolas; Li, Ming; James, Anthony P; Dietzgen, Ralf G; Pearson, Michael N; Revill, Peter A; Harding, Robert M

    2016-03-01

    We report the first genome sequence of a Colocasia bobone disease-associated virus (CBDaV) derived from bobone-affected taro [Colocasia esculenta L. Schott] from Solomon Islands. The negative-strand RNA genome is 12,193 nt long, with six major open reading frames (ORFs) with the arrangement 3'-N-P-P3-M-G-L-5'. Typical of all rhabdoviruses, the 3' leader and 5' trailer sequences show complementarity to each other. Phylogenetic analysis indicated that CBDaV is a member of the genus Cytorhabdovirus, supporting previous reports of virus particles within the cytoplasm of bobone-infected taro cells. The availability of the CBDaV genome sequence now makes it possible to assess the role of this virus in bobone, and possibly alomae disease of taro and confirm that this sequence is that of Colocasia bobone disease virus (CBDV).

  4. Complete genome sequence of Colocasia bobone disease-associated virus, a putative cytorhabdovirus infecting taro.

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    Higgins, Colleen M; Bejerman, Nicolas; Li, Ming; James, Anthony P; Dietzgen, Ralf G; Pearson, Michael N; Revill, Peter A; Harding, Robert M

    2016-03-01

    We report the first genome sequence of a Colocasia bobone disease-associated virus (CBDaV) derived from bobone-affected taro [Colocasia esculenta L. Schott] from Solomon Islands. The negative-strand RNA genome is 12,193 nt long, with six major open reading frames (ORFs) with the arrangement 3'-N-P-P3-M-G-L-5'. Typical of all rhabdoviruses, the 3' leader and 5' trailer sequences show complementarity to each other. Phylogenetic analysis indicated that CBDaV is a member of the genus Cytorhabdovirus, supporting previous reports of virus particles within the cytoplasm of bobone-infected taro cells. The availability of the CBDaV genome sequence now makes it possible to assess the role of this virus in bobone, and possibly alomae disease of taro and confirm that this sequence is that of Colocasia bobone disease virus (CBDV). PMID:26687584

  5. Detection of diverse astroviruses from bats in China.

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    Zhu, Hua Chen; Chu, Daniel K.W.; Liu, Wei; Dong, Bai Qing; Zhang, Shu Yi; Zhang, Jin Xia; Li, Li Feng; Vijaykrishna, Dhanasekaran; Smith, Gavin J. D.; Chen, Hong Lin; Leo L M Poon; Peiris, J. S. Malik; Guan, Yi

    2009-01-01

    Astroviruses infect humans and many different animal species and are associated with gastroenteritis. Recent studies first detected the virus from bat species in Hong Kong. To understand astrovirus distribution in the wider region further, we examined the prevalence of this virus family in bat specimens collected from a large geographical region of mainland China. We collected 500 anal swabs from 20 bat species in 51 natural habitats from 11 provinces of China and tested these for astroviruse...

  6. Astrovirus as a cause of gastroenteritis in Japan.

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    Utagawa, E T; Nishizawa, S; Sekine, S; Hayashi, Y.; Ishihara, Y.; Oishi, I; Iwasaki, A; Yamashita, I; Miyamura, K; Yamazaki, S.

    1994-01-01

    We used an enzyme immunoassay (EIA) to screen for astrovirus in stool specimens from outbreaks and sporadic cases of gastroenteritis collected between 1982 and 1992 in six prefectural public health institutes in Japan. Three outbreaks of gastroenteritis involving schoolchildren and adults were confirmed to be attributable to astrovirus. Astrovirus was detected in 6 to 10% of the specimens from patients with sporadic gastroenteritis from whom no other bacterial or viral agent had been identifi...

  7. Nosocomial diarrhea in children:is astrovirus the leading pathogen?

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    Anita Chakravarti; Manisha Jain; Mayank Singh Chauhan; Anju Sharma; Sayani Tewari

    2010-01-01

    Objective:To screen for the presence of mixed infection with rotavirus. Methods:The present study included 140 children aged less than 2 years with acute diarrhea. Fecal samples of all these patients were analyzed for the presence of astroviral antigen by enzyme immunoassay. Also 40 rotavirus positive fecal samples were screened for the presence of astrovirus. Results:In case of acute diarrhea in children the prevalence of astrovirus was around 34%(48/140). It was seen that even in rotavirus positive cases astrovirus co infection was 25%. Conclusions:Astrovirus is a growing problem which is often underrecognised. With the rotavirus vaccine licensure being imminent astrovirus will emerge out as the single most important cause of viral diarrhea.

  8. Novel Coronaviruses and Astroviruses in Bats

    Institute of Scientific and Technical Information of China (English)

    Daniel K. W. Chu; J. S. Malik Peiris; Leo L. M. Poon

    2009-01-01

    Zoonotic transmissions of emerging pathogens from wildlife to human have shaped the history of mankind. These events have also highlighted our poor understanding of microorganisms circulated in wild animals. Coronaviruses and astroviruses, which can be found from a wide range of mammals, were recently detected in bats. Strikingly, these bat viruses are genetically highly diverse and these interesting findings might help to better understand the evolution and ecology of these viruses. The discoveries of these novel bats viruses not only suggested that bats are important hosts for these virus families, but also reiterated the role of bats as a reservoir of viruses that might pose a zoonotic threat to human health.

  9. Detection of Diverse Novel Bat Astrovirus Sequences in the Czech Republic.

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    Dufkova, Lucie; Straková, Petra; Širmarová, Jana; Salát, Jiří; Moutelíková, Romana; Chrudimský, Tomáš; Bartonička, Tomáš; Nowotny, Norbert; Růžek, Daniel

    2015-08-01

    Astroviruses are a major cause of gastroenteritis in humans and animals. Recently, novel groups of astroviruses were identified in apparently healthy insectivorous bats. We report the detection of diverse novel astrovirus sequences in nine different European bat species: Eptesicus serotinus, Hypsugo savii, Myotis emarginatus, M. mystacinus, Nyctalus noctula, Pipistrellus nathusii or P. pygmaeus, P. pipistrellus, Vespertilio murinus, and Rhinolophus hipposideros. In six bat species, astrovirus sequences were detected for the first time. One astrovirus strain detected in R. hipposideros clustered phylogenetically with Chinese astrovirus strains originating from bats of the families Rhinolophidae and Hipposideridae. All other Czech astrovirus sequences from vesper bats formed, together with one Hungarian sequence, a separate monophyletic lineage within the bat astrovirus group. These findings provide new insights into the molecular epidemiology, ecology, and prevalence of astroviruses in European bat populations. PMID:26273815

  10. Alfalfa dwarf cytorhabdovirus P protein is a local and systemic RNA silencing supressor which inhibits programmed RISC activity and prevents transitive amplification of RNA silencing.

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    Bejerman, Nicolás; Mann, Krin S; Dietzgen, Ralf G

    2016-09-15

    Plants employ RNA silencing as an innate defense mechanism against viruses. As a counter-defense, plant viruses have evolved to express RNA silencing suppressor proteins (RSS), which target one or more steps of the silencing pathway. In this study, we show that the phosphoprotein (P) encoded by the negative-sense RNA virus alfalfa dwarf virus (ADV), a species of the genus Cytorhabdovirus, family Rhabdoviridae, is a suppressor of RNA silencing. ADV P has a relatively weak local RSS activity, and does not prevent siRNA accumulation. On the other hand, ADV P strongly suppresses systemic RNA silencing, but does not interfere with the short-distance spread of silencing, which is consistent with its lack of inhibition of siRNA accumulation. The mechanism of suppression appears to involve ADV P binding to RNA-induced silencing complex proteins AGO1 and AGO4 as shown in protein-protein interaction assays when ectopically expressed. In planta, we demonstrate that ADV P likely functions by inhibiting miRNA-guided AGO1 cleavage and prevents transitive amplification by repressing the production of secondary siRNAs. As recently described for lettuce necrotic yellows cytorhabdovirus P, but in contrast to other viral RSS known to disrupt AGO activity, ADV P sequence does not contain any recognizable GW/WG or F-box motifs, which suggests that cytorhabdovirus P proteins may use alternative motifs to bind to AGO proteins. PMID:27543392

  11. Neurotropic astrovirus in cattle with nonsuppurative encephalitis in Europe.

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    Bouzalas, Ilias G; Wüthrich, Daniel; Walland, Julia; Drögemüller, Cord; Zurbriggen, Andreas; Vandevelde, Marc; Oevermann, Anna; Bruggmann, Rémy; Seuberlich, Torsten

    2014-09-01

    Encephalitis is a frequently diagnosed condition in cattle with neurological diseases. Many affected animals present with a nonsuppurative inflammatory reaction pattern in the brain. While this pattern supports a viral etiology, the causative pathogen remains unknown in a large proportion of cases. Using viral metagenomics, we identified an astrovirus (bovine astrovirus [BoAstV]-CH13) in the brain of a cow with nonsuppurative encephalitis. Additionally, BoAstV RNA was detected with reverse transcription-PCR and in situ hybridization in about one fourth (5/22 animals) of cattle with nonsuppurative encephalitis of unknown etiology. Viral RNA was found primarily in neurons and at the site of pathology. These findings support the notion that BoAstV infection is a common cause of encephalitis in cattle. Phylogenetically, BoAstV-CH13 was closely related to rare astrovirus isolates from encephalitis cases in animals and a human patient. Future research needs to be directed toward the pathogenic mechanisms, epidemiology, and potential cross-species transmission of these neurotropic astroviruses.

  12. Potential Role of Fomites in the Vehicular Transmission of Human Astroviruses

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    Abad, F. Xavier; Villena, Cristina; Guix, Susana; Caballero, Santiago; Pintó, Rosa M.; Bosch, Albert

    2001-01-01

    The persistence of human astroviruses dried on representative porous (paper) and nonporous (china) surfaces was investigated. Long-term astrovirus survival on fomites was monitored by an integrated cell culture-reverse transcription-PCR procedure. Viruses were applied to inanimate surfaces in the presence and absence of fecal material, and their survival was assayed at 4 and 20°C with high relative humidity. Astroviruses exhibited a notable persistence when dried on porous and nonporous mater...

  13. Astrovirus infection in young children with diarrhea hospitalized at Beijing Children's Hospital

    Institute of Scientific and Technical Information of China (English)

    刘春艳; 申昆玲; 王树欣; 刘亚谊; 照日格图

    2004-01-01

    Background This study was to assess certain epidemiological and clinical characteristics of astrovirus infection in children with diarrhea below 5 years old hospitalized at the Beijing Children's Hospital. Methods From September 1999 to August 2001, a total of 288 children with diarrhea below 5 years old hospitalized at Beijing Children's Hospital were studied. Fecal specimens collected from each patient were tested for astrovirus by using enzyme immunoassay (EIA) and further serotyped by reverse-transcription polymerase chain reaction (RT-PCR) using serotype-specific primers. Results Astrovirus antigen was positive in 9.0% of the patients, and the rate of coinfection with rotavirus was 19.2% among the astrovirus positive patients. The patients with astrovirus infection were at the age of 7 days to 17 months, most (92.3%) of them were less than 12 months. Astrovirus infection occurred mainly between October and March of the following year. Main symptoms included watery stool, vomiting, fever, and dehydration. Increased activity of myocardial enzyme was seen in 4 patients. Of the 22 astrovirus positive specimens, 14 were successfully serotyped by RT-PCR and they were all serotype 1. Conclusions The overall incidence of astrovirus infection in young children with diarrhea hospitalized at the Beijing Children's Hospital was 9.0%. The predominant serotype was type 1. Astrovirus may play an important role in viral diarrhea in young children in Beijing, China.

  14. Crystal Structure of the Human Astrovirus Capsid Protein

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    Toh, Yukimatsu; Harper, Justin; Dryden, Kelly A.; Yeager, Mark; Méndez, Ernesto

    2016-01-01

    ABSTRACT Human astrovirus (HAstV) is a leading cause of viral diarrhea in infants and young children worldwide. HAstV is a nonenveloped virus with a T=3 capsid and a positive-sense RNA genome. The capsid protein (CP) of HAstV is synthesized as a 90-kDa precursor (VP90) that can be divided into three linear domains: a conserved N-terminal domain, a hypervariable domain, and an acidic C-terminal domain. Maturation of HAstV requires proteolytic processing of the astrovirus CP both inside and outside the host cell, resulting in the removal of the C-terminal domain and the breakdown of the rest of the CP into three predominant protein species with molecular masses of ∼34, 27/29, and 25/26 kDa, respectively. We have now solved the crystal structure of VP9071–415 (amino acids [aa] 71 to 415 of VP90) of human astrovirus serotype 8 at a 2.15-Å resolution. VP9071–415 encompasses the conserved N-terminal domain of VP90 but lacks the hypervariable domain, which forms the capsid surface spikes. The structure of VP9071–415 is comprised of two domains: an S domain, which adopts the typical jelly-roll β-barrel fold, and a P1 domain, which forms a squashed β-barrel consisting of six antiparallel β-strands similar to what was observed in the hepatitis E virus (HEV) capsid structure. Fitting of the VP9071–415 structure into the cryo-electron microscopy (EM) maps of HAstV produced an atomic model for a continuous, T=3 icosahedral capsid shell. Our pseudoatomic model of the human HAstV capsid shell provides valuable insights into intermolecular interactions required for capsid assembly and trypsin-mediated proteolytic maturation needed for virus infectivity. Such information has potential applications in the development of a virus-like particle (VLP) vaccine as well as small-molecule drugs targeting astrovirus assembly/maturation. IMPORTANCE Human astrovirus (HAstV) is a leading cause of viral diarrhea in infants and young children worldwide. As a nonenveloped virus

  15. Turkey Astrovirus Type 1 (TAstV-1) and Chicken Astrovirus (CAstV) Detection in Brazilian Chicken Flocks.

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    Espinoza, Luis Luna; Beserra, Laila A R; Soares, Rodrigo M; Gregori, Fabio

    2016-09-01

    Astrovirus is a common cause of enteritis in humans and domestic animals. Here we report the detection of turkey astrovirus type 1 (TAstV-1) and chicken astrovirus (CAstV) in avian farms. Sixty fecal sample pools (five or six birds of the same flock), from chickens without apparent clinical symptoms of enteric disease from farms located in six Brazilian states, were screened by an ORF1b PCR, followed by nucleotide sequencing of amplified products and phylogenetic analysis. Six samples tested positive for TAstV-1 and two for CAstV. One positive sample of each detected virus (TAstV-1 and CAstV) had the complete ORF2 sequenced. Data for the ORF2 sequence indicate that Brazilian TAstV-1 was divergent from TAstV-1 (United States), previously described infecting turkeys, and Brazilian CAstV clustered together with the U.K. group, subgroup B-II, associated with enteritis and growth retardation in chicks. This study provides updated information about CAstV and the first report of detection of TAstV-1 in Brazilian chickens, supporting the diagnostic of enteritis and epidemiologic surveillance in poultry health. PMID:27610731

  16. Childhood astrovirus-associated diarrhea in the ambulatory setting in a Public Hospital in Cordoba city, Argentina

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    Giordano Miguel O.

    2004-01-01

    Full Text Available Human astroviruses have been increasingly identified as important agents of diarrheal disease in children. However, the disease burden of astrovirus infection is still incompletely assessed. This paper reports results on the epidemiological and clinical characteristics of astrovirus-associated diarrhea, as well as the impact of astrovirus infection on the ambulatory setting at a Public Hospital in Córdoba city, Argentina. From February 2001 through January 2002, 97 randomly selected outpatient visits for diarrhea among children 0.05. According to our estimation about one out of seventy-four children in this cohort would be assisted annually for an astroviral-diarrheal episode in the Public Hospital and one out of eight diarrheal cases could be attributed to astrovirus infection. Astrovirus is a common symptomatic infection in pediatric outpatient visits in the public hospital in the study area, contributing 12.37% of the overall morbidity from diarrhea.

  17. Full genome analysis of bovine astrovirus from fecal samples of cattle in Japan: identification of possible interspecies transmission of bovine astrovirus.

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    Nagai, Makoto; Omatsu, Tsutomu; Aoki, Hiroshi; Otomaru, Konosuke; Uto, Takehiko; Koizumi, Motoya; Minami-Fukuda, Fujiko; Takai, Hikaru; Murakami, Toshiaki; Masuda, Tsuneyuki; Yamasato, Hiroshi; Shiokawa, Mai; Tsuchiaka, Shinobu; Naoi, Yuki; Sano, Kaori; Okazaki, Sachiko; Katayama, Yukie; Oba, Mami; Furuya, Tetsuya; Shirai, Junsuke; Mizutani, Tetsuya

    2015-10-01

    A viral metagenomics approach was used to investigate fecal samples of Japanese calves with and without diarrhea. Of the different viral pathogens detected, read counts gave nearly complete astrovirus-related RNA sequences in 15 of the 146 fecal samples collected in three distinct areas (Hokkaido, Ishikawa, and Kagoshima Prefectures) between 2009 and 2015. Due to the lack of genetic information about bovine astroviruses (BoAstVs) in Japan, these sequences were analyzed in this study. Nine of the 15 Japanese BoAstVs were closely related to Chinese BoAstVs and clustered into a lineage (tentatively named lineage 1) in all phylogenetic trees. Three of 15 strains were phylogenetically separate from lineage 1, showing low sequence identities, and clustered instead with an American strain isolated from cattle with respiratory disease (tentatively named lineage 2). Interestingly, two of 15 strains clustered with lineage 1 in the open reading frame (ORF)1a and ORF1b regions, while they clustered with lineage 2 in the ORF2 region. Remarkably, one of 15 strains exhibited low amino acid sequence similarity to other BoAstVs and was clustered separately with porcine astrovirus type 5 in all trees, and ovine astrovirus in the ORF2 region, suggesting past interspecies transmission.

  18. Detection of a Novel Bovine Astrovirus in a Cow with Encephalitis.

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    Schlottau, K; Schulze, C; Bilk, S; Hanke, D; Höper, D; Beer, M; Hoffmann, B

    2016-06-01

    Encephalitis can be caused by several infectious agents, including bacteria, fungi, parasites and viruses. In many cases, the causative agent cannot be identified, because the pathogens are unknown or detection methods are not routinely available. In our case, a 15-month-old cow developed central nervous disorders and died within 6 days after the onset of clinical signs. The histopathology revealed an acute encephalitis, predominantly in the brain stem, and a ganglionitis of the trigeminal ganglion with massive neuronal necroses in both the brain and the ganglion. However, a relevant panel of bacterial and viral infections of cattle could be routinely excluded. Therefore, a brain sample from the cow was analysed using a metagenomics approach with next-generation sequencing. A novel bovine astrovirus (BoAstV-BH89/14) could be identified using the analysis pipeline RIEMS, and the finding could be confirmed with a specific BoAstV RT-qPCR. The genome of the bovine astrovirus (BoAstV), belonging to the family Astroviridae in the genus Mamastrovirus, has a length of 6478 bp. Sequence identities between 71% to a sheep astrovirus and 69% to two recently described bovine astroviruses from the USA and Switzerland were ascertained. The latter were also connected to encephalitis cases in cattle. Like these, the new virus described here was detected in different brain sections using the specific BoAstV RT-qPCR and fluorescent in situ hybridization. In conclusion, while astroviruses so far were mainly found in relation to gastroenteritis in animals and humans, recently detected astrovirus infections were also related to encephalitis. PMID:26948516

  19. Detection of a mammalian-like astrovirus in bird, European roller (Coracias garrulus).

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    Pankovics, Péter; Boros, Ákos; Kiss, Tamás; Delwart, Eric; Reuter, Gábor

    2015-08-01

    Astroviruses are small, non-enveloped viruses with positive sense, single-stranded RNA genomes. The family Astroviridae contains two genera, Mamastrovirus and Avastrovirus, which – based upon our current knowledge – infect mammals and birds, respectively. However, recent seroprevalence study indicated that people with contact to turkeys can develop serological responses to the turkey astrovirus and minks might have been infected with the avastrovirus. These data suggest that the "host species/astrovirus genus" association should be permeable; however, mamastrovirus infection has not been reported from avian species, yet. In this study, a novel astrovirus was identified by viral metagenomics and RT-PCR methods in 2 (11%) out of 19 faecal samples collected from a wild, carnivorous bird species, European rollers (Coracias garrulus) from two breeding territories in Hungary. The complete genome sequence of astrovirus Er/SZAL6/HUN/2011 (KP663426) was 7025 nt-long and had some unique genomic features including an unusually long spacer between the subgenomic RNA promoter and the ORF2 initiation codon. Using the BLASTp Er/SZAL6/HUN/2011 had the highest aa identities 35%, 61% and 34% to MAstV 32 (JF713710, host: porcine), to MAstV 23 (JF729316, host: rabbit) and to unclassified porcine astrovirus (JX684071) in ORF1a, ORF1b and ORF2, respectively. The same proteins of Er/SZAL6/HUN/2011 had 25%, 66% and 33% aa identities to the corresponding proteins of murine astrovirus (JX544743) as the closest strain. The sequence- and phylogenetic analysis indicated that Er/SZAL6/HUN/2011 represents the first member of a novel mamastrovirus species. Data suggest that both mammals and birds could have been exposed to mamastroviruses and avastroviruses providing opportunities for cross-species infection and viral adaptation with cross-class astroviruses especially in carnivorous animals. Further investigation is needed to determine the origin, natural host species spectrum, distribution

  20. Molecular characterization of a novel astrovirus associated with disease in mink

    DEFF Research Database (Denmark)

    Mittelholzer, C.; Hedlund, K.O.; Englund, L.;

    2003-01-01

    . In this report, the molecular characterization, origin and evolution of this novel astrovirus of mink are discussed. The polyadenylated, positive-stranded RNA genome was sequenced and found to contain 6610 nt, organized into three ORFs and two short UTRs. A ribosomal frameshift sequence links the 5' two ORFs...

  1. Astrovirus infection in children living in the Central West region of Brazil

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    Rodrigo Alessandro Tôgo Santos

    2007-03-01

    Full Text Available This study presents data regarding the circulation of astrovirus in Goiânia-GO and Brasília-DF. These viruses were detected in fecal samples from hospitalized children up to five years old with and without acute gastroenteritis. A total of 1244 fecal samples were collected in two periods, 1994 to 1996 (Brasília and 1998 to 2002 (Goiânia and Brasília, and were analyzed for viral RNA using the reverse transcription-polymerase chain reaction (RT-PCR. Positivity rates of 4.3 and 0.5% for astrovirus were observed in children with acute gastroenteritis and those without gastroenteritis, respectively. Among children with gastroenteritis no statistically significant difference was seen with regards to viral positivity rates in relation to gender and age. However, a higher incidence rate was observed for children from Brasília aged 36 months or more. Overall, astroviruses occurred predominantly from September to March in the two cities, suggesting a seasonal pattern for these viruses which coincides with the highest relative air humidity period. The results of this study highlight the importance of astrovirus as an etiologic agent of acute gastroenteritis in children of the Central West region of Brazil.

  2. Population-Based Incidence Rates of Diarrheal Disease Associated with Norovirus, Sapovirus, and Astrovirus in Kenya

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    Shioda, Kayoko; Cosmas, Leonard; Audi, Allan; Gregoricus, Nicole; Vinjé, Jan; Parashar, Umesh D.; Montgomery, Joel M.; Feikin, Daniel R.; Breiman, Robert F.; Hall, Aron J.

    2016-01-01

    Background Diarrheal diseases remain a major cause of mortality in Africa and worldwide. While the burden of rotavirus is well described, population-based rates of disease caused by norovirus, sapovirus, and astrovirus are lacking, particularly in developing countries. Methods Data on diarrhea cases were collected through a population-based surveillance platform including healthcare encounters and household visits in Kenya. We analyzed data from June 2007 to October 2008 in Lwak, a rural site in western Kenya, and from October 2006 to February 2009 in Kibera, an urban slum. Stool specimens from diarrhea cases of all ages who visited study clinics were tested for norovirus, sapovirus, and astrovirus by RT-PCR. Results Of 334 stool specimens from Lwak and 524 from Kibera, 85 (25%) and 159 (30%) were positive for norovirus, 13 (4%) and 31 (6%) for sapovirus, and 28 (8%) and 18 (3%) for astrovirus, respectively. Among norovirus-positive specimens, genogroup II predominated in both sites, detected in 74 (87%) in Lwak and 140 (88%) in Kibera. The adjusted community incidence per 100,000 person-years was the highest for norovirus (Lwak: 9,635; Kibera: 4,116), followed by astrovirus (Lwak: 3,051; Kibera: 440) and sapovirus (Lwak: 1,445; Kibera: 879). For all viruses, the adjusted incidence was higher among children aged <5 years (norovirus: 22,225 in Lwak and 17,511 in Kibera; sapovirus: 5,556 in Lwak and 4,378 in Kibera; astrovirus: 11,113 in Lwak and 2,814 in Kibera) compared to cases aged ≥5 years. Conclusion Although limited by a lack of controls, this is the first study to estimate the outpatient and community incidence rates of norovirus, sapovirus, and astrovirus across the age spectrum in Kenya, suggesting a substantial disease burden imposed by these viruses. By applying adjusted rates, we estimate approximately 2.8–3.3 million, 0.45–0.54 million, and 0.77–0.95 million people become ill with norovirus, sapovirus, and astrovirus, respectively, every year in

  3. Population-Based Incidence Rates of Diarrheal Disease Associated with Norovirus, Sapovirus, and Astrovirus in Kenya.

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    Kayoko Shioda

    Full Text Available Diarrheal diseases remain a major cause of mortality in Africa and worldwide. While the burden of rotavirus is well described, population-based rates of disease caused by norovirus, sapovirus, and astrovirus are lacking, particularly in developing countries.Data on diarrhea cases were collected through a population-based surveillance platform including healthcare encounters and household visits in Kenya. We analyzed data from June 2007 to October 2008 in Lwak, a rural site in western Kenya, and from October 2006 to February 2009 in Kibera, an urban slum. Stool specimens from diarrhea cases of all ages who visited study clinics were tested for norovirus, sapovirus, and astrovirus by RT-PCR.Of 334 stool specimens from Lwak and 524 from Kibera, 85 (25% and 159 (30% were positive for norovirus, 13 (4% and 31 (6% for sapovirus, and 28 (8% and 18 (3% for astrovirus, respectively. Among norovirus-positive specimens, genogroup II predominated in both sites, detected in 74 (87% in Lwak and 140 (88% in Kibera. The adjusted community incidence per 100,000 person-years was the highest for norovirus (Lwak: 9,635; Kibera: 4,116, followed by astrovirus (Lwak: 3,051; Kibera: 440 and sapovirus (Lwak: 1,445; Kibera: 879. For all viruses, the adjusted incidence was higher among children aged <5 years (norovirus: 22,225 in Lwak and 17,511 in Kibera; sapovirus: 5,556 in Lwak and 4,378 in Kibera; astrovirus: 11,113 in Lwak and 2,814 in Kibera compared to cases aged ≥5 years.Although limited by a lack of controls, this is the first study to estimate the outpatient and community incidence rates of norovirus, sapovirus, and astrovirus across the age spectrum in Kenya, suggesting a substantial disease burden imposed by these viruses. By applying adjusted rates, we estimate approximately 2.8-3.3 million, 0.45-0.54 million, and 0.77-0.95 million people become ill with norovirus, sapovirus, and astrovirus, respectively, every year in Kenya.

  4. Different rates of (non-synonymous mutations in astrovirus genes; correlation with gene function

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    Berkhout Ben

    2007-03-01

    Full Text Available Abstract Background Complete genome sequences of the Astroviridae include human, non-human mammalian and avian species. A consensus topology of astroviruses has been derived from nucleotide substitutions in the full-length genomes and from non-synonymous nucleotide substitutions in each of the three ORFs. Analyses of synonymous substitutions displayed a loss of tree structure, suggesting either saturation of the substitution model or a deviant pattern of synonymous substitutions in certain virus species. Results We analyzed the complete Astroviridae family for the inference of adaptive molecular evolution at sites and in branches. High rates of synonymous mutations are observed among the non-human virus species. Deviant patterns of synonymous substitutions are found in the capsid structural genes. Purifying selection is a dominant force among all astrovirus genes and only few codon sites showed values for the dN/dS ratio that may indicate site-specific molecular adaptation during virus evolution. One of these sites is the glycine residue of a RGD motif in ORF2 of human astrovirus serotype 1. RGD or similar integrin recognition motifs are present in nearly all astrovirus species. Conclusion Phylogenetic analysis directed by maximum likelihood approximation allows the inclusion of significantly more evolutionary history and thereby, improves the estimation of dN and dS. Sites with enhanced values for dN/dS are prominent at domains in charge of environmental communication (f.i. VP27 and domain 4 in ORF1a more than at domains dedicated to intrinsic virus functions (f.i. VP34 and ORF1b (the virus polymerase. Integrin recognition may play a key role in astrovirus to target cell attachment.

  5. Reseanh Advance in Human Astrovirus%人星状病毒研究进展

    Institute of Scientific and Technical Information of China (English)

    王永霞; 段招军; 李宇宁

    2012-01-01

    Human astroviruses have been recognized as one of the important causes of viral gastroenteritis in infants and young children. In the present work, we reviewed the progress of astrovirus infections in humans, focusing on the serotypes molecular biological, characteristics of disease, pathogenic mechanism, epidemiology and detection methods, and concluded that there were multiple astroviruses circulating in the world, and several novel astroviruses were discovered in recent years. Human astrovirus 1 was the most prevailing serotype. Which caused intestinal and parenteral infections, and the characteristics of infections were similar to other diarrheal viruses. However, the pathogenic mechanism remained unknown. Only limited data was available about the correlation between the novel astroviruses and diseases, and the laboratory detection methods needed to be established.%人星状病毒是引起婴幼儿病毒性腹泻的重要病原之一,本文回顾了其分子生物学特征、型别、所致疾病特征、致病机制、流行病学特征及检测方法等方面的文献,指出人星状病毒目前存在多种型别,尤其是近年来发现了多种新型的星状病毒,主要的流行型别是血清型1型,不仅引起肠道内感染,还可以引起其他系统疾病,所致疾病特征和其他腹泻相关病毒相似,但是其致病机制的研究尚不清楚,对于几种新发现的星状病毒,其与疾病的相关性研究较少,且未建立完善的实验室检测方法,还需要进一步的研究.

  6. Prevalence of Rotavirus, Adenovirus, and Astrovirus Infections Among Patients with Acute Gastroenteritis in, Northern Iran

    OpenAIRE

    R Savad-Koohi; A Pakfetrat; AA Poor-Babaei; S Vaziri; L Adibi; Jalilvand, S; K Nourijelyani; Noroozi, M.; Y Yahyapour; Hamkar, R

    2010-01-01

    Background: The aim of the study was to determine the incidence of non-bacterial acute gastroenteritis associated with diarrheal diseases in Mazandaran Province, northern Iran. Methods: A total of 400 symptomatic cases from patients with acute gastroenteritis from Mazandaran Province in Iran were screened using EIA method for the presence of rotavirus, adenovirus and astrovirus during 2005–2006. Chi-square tests were used for testing relationships between different variables. Results: Rotavir...

  7. Molecular detection of human astrovirus in an urban sewage treatment plant in Rio de Janeiro, Brazil

    OpenAIRE

    Flávia Ramos Guimarães; Fabiana Fioretti Martins Ferreira; Carmen Baur Vieira; Tulio Machado Fumian; Tatsuo Shubo; José Paulo Gagliardi Leite; Marize Pereira Miagostovich

    2008-01-01

    The objective of this study was to evaluate the prevalence and dissemination of human astroviruses (HAstV) in the environment by analyzing urban sewage samples from a wastewater treatment plant in the city of Rio de Janeiro, Brazil. A one-year study was performed with a total of 48 raw and treated sewage composite samples, which were collected biweekly from an activated sludge plant. Virus particles were concentrated by the adsorption-elution method using negatively charged membranes associat...

  8. Non-Human Primates Harbor Diverse Mammalian and Avian Astroviruses Including Those Associated with Human Infections.

    Directory of Open Access Journals (Sweden)

    Erik A Karlsson

    Full Text Available Astroviruses (AstVs are positive sense, single-stranded RNA viruses transmitted to a wide range of hosts via the fecal-oral route. The number of AstV-infected animal hosts has rapidly expanded in recent years with many more likely to be discovered because of the advances in viral surveillance and next generation sequencing. Yet no study to date has identified human AstV genotypes in animals, although diverse AstV genotypes similar to animal-origin viruses have been found in children with diarrhea and in one instance of encephalitis. Here we provide important new evidence that non-human primates (NHP can harbor a wide variety of mammalian and avian AstV genotypes, including those only associated with human infection. Serological analyses confirmed that >25% of the NHP tested had antibodies to human AstVs. Further, we identified a recombinant AstV with parental relationships to known human AstVs. Phylogenetic analysis suggests AstVs in NHP are on average evolutionarily much closer to AstVs from other animals than are AstVs from bats, a frequently proposed reservoir. Our studies not only demonstrate that human astroviruses can be detected in NHP but also suggest that NHP are unique in their ability to support diverse AstV genotypes, further challenging the paradigm that astrovirus infection is species-specific.

  9. Adenovirus, calicivirus and astrovirus detection in fecal samples of hospitalized children with acute gastroenteritis from Campo Grande, MS, Brazil

    Directory of Open Access Journals (Sweden)

    Marcia Sueli Assis Andreasi

    2008-11-01

    Full Text Available We analyzed fecal samples from hospitalized children up to three years of age with acute gastroenteritis at Campo Grande, Mato Grosso do Sul, Brazil, from May 2000-January 2004. Astrovirus and calicivirus were detected by Reverse Transcription-Polymerase Chain Reaction and adenovirus was detected using the Rotavirus and Adenovirus combined immunoenzyme assay. Astrovirus, adenovirus and calicivirus were detected at rates of 3.1%, 3.6% and 7.6%, respectively. These results re-emphasize the need for the establishment of regional vigilance systems to evaluate the impact of enteric viruses on viral gastroenteritis.

  10. Astrovirus infection in children living in the Central West region of Brazil

    OpenAIRE

    Rodrigo Alessandro Tôgo Santos; Ana Maria Tavares Borges; Paulo Sérgio Sucasas da Costa; José Marcus Sócrates Teixeira; Loreny Gimenes Giugliano; José Paulo Gagliardi Leite; Divina das Dôres de Paula Cardoso

    2007-01-01

    This study presents data regarding the circulation of astrovirus in Goiânia-GO and Brasília-DF. These viruses were detected in fecal samples from hospitalized children up to five years old with and without acute gastroenteritis. A total of 1244 fecal samples were collected in two periods, 1994 to 1996 (Brasília) and 1998 to 2002 (Goiânia and Brasília), and were analyzed for viral RNA using the reverse transcription-polymerase chain reaction (RT-PCR). Positivity rates of 4.3 and 0.5% for astro...

  11. Insectivorous bats carry host specific astroviruses and coronaviruses across different regions in Germany.

    Science.gov (United States)

    Fischer, Kerstin; Zeus, Veronika; Kwasnitschka, Linda; Kerth, Gerald; Haase, Martin; Groschup, Martin H; Balkema-Buschmann, Anne

    2016-01-01

    Recently several infectious agents with a zoonotic potential have been detected in different bat species. However, there is still a lack of knowledge on the transmission dynamics within and between bat species, as well as from bats to other mammals. To better understand these processes, it is important to compare the phylogenetic relationships between different agents to that of their respective hosts. In this study, we analysed more than 950 urine, faeces and oral swab samples collected from 653 bats from mainly four species (Myotis nattereri, Myotis bechsteinii, Myotis daubentonii, and Plecotus auritus) for the presence of coronavirus, paramyxovirus and astrovirus related nucleic acids located in three different regions of Germany. Using hemi-nested reverse transcriptase (RT)-PCR amplification of fragments within the highly conserved regions of the respective RNA dependent RNA polymerase (RdRp) genes, we detected astrovirus sequences at an overall detection rate of 25.8% of the analysed animals, with a maximum of 65% in local populations. The detection rates for coronaviruses and paramyxoviruses were distinctly lower, ranging between 1.4% and 3.1%. Interestingly, the sequence similarities in samples collected from the same bat species in different geographical areas were distinctly larger than the sequence similarities between samples from different species sampled at the same location. This indicates that host specificity may be more important than host ecology for the presence of certain viruses in bats.

  12. Nearly full-length genome sequence of a novel astrovirus isolated from chickens with 'white chicks' condition.

    Science.gov (United States)

    Sajewicz-Krukowska, Joanna; Domanska-Blicharz, Katarzyna

    2016-09-01

    Avian astroviruses (aAstVs) are divided into three species, Avastrovirus 1, Avastrovirus 2, and Avastrovirus 3, but there are a few strains are waiting to be assigned to an official taxonomic group. This study presents the molecular characterization of chicken astrovirus (CAstV), PL/G059/2014, which is involved in the induction of "white chicks" condition. The 7382-nucleotide-long genome sequence was determined by next-generation sequencing using an Illumina MiSeq System. Phylogenetic analysis showed that it has the characteristics that are typical of avian astroviruses. However, overall degree of nucleotide sequence identity was 43.6 % to 73.7 % between PL/G059/2014 and other available genome sequences of aAstV strains. The amino acid sequences of the proteins encoded by ORF1a and ORF1b of the studied strain were very similar (86.5-93.8 % identity) to those of CAstVs 4175 and GA2011, but they were only 32.7-35.2 % identical in the case of ORF2, which is used officially for astrovirus species demarcation. These features could suggest that the PL/G059/2014 strain should be assigned to a new species in the genus Avastrovirus. Moreover, the different phylogenetic topology of PL/G059/2014 and its nucleotide sequence similarity in different genomic regions could suggest that a recombination event occurred during its evolution and that it has ancestors in common with duck astroviruses. PMID:27339687

  13. Astrovirus infection in hospitalized infants with severe combined immunodeficiency after allogeneic hematopoietic stem cell transplantation.

    Directory of Open Access Journals (Sweden)

    Werner Wunderli

    Full Text Available Infants with severe primary combined immunodeficiency (SCID and children post-allogeneic hematopoietic stem cell transplantation (HSCT are extremely susceptible to unusual infections. The lack of generic tools to detect disease-causing viruses among more than 200 potential human viral pathogens represents a major challenge to clinicians and virologists. We investigated retrospectively the causes of a fatal disseminated viral infection with meningoencephalitis in an infant with gamma C-SCID and of chronic gastroenteritis in 2 other infants admitted for HSCT during the same time period. Analysis was undertaken by combining cell culture, electron microscopy and sequence-independent single primer amplification (SISPA techniques. Caco-2 cells inoculated with fecal samples developed a cytopathic effect and non-enveloped viral particles in infected cells were detected by electron microscopy. SISPA led to the identification of astrovirus as the pathogen. Both sequencing of the capsid gene and the pattern of infection suggested nosocomial transmission from a chronically excreting index case to 2 other patients leading to fatal infection in 1 and to transient disease in the others. Virus-specific, real-time reverse transcription polymerase chain reaction was then performed on different stored samples to assess the extent of infection. Infection was associated with viremia in 2 cases and contributed to death in 1. At autopsy, viral RNA was detected in the brain and different other organs, while immunochemistry confirmed infection of gastrointestinal tissues. This report illustrates the usefulness of the combined use of classical virology procedures and modern molecular tools for the diagnosis of unexpected infections. It illustrates that astrovirus has the potential to cause severe disseminated lethal infection in highly immunocompromised pediatric patients.

  14. Molecular epidemiology and phylogenetic analysis of diverse bovine astroviruses associated with diarrhea in cattle and water buffalo calves in China.

    Science.gov (United States)

    Alfred, Niyokwishimira; Liu, Huan; Li, Mu Lan; Hong, Shao Feng; Tang, Hai Bo; Wei, Zu Zhang; Chen, Ying; Li, Fa Kai; Zhong, Yi Zhi; Huang, Wei Jian

    2015-06-01

    Astroviruses are the principal causative agents of gastroenteritis in humans and have been associated with diarrhea in other mammals as well as birds. However, astroviral infection of animals had been poorly studied. In the present study, 211 rectal swabs collected from cattle and water buffalo calves with mild to severe diarrhea were tested for bovine astrovirus (BAstV) by RT-PCR. Results: 92/211 (43.6%) samples were positive for BAstV, at a rate of 46.10% (71/154) in cattle and 36.84% (21/57) in water buffalo. Phylogenetic analysis based on the partial and full-length of 25 ORF2 amino acid sequences obtained in this study classified the Guangxi BAstVs isolates into five subgroups under the genus of Mamastrovirus, genotype MAstV33, which suggested that the water buffalo was a new host of this genogroup that previously included only cattle and roe deer. Despite the origin of the host, the Guangxi BAstV isolates were closely related to the BAstV Hong Kong isolates (B18/HK and B76-2/HK), but highly divergent from the BAstV NeuroS1 isolate previously associated with neurologic disease in cattle in the U.S.A. Nucleotide sequence-based characterization of the ORF1b/ORF2 junction and corresponding overlapping regions showed distinctive properties, which may be common to BAstVs. Our results suggested that cattle and water buffalo are prone to infection of closely related astroviruses, which probably evolved from the same ancestor. The current study described astroviruses in water buffalo for the first time and is thus far among the largest epidemiological investigations of BAstV infection in cattle conducted in China.

  15. [Construction and expression of six deletion mutants of human astrovirus C-terminal nsP1a/4 protein].

    Science.gov (United States)

    Zhao, Wei; Niu, Ke; Zhao, Jian; Jin, Yi-ming; Sui, Ting-ting; Wang, Wen

    2013-09-01

    Human astrovirus (HAstV) is one of the leading causes of actue virual diarrhea in infants. HAstV-induced epithdlial cell apoptosis plays an important role in the pathogenesis of HAstV infection. Our previous study indicated that HAstV non-structural protein nsPla C-terminal protein nsPla/4 was the major apoptosis functional protein and probably contained the main apoptosis domains. In order to screen for astrovirus encoded apoptotic protien, nsPla/4 and six turncated proteins, which possessed nsPla/4 protein different function domain ,were cloned into green fluorescent protein (GFP) vector pEG-FP-N3. After 24-72 h transfection, the fusion protein expression in BHK21 cells, was analysis by fluorescence microscope and Western blot. The results indicated seven fusion proteins were observed successfully in BHK21 cell after transfected for 24 h. Western blot analysis showed that the level of fusion protein expressed in BHK21 cells was increased significantly at 72h compared to 48h in transfected cells. The successful expression of deletion mutants of nsPla/4 protein was an important foundation to gain further insights into the function of apoptosis domains of nsPla/4 protein and it would also provide research platform to further confirm the molecule pathogenic mechanism of human astrovirus. PMID:24386845

  16. [Construction and expression of six deletion mutants of human astrovirus C-terminal nsP1a/4 protein].

    Science.gov (United States)

    Zhao, Wei; Niu, Ke; Zhao, Jian; Jin, Yi-ming; Sui, Ting-ting; Wang, Wen

    2013-09-01

    Human astrovirus (HAstV) is one of the leading causes of actue virual diarrhea in infants. HAstV-induced epithdlial cell apoptosis plays an important role in the pathogenesis of HAstV infection. Our previous study indicated that HAstV non-structural protein nsPla C-terminal protein nsPla/4 was the major apoptosis functional protein and probably contained the main apoptosis domains. In order to screen for astrovirus encoded apoptotic protien, nsPla/4 and six turncated proteins, which possessed nsPla/4 protein different function domain ,were cloned into green fluorescent protein (GFP) vector pEG-FP-N3. After 24-72 h transfection, the fusion protein expression in BHK21 cells, was analysis by fluorescence microscope and Western blot. The results indicated seven fusion proteins were observed successfully in BHK21 cell after transfected for 24 h. Western blot analysis showed that the level of fusion protein expressed in BHK21 cells was increased significantly at 72h compared to 48h in transfected cells. The successful expression of deletion mutants of nsPla/4 protein was an important foundation to gain further insights into the function of apoptosis domains of nsPla/4 protein and it would also provide research platform to further confirm the molecule pathogenic mechanism of human astrovirus.

  17. Identification of an astrovirus commonly infecting laboratory mice in the US and Japan.

    Science.gov (United States)

    Ng, Terry Fei Fan; Kondov, Nikola O; Hayashimoto, Nobuhito; Uchida, Ritsuki; Cha, Yunhee; Beyer, Ashley I; Wong, Walt; Pesavento, Patricia A; Suemizu, Hiroshi; Muench, Marcus O; Delwart, Eric

    2013-01-01

    Mice (Mus musculus) are the most commonly used laboratory animals. Viral metagenomics on tissues of immunodeficient mice revealed sequences of a novel mammalian astrovirus. Using PCR, we screened mice from 4 breeders, 4 pharmaceutical companies, 14 research institutes and 30 universities in the US and Japan. Mice from one US breeder tested positive while none from Japanese breeders were positive for MuAstV. Mice in over half of the universities (19/30), institutes (7/14) and pharmaceutical animal facilities (2/4) investigated revealed the presence of MuAstV. Nine mice strains tested positive including both immunodeficient strains (NSG, NOD-SCID, NSG-3GS, C57BL6-Timp-3 (-/-), and uPA-NOG) and immunocompetent strains (B6J, ICR, Bash2, BALB/c). Our data indicates that MuAstV has a wide geographical, institutional and host strain distribution. Comparison of the MuAstV RdRp sequences showed numerous mutations indicating ongoing viral divergence in different facilities. This study demonstrates the need for metagenomic screening of laboratory animals to identify adventitious infections that may affect experimental outcomes.

  18. Molecular detection of human astrovirus in an urban sewage treatment plant in Rio de Janeiro, Brazil

    Directory of Open Access Journals (Sweden)

    Flávia Ramos Guimarães

    2008-12-01

    Full Text Available The objective of this study was to evaluate the prevalence and dissemination of human astroviruses (HAstV in the environment by analyzing urban sewage samples from a wastewater treatment plant in the city of Rio de Janeiro, Brazil. A one-year study was performed with a total of 48 raw and treated sewage composite samples, which were collected biweekly from an activated sludge plant. Virus particles were concentrated by the adsorption-elution method using negatively charged membranes associated to a Centriprep Concentrator® 50 (Nihon Millipore. HAstV were detected in 16.7% of the samples in raw and treated sewage by using both qualitative and quantitative reverse transcriptase-polymerase chain reactions (RT-PCR and qPCR, respectively. Positive untreated sewage sample exhibited mean values of 1.1 x 10(4 gEq/mL. The qPCR sensitivity was 18 gEq/reaction. Through utilization of qPCR, a HAstV recovery efficiency of 4.2% and 4.3% was demonstrated for raw and treated sewage samples, respectively. The presence of HAstV in both the raw and treated sewage samples demonstrated the dissemination of these viruses in the environment as well as viral permanence after sewage treatment. There was a reduction in the total and faecal coliform levels, indicating efficiency of the wastewater treatment plant.

  19. Identification of an astrovirus commonly infecting laboratory mice in the US and Japan.

    Directory of Open Access Journals (Sweden)

    Terry Fei Fan Ng

    Full Text Available Mice (Mus musculus are the most commonly used laboratory animals. Viral metagenomics on tissues of immunodeficient mice revealed sequences of a novel mammalian astrovirus. Using PCR, we screened mice from 4 breeders, 4 pharmaceutical companies, 14 research institutes and 30 universities in the US and Japan. Mice from one US breeder tested positive while none from Japanese breeders were positive for MuAstV. Mice in over half of the universities (19/30, institutes (7/14 and pharmaceutical animal facilities (2/4 investigated revealed the presence of MuAstV. Nine mice strains tested positive including both immunodeficient strains (NSG, NOD-SCID, NSG-3GS, C57BL6-Timp-3 (-/-, and uPA-NOG and immunocompetent strains (B6J, ICR, Bash2, BALB/c. Our data indicates that MuAstV has a wide geographical, institutional and host strain distribution. Comparison of the MuAstV RdRp sequences showed numerous mutations indicating ongoing viral divergence in different facilities. This study demonstrates the need for metagenomic screening of laboratory animals to identify adventitious infections that may affect experimental outcomes.

  20. Association of the Astrovirus Structural Protein VP90 with Membranes Plays a Role in Virus Morphogenesis▿

    Science.gov (United States)

    Méndez, Ernesto; Aguirre-Crespo, Gabriela; Zavala, Guadalupe; Arias, Carlos F.

    2007-01-01

    VP90, the capsid polyprotein precursor of human astrovirus Yuc8, is assembled into viral particles, and its processing at the carboxy terminus by cellular caspases, to yield VP70, has been correlated with the cell release of the virus. Here, we characterized the effect of the VP90-VP70 processing on the properties of these proteins, as well as on their intracellular distribution. VP90 was found in membrane-enriched fractions (mVP90), as well as in fractions enriched in cytosolic proteins (cVP90), while VP70 was found exclusively in the latter fractions. Upon trypsin activation, infectivity was detected in all VP90-containing fractions, confirming that both mVP90 and cVP90 are able to assemble into particles; however, the two forms of VP90 showed differential sensitivities to trypsin, especially at their carboxy termini, which in the case of mVP90 was shown to remain membrane associated after protease digestion. Structural protein oligomers were detected in purified VP70-containing viruses, as well as in membrane-enriched fractions, but they were less evident in cytosolic fractions. Ultrastructural studies of infected cells revealed different types of viral particles, some of which appeared to be associated with membranes. By immunoelectron microscopy, structural proteins were shown to form virus particles in clusters and to associate with the edges of vesicles induced during infection, which also appear to contain subviral particles inside. Nonstructural proteins and viral RNA colocalized with mVP90, but not with cVP90, suggesting that mVP90 might represent the form of the protein that is initially assembled into particles, at the sites where the virus genome is being replicated. PMID:17652389

  1. Serological studies confirm the novel astrovirus HMOAstV-C as a highly prevalent human infectious agent.

    Directory of Open Access Journals (Sweden)

    Peter D Burbelo

    Full Text Available Molecular identification of a microbe is the first step in determining its prevalence of infection and pathogenic potential. Detection of specific adaptive immune responses can provide insights into whether a microbe is a human infectious agent and its epidemiology. Here we characterized human anti-IgG antibody responses by luciferase immunoprecipitation systems (LIPS against two protein fragments derived from the capsid protein of the novel HMOAstV-C astrovirus. While antibodies to the N-terminal fragment were not informative, the C-terminal capsid fragment of HMOAstV-C showed a high frequency of immunoreactivity with serum from healthy blood donors. In contrast, a similar C-terminal capsid fragment from the related HMOAstV-A astrovirus failed to show immunoreactivity. Detailed analysis of adult serum from the United Sates using a standardized threshold demonstrated HMOAstV-C seropositivity in approximately 65% of the samples. Evaluation of serum samples from different pediatric age groups revealed that the prevalence of antibodies in 6-12 month, 1-2 year, 2-5 year and 5-10 year olds was 20%, 23%, 32% and 36%, respectively, indicating rising seroprevalence with age. Additionally, 50% (11/22 of the 0-6 month old children showed anti-HMOAstV-C antibody responses, likely reflecting maternal antibodies. Together these results document human humoral responses to HMOAstV-C and validate LIPS as a facile and effective approach for identifying humoral responses to novel infectious agents.

  2. Establishment of Stably Transfected Cells Constitutively Expressing the Full-Length and Truncated Antigenic Proteins of Two Genetically Distinct Mink Astroviruses

    DEFF Research Database (Denmark)

    Bidokhti, Mehdi R. M.; Ullman, Karin; Jensen, Trine Hammer;

    2013-01-01

    to circumvent this drawback, we have developed stably transfected mink fetal cells and BHK21 cells constitutively expressing the full-length and truncated capsid proteins of two distinct genotypes of mink astrovirus. Protein expression in these stably transfected cells was demonstrated by strong signals...

  3. Prevalence of group a rotavirus, enteric adenovirus, norovirus and astrovirus infections among children with acute gastroenteritis in al-qassim, saudi arabia

    International Nuclear Information System (INIS)

    To investigate the prevalence of Rotavirus, Adenovirus, Norovirus, and Astrovirus among Saudi children with gastroenteritis. This study was conducted at the Department of Medical Laboratories, Qassim University during the winter seasons of the years 2004 and 2005. A total of 284 diarrhoeal fecal specimens collected from children were tested for the gastroenteritis causing viruses using enzyme immunoassay. Of the 284 specimens, 142 (50%) were found to be positive for viruses causing gastroenteritis. Rotavirus (66.2%) was the most frequently detected, followed by adenovirus (15.5%), norovirus and astrovirus each with 9.2%. All of rotavirus detected belonged to group A. Eight specimens were found positive by two viruses. The introduction of simple and rapid tests for diagnosis of viruses causing gastroenteritis in our pediatric hospitals will improve patient care by reducing unnecessary treatments and hospital stay for patients. (author)

  4. Development and evaluation of two subunit vaccine candidates containing antigens of hepatitis E virus, rotavirus, and astrovirus

    Science.gov (United States)

    Xia, Ming; Wei, Chao; Wang, Leyi; Cao, Dianjun; Meng, Xiang-Jin; Jiang, Xi; Tan, Ming

    2016-01-01

    Hepatitis E virus (HEV), rotavirus (RV), and astrovirus (AstV) are important pathogens that transmit through a common fecal-oral route, causing hepatitis (HEV) and gastroenteritis (RV and AstV) respectively in humans. In this study, we developed and evaluated two subunit vaccine candidates that consisted of the same protruding or spike protein antigens of the three viruses in two formats, a fusion of the three antigens into one molecule (fused vaccine) vs. a mixture of the three free antigens together (mixed vaccine). Both vaccines were easily made via E. coli expression system. Mouse immunization experiments showed that the fused vaccine elicited significantly higher antibody responses against the three viral antigens than those induced by the mixed vaccine. In addition, the mouse post-immune antisera of the fused vaccine revealed significantly higher neutralizing titers against HEV infection in cell culture, as well as significantly higher 50% blocking titers (BT50) against RV VP8-HBGA receptor interactions than those of the post-immune antisera after immunization of the mixed vaccine. Thus, the fused vaccine is a promising trivalent vaccine candidate against HEV, RV, and AstV, which is worth for further development. PMID:27194006

  5. Development and evaluation of two subunit vaccine candidates containing antigens of hepatitis E virus, rotavirus, and astrovirus.

    Science.gov (United States)

    Xia, Ming; Wei, Chao; Wang, Leyi; Cao, Dianjun; Meng, Xiang-Jin; Jiang, Xi; Tan, Ming

    2016-01-01

    Hepatitis E virus (HEV), rotavirus (RV), and astrovirus (AstV) are important pathogens that transmit through a common fecal-oral route, causing hepatitis (HEV) and gastroenteritis (RV and AstV) respectively in humans. In this study, we developed and evaluated two subunit vaccine candidates that consisted of the same protruding or spike protein antigens of the three viruses in two formats, a fusion of the three antigens into one molecule (fused vaccine) vs. a mixture of the three free antigens together (mixed vaccine). Both vaccines were easily made via E. coli expression system. Mouse immunization experiments showed that the fused vaccine elicited significantly higher antibody responses against the three viral antigens than those induced by the mixed vaccine. In addition, the mouse post-immune antisera of the fused vaccine revealed significantly higher neutralizing titers against HEV infection in cell culture, as well as significantly higher 50% blocking titers (BT50) against RV VP8-HBGA receptor interactions than those of the post-immune antisera after immunization of the mixed vaccine. Thus, the fused vaccine is a promising trivalent vaccine candidate against HEV, RV, and AstV, which is worth for further development. PMID:27194006

  6. An outbreak of gastroenteritis associated with astrovirus serotype 1 in a day care center, in Rio de Janeiro, Brazil

    Directory of Open Access Journals (Sweden)

    AMV Silva

    2001-11-01

    Full Text Available Between June 4th and June 20th1996 rotavirus, adenovirus, and astrovirus (HAstrV were investigated in fecal samples from 27 children under three years old with acute diarrhea, attending the Bertha Lutz day care center, in Rio de Janeiro. All fecal samples were analyzed by polyacrylamide gel electrophoresis (PAGE, reverse transcriptase polymerase chain reaction (RT-PCR, enzyme immunoassays (EIA, and electron microscopy (EM. Nine of them (33% showed positive results for HAstrV by at least one of the employed methodologies. Eight were positive by RT-PCR and EIA, and six by EM. All positive samples were inoculated onto HT-29 (human colon adenocarcinoma cultured cells for HAstrV isolation and seven were positive after three passages. The sequencing analysis of eight RT-PCR products (449 bp from gene that codifies VP2 protein, showed a total nucleotide identity among them and 98% with HAstrV-1 (strain Oxford type 1. This is the first report of a gastroenteritis outbreak associated with HAstrv-1 in a day care center in Rio de Janeiro and it reinforces the importance of this virus in association with infantile acute gastroenteritis.

  7. PTB Binds to the 3’ Untranslated Region of the Human Astrovirus Type 8: A Possible Role in Viral Replication

    Science.gov (United States)

    Espinosa-Hernández, Wendy; Velez-Uriza, Dora; Valdés, Jesús; Vélez-Del Valle, Cristina; Salas-Benito, Juan; Martínez-Contreras, Rebeca; García-Espítia, Matilde; Salas-Benito, Mariana; Vega-Almeida, Tania; De Nova-Ocampo, Mónica

    2014-01-01

    The 3′ untranslated region (3′UTR) of human astroviruses (HAstV) consists of two hairpin structures (helix I and II) joined by a linker harboring a conserved PTB/hnRNP1 binding site. The identification and characterization of cellular proteins that interact with the 3′UTR of HAstV-8 virus will help to uncover cellular requirements for viral functions. To this end, mobility shift assays and UV cross-linking were performed with uninfected and HAstV-8-infected cell extracts and HAstV-8 3′UTR probes. Two RNA-protein complexes (CI and CII) were recruited into the 3′UTR. Complex CII formation was compromised with cold homologous RNA, and seven proteins of 35, 40, 45, 50, 52, 57/60 and 75 kDa were cross-linked to the 3′UTR. Supermobility shift assays indicated that PTB/hnRNP1 is part of this complex, and 3′UTR-crosslinked PTB/hnRNP1 was immunoprecipitated from HAstV-8 infected cell-membrane extracts. Also, immunofluorescence analyses revealed that PTB/hnRNP1 is distributed in the nucleus and cytoplasm of uninfected cells, but it is mainly localized perinuclearly in the cytoplasm of HAstV-8 infected cells. Furthermore, the minimal 3′UTR sequences recognized by recombinant PTB are those conforming helix I, and an intact PTB/hnRNP1-binding site. Finally, small interfering RNA-mediated PTB/hnRNP1 silencing reduced synthesis viral genome and virus yield in CaCo2 cells, suggesting that PTB/hnRNP1 is required for HAstV replication. In conclusion, PTB/hnRNP1 binds to the 3′UTR HAstV-8 and is required or participates in viral replication. PMID:25406089

  8. The prevalence of norovirus, astrovirus and adenovirus infections among hospitalised children with acute gastroenteritis in Porto Velho, state of Rondônia, western Brazilian Amazon

    Science.gov (United States)

    Amaral, Maria Sandra Costa; Estevam, Grecy Kelli; Penatti, Marilene; Lafontaine, Roger; Lima, Ian Carlos Gomes; Spada, Paula Katharine Pontes; Gabbay, Yvone Benchimol; Matos, Najla Benevides

    2015-01-01

    Although viruses are well-established causes of acute gastroenteritis, few data on the circulation of these pathogens in Porto Velho, state of Rondônia, Brazil, are available. Thus, faecal samples from hospitalised diarrhoeic children, under six years of age, were collected and tested for the presence of norovirus (NoV), adenovirus (AdV) and astrovirus (AstV) from February 2010-February 2012. Specimens were screened by reverse-transcription polymerase chain reaction and viruses were found in 10.7% (63/591) of the cases. NoV, AdV and AstV were detected in 7.8%, 2% and 0.8% of the samples, respectively. NoV infection was observed at all ages and was most prevalent in zero-18-month-old children (84.7%; p = 0.002). A higher incidence of NoV was detected from February-April 2010, when it was found in 52.2% of the cases. Co-infections involving these viruses, rotavirus and enteropathogenic bacteria were detected in 44.4% (28/63) of the children with viral diarrhoea. Nosocomial infections were demonstrated in 28.6% (18/63) of the cases in which viruses were detected. The present paper reports, for the first time, the circulation of NoV and AstV among the paediatric population of Porto Velho and it contributes to our understanding of the roles of these pathogens in gastrointestinal infections. PMID:25946245

  9. The prevalence of norovirus, astrovirus and adenovirus infections among hospitalised children with acute gastroenteritis in Porto Velho, state of Rondônia, western Brazilian Amazon

    Directory of Open Access Journals (Sweden)

    Maria Sandra Costa Amaral

    2015-04-01

    Full Text Available Although viruses are well-established causes of acute gastroenteritis, few data on the circulation of these pathogens in Porto Velho, state of Rondônia, Brazil, are available. Thus, faecal samples from hospitalised diarrhoeic children, under six years of age, were collected and tested for the presence of norovirus (NoV, adenovirus (AdV and astrovirus (AstV from February 2010-February 2012. Specimens were screened by reverse-transcription polymerase chain reaction and viruses were found in 10.7% (63/591 of the cases. NoV, AdV and AstV were detected in 7.8%, 2% and 0.8% of the samples, respectively. NoV infection was observed at all ages and was most prevalent in zero-18-month-old children (84.7%; p = 0.002. A higher incidence of NoV was detected from February-April 2010, when it was found in 52.2% of the cases. Co-infections involving these viruses, rotavirus and enteropathogenic bacteria were detected in 44.4% (28/63 of the children with viral diarrhoea. Nosocomial infections were demonstrated in 28.6% (18/63 of the cases in which viruses were detected. The present paper reports, for the first time, the circulation of NoV and AstV among the paediatric population of Porto Velho and it contributes to our understanding of the roles of these pathogens in gastrointestinal infections.

  10. Detection and molecular characterization of chicken astrovirus associated with chicks that have an unusual condition known as "white chicks" in Brazil.

    Science.gov (United States)

    Nuñez, L F N; Santander Parra, S H; Carranza, C; Astolfi-Ferreira, C S; Buim, M R; Piantino Ferreira, A J

    2016-06-01

    Chicken astrovirus (CAstV) is one of many viruses related to enteric diseases in poultry that are associated with Runting-Stunting Syndrome (RSS), which affects young chickens. CAstV was also recently associated with an unusual condition in chicks called "white chicks." Some hatcheries in certain states of Brazil have reported several incubation problems, mortality, and the presence of chicks with white plumages over the past several months. These chicks were termed locally as "white chicks." The present work investigated 30 chicks with this unusual condition using a multidisciplinary approach. Postmortem examination of each chick showed enlarged livers and intestines that were full of liquid and gas (30/30). The pancreas, kidneys, and spleen were pale (30/30). The other organs did not show any macroscopic alterations. CAstV, chicken parvovirus (ChPV), avian nephritis virus (ANV), avian rotavirus (ARtV), avian reovirus (AReoV), infectious bronchitis virus (IBV), and fowl adenovirus group I (FAdV-1) were tested in the intestines, pancreas, proventriculus, gizzard, liver, spleen, bursa, kidneys, thymus, lung, heart, brain, and yolk sac in each chick. All organs and yolk sacs were positive for CAstV in different titres and negative for the other tested viruses. The partial molecular characterization of the ORF 1b gene of CAstV using 28 sequences revealed a high similarity of the nucleotides and amino acids with sequences of CAstV from North America, Europe, and Asia, and our CAstV sequences clustered into a unique group that was separate from the other sequences. These results demonstrated that CAstV was associated with the white chick condition in Brazil. The virus was distributed in most organs, including the brain and yolk sac. These results suggest that the virus could be transmitted vertically. The molecular characterization also revealed that the CAstV associated with white chick condition was molecularly related to other CAstV sequences found worldwide. PMID

  11. 人星状病毒临床分离株感染 CaCo-2细胞的转录组分析%Transcriptome analysis of clinically isolated human astrovirus in CaCo-2 cells

    Institute of Scientific and Technical Information of China (English)

    吴立梦; 滕峥; 刘晶; 张曦; 崔晓娴; 林庆能; 吴寰宇; 袁政安; 谢幼华

    2016-01-01

    人星状病毒(human astrovirus ,HAstV)是引起婴幼儿病毒性腹泻的重要病原之一,但其致病机制及与宿主相互作用的数据非常有限。本研究旨在了解HAstV感染细胞后对宿主基因在转录水平上的影响。首先,利用临床分离 HAstV毒株感染 CaCo‐2细胞,用实时定量反转录‐聚合酶链反应(reverse transcriptase‐polymerase chain reaction ,RT‐PCR)检测细胞培养上清液中的病毒总RNA ,结果显示接种后9~24 h病毒总RNA拷贝数明显增加。然后,利用转录组测序全面比较感染与未感染 HAstV的CaCo‐2细胞转录本,筛选两者间的差异表达基因;并应用KEGG信号通路富集性方法分析差异表达基因相关的信号通路。结果显示,差异基因富集在两条信号通路上(P<0.05),分别为轴突导向通路和Ras信号通路。本研究首次利用深度测序技术分析了HAstV感染对宿主基因在转录水平上的影响,为进一步研究HAstV致病机制等提供了方向。%Human astrovirus (HAstV) is one of the major causes of viral gastroenteritis in infants and young children .However ,data on the host response to and pathogenesis of HAstV infection are limited . The primary goal of this study was to identify differentially expressed genes and enriched pathways associated with HAstV infection in human CaCo‐2 cells .The clinical isolates of HAstV were used to infect CaCo‐2 cells and total viral RNAs in the extracellular medium were quantitatively detected . Real‐time reverse transcriptase‐polymerase chain reaction (RT‐PCR ) assay was applied to clearly demonstrate a significant increase in the amount of viral RNAs in the culture supernatant at 9‐24 h post‐infection . Finally , RNA sequencing was performed to compare the transcriptomes of CaCo‐2 cells infected with and without a clinically isolated HAstV strain .Statistical analyses on differentially expressed genes revealed that axon

  12. Identification and characterization of deer astroviruses

    DEFF Research Database (Denmark)

    Smits, Saskia L.; van Leeuwen, Marije; Kuiken, Thijs;

    2010-01-01

    The threat of emerging infectious viruses in humans requires a more effective approach regarding virus surveillance. A thorough understanding of virus diversity in wildlife provides epidemiological baseline information about pathogens and may lead to the identification of newly emerging pathogens...

  13. Astrovirus epidemiologically linked to pre-weaning diarrhoea in mink

    DEFF Research Database (Denmark)

    Englund, L.; Chriél, Mariann; Dietz, H.H.;

    2002-01-01

    in abundance and found to be a significant risk factor both at farm level (OR = 21.60, p body weight, coccoid bacteria adherent to the enteric villi, and presence of calicivirus were also shown to increase the risk of pre...

  14. Recombinant proteins as vaccines for protection against disease induced by infection with mink astrovirus

    DEFF Research Database (Denmark)

    2012-01-01

    Pre-weaning diarrhoea, has been a problem in mink farms for many years. The "greasy kits" syndrome is a condition of newborn mink characterised by diarrhoea accompanied by skin swelling and redness, skin exudates and blackness of the nails. The present invention relates to polynucleotides and pol...

  15. Molecular detection and genetic characterization of kobuviruses and astroviruses in asymptomatic local pigs in East Africa

    OpenAIRE

    Amimo, Joshua O.; Okoth, Edward; Junga, Joseph O.; Ogara, William O; Njahira, Moses N.; Wang, Qiuhong; Vlasova, Anastasia N.; Saif, Linda J; Djikeng, Appolinaire

    2013-01-01

    In this study, swine fecal specimens (n = 251) collected from nursing and weaned piglets raised under smallholder production systems were screened for the presence of kobuviruses by RT-PCR. Porcine kobuviruses were detected in 13.1 % (33/251) of the samples. We demonstrated that porcine kobuvirus infections exist in indigenous pigs in Kenya and Uganda and that the prevalence was higher in young piglets than older pigs: nursing piglets (15 %), post-weaning (3-month-old) pigs (17 %), 4-month-ol...

  16. Gastroenteritis Attributable to 16 Enteropathogens in Children Attending Day Care Significant Effects of Rotavirus, Norovirus, Astrovirus, Cryptosporidium and Giardia

    NARCIS (Netherlands)

    Enserink, Remko; van den Wijngaard, Cees; Bruijning-Verhagen, Patricia; van Asten, Liselotte; Mughini-Gras, Lapo; Duizer, Erwin; Kortbeek, Titia; Scholts, Rianne; Nagelkerke, Nico; Smit, Henriette A.; Kooistra-Smid, Mirjam; van Pelt, Wilfrid

    2015-01-01

    Background: Children attending day care experience substantial gastrointestinal morbidity due to circulating seasonal enteropathogens in the day-care environment. The lack of a distinct clinical presentation of gastroenteritis (GE) in these children, in combination with the high diversity of enterop

  17. Molecular epidemiology of enteric viruses and genotyping of rotavirus A, adenovirus and astrovirus among children under 5 years old in Gabon

    Directory of Open Access Journals (Sweden)

    Sonia Etenna Lekana-Douki

    2015-05-01

    Conclusions: These findings improve our knowledge of circulating enteric viruses in Gabon. The emergence of unusual G6P[6] strain of rotavirus A, predominant, suggested a particular epidemiological surveillance of circulating rotavirus strains during the introduction of vaccination in Gabon.

  18. 猪嵴病毒和猪星状病毒双重RT-PCR检测方法的建立%Establishment and a duplex RT-PCR assay for identification of porcine Kobuvirus and porcine astrovirus

    Institute of Scientific and Technical Information of China (English)

    顾凡; 覃娟娟; 蔡雨函; 李新琼; 黄剑波; 朱玲; 刘书亮; 徐志文

    2015-01-01

    为建立同时检测猪嵴病毒(PKV)和猪星状病毒(AstV)的检测方法,本研究根据PKV 3D基因和AstVORF2基因设计了两对特异性引物,通过优化反应条件,首次建立了PKV和AstV双重RT-PCR检测方法.该方法可以同时扩增出PKV的358 bp和AstV的938 bp特异性片段,而对猪伪狂犬病病毒、猪流行性腹泻病毒、猪传染性胃肠炎病毒及大肠杆菌等病原核酸扩增结果均为阴性,具有较强的特异性;对PKV和AstV的最低检出量分别为1.51×106拷贝/μL和1.19×106拷贝/μL;利用该方法和单项RT-PCR方法对35份来自四川省部分猪场的仔猪腹泻病料样品进行检测.结果显示,PKV和AstV的阳性检出率分别为80%和31.4%,两者符合率为100%.本研究建立的方法对PKV和AstV的鉴别诊断和混合感染检测具有重要的应用价值.

  19. Dicty_cDB: Contig-U16482-1 [Dicty_cDB

    Lifescience Database Archive (English)

    Full Text Available 683_1( FJ693683 |pid:none) Turkey astrovirus 2 isolate TK/MN/... 34 4.0 (A6VI47) RecName: Full=50S ribosomal...34 4.0 FJ693660_1( FJ693660 |pid:none) Turkey astrovirus 2 isolate TK/MN/... 33 9

  20. AcEST: BP917675 [AcEST

    Lifescience Database Archive (English)

    Full Text Available SD_TASV2 Capsid polyprotein OS=Turkey astrovirus 2 ... 30 4.2 sp|P09001|RM03_HUMAN 39S ribosomal protein L3,...RINELRRLKRKKEYH------NDEYKDDEIYLDNILKG 315 >sp|Q9Q3G5|CAPSD_TASV2 Capsid polyprotein OS=Turkey astrovirus 2

  1. Year-round screening of noncommercial and commercial oysters for the presence of human pathogenic viruses

    NARCIS (Netherlands)

    Lodder-Verschoor, F.; Husman, A.M.R.; Berg, van den H.H.J.L.; Stein, A.; Pelt-Heerschap, van H.M.L.; Poel, van der W.H.M.

    2005-01-01

    Consumption of virus-contaminated shellfish has caused numerous outbreaks of gastroenteritis and hepatitis worldwide. In The Netherlands, oysters are cultured and imported both for consumption and export; therefore, the presence of noroviruses, rotaviruses, astroviruses, hepatitis A viruses, and ent

  2. Establishment and clinical application of a multiplex RT-PCR for detection of porcine kobuvirus, porcine astrovirus and porcine torovirus%猪嵴病毒和猪星状病毒及猪环曲病毒多重RT-PCR检测方法的建立及临床应用

    Institute of Scientific and Technical Information of China (English)

    顾凡; 周远成; 黄剑波; 樊毅; 赵洲; 乔小改; 朱玲; 刘书亮; 徐志文

    2015-01-01

    根据猪嵴病毒(PKV)3D基因、猪星状病毒(PAstV) ORF2基因和猪环曲病毒(PToV)M基因的序列,设计了3对引物,通过反应体系和条件的优化,首次建立了检测猪嵴病毒、猪星状病毒和猪环曲病毒的多重RT-PCR.本研究建立的多重RT-PCR对PKV、PAstV和PToV的最低检出限分别为1.51×104、1.19×103、1.26×104 copies/μL,同时也具有较强的特异性和良好的重复性.用该方法检测了40份来自四川省部分猪场的仔猪腹泻病样.结果显示,PKV、PAstV、PToV的阳性检出率分别为75.0%、30.0%和22.5%.与单一RT-PCR检测结果一致.本方法的建立对PKV、PAstV、PToV的鉴别诊断和混合感染检测具有重要的应用价值.

  3. Complete genome sequence and integrated protein localization and interaction map for alfalfa dwarf virus, which combines properties of both cytoplasmic and nuclear plant rhabdoviruses

    Energy Technology Data Exchange (ETDEWEB)

    Bejerman, Nicolás, E-mail: n.bejerman@uq.edu.au [Instituto de Patología Vegetal (IPAVE), Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria INTA, Camino a 60 Cuadras k 5,5, Córdoba X5020ICA (Argentina); Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072 (Australia); Giolitti, Fabián; Breuil, Soledad de; Trucco, Verónica; Nome, Claudia; Lenardon, Sergio [Instituto de Patología Vegetal (IPAVE), Centro de Investigaciones Agropecuarias (CIAP), Instituto Nacional de Tecnología Agropecuaria INTA, Camino a 60 Cuadras k 5,5, Córdoba X5020ICA (Argentina); Dietzgen, Ralf G. [Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072 (Australia)

    2015-09-15

    Summary: We have determined the full-length 14,491-nucleotide genome sequence of a new plant rhabdovirus, alfalfa dwarf virus (ADV). Seven open reading frames (ORFs) were identified in the antigenomic orientation of the negative-sense, single-stranded viral RNA, in the order 3′-N-P-P3-M-G-P6-L-5′. The ORFs are separated by conserved intergenic regions and the genome coding region is flanked by complementary 3′ leader and 5′ trailer sequences. Phylogenetic analysis of the nucleoprotein amino acid sequence indicated that this alfalfa-infecting rhabdovirus is related to viruses in the genus Cytorhabdovirus. When transiently expressed as GFP fusions in Nicotiana benthamiana leaves, most ADV proteins accumulated in the cell periphery, but unexpectedly P protein was localized exclusively in the nucleus. ADV P protein was shown to have a homotypic, and heterotypic nuclear interactions with N, P3 and M proteins by bimolecular fluorescence complementation. ADV appears unique in that it combines properties of both cytoplasmic and nuclear plant rhabdoviruses. - Highlights: • The complete genome of alfalfa dwarf virus is obtained. • An integrated localization and interaction map for ADV is determined. • ADV has a genome sequence similarity and evolutionary links with cytorhabdoviruses. • ADV protein localization and interaction data show an association with the nucleus. • ADV combines properties of both cytoplasmic and nuclear plant rhabdoviruses.

  4. Complete genome sequence and integrated protein localization and interaction map for alfalfa dwarf virus, which combines properties of both cytoplasmic and nuclear plant rhabdoviruses

    International Nuclear Information System (INIS)

    Summary: We have determined the full-length 14,491-nucleotide genome sequence of a new plant rhabdovirus, alfalfa dwarf virus (ADV). Seven open reading frames (ORFs) were identified in the antigenomic orientation of the negative-sense, single-stranded viral RNA, in the order 3′-N-P-P3-M-G-P6-L-5′. The ORFs are separated by conserved intergenic regions and the genome coding region is flanked by complementary 3′ leader and 5′ trailer sequences. Phylogenetic analysis of the nucleoprotein amino acid sequence indicated that this alfalfa-infecting rhabdovirus is related to viruses in the genus Cytorhabdovirus. When transiently expressed as GFP fusions in Nicotiana benthamiana leaves, most ADV proteins accumulated in the cell periphery, but unexpectedly P protein was localized exclusively in the nucleus. ADV P protein was shown to have a homotypic, and heterotypic nuclear interactions with N, P3 and M proteins by bimolecular fluorescence complementation. ADV appears unique in that it combines properties of both cytoplasmic and nuclear plant rhabdoviruses. - Highlights: • The complete genome of alfalfa dwarf virus is obtained. • An integrated localization and interaction map for ADV is determined. • ADV has a genome sequence similarity and evolutionary links with cytorhabdoviruses. • ADV protein localization and interaction data show an association with the nucleus. • ADV combines properties of both cytoplasmic and nuclear plant rhabdoviruses

  5. 海南省虫媒病毒调查研究状况%Review on arbovirus studies in Hainan province, China

    Institute of Scientific and Technical Information of China (English)

    郑雅匀; 王志玉; 梁国栋

    2011-01-01

    North to Torrid Zone, Hainan province has favorable natural conditions to arthropod reproduction and the spread of arboviruses, as evidenced by several outbreaks of dengue fever and endemic Japanese encephalitis (JE). Arboviruses, including four alphaviruses (Chikungunya virus, Mayaro virus, Getah virus, Ross River virus), two flaviviruses (JE virus and Dengue virus) and one seadornavirus, have been isolated from various vectors and host animals in this province. This article reviews current studies on arboviruses and arboviral infections to humans and livestocks, in order to inform prevention and control both locally and nationwide.%海南省地处热带北缘,自然条件适合节肢动物繁殖及虫媒病毒传播,曾发生过多次登革热大流行,也是流行性乙型脑炎(乙脑)地方性流行区.以往从海南省多种媒介和宿主动物中分离到4种甲病毒(基孔肯雅、马雅罗、盖塔和罗斯河病毒)、2种黄病毒(乙脑和登革热病毒)和1种Seadornavirus.现对海南省新分离虫媒病毒及其人畜感染状况进行回顾整理,为当地以及我国虫媒病毒病的预防控制提供依据.

  6. Determination and analysis of the full-length chicken parvovirus genome.

    Science.gov (United States)

    Viral enteric disease in poultry is an ongoing problem in many parts of the world. Many enteric viruses have been identified in turkeys and chickens, including avian astroviruses, rotaviruses, reoviruses, and coronaviruses. Through the application of a molecular screening method targeting particle-a...

  7. An Otofuke-like virus associated with diarrhoea. Case report and electronmicroscopic study.

    Science.gov (United States)

    O'Neill, H J; Connolly, J H; Redmond, A O; Dermott, E

    1985-04-01

    Virus particles similar to Otofuke virus have been found, together with rotaviruses and astroviruses, by electronmicroscopy in faeces from an infant with diarrhoea in Northern Ireland. Previously Otofuke virus has been found only in Japan whence it may have been carried to this country by a businessman. PMID:4082360

  8. Novel genotype 3 human bufavirus from children with severe diarrhea in Bhutan

    OpenAIRE

    八尋, 隆明

    2014-01-01

    We identified a new genotype of bufavirus, BuV3, in samples (0.8%) collected to determine the viral etiology of diarrhea in Bhutanese children. Norovirus GII.6 was codetected in one sample; no norovirus, bocavirus, adenovirus, astrovirus, salivirus, cosavirus, aichivirus, and rotavirus were detected in others, suggesting BuV3 a possible cause of diarrhea.

  9. A Systematic Approach to Elucidate Causes of Gastroenteritis Outbreaks of Suspected Viral Etiology

    NARCIS (Netherlands)

    S. Svraka-Latifovic (Sanela)

    2011-01-01

    textabstractThe main objective of this thesis was to investigate the etiology of outbreaks of viral gastroenteritis that remained without diagnosis after testing for common viral pathogens causing gastroenteritis, e.g. noroviruses, rotaviruses, sapoviruses, adenoviruses, and astroviruses. No causati

  10. Global issues related to enteric viral infections

    OpenAIRE

    Desselberger, Ulrich

    2014-01-01

    Acute viral gastroenteritis is a major health issue worldwide and is associated with high annual mortality, particularly in children of developing countries. Rotaviruses, caliciviruses and astroviruses are the main causes. Accurate diagnoses are possible by recently developed molecular techniques. In many setups, zoonotic transmission is an important epidemiological factor. Treatment consists of rehydration and is otherwise symptomatic. The worldwide introduction of universal rotavirus vaccin...

  11. Molecular Epidemiology of Viral Gastroenteritis in Hajj pilgrimage

    KAUST Repository

    Padron Regalado, Eriko

    2014-05-01

    Hajj is the annual gathering of Islam practitioners in Mecca, Saudi Arabia. During the event, gastrointestinal infections are usually experienced and outbreaks have always been a concern; nevertheless, a deep and integrative study of the etiological agents has never been carried out. Here, I describe for the first time the epidemiology of pathogenic enteric viruses during Hajj 2011, 2012 and 2013. The focus of this study was the common enteric viruses Astrovirus, Norovirus, Rotavirus and Adenovirus. An enzyme Immunoassay established their presence in 14.9%, 15.0% and 6.6% of the reported cases of acute diarrhea for 2011, 2012 and 2013, respectively. For the three years of study, Astrovirus accounted for the majority of the viral infections. To our knowledge, this is the first time an epidemiological study depicts Astrovirus as the main viral agent of gastroenteritis in a mass gathering event. Hajj is rich in strains of Astrovirus, Norovirus and Rotavirus. A first screening by RT-PCR resulted in ten different genotypes. Strains HAstV 2, HAstV 1 and HAstV 5 were identified for Astrovirus. GI.6, GII.3, GII.4 and GII.1 were described for Norovirus and G1P[8], G4P[8] and G3P[8] were found for Rotavirus. The majority of the Astrovirus isolates could not be genotyped suggesting the presence of a new variant(s). Cases like this encourage the use of metagenomics (and nextgeneration sequencing) as a state-of-the-art technology in clinical diagnosis. A sample containing Adenovirus particles is being used to standardize a process for detection directly from stool samples and results will be obtained in the near future. The overall findings of the present study support the concept of Hajj as a unique mass gathering event that potentiates the transmission of infectious diseases. The finding of Norovirus GII.4 Sydney, a variant originated from Australia, suggests that Hajj is a receptor of infectious diseases worldwide. This work is part of the Hajj project, a collaborative

  12. Viral gastrointestinal syndrome in our environment

    Directory of Open Access Journals (Sweden)

    Patić A.

    2014-01-01

    Full Text Available Viral gastrointestinal syndrome is a cause of morbidity and death worldwide. Infection is spread through contact with an infected person, as well as through contaminated food and water. A lethal outcome is possible in infants and young children due to dehydration and electrolyte imbalance. The study included 141 patients with gastroenteritis from Vojvodina. Real-Time PCR method in stool samples was used to determine the presence of rota-, noro-, and astrovirus nucleic acid. Out of 141 patients with gastroenteritis, 60.3% were confirmed to have one of the three viruses. Rotavirus was significantly more common in children up to 3 years of age (43.3%. Norovirus was more frequently detected in patients older than 20 (50%. These infections started in collectives. Astrovirus was detected in four patients (2.8%. The results confirm the necessity to implement PCR in routine diagnostics for the proper treatment of patients.

  13. Identification of multiple novel viruses, including a parvovirus and a hepevirus, in feces of red foxes.

    Science.gov (United States)

    Bodewes, Rogier; van der Giessen, Joke; Haagmans, Bart L; Osterhaus, Albert D M E; Smits, Saskia L

    2013-07-01

    Red foxes (Vulpes vulpes) are the most widespread members of the order of Carnivora. Since they often live in (peri)urban areas, they are a potential reservoir of viruses that transmit from wildlife to humans or domestic animals. Here we evaluated the fecal viral microbiome of 13 red foxes by random PCR in combination with next-generation sequencing. Various novel viruses, including a parvovirus, bocavirus, adeno-associated virus, hepevirus, astroviruses, and picobirnaviruses, were identified.

  14. High prevalence of turkey parvovirus in turkey flocks from Hungary experiencing enteric disease syndromes.

    Science.gov (United States)

    Palade, Elena Alina; Demeter, Zoltán; Hornyák, Akos; Nemes, Csaba; Kisary, János; Rusvai, Miklós

    2011-09-01

    Samples collected in 2008 and 2009, from 49 turkey flocks of 6 to 43 days in age and presenting clinical signs of enteric disease and high mortality, were tested by polymerase chain reaction and reverse transcription-polymerase chain reaction for the presence of viruses currently associated with enteric disease (ED) syndromes: astrovirus, reovirus, rotavirus, coronavirus, adenovirus, and parvovirus. Turkey astroviruses were found in 83.67% of the cases and turkey astrovirus 2 (TAst-2) in 26.53%. The investigations directly demonstrated the high prevalence of turkey parvovirus (TuPV) in 23 flocks (46.9%) experiencing signs of ED, making this pathogen the second most identified after astroviruses. Phylogenetic analysis on a 527 base pair-long region from the NS1 gene revealed two main clusters, a chicken parvovirus (ChPV) and a TuPV group, but also the presence of a divergent branch of tentatively named "TuPV-like ChPV" strains. The 23 Hungarian TuPV strains were separately positioned in two groups from the American origin sequences in the TuPV cluster. An Avail-based restriction fragment length polymorphism assay has also been developed for the quick differentiation of TuPV, ChPV, and divergent TuPV-like ChPV strains. As most detected enteric viruses have been directly demonstrated in healthy turkey flocks as well, the epidemiology of this disease complex remains unclear, suggesting that a certain combination of pathogens, environmental factors, or both are necessary for the development of clinical signs.

  15. Prevalence and Genetic Diversity of Enteric Viruses in Children with Diarrhea in Ouagadougou, Burkina Faso.

    Science.gov (United States)

    Ouédraogo, Nafissatou; Kaplon, Jérôme; Bonkoungou, Isidore Juste O; Traoré, Alfred Sababénédjo; Pothier, Pierre; Barro, Nicolas; Ambert-Balay, Katia

    2016-01-01

    Enteric viruses are a major cause of diarrhea in children, especially those under five years old. Identifying the viral agents is critical to the development of effective preventive measures. This study aimed to determine the prevalence and genetic diversity of common enteric viruses in children under five years old in Burkina Faso. Stool samples from children with (n = 263) and without (n = 50) diarrhea disorders were collected in Ouagadougou, Burkina Faso from November 2011 to September 2012. Rotavirus, norovirus, sapovirus, astrovirus, adenovirus and Aichivirus A were detected using real-time or end-point (RT-)PCR. Rotavirus strains were G and P genotyped by multiplex RT-PCR and other viral strains were characterized by sequencing of viral subgenomic segements. At least one viral agent was detected in 85.6% and 72% of the symptomatic and asymptomatic patients, respectively. Rotavirus (63.5%), adenovirus (31.2%) and genogroup II norovirus (18.2%) were the most prevalent viruses in symptomatic patients, but only rotavirus and genogroup II norovirus were significantly associated with diarrhea (OR: 7.9, 95%CI: 3.7-17; OR: 3.5, 95%CI: 1-11.7, respectively). Sapovirus (10.3%), astrovirus (4.9%), genogroup I norovirus (2.7%) and Aichivirus A (0.8%) were less prevalent. The predominant genotype of rotavirus was G9P[8] (36.5%), and the predominant norovirus strain was GII.4 variant 2012 (71.4%). Among sapovirus, the genogroup II (87.5%) predominated. Astrovirus type 1 (41.7%) was the most frequent astrovirus identified. Aichivirus A belonged to the three genotypes (A, B and C). Enteric adenoviruses type 40 and 41 were identified in 10.2% and 5.1% respectively. Several cases of co-infections were detected. The results highlight the high prevalence and the high diversity of enteric viruses in Burkinabe children. PMID:27092779

  16. A Systematic Approach to Elucidate Causes of Gastroenteritis Outbreaks of Suspected Viral Etiology

    OpenAIRE

    Svraka-Latifovic, Sanela

    2011-01-01

    textabstractThe main objective of this thesis was to investigate the etiology of outbreaks of viral gastroenteritis that remained without diagnosis after testing for common viral pathogens causing gastroenteritis, e.g. noroviruses, rotaviruses, sapoviruses, adenoviruses, and astroviruses. No causative pathogen could be detected in over 10% of these outbreaks. Viral gastroenteritis is about the most frequent disease in humans and this unexplained fraction concerns about 150000 cases in the Net...

  17. Simultaneous Detection of Seven Enteric Viruses Associated with Acute Gastroenteritis by a Multiplexed Luminex-Based Assay

    OpenAIRE

    Liu, Yan; Xu, Zi-qian; Zhang, Qing; Jin, Miao; Yu, Jie-mei; Li, Jin-song; Liu, Na; Cui, Shu-Xian; Kong, Xiang-Yu; Wang, Hong; Li, Hui-Ying; Cheng, Wei-Xia; Ma, Xue-Jun; Duan, Zhao-jun

    2012-01-01

    Rapid and broad diagnostic methods are needed for the identification of viral agents of gastroenteritis. In this study, we used Luminex xMAP technology to develop a multiplexed assay for the simultaneous identification of major enteric viral pathogens, including rotavirus A (RVA), noroviruses (NoVs) (including genogroups GI and GII), sapoviruses (SaV), human astrovirus (HAstV), enteric adenoviruses (EAds), and human bocavirus 2 (HBoV2). The analytical sensitivity allowed detection of 103 (EAd...

  18. Recent viral pathogen in acute gastroenteritis: a retrospective study at a tertiary hospital for 1 year

    OpenAIRE

    Jin, Hye Il; Lee, Yoo Mi; Choi, You Jin; Jeong, Su Jin

    2016-01-01

    Purpose Viral gastroenteritis among children is mainly caused by rotavirus, norovirus, astrovirus, or adenovirus strains. However, changing socioeconomic conditions and a rotavirus vaccination program may be affecting the prevalence of these viral infections. Therefore, we aimed to elucidate the season-specific trends in viral infections for facilitating prophylaxis and surveillance in our region. Methods We evaluated 345 pediatric patients (203 males, 142 females; age, 1 month to 16 years) w...

  19. Aetiology of childhood viral gastroenteritis in Lucknow, north India

    OpenAIRE

    Shilpi Gupta; Singh, K. P.; Amita Jain; Shilpi Srivastava; Vishwajeet Kumar; Mastan Singh

    2015-01-01

    Background & objectives: Due to limited availability of data on viral aetiology of acute gastroenteritis in north India, the present study was planned to detect rotavirus, norovirus, sapovirus and astrovirus in stool samples of both in hospitalized and non-hospitalized children less than five years of age presenting with acute gastroenteritis. Methods: A total of 278 stool samples from equal number of children were tested for rotavirus antigen using ELISA and for norovirus, sapovirus and...

  20. Evaluation of the results of acute viral gastroenteritis data in Refik Saydam National Public Health Agency, Virology Reference and Research Laboratory in 2009

    OpenAIRE

    Albayrak, Nurhan; Dilek YAĞCI-ÇAĞLAYIK; Ayşe Başak ALTAŞ; Korukluoğlu, Gülay; Ertek, Mustafa

    2011-01-01

    Objective: Norovirus, Rotavirus, Adenovirus and Astrovirus are responsible for most non-bacterial acute gastroenteritis. The incidence of these viral agents in Turkey is not well known. In this study, it was aimed to document the viral etiology of the stool samples which were send to Refik Saydam National Public Health Agency (RSNPHA), Virology Reference and Research Laboratory for investigation of viral acute gastroenteritis agents. Method: A total of 147 stool samples from 11 different ...

  1. Prevalence and Genetic Diversity of Enteric Viruses in Children with Diarrhea in Ouagadougou, Burkina Faso.

    Directory of Open Access Journals (Sweden)

    Nafissatou Ouédraogo

    Full Text Available Enteric viruses are a major cause of diarrhea in children, especially those under five years old. Identifying the viral agents is critical to the development of effective preventive measures. This study aimed to determine the prevalence and genetic diversity of common enteric viruses in children under five years old in Burkina Faso. Stool samples from children with (n = 263 and without (n = 50 diarrhea disorders were collected in Ouagadougou, Burkina Faso from November 2011 to September 2012. Rotavirus, norovirus, sapovirus, astrovirus, adenovirus and Aichivirus A were detected using real-time or end-point (RT-PCR. Rotavirus strains were G and P genotyped by multiplex RT-PCR and other viral strains were characterized by sequencing of viral subgenomic segements. At least one viral agent was detected in 85.6% and 72% of the symptomatic and asymptomatic patients, respectively. Rotavirus (63.5%, adenovirus (31.2% and genogroup II norovirus (18.2% were the most prevalent viruses in symptomatic patients, but only rotavirus and genogroup II norovirus were significantly associated with diarrhea (OR: 7.9, 95%CI: 3.7-17; OR: 3.5, 95%CI: 1-11.7, respectively. Sapovirus (10.3%, astrovirus (4.9%, genogroup I norovirus (2.7% and Aichivirus A (0.8% were less prevalent. The predominant genotype of rotavirus was G9P[8] (36.5%, and the predominant norovirus strain was GII.4 variant 2012 (71.4%. Among sapovirus, the genogroup II (87.5% predominated. Astrovirus type 1 (41.7% was the most frequent astrovirus identified. Aichivirus A belonged to the three genotypes (A, B and C. Enteric adenoviruses type 40 and 41 were identified in 10.2% and 5.1% respectively. Several cases of co-infections were detected. The results highlight the high prevalence and the high diversity of enteric viruses in Burkinabe children.

  2. A Predominant Role for Norwalk-like Viruses as Agents of Epidemic Gastroenteritis in Maryland Nursing Homes for the Elderly

    OpenAIRE

    Green, Kim Y.; Belliot, Gaël; Taylor, Jean Lin; Valdesuso, José; Lew, Judy F.; Kapikian, Albert Z.; Lin, Feng-Ying C.

    2002-01-01

    Stool specimens from 156 Maryland nursing home residents, who became ill during 20 outbreaks of gastroenteritis from November 1987 through February 1988, were analyzed. All tested negative for astroviruses, enteroviruses, Group A rotaviruses, Sapporo-like caliciviruses, and enteric bacteria (i.e., Salmonella, Clostridium, and Shigella species). Eighty-two (52%) were positive for Norwalk-like viruses (NLVs), members of the family Caliciviridae. Six distinct genetic clusters within genogroups I...

  3. Epidemiology of gastroenteritis viruses in Japan: Prevalence, seasonality, and outbreak.

    Science.gov (United States)

    Thongprachum, Aksara; Khamrin, Pattara; Maneekarn, Niwat; Hayakawa, Satoshi; Ushijima, Hiroshi

    2016-04-01

    Acute gastroenteritis has been recognized as one of the most common diseases in humans and continues to be a major public health problem worldwide. Several groups of viruses have been reported as the causative agents of acute gastroenteritis, including rotavirus, norovirus, sapovirus, human astrovirus, adenovirus, and an increasing number of others which have been reported more recently. The epidemiology, prevalence, seasonality, and outbreaks of these viruses have been reviewed in a number of studies conducted in Japan over three decades. Rotavirus and norovirus were the two most common viruses detected almost equally in children under 5 years of age who were suffering from acute gastroenteritis. Like many other countries, the main rotavirus strains circulating in pediatric patients in Japan are G1P[8], G2P[4], G3P[8], and G9P[8]. Norovirus GII.4 was involved in most outbreaks in Japan and found to be associated with the emergence of new variants Sydney_2012. The classic human astrovirus, MLB, and VA clades astroviruses were also commonly found in pediatric patients with acute diarrhea. The sapovirus and adenovirus have been identified as the minor viral causative agents for acute gastroenteritis in Japan.

  4. Application of qPCR assays for diagnosing causes of viral mink diarrhea. Preliminary results

    DEFF Research Database (Denmark)

    Hartby, Christina Marie; Kvisgaard, Lise Kirstine; Larsen, Lars Erik;

    for a quantitative diagnostic approach. We have developed new or adapted previously published real-time PCR/RT-PCR assays for MEV, astrovirus, rota- and coronavirus diagnostics. The technical test validation was initially carried out on archived diarrhea samples from diagnosed positive animals and on normal...... and diarrhea samples from a case-control study. In order to further validate the applicability of the assays, a testing scheme for normal and affected farms was set up and initiated in June 2015. This protocol will allow optimization of test characteristics (sensitivity, specificity and predictive value......) and assessment of the validity of using pooled samples in order to reduce test costs....

  5. A non-enteric adenovirus A12 gastroenteritis outbreak in Rio de Janeiro, Brazil

    OpenAIRE

    Silvana Augusta Rodrigues Portes; Eduardo de Mello Volotão; Monica Simões Rocha; Maria Cristina Rebelo; Maria da Penha Trindade Pinheiro Xavier; Rosane Maria de Assis; Tatiana Lundgren Rose; Marize Pereira Miagostovich; José Paulo Gagliardi Leite; Filipe Anibal Carvalho-Costa

    2016-01-01

    A gastroenteritis outbreak that occurred in 2013 in a low-income community in Rio de Janeiro was investigated for the presence of enteric viruses, including species A rotavirus (RVA), norovirus (NoV), astrovirus (HAstV), bocavirus (HBoV), aichivirus (AiV), and adenovirus (HAdV). Five of nine stool samples (83%) from patients were positive for HAdV, and no other enteric viruses were detected. Polymerase chain reaction products were sequenced and subjected to phylogenetic analysis, which reveal...

  6. Feeding of the probiotic bacterium Enterococcus faecium NCIMB 10415 differentially affects shedding of enteric viruses in pigs

    Directory of Open Access Journals (Sweden)

    Kreuzer Susanne

    2012-07-01

    Full Text Available Abstract Effects of probiotic bacteria on viral infections have been described previously. Here, two groups of sows and their piglets were fed with or without feed supplementation of the probiotic bacterium Enterococcus faecium NCIMB 10415. Shedding of enteric viruses naturally occurring in these pigs was analyzed by quantitative real-time RT-PCR. No differences between the groups were recorded for hepatitis E virus, encephalomyocarditis virus and norovirus. In contrast, astrovirus was exclusively detected in the non-supplemented control group. Rotavirus was shedded later and with lower amounts in the probiotic piglet group (p p p p p p 

  7. Enfermedad diarréica aguda (EDA) nuevos agentes virales

    OpenAIRE

    Peláez, Dioselina

    2004-01-01

    La EDA es una de las enfermedades más importantes en términos de morbilidad y mortalidad a nivel mundial. Cada año ocurren más de un billón de episodios diarreicos en niños menores de 5 años con altos costos hospitalarios y pérdida de la productividad. Agentes bacterianos ( E.coli, Salmonella, Shiguella , toxinas), parasitarios (Giardia, Cryptosporidium, Entamoeba), virales (Rotavirus, Adenovirus, Astrovirus, Norovirus, Enterovirus ) y otros (intolerancias a ...

  8. Genome Sequence Analysis of CsRV1: A Pathogenic Reovirus that Infects the Blue Crab Callinectes sapidus Across Its Trans-Hemispheric Range.

    Science.gov (United States)

    Flowers, Emily M; Bachvaroff, Tsvetan R; Warg, Janet V; Neill, John D; Killian, Mary L; Vinagre, Anapaula S; Brown, Shanai; Almeida, Andréa Santos E; Schott, Eric J

    2016-01-01

    The blue crab, Callinectes sapidus Rathbun, 1896, which is a commercially important trophic link in coastal ecosystems of the western Atlantic, is infected in both North and South America by C. sapidus Reovirus 1 (CsRV1), a double stranded RNA virus. The 12 genome segments of a North American strain of CsRV1 were sequenced using Ion Torrent technology. Putative functions could be assigned for 3 of the 13 proteins encoded in the genome, based on their similarity to proteins encoded in other reovirus genomes. Comparison of the CsRV1 RNA-dependent RNA polymerase (RdRP) sequence to genomes of other crab-infecting reoviruses shows that it is similar to the mud crab reovirus found in Scylla serrata and WX-2012 in Eriocheir sinensis, Chinese mitten crab, and supports the idea that there is a distinct "Crabreo" genus, different from Seadornavirus and Cardoreovirus, the two closest genera in the Reoviridae. A region of 98% nucleotide sequence identity between CsRV1 and the only available sequence of the P virus of Macropipus depurator suggests that these two viruses may be closely related. An 860 nucleotide region of the CsRV1 RdRP gene was amplified and sequenced from 15 infected crabs collected from across the geographic range of C. sapidus. Pairwise analysis of predicted protein sequences shows that CsRV1 strains in Brazil can be distinguished from those in North America based on conserved residues in this gene. The sequencing, annotation, and preliminary population metrics of the genome of CsRV1 should facilitate additional studies in diverse disciplines, including structure-function relationships of reovirus proteins, investigations into the evolution of the Reoviridae, and biogeographic research on the connectivity of C. sapidus populations across the Northern and Southern hemispheres. PMID:26904003

  9. Isolates of Liao ning virus from wild-caught mosquitoes in the Xinjiang province of China in 2005.

    Directory of Open Access Journals (Sweden)

    Xinjun Lv

    Full Text Available Liao ning virus (LNV is related to Banna virus, a known human-pathogen present in south-east Asia. Both viruses belong to the genus Seadornavirus, family Reoviridae. LNV causes lethal haemorrhage in experimentally infected mice. Twenty seven isolates of LNV were made from mosquitoes collected in different locations within the Xinjiang province of north-western China during 2005. These mosquitoes were caught in the accommodation of human patients with febrile manifestations, or in animal barns where sheep represent the main livestock species. The regions where LNV was isolated are affected by seasonal encephalitis, but are free of Japanese encephalitis (JE. Genome segment 10 (Seg-10 (encoding cell-attachment and serotype-determining protein VP10 and Seg-12 (encoding non-structural protein VP12 were sequenced for multiple LNV isolates. Phylogenetic analyses showed a less homogenous Seg-10 gene pool, as compared to segment 12. However, all of these isolates appear to belong to LNV type-1. These data suggest a relatively recent introduction of LNV into Xinjiang province, with substitution rates for LNV Seg-10 and Seg-12, respectively, of 2.29×10(-4 and 1.57×10(-4 substitutions/nt/year. These substitution rates are similar to those estimated for other dsRNA viruses. Our data indicate that the history of LNV is characterized by a lack of demographic fluctuations. However, a decline in the LNV population in the late 1980s-early 1990s, was indicated by data for both Seg-10 and Seg-12. Data also suggest a beginning of an expansion in the late 1990s as inferred from Seg-12 skyline plot.

  10. Comparative study of enteric viruses, coliphages and indicator bacteria for evaluating water quality in a tropical high-altitude system

    Directory of Open Access Journals (Sweden)

    Mazari-Hiriart Marisa

    2009-10-01

    Full Text Available Abstract Background Bacteria used as indicators for pathogenic microorganisms in water are not considered adequate as enteric virus indicators. Surface water from a tropical high-altitude system located in Mexico City that receives rainwater, treated and non-treated wastewater used for irrigation, and groundwater used for drinking, was studied. Methods The presence of enterovirus, rotavirus, astrovirus, coliphage, coliform bacteria, and enterococci was determined during annual cycles in 2001 and 2002. Enteric viruses in concentrated water samples were detected by reverse transcriptase-polymerase chain reaction (RT-PCR. Coliphages were detected using the double agar layer method. Bacteria analyses of the water samples were carried out by membrane filtration. Results The presence of viruses and bacteria in the water used for irrigation showed no relationship between current bacterial indicator detection and viral presence. Coliphages showed strong association with indicator bacteria and enterovirus, but weak association with other enteric viruses. Enterovirus and rotavirus showed significant seasonal differences in water used for irrigation, although this was not clear for astrovirus. Conclusion Coliphages proved to be adequate faecal pollution indicators for the irrigation water studied. Viral presence in this tropical high-altitude system showed a similar trend to data previously reported for temperate zones.

  11. Incidence of Norovirus and Other Viral Pathogens That Cause Acute Gastroenteritis (AGE among Kaiser Permanente Member Populations in the United States, 2012-2013.

    Directory of Open Access Journals (Sweden)

    Scott P Grytdal

    Full Text Available Noroviruses and other viral pathogens are increasingly recognized as frequent causes of acute gastroenteritis (AGE. However, few laboratory-based data are available on the incidence of AGE caused by viral pathogens in the U.S. This study examined stool specimens submitted for routine clinical diagnostics from patients enrolled in Kaiser Permanente (KP health plans in metro Portland, OR, and the Maryland, District of Columbia, and northern Virginia geographic areas to estimate the incidence of viral enteropathogens in these populations. Over a one-year study period, participating laboratories randomly selected stools submitted for routine clinical diagnostics for inclusion in the study along with accompanying demographic and clinical data. Selected stools were tested for norovirus, rotavirus, sapovirus, and astrovirus using standardized real-time RT-PCR protocols. Each KP site provided administrative data which were used in conjunction with previously published data on healthcare utilization to extrapolate pathogen detection rates into population-based incidence rates. A total of 1,099 specimens collected during August 2012 to September 2013 were included. Mean age of patients providing stool specimens was 46 years (range: 0-98 years. Noroviruses were the most common viral pathogen identified among patients with AGE (n = 63 specimens, 6% of specimens tested. In addition, 22 (2% of specimens were positive for rotavirus; 19 (2% were positive for sapovirus; and 7 (1% were positive for astrovirus. Incidence of norovirus-associated outpatient visits was 5.6 per 1,000 person-years; incidence of norovirus disease in the community was estimated to be 69.5 per 1,000 person-years. Norovirus incidence was highest among children 65 years (outpatient incidence = 7.8 per 1,000 person-years; community incidence = 75.8 per 1,000 person-years. Outpatient incidence rates of rotavirus, sapovirus, and astrovirus were 2.0, 1.6, 0.6 per 1,000 person

  12. Incidence of Norovirus and Other Viral Pathogens That Cause Acute Gastroenteritis (AGE) among Kaiser Permanente Member Populations in the United States, 2012-2013.

    Science.gov (United States)

    Grytdal, Scott P; DeBess, Emilio; Lee, Lore E; Blythe, David; Ryan, Patricia; Biggs, Christianne; Cameron, Miriam; Schmidt, Mark; Parashar, Umesh D; Hall, Aron J

    2016-01-01

    Noroviruses and other viral pathogens are increasingly recognized as frequent causes of acute gastroenteritis (AGE). However, few laboratory-based data are available on the incidence of AGE caused by viral pathogens in the U.S. This study examined stool specimens submitted for routine clinical diagnostics from patients enrolled in Kaiser Permanente (KP) health plans in metro Portland, OR, and the Maryland, District of Columbia, and northern Virginia geographic areas to estimate the incidence of viral enteropathogens in these populations. Over a one-year study period, participating laboratories randomly selected stools submitted for routine clinical diagnostics for inclusion in the study along with accompanying demographic and clinical data. Selected stools were tested for norovirus, rotavirus, sapovirus, and astrovirus using standardized real-time RT-PCR protocols. Each KP site provided administrative data which were used in conjunction with previously published data on healthcare utilization to extrapolate pathogen detection rates into population-based incidence rates. A total of 1,099 specimens collected during August 2012 to September 2013 were included. Mean age of patients providing stool specimens was 46 years (range: 0-98 years). Noroviruses were the most common viral pathogen identified among patients with AGE (n = 63 specimens, 6% of specimens tested). In addition, 22 (2%) of specimens were positive for rotavirus; 19 (2%) were positive for sapovirus; and 7 (1%) were positive for astrovirus. Incidence of norovirus-associated outpatient visits was 5.6 per 1,000 person-years; incidence of norovirus disease in the community was estimated to be 69.5 per 1,000 person-years. Norovirus incidence was highest among children 65 years (outpatient incidence = 7.8 per 1,000 person-years; community incidence = 75.8 per 1,000 person-years). Outpatient incidence rates of rotavirus, sapovirus, and astrovirus were 2.0, 1.6, 0.6 per 1,000 person-years, respectively; community

  13. Acute diarrhea in West African children: diverse enteric viruses and a novel parvovirus genus.

    Science.gov (United States)

    Phan, Tung G; Vo, Nguyen P; Bonkoungou, Isidore J O; Kapoor, Amit; Barro, Nicolas; O'Ryan, Miguel; Kapusinszky, Beatrix; Wang, Chunling; Delwart, Eric

    2012-10-01

    Parvoviruses cause a variety of mild to severe symptoms or asymptomatic infections in humans and animals. During a viral metagenomic analysis of feces from children with acute diarrhea in Burkina Faso, we identified in decreasing prevalence nucleic acids from anelloviruses, dependoviruses, sapoviruses, enteroviruses, bocaviruses, noroviruses, adenoviruses, parechoviruses, rotaviruses, cosavirus, astroviruses, and hepatitis B virus. Sequences from a highly divergent parvovirus, provisionally called bufavirus, were also detected whose NS1 and VP1 proteins showed parvoviruses. Four percent of the fecal samples were PCR positive for this new parvovirus, including a related bufavirus species showing only 72% identity in VP1. The high degree of genetic divergence of these related genomes from those of other parvoviruses indicates the presence of a proposed new Parvoviridae genus containing at least two species. Studies of the tropism and pathogenicity of these novel parvoviruses will be facilitated by the availability of their genome sequences.

  14. Identification of GBV-D, a novel GB-like flavivirus from old world frugivorous bats (Pteropus giganteus in Bangladesh.

    Directory of Open Access Journals (Sweden)

    Jonathan H Epstein

    Full Text Available Bats are reservoirs for a wide range of zoonotic agents including lyssa-, henipah-, SARS-like corona-, Marburg-, Ebola-, and astroviruses. In an effort to survey for the presence of other infectious agents, known and unknown, we screened sera from 16 Pteropus giganteus bats from Faridpur, Bangladesh, using high-throughput pyrosequencing. Sequence analyses indicated the presence of a previously undescribed virus that has approximately 50% identity at the amino acid level to GB virus A and C (GBV-A and -C. Viral nucleic acid was present in 5 of 98 sera (5% from a single colony of free-ranging bats. Infection was not associated with evidence of hepatitis or hepatic dysfunction. Phylogenetic analysis indicates that this first GBV-like flavivirus reported in bats constitutes a distinct species within the Flaviviridae family and is ancestral to the GBV-A and -C virus clades.

  15. Etiology of diarrhea in young children in Denmark: a case-control study

    DEFF Research Database (Denmark)

    Olesen, B.; Neimann, J.; Bottiger, B.;

    2005-01-01

    -matched controls were examined, and their parents were interviewed concerning symptoms. Rotavirus, adenovirus, and astrovirus were detected by enzyme-linked immunosorbent assay, and norovirus and sapovirus were detected by PCR. Salmonella, thermotolerant Campylobacter, Yersinia, Shigella, and Vibrio spp. were...... by microscopy. Overall, a potential pathogen was found in 54% of cases. More cases than controls were infected with rotavirus, Salmonella, norovirus, adenovirus, Campylobacter, sapovirus, STEC, classical EPEC, Yersinia, and Cryptosporidium strains, whereas A/EEC, although common, was not associated with illness....... The single most important cause of diarrhea was rotavirus, which points toward the need for a childhood vaccine for this pathogen, but norovirus, adenovirus, and sapovirus were also major etiologies. Salmonella sp. was the most common bacterial pathogen, followed by Campylobacter, STEC, Yersinia...

  16. Development of the Intestinal RNA Virus Community of Healthy Broiler Chickens.

    Science.gov (United States)

    Shah, Jigna D; Desai, Prerak T; Zhang, Ying; Scharber, Sarah K; Baller, Joshua; Xing, Zheng S; Cardona, Carol J

    2016-01-01

    Several RNA viruses such as astrovirus, rotavirus, reovirus and parvovirus have been detected in both healthy and diseased commercial poultry flocks. The aim of this study was to characterize (a) the development of the RNA viral community in the small intestines of healthy broiler chickens from hatch through 6 weeks of age (market age) and (b) the contribution of the breeder source vs. bird age in development of the community structure. Intestinal tissue samples were harvested from breeders and their progeny, processed for viral RNA extraction and sequenced using Illumina Hiseq sequencing technology resulting in 100 bp PE reads. The results from this study indicated that the breeder source influenced the RNA viral community only at hatch but later environment i.e. bird age had the more significant effect. The most abundant RNA viral family detected at 2, 4 and 6 weeks of age was Astroviridae, which decreased in abundance with age while the abundance of Picornaviridae increased with age.

  17. Viral immunity. Transkingdom control of viral infection and immunity in the mammalian intestine.

    Science.gov (United States)

    Pfeiffer, Julie K; Virgin, Herbert W

    2016-01-15

    Viruses that infect the intestine include major human pathogens (retroviruses, noroviruses, rotaviruses, astroviruses, picornaviruses, adenoviruses, herpesviruses) that constitute a serious public health problem worldwide. These viral pathogens are members of a large, complex viral community inhabiting the intestine termed "the enteric virome." Enteric viruses have intimate functional and genetic relationships with both the host and other microbial constituents that inhabit the intestine, such as the bacterial microbiota, their associated phages, helminthes, and fungi, which together constitute the microbiome. Emerging data indicate that enteric viruses regulate, and are in turn regulated by, these other microbes through a series of processes termed "transkingdom interactions." This represents a changing paradigm in intestinal immunity to viral infection. Here we review recent advances in the field and propose new ways in which to conceptualize this important area.

  18. Development and application of an RT-PCR test for detecting avian nephritis virus.

    Science.gov (United States)

    Todd, D; Trudgett, J; McNeilly, F; McBride, N; Donnelly, B; Smyth, V J; Jewhurst, H L; Adair, B M

    2010-06-01

    The development of a reverse transcriptase-polymerase chain reaction (RT-PCR) test for detecting avian nephritis virus (ANV) is described. Primers, which amplified a fragment of 182 base pairs (bp), were located in the conserved 3' untranslated region (UTR) of the genome. The limit of detection of the test was estimated to be approximately 18 viral copies using a 10-fold dilution series of in vitro transcribed RNA. Positive signals were produced with representative ANV samples, some of which were not detected by previously described RT-PCR tests for detecting ANV, but other avian astroviruses including chicken astrovirus isolates and duck hepatitis virus types 2 and 3 tested negative. When applied to gut content samples from UK, German and US broiler flocks with enteritis/growth problems, ANVs were detected by RT-PCR in 82/82 (100%) samples. ANVs were also detected in 80/96 (83%) pooled gut content samples from longitudinal surveys of four broiler flocks displaying below-average performance. Whereas all samples collected on day 0 from the surveys were negative for ANV, all samples collected at days 4/5, 7, 10, 14, 21 and 28 tested positive. Sequence determinations performed with amplicons produced with 14 field samples confirmed the ANV specificity of the test, while comparative and phylogenetic analyses based on 109-nucleotide 3'-UTR sequences demonstrated that the majority of ANVs investigated were more closely related to the serotype 2 ANV (accession number AB 046864) than to the serotype 1 ANV (accession number NC 003790).

  19. LAS GASTROENTERITIS VÍRICAS: UN PROBLEMA DE SALUD PÚBLICA

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    Angela Domínguez

    2009-01-01

    Full Text Available Las gastroenteritis agudas (GA constituyen un problema de salud importante, pudiendo estar causadas por bacterias, parásitos y virus enteropatógenos, entre los que se han reconocido hasta la actualidad rotavirus, astrovirus, adenovirus y calicivirus. La frecuencia de rotavirus como causa de casos esporádicos de GA oscila entre el 17,3% y el 37,4%. Aunque se ha sugerido que la exposición común no tiene mucha importancia para la difusión de este virus, resulta difícil relacionar casos aparentemente esporádicos, por lo que probablemente haya brotes que no llegan a detectarse. Los astrovirus causan GA con una frecuencia que oscila entre un 2 y un 26% y se han descrito brotes en escuelas y guarderías, pero también en población adulta y en ancianos. La frecuencia con que se identifican los adenovirus 40 y 41 como causa de GA esporádica en niños no inmunodeprimidos oscila entre 0,7% y 31,5%, aunque probablemente haya subdetección debido a que la sensibilidad de las técnicas convencionales es baja. Los calicivirus se separan filogenéticamente en dos géneros: Norovirus y Sapovirus. Los Norovirus se asocian frecuentemente con brotes de GA transmitidos por agua y alimentos . Se estima que el 40% de los casos de GA por Norovirus están vehiculados por alimentos. En Suecia y en algunas zonas de Estados Unidos es la primera causa de brotes de toxiinfecciones alimentarias. Recientemente se han descrito en Canadà y Japón brotes de transmisión persona a persona y también de transmisión alimentaria causados por Sapovirus, afectando tanto a población infantil como adulta.

  20. Acute viral gastroenteritis in children hospitalized in Iksan, Korea during December 2010 - June 2011

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    Cheol Whoan So

    2013-09-01

    Full Text Available Purpose: Viral etiology is common in cases of children with acute diarrhea, and antibiotic therapy is usually not required. Therefore, it is important to determine the distribution of common viruses among children hospitalized with acute diarrhea. Methods: We included 186 children who suffered from acute diarrhea and were hospitalized at the Wonkwang University Hospital Pediatric ward from December 1, 2010 to June 30, 2011 in this study. Stool samples were collected and multiplex reverse transcriptase polymerase chain reaction (multiplex RT-PCR was used to simultaneously determine the viral etiology such as rotavirus, norovirus, astrovirus, or adenovirus.&lt;br&gt; Results: Causative viruses were detected in 72 of the 186 cases (38.7%. The mean age of the viruspositive cases was 1 year and 9 months (range, 1 month to 11 years. Rotavirus was detected in 50/186 (26.9%; norovirus, in 18/186 (9.7%; and astrovirus, in 3/186 cases (1.6%. Adenovirus was not detected in any of the cases. Proportions of norovirus genogroups I and II were 21.1% and 78.9%, respectively. Four of the 51 rotavirus-positive cases (7.8% had received rotavirus vaccination at least once. The mean duration of diarrhea was 2.8 days (range, 1 to 10 days and vomiting occurred in 39 of the 72 cases (54.2%.&lt;br&gt; Conclusion: Viral etiology was confirmed in about one-third of the children with acute diarrhea, and the most common viral agent was rotavirus, followed by norovirus.

  1. ACUTE ENTERIC INFECTIONS POLYMERASE CHAIN REACTION ASSAY IN PEDIATRIC PRACTICE: OPPORTUNITIES AND CHALLENGES

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    E. D. Sokolova

    2016-01-01

    Full Text Available The aim of the study is estimate the opportunities of local multi-prime PCR reagents kits in children enteric infections etiological diagnostics amongst the patients with diarrhoea vs traditional bacteriological methods. We used 4 kits of reagents that provide multiple pathogens simultaneous indication in one sample: 1 Rotavirus, Norovirus, Astrovirus; 2 Shigella spp./EIEC, Salmonella spp., Campylobacter spp.; 3 Yersinia enterocolitica and Yersinia pseudotuberculosis; 4 E. coli: EIEC (enteroinvasive, EPEC (enteropathogenic, ETEC (enterotoxigenic, EHEC (enterohaemorrhagic, EAgEC (enteroaggregative. It has been shown that the viral intestinal infections is increased by 14%, bacterial — in 2,5 times. PCR diagnostics identified in 62% of patients the viral gastroenteritis: Rotavirus (52%, Norovirus (9%, Astrovirus (1%. Detected bacterial pathogens PCR markers number proved up to 2.5 times high than according to bacteriological examination. The spectrum of bacterial agents increased due to E. coli and Y. enterocolitica. PCR diagnostics increased detection of Campylobacter up to 2 times. Detected E. coli DNA prevalence: EPEC — 66%, EAgEC, ETEC and EHEC were 31%, 9% and 4%, respectively. DNA Campylobacter spp. and E. coli constituted 2/3 of all findings: Campylobacter spp. (41%, E. coli (24%, Salmonella spp. (19%, Yersinia spp. (11%, Shigella spp./EIEC (5%. The positive results of bacteriological and serological methods duplicate the positive results of PCR diagnostics. In general, the positive results of PCR diagnosis of bacterial pathogens were detected in 46.35% of the examined patients. In 48.4% of patients identified PCR markers viral — bacterial infection, in 5.25% — of bacterial associations, in 11% of them were found the DNA 2–3 bacterial pathogens. The study was shown in children in St. Petersburg in 2012–2014 dominated rotavirus infection, campylobacteriosis and escherichiosis. The prevalence of viral-bacterial confections is more

  2. Evaluation of the results of acute viral gastroenteritis data in Refik Saydam National Public Health Agency, Virology Reference and Research Laboratory in 2009

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    Nurhan ALBAYRAK

    2011-01-01

    Full Text Available Objective: Norovirus, Rotavirus, Adenovirus and Astrovirus are responsible for most non-bacterial acute gastroenteritis. The incidence of these viral agents in Turkey is not well known. In this study, it was aimed to document the viral etiology of the stool samples which were send to Refik Saydam National Public Health Agency (RSNPHA, Virology Reference and Research Laboratory for investigation of viral acute gastroenteritis agents. Method: A total of 147 stool samples from 11 different provinces were send to the Virology Laboratory for Reference and Research of RSNPHA in 2009. Samples were collected from patients admitted because of acute gastroenteritis and from the cases with the signs of illness at different times of the year and sent by the Provincial Health Directorates to our laboratory. The samples were examined in the laboratory using the commercial multiplex real-time PCR kit for norovirus genotype I, norovirus genotype II, rotavirus, adenovirus and astrovirus. Results: 65 (44.2 % samples were found to be positive at least for one viral agent and 10 (6.8 % samples for more than one viral agent. Norovirus (particularly genotype II infections were detected as the most prevalent viral agent in acute gastroenteritis patients in this period. Rotavirus infections were determined as the second most common infection after norovirus infections. Adenovirus infections have been found to be the least prevalent agent in the laboratory. Conclusion: Results of this study showed that norovirus genotype II has been more commonly responsible for acute diarrhea than the other viral pathogens. The viral agents we have studied should be considered as pathogens that can be seen in all seasons. Viral factors should not be underestimated as the cause of acute gastroenteritis; additionally it should be noted that acute gastroenteritis could be caused by coinfection of viral agents.

  3. Hepatitis Virus Infections in Poultry.

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    Yugo, Danielle M; Hauck, Ruediger; Shivaprasad, H L; Meng, Xiang-Jin

    2016-09-01

    Viral hepatitis in poultry is a complex disease syndrome caused by several viruses belonging to different families including avian hepatitis E virus (HEV), duck hepatitis B virus (DHBV), duck hepatitis A virus (DHAV-1, -2, -3), duck hepatitis virus Types 2 and 3, fowl adenoviruses (FAdV), and turkey hepatitis virus (THV). While these hepatitis viruses share the same target organ, the liver, they each possess unique clinical and biological features. In this article, we aim to review the common and unique features of major poultry hepatitis viruses in an effort to identify the knowledge gaps and aid the prevention and control of poultry viral hepatitis. Avian HEV is an Orthohepevirus B in the family Hepeviridae that naturally infects chickens and consists of three distinct genotypes worldwide. Avian HEV is associated with hepatitis-splenomegaly syndrome or big liver and spleen disease in chickens, although the majority of the infected birds are subclinical. Avihepadnaviruses in the family of Hepadnaviridae have been isolated from ducks, snow geese, white storks, grey herons, cranes, and parrots. DHBV evolved with the host as a noncytopathic form without clinical signs and rarely progressed to chronicity. The outcome for DHBV infection varies by the host's ability to elicit an immune response and is dose and age dependent in ducks, thus mimicking the pathogenesis of human hepatitis B virus (HBV) infections and providing an excellent animal model for human HBV. DHAV is a picornavirus that causes a highly contagious virus infection in ducks with up to 100% flock mortality in ducklings under 6 wk of age, while older birds remain unaffected. The high morbidity and mortality has an economic impact on intensive duck production farming. Duck hepatitis virus Types 2 and 3 are astroviruses in the family of Astroviridae with similarity phylogenetically to turkey astroviruses, implicating the potential for cross-species infections between strains. Duck astrovirus (DAstV) causes

  4. Absence of Genetic Differences among G10P[11] Rotaviruses Associated with Asymptomatic and Symptomatic Neonatal Infections in Vellore, India

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    Libonati, Margaret H.; Dennis, Allison F.; Ramani, Sasirekha; McDonald, Sarah M.; Akopov, Asmik; Kirkness, Ewen F.; Kang, Gagandeep

    2014-01-01

    ABSTRACT Rotaviruses (RVs) are leading causes of severe diarrhea and vomiting in infants and young children. RVs with G10P[11] genotype specificity have been associated with symptomatic and asymptomatic neonatal infections in Vellore, India. To identify possible viral genetic determinants responsible for differences in symptomology, the genome sequences of G10P[11] RVs in stool samples of 19 neonates with symptomatic infections and 20 neonates with asymptomatic infections were determined by Sanger and next-generation sequencing. The data showed that all 39 viruses had identical genotype constellations (G10-P[11]-I2-R2-C2-M2-A1-N1-T1-E2-H3), the same as those of the previously characterized symptomatic N155 Vellore isolate. The data also showed that the RNA and deduced protein sequences of all the Vellore G10P[11] viruses were nearly identical; no nucleotide or amino acid differences were found that correlated with symptomatic versus asymptomatic infection. Next-generation sequencing data revealed that some stool samples, both from neonates with symptomatic infections and from neonates with asymptomatic infections, also contained one or more positive-strand RNA viruses (Aichi virus, astrovirus, or salivirus/klassevirus) suspected of being potential causes of pediatric gastroenteritis. However, none of the positive-strand RNA viruses could be causally associated with the development of symptoms. These results indicate that the diversity of clinical symptoms in Vellore neonates does not result from genetic differences among G10P[11] RVs; instead, other undefined factors appear to influence whether neonates develop gastrointestinal disease symptoms. IMPORTANCE Rotavirus (RV) strains have been identified that preferentially replicate in neonates, in some cases, without causing gastrointestinal disease. Surveillance studies have established that G10P[11] RVs are a major cause of neonatal infection in Vellore, India, with half of infected neonates exhibiting symptoms. We

  5. Proceedings of the 2015 National Toxicology Program Satellite Symposium.

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    Elmore, Susan A; Farman, Cindy A; Hailey, James R; Kovi, Ramesh C; Malarkey, David E; Morrison, James P; Neel, Jennifer; Pesavento, Patricia A; Porter, Brian F; Szabo, Kathleen A; Teixeira, Leandro B C; Quist, Erin M

    2016-06-01

    The 2015 Annual National Toxicology Program Satellite Symposium, entitled "Pathology Potpourri" was held in Minneapolis, Minnesota, at the American College of Veterinary Pathologists/American Society for Veterinary Clinical Pathology/Society of Toxicologic Pathology combined meeting. The goal of this symposium is to present and discuss diagnostic pathology challenges or nomenclature issues. Because of the combined meeting, both laboratory and domestic animal cases were presented. This article presents summaries of the speakers' talks, including challenging diagnostic cases or nomenclature issues that were presented, along with select images that were used for audience voting and discussion. Some lesions and topics covered during the symposium included hepatocellular lesions, a proposed harmonized diagnostic approach to rat cardiomyopathy, crop milk in a bird, avian feeding accoutrement, heat exchanger in a tuna, metastasis of a tobacco carcinogen-induced pulmonary carcinoma, neurocytoma in a rat, pituicytoma in a rat, rodent mammary gland whole mounts, dog and rat alveolar macrophage ultrastructure, dog and rat pulmonary phospholipidosis, alveolar macrophage aggregation in a dog, degenerating yeast in a cat liver aspirate, myeloid leukemia in lymph node aspirates from a dog, Trypanosoma cruzi in a dog, solanum toxicity in a cow, bovine astrovirus, malignant microglial tumor, and nomenclature challenges from the Special Senses International Harmonization of Nomenclature and Diagnostic Criteria Organ Working Group. PMID:27075180

  6. Surveillance of Food- and Smear-Transmitted Pathogens in European Soldiers with Diarrhea on Deployment in the Tropics: Experience from the European Union Training Mission (EUTM) Mali

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    Frickmann, Hagen; Warnke, Philipp; Frey, Claudia; Schmidt, Salvatore; Janke, Christian; Erkens, Kay; Schotte, Ulrich; Köller, Thomas; Maaßen, Winfried; Podbielski, Andreas; Binder, Alfred; Hinz, Rebecca; Queyriaux, Benjamin; Wiemer, Dorothea; Schwarz, Norbert Georg; Hagen, Ralf Matthias

    2015-01-01

    Introduction. Since 2013, European soldiers have been deployed on the European Union Training Mission (EUTM) in Mali. From the beginning, diarrhea has been among the most “urgent” concerns. Diarrhea surveillance based on deployable real-time PCR equipment was conducted between December 2013 and August 2014. Material and Methods. In total, 53 stool samples were obtained from 51 soldiers with acute diarrhea. Multiplex PCR panels comprised enteroinvasive bacteria, diarrhea-associated Escherichia coli (EPEC, ETEC, EAEC, and EIEC), enteropathogenic viruses, and protozoa. Noroviruses were characterized by sequencing. Cultural screening for Enterobacteriaceae with extended-spectrum beta-lactamases (ESBL) with subsequent repetitive sequence-based PCR (rep-PCR) typing was performed. Clinical information was assessed. Results. Positive PCR results for diarrhea-associated pathogens were detected in 43/53 samples, comprising EPEC (n = 21), ETEC (n = 19), EAEC (n = 15), Norovirus (n = 10), Shigella spp./EIEC (n = 6), Cryptosporidium parvum (n = 3), Giardia duodenalis (n = 2), Salmonella spp. (n = 1), Astrovirus (n = 1), Rotavirus (n = 1), and Sapovirus (n = 1). ESBL-positive Enterobacteriaceae were grown from 13 out of 48 samples. Simultaneous infections with several enteropathogenic agents were observed in 23 instances. Symptoms were mild to moderate. There were hints of autochthonous transmission. Conclusions. Multiplex real-time PCR proved to be suitable for diarrhea surveillance on deployment. Etiological attribution is challenging in cases of detection of multiple pathogens. PMID:26525953

  7. Surveillance of Food- and Smear-Transmitted Pathogens in European Soldiers with Diarrhea on Deployment in the Tropics: Experience from the European Union Training Mission (EUTM Mali

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    Hagen Frickmann

    2015-01-01

    Full Text Available Introduction. Since 2013, European soldiers have been deployed on the European Union Training Mission (EUTM in Mali. From the beginning, diarrhea has been among the most “urgent” concerns. Diarrhea surveillance based on deployable real-time PCR equipment was conducted between December 2013 and August 2014. Material and Methods. In total, 53 stool samples were obtained from 51 soldiers with acute diarrhea. Multiplex PCR panels comprised enteroinvasive bacteria, diarrhea-associated Escherichia coli (EPEC, ETEC, EAEC, and EIEC, enteropathogenic viruses, and protozoa. Noroviruses were characterized by sequencing. Cultural screening for Enterobacteriaceae with extended-spectrum beta-lactamases (ESBL with subsequent repetitive sequence-based PCR (rep-PCR typing was performed. Clinical information was assessed. Results. Positive PCR results for diarrhea-associated pathogens were detected in 43/53 samples, comprising EPEC (n=21, ETEC (n=19, EAEC (n=15, Norovirus (n=10, Shigella spp./EIEC (n=6, Cryptosporidium parvum (n=3, Giardia duodenalis (n=2, Salmonella spp. (n=1, Astrovirus (n=1, Rotavirus (n=1, and Sapovirus (n=1. ESBL-positive Enterobacteriaceae were grown from 13 out of 48 samples. Simultaneous infections with several enteropathogenic agents were observed in 23 instances. Symptoms were mild to moderate. There were hints of autochthonous transmission. Conclusions. Multiplex real-time PCR proved to be suitable for diarrhea surveillance on deployment. Etiological attribution is challenging in cases of detection of multiple pathogens.

  8. A non-enteric adenovirus A12 gastroenteritis outbreak in Rio de Janeiro, Brazil

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    Portes, Silvana Augusta Rodrigues; Volotão, Eduardo de Mello; Rocha, Monica Simões; Rebelo, Maria Cristina; Xavier, Maria da Penha Trindade Pinheiro; de Assis, Rosane Maria; Rose, Tatiana Lundgren; Miagostovich, Marize Pereira; Leite, José Paulo Gagliardi; Carvalho-Costa, Filipe Anibal

    2016-01-01

    A gastroenteritis outbreak that occurred in 2013 in a low-income community in Rio de Janeiro was investigated for the presence of enteric viruses, including species A rotavirus (RVA), norovirus (NoV), astrovirus (HAstV), bocavirus (HBoV), aichivirus (AiV), and adenovirus (HAdV). Five of nine stool samples (83%) from patients were positive for HAdV, and no other enteric viruses were detected. Polymerase chain reaction products were sequenced and subjected to phylogenetic analysis, which revealed four strains and one strain of non-enteric HAdV-A12 and HAdV-F41, respectively. The HAdV-A12 nucleotide sequences shared 100% nucleotide similarity. Viral load was assessed using a TaqMan real-time PCR assay. Stool samples that were positive for HAdV-A12 had high viral loads (mean 1.9 X 107 DNA copies/g stool). All four patients with HAdV-A12 were < 25 months of age and had symptoms of fever and diarrhoea. Evaluation of enteric virus outbreaks allows the characterisation of novel or unique diarrhoea-associated viruses in regions where RVA vaccination is routinely performed. PMID:27223654

  9. Comparative pathology of infection by novel diarrhoea viruses.

    Science.gov (United States)

    Hall, G A

    1987-01-01

    Examination of diarrhoeic faeces in the electron microscope often reveals viruses that are presumed to be enteropathogenic. Lesions caused by novel rotaviruses were similar to those of group A rotaviruses, but enterocyte syncytia were seen which are probably pathognomonic for novel rotaviruses. In adenovirus infection in piglets, mature enterocytes were infected and destroyed; intranuclear inclusion bodies were seen in infected enterocytes. Calici-like viruses infected mature enterocytes in calves and the lesions were similar to those described in humans infected with calici-like viruses; in both host species it was impossible to demonstrate virus particles in enterocytes examined in the electron microscope. The Breda virus infected villi and crypts in the lower small intestine and the surface and crypts in the large intestine; it was the only enteropathogenic virus to show this distribution of infection and lesions. Astrovirus infection in lambs was comparable to a mild rotavirus infection, but in calves the epithelium of the dome villi of Peyer's patches was infected. Parvovirus in cats and dogs infected and destroyed small intestinal crypt cells, causing dilated crypts and stunted villi; intranuclear inclusion bodies were prominent. PMID:3036441

  10. Risk factors for gastroenteritis in child day care.

    Science.gov (United States)

    Enserink, R; Mughini-Gras, L; Duizer, E; Kortbeek, T; Van Pelt, W

    2015-10-01

    The child day-care centre (DCC) is often considered as one risk factor for gastroenteritis (GE) rather than a complex setting in which the interplay of many factors may influence the epidemiology of GE. This study aimed to identify DCC-level risk factors for GE and major enteropathogen occurrence. A dynamic network of 100 and 43 DCCs participated in a syndromic and microbiological surveillance during 2010-2013. The weekly incidence of GE events and weekly prevalence of five major enteropathogens (rotavirus, norovirus, astrovirus, Giardia lamblia, Cryptosporidium hominis/parvum) were modelled per DCC using mixed-effects negative binomial/Poisson regression models. Sixteen hundred children were surveyed up to 3 years, during which 1829 GE episodes were reported and 5197 faecal samples were analysed. Identified risk factors were: large DCC capacity, crowding, having animals, nappy changing areas, sandpits, paddling pools, cleaning potties in normal sinks, cleaning vomit with paper towels (but without cleaner), mixing of staff between child groups, and staff members with multiple daily duties. Protective factors were: disinfecting fomites with chlorine, cleaning vomit with paper towels (and cleaner), daily cleaning of bed linen/toys, cohorting and exclusion policies for ill children and staff. Targeting these factors may reduce the burden of DCC-related GE. PMID:25592679

  11. Development of the Intestinal RNA Virus Community of Healthy Broiler Chickens.

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    Jigna D Shah

    Full Text Available Several RNA viruses such as astrovirus, rotavirus, reovirus and parvovirus have been detected in both healthy and diseased commercial poultry flocks. The aim of this study was to characterize (a the development of the RNA viral community in the small intestines of healthy broiler chickens from hatch through 6 weeks of age (market age and (b the contribution of the breeder source vs. bird age in development of the community structure. Intestinal tissue samples were harvested from breeders and their progeny, processed for viral RNA extraction and sequenced using Illumina Hiseq sequencing technology resulting in 100 bp PE reads. The results from this study indicated that the breeder source influenced the RNA viral community only at hatch but later environment i.e. bird age had the more significant effect. The most abundant RNA viral family detected at 2, 4 and 6 weeks of age was Astroviridae, which decreased in abundance with age while the abundance of Picornaviridae increased with age.

  12. Molecular detection of chicken parvovirus in broilers with enteric disorders presenting curving of duodenal loop, pancreatic atrophy, and mesenteritis.

    Science.gov (United States)

    Nuñez, L F N; Sá, L R M; Parra, S H S; Astolfi-Ferreira, C S; Carranza, C; Ferreira, A J P

    2016-04-01

    Enteric disorders are an important cause of economic losses in broiler chickens worldwide. Several agents have been associated with enteric problems, such as viruses, bacteria, and parasites. In this study, broiler chickens showing signs of enteric disorders were subjected to molecular diagnosis for several viral agents and also for pathological examination for elucidating this problem. Thus, the chickens were screened for avian nephritis virus (ANV), chicken astrovirus (CAstV), avian rotavirus (ArtV), avian reovirus (AReoV), infectious bronchitis virus (IBV), fowl adenovirus group I (FAdV-1), and chicken parvovirus (ChPV). Postmortem examinations revealed a curving of the duodenal loop (J-like appearance) and intestines filled with liquid and gaseous content. Histopathological analysis of the duodenal loop showed pancreatic atrophy, acute mesenteritis, and enteritis. PCR results showed that ChPV was the sole viral agent detected in samples with lesions such as the curved duodenal loop and pancreatic atrophy. Molecular characterization of the nucleotide and deduced amino acid sequences revealed a high similarity with other strains of ChPV from Brazil, Canada, United States, Europe, and Asia. These findings suggest an association between ChPV and the development of enteritis, pancreatitis, and pancreatic atrophy, which may lead to curling of the duodenal loop. Together, these alterations may disrupt the normal functioning of the digestive system, diminishing digestion and the absorption of dietary nutrients and consequently leading to reduced weight gain, flock impairment, dwarfism, and an elevated feed conversion rate. PMID:26908891

  13. A non-enteric adenovirus A12 gastroenteritis outbreak in Rio de Janeiro, Brazil

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    Silvana Augusta Rodrigues Portes

    2016-06-01

    Full Text Available A gastroenteritis outbreak that occurred in 2013 in a low-income community in Rio de Janeiro was investigated for the presence of enteric viruses, including species A rotavirus (RVA, norovirus (NoV, astrovirus (HAstV, bocavirus (HBoV, aichivirus (AiV, and adenovirus (HAdV. Five of nine stool samples (83% from patients were positive for HAdV, and no other enteric viruses were detected. Polymerase chain reaction products were sequenced and subjected to phylogenetic analysis, which revealed four strains and one strain of non-enteric HAdV-A12 and HAdV-F41, respectively. The HAdV-A12 nucleotide sequences shared 100% nucleotide similarity. Viral load was assessed using a TaqMan real-time PCR assay. Stool samples that were positive for HAdV-A12 had high viral loads (mean 1.9 X 107 DNA copies/g stool. All four patients with HAdV-A12 were < 25 months of age and had symptoms of fever and diarrhoea. Evaluation of enteric virus outbreaks allows the characterisation of novel or unique diarrhoea-associated viruses in regions where RVA vaccination is routinely performed.

  14. Large scale survey of enteric viruses in river and waste water underlines the health status of the local population.

    Science.gov (United States)

    Prevost, B; Lucas, F S; Goncalves, A; Richard, F; Moulin, L; Wurtzer, S

    2015-06-01

    Although enteric viruses constitute a major cause of acute waterborne diseases worldwide, environmental data about occurrence and viral load of enteric viruses in water are not often available. In this study, enteric viruses (i.e., adenovirus, aichivirus, astrovirus, cosavirus, enterovirus, hepatitis A and E viruses, norovirus of genogroups I and II, rotavirus A and salivirus) were monitored in the Seine River and the origin of contamination was untangled. A total of 275 water samples were collected, twice a month for one year, from the river Seine, its tributaries and the major WWTP effluents in the Paris agglomeration. All water samples were negative for hepatitis A and E viruses. AdV, NVGI, NVGII and RV-A were the most prevalent and abundant populations in all water samples. The viral load and the detection frequency increased significantly between the samples collected the most upstream and the most downstream of the Paris urban area. The calculated viral fluxes demonstrated clearly the measurable impact of WWTP effluents on the viral contamination of the Seine River. The viral load was seasonal for almost all enteric viruses, in accordance with the gastroenteritis recordings provided by the French medical authorities. These results implied the existence of a close relationship between the health status of inhabitants and the viral contamination of WWTP effluents and consequently surface water contamination. Subsequently, the regular analysis of wastewater could serve as a proxy for the monitoring of the human viruses circulating in both a population and surface water. PMID:25795193

  15. Eight different viral agents in childhood acute gastroenteritis.

    Science.gov (United States)

    Bozkurt, Derya; Selimoğlu, Mukadder Ayşe; Otlu, Barış; Sandıkkaya, Ayşe

    2015-01-01

    Viral gastroenteritis is the most frequent cause of acute gastroenteritis (AGE) of childhood. The aim of this study was to determine the prevalence of viral agents including astrovirus, rotavirus, adenovirus, enterovirus, norovirus, parechovirus, Aichivirus and sapovirus in children with AGE in a pediatric Turkish population. Fecal specimens of 240 children with AGE were investigated by polymerase chain reaction, and viral agents were identified in 131 (54.6%) samples. The distribution of viral agents was as follows: 56 (42.8%) norovirus, 44 (33.6%) rotavirus, 29 (22.1%) enterovirus, 21 (16.0%) adenovirus, 21 (16.0%) parechovirus, 5 (3.8%) sapovirus and 1 (0.8%) Aichivirus. Single and multiple viral agents were detected in 38.8% and 15.8% of patients, respectively. The duration of hospitalization was longer in children with multiple viral agents than in those infected with a single viral agent (p<0.001). While the highest rate of rotavirus infection was detected in winter, the highest rate of norovirus was found in the summer. In conclusion, norovirus and rotavirus are the most frequent causes of childhood AGE in our country. PMID:26613223

  16. [Diagnosis and molecular epidemiology of viral gastroenteritis in the past, present and future].

    Science.gov (United States)

    Ushijima, Hiroshi

    2009-06-01

    Outline, history of research, diagnosis and molecular epidemiology of viral gastroenteritis were described. Rotavirus, adenovirus, norovirus, sapovirus, astrovirus, human parechovirus, Aichivirus, and human bocavirus are the major target viruses which cause acute gastroenteritis. The viruses were differentiated into genogroup, genotypes and subgenotypes/clusters/lineages. The changing of their genetic backgrounds was well recognized in different areas and years. Some reassortments or recombinations were observed not only between humans and humans but also between humans and animals. Viral gastroenteritis diseases were transmitted by food-borne and humans to humans contact. The environmental factors were also impacted on the infections. Recently, situation of the diseases in the natural ecosystem is becoming clearly. Diagnoses by immunological methods and gene technology are available for the known viruses. Further development of diagnosis and discovery of new viruses will be expected. Therefore, the research on molecular epidemiology is needed to be conducted continuously and then new findings will appear. We need to precede the research by using new techniques and we need to cope with the demand of society especially during acute gastroenteritis outbreak seasons. PMID:19927992

  17. A non-enteric adenovirus A12 gastroenteritis outbreak in Rio de Janeiro, Brazil.

    Science.gov (United States)

    Portes, Silvana Augusta Rodrigues; Volotão, Eduardo de Mello; Rocha, Monica Simões; Rebelo, Maria Cristina; Xavier, Maria da Penha Trindade Pinheiro; Assis, Rosane Maria de; Rose, Tatiana Lundgren; Miagostovich, Marize Pereira; Leite, José Paulo Gagliardi; Carvalho-Costa, Filipe Anibal

    2016-05-24

    A gastroenteritis outbreak that occurred in 2013 in a low-income community in Rio de Janeiro was investigated for the presence of enteric viruses, including species A rotavirus (RVA), norovirus (NoV), astrovirus (HAstV), bocavirus (HBoV), aichivirus (AiV), and adenovirus (HAdV). Five of nine stool samples (83%) from patients were positive for HAdV, and no other enteric viruses were detected. Polymerase chain reaction products were sequenced and subjected to phylogenetic analysis, which revealed four strains and one strain of non-enteric HAdV-A12 and HAdV-F41, respectively. The HAdV-A12 nucleotide sequences shared 100% nucleotide similarity. Viral load was assessed using a TaqMan real-time PCR assay. Stool samples that were positive for HAdV-A12 had high viral loads (mean 1.9 X 107 DNA copies/g stool). All four patients with HAdV-A12 were < 25 months of age and had symptoms of fever and diarrhoea. Evaluation of enteric virus outbreaks allows the characterisation of novel or unique diarrhoea-associated viruses in regions where RVA vaccination is routinely performed. PMID:27223654

  18. 2009-2010年湖南省哨点医院婴幼儿病毒性腹泻病原学研究%Etiological Study on Viral Diarrhea Among Infants and Young Children in Surveillance Hospitals of Hunan Province from 2009 to 2010

    Institute of Scientific and Technical Information of China (English)

    李俊华; 刘富强; 陈雨; 张红; 周帅锋; 刘运芝; 邓志红; 黄威; 李丹地; 张帆; 姚正才; 袁丹

    2012-01-01

    Objective To investigate the etiological characteristics of common diarrhea viruses in sentinel hospitals of Hunan Province from 2009 to 2010, and to provide the scientific reference for comprehensive prevention and treatment of viral diarrhea. Methods A total of 759 stool specimens were collected from children less than 5 years old with an acute gastroenteritis admitted to surveillance hospitals of Hunan Province from 2009 to 2010. Dako- IDEIATM kits were used for detection of rota-virus, and the strain characterization of rotavirus was carried out with reverse transcription- polymerase chain reactions (RT-PCR). The detection of calicivirus, adenovirus and astrovirus was done by multiple RT- PCR. Part of the PCR products (DNA) which were positive for samples of calicivirus, adenovirus and astrovirus were analyzed by nucleotide sequencing, respectively. Results Rotavirus was detected in 22.79% (173/759) of all cases, calicivirus detected in 9.22% (70/759), adenovirus detected in 4.61% (35/759), and astrovirus detected in 0.79% (6/759), respectively. Mix infections were found in 2.50% (19/759) of all samples. Among 173 rotavirus positive samples, serotypes G1, G3 and P[4] were the most predominant strains. The four types of diarrhea viruses mostly attacked the children less than 2 years old, and moreover, the seasonal variations of viral diarrhea were obvious. Sequence analysis showed that the 12 positive strains were confirmed as the corresponding virus. Conclusions Rotavirus was the main pathogen for viral diarrhea in surveillance hospitals of Hunan Province from 2009 to 2010, followed by calicivirus, adenovirus and astrovirus.%目的 了解湖南省哨点医院2009-2010年常见腹泻病毒的病原学特征,为病毒性腹泻的综合防治提供科学依据. 方法 收集湖南省哨点医院2009-2010年5岁以下住院腹泻患儿的粪便标本,采用Dako公司酶免疫试剂盒检测轮状病毒,采用逆转录-聚合酶联反应(RT-PCR)进行分型鉴定

  19. Acute gastroenteritis and enteric viruses in hospitalised children in southern Brazil: aetiology, seasonality and clinical outcomes

    Directory of Open Access Journals (Sweden)

    Sonia Maria Raboni

    2014-07-01

    Full Text Available Viral acute gastroenteritis (AG is a significant cause of hospitalisation in children younger than five years. Group A rotavirus (RVA is responsible for 30% of these cases. Following the introduction of RVA immunisation in Brazil in 2006, a decreased circulation of this virus has been observed. However, AG remains an important cause of hospitalisation of paediatric patients and only limited data are available regarding the role of other enteric viruses in these cases. We conducted a prospective study of paediatric patients hospitalised for AG. Stool samples were collected to investigate human adenovirus (HAdV, RVA, norovirus (NoV and astrovirus (AstV. NoV typing was performed by nucleotide sequencing and phylogenetic analysis. From the 225 samples tested, 60 (26% were positive for at least one viral agent. HAdV, NoV, RVA and AstV were detected in 16%, 8%, 6% and 0% of the samples, respectively. Mixed infections were found in nine patients: HAdV/RVA (5, HAdV/NoV (3 and HAdV/NoV/RVA (1. The frequency of fever and lymphocytosis was significantly higher in virus-infected patients. Phylogenetic analysis of NoV indicated that all of these viruses belonged to genotype GII.4. The significant frequency of these pathogens in patients with AG highlights the need to routinely implement laboratory investigations.

  20. Molecular detection of chicken parvovirus in broilers with enteric disorders presenting curving of duodenal loop, pancreatic atrophy, and mesenteritis.

    Science.gov (United States)

    Nuñez, L F N; Sá, L R M; Parra, S H S; Astolfi-Ferreira, C S; Carranza, C; Ferreira, A J P

    2016-04-01

    Enteric disorders are an important cause of economic losses in broiler chickens worldwide. Several agents have been associated with enteric problems, such as viruses, bacteria, and parasites. In this study, broiler chickens showing signs of enteric disorders were subjected to molecular diagnosis for several viral agents and also for pathological examination for elucidating this problem. Thus, the chickens were screened for avian nephritis virus (ANV), chicken astrovirus (CAstV), avian rotavirus (ArtV), avian reovirus (AReoV), infectious bronchitis virus (IBV), fowl adenovirus group I (FAdV-1), and chicken parvovirus (ChPV). Postmortem examinations revealed a curving of the duodenal loop (J-like appearance) and intestines filled with liquid and gaseous content. Histopathological analysis of the duodenal loop showed pancreatic atrophy, acute mesenteritis, and enteritis. PCR results showed that ChPV was the sole viral agent detected in samples with lesions such as the curved duodenal loop and pancreatic atrophy. Molecular characterization of the nucleotide and deduced amino acid sequences revealed a high similarity with other strains of ChPV from Brazil, Canada, United States, Europe, and Asia. These findings suggest an association between ChPV and the development of enteritis, pancreatitis, and pancreatic atrophy, which may lead to curling of the duodenal loop. Together, these alterations may disrupt the normal functioning of the digestive system, diminishing digestion and the absorption of dietary nutrients and consequently leading to reduced weight gain, flock impairment, dwarfism, and an elevated feed conversion rate.

  1. Viral metagenomics analysis demonstrates the diversity of viral flora in piglet diarrhoeic faeces in China.

    Science.gov (United States)

    Zhang, Bin; Tang, Cheng; Yue, Hua; Ren, Yupeng; Song, Zhigang

    2014-07-01

    To investigate the diversity of viral flora, we used metagenomics to study the viral communities in a pooled faecal sample of 27 diarrhoeic piglets from intensive commercial farms in China. The 15 distinct mammalian viruses identified in the pooled diarrhoeic sample were, in order of abundance of nucleic acid sequence, Porcine epidemic diarrhea virus (PEDV), sapovirus, porcine bocavirus-4 (PBoV-4), sapelovirus, torovirus, coronavirus, PBoV-2, stool-associated single-stranded DNA virus (poSCV), astrovirus (AstV), kobuvirus, posavirus-1, porcine enterovirus-9 (PEV-9), porcine circovirus-like (po-circo-like) virus, picobirnavirus (PBV) and Torque teno sus virus 2 (TTSuV-2). The prevalence rate of each virus was verified from diarrhoeic and healthy piglets by PCR assay. A mean of 5.5 different viruses were shed in diarrhoeic piglets, and one piglet was in fact co-infected with 11 different viruses. By contrast, healthy piglets shed a mean of 3.2 different viruses. Compared with samples from healthy piglets, the co-infection of PEDV and PBoV had a high prevalence rate in diarrhoea samples, suggesting a correlation with the appearance of diarrhoea in piglets. Furthermore, we report here for the first time the presence of several recently described viruses in China, and the identification of novel genotypes. Therefore, our investigation results provide an unbiased survey of viral communities and prevalence in faecal samples of piglets.

  2. Viral infections of rabbits.

    Science.gov (United States)

    Kerr, Peter J; Donnelly, Thomas M

    2013-05-01

    Viral diseases of rabbits have been used historically to study oncogenesis (e.g. rabbit fibroma virus, cottontail rabbit papillomavirus) and biologically to control feral rabbit populations (e.g. myxoma virus). However, clinicians seeing pet rabbits in North America infrequently encounter viral diseases although myxomatosis may be seen occasionally. The situation is different in Europe and Australia, where myxomatosis and rabbit hemorrhagic disease are endemic. Advances in epidemiology and virology have led to detection of other lapine viruses that are now recognized as agents of emerging infectious diseases. Rabbit caliciviruses, related to rabbit hemorrhagic disease, are generally avirulent, but lethal variants are being identified in Europe and North America. Enteric viruses including lapine rotavirus, rabbit enteric coronavirus and rabbit astrovirus are being acknowledged as contributors to the multifactorial enteritis complex of juvenile rabbits. Three avirulent leporid herpesviruses are found in domestic rabbits. A fourth highly pathogenic virus designated leporid herpesvirus 4 has been described in Canada and Alaska. This review considers viruses affecting rabbits by their clinical significance. Viruses of major and minor clinical significance are described, and viruses of laboratory significance are mentioned. PMID:23642871

  3. Novel divergent nidovirus in a python with pneumonia.

    Science.gov (United States)

    Bodewes, Rogier; Lempp, Charlotte; Schürch, Anita C; Habierski, Andre; Hahn, Kerstin; Lamers, Mart; von Dörnberg, Katja; Wohlsein, Peter; Drexler, Jan Felix; Haagmans, Bart L; Smits, Saskia L; Baumgärtner, Wolfgang; Osterhaus, Albert D M E

    2014-11-01

    The order Nidovirales contains large, enveloped viruses with a non-segmented positive-stranded RNA genome. Nidoviruses have been detected in man and various animal species, but, to date, there have been no reports of nidovirus in reptiles. In the present study, we describe the detection, characterization, phylogenetic analyses and disease association of a novel divergent nidovirus in the lung of an Indian python (Python molurus) with necrotizing pneumonia. Characterization of the partial genome (>33 000 nt) of this virus revealed several genetic features that are distinct from other nidoviruses, including a very large polyprotein 1a, a putative ribosomal frameshift signal that was identical to the frameshift signal of astroviruses and retroviruses and an accessory ORF that showed some similarity with the haemagglutinin-neuraminidase of paramyxoviruses. Analysis of genome organization and phylogenetic analysis of polyprotein 1ab suggests that this virus belongs to the subfamily Torovirinae. Results of this study provide novel insights into the genetic diversity within the order Nidovirales.

  4. New viruses in veterinary medicine, detected by metagenomic approaches.

    Science.gov (United States)

    Belák, Sándor; Karlsson, Oskar E; Blomström, Anne-Lie; Berg, Mikael; Granberg, Fredrik

    2013-07-26

    In our world, which is faced today with exceptional environmental changes and dramatically intensifying globalisation, we are encountering challenges due to many new factors, including the emergence or re-emergence of novel, so far "unknown" infectious diseases. Although a broad arsenal of diagnostic methods is at our disposal, the majority of the conventional diagnostic tests is highly virus-specific or is targeted entirely towards a limited group of infectious agents. This specificity complicates or even hinders the detection of new or unexpected pathogens, such as new, emerging or re-emerging viruses or novel viral variants. The recently developed approaches of viral metagenomics provide an effective novel way to screen samples and detect viruses without previous knowledge of the infectious agent, thereby enabling a better diagnosis and disease control, in line with the "One World, One Health" principles (www.oneworldonehealth.org). Using metagenomic approaches, we have recently identified a broad variety of new viruses, such as novel bocaviruses, Torque Teno viruses, astroviruses, rotaviruses and kobuviruses in porcine disease syndromes, new virus variants in honeybee populations, as well as a range of other infectious agents in further host species. These findings indicate that the metagenomic detection of viral pathogens is becoming now a powerful, cultivation-independent, and useful novel diagnostic tool in veterinary diagnostic virology. PMID:23428379

  5. Detection of enteric pathogens in Turkey flocks affected with severe enteritis, in Brazil.

    Science.gov (United States)

    Moura-Alvarez, Joelma; Nuñez, Luis F N; Astolfi-Ferreira, Claudete S; Knöbl, Terezinha; Chacón, Jorge L; Moreno, Andrea M; Jones, Richard C; Ferreira, Antonio J Piantino

    2014-08-01

    Twenty-two flocks of turkeys affected by enteric problems, with ages between 10 and 104 days and located in the Southern region of Brazil, were surveyed for turkey by PCR for turkey astrovirus type 2 (TAstV-2), turkey coronavirus (TCoV), hemorrhagic enteritis virus (HEV), rotavirus, reovirus, Salmonella spp., and Lawsonia intracellularis (Li) infections. Eleven profiles of pathogen combination were observed. The most frequently encountered pathogen combinations were TCoV-Li, followed by TCoV-TAstV-2-Li, TCoV-TastV-2. Only TCoV was detected as the sole pathogen in three flocks. Eight and 19 flocks of the 22 were positive for TAstV-2 and TCoV, respectively. Six were positive for Salmonella spp. and L. intracellularis was detected in 12 turkey flocks. Reovirus and HEV were not detected in this survey. These results throw new light on the multiple etiology of enteritis in turkeys. The implications of these findings and their correlation with the clinical signs are comprehensively discussed, illustrating the complexity of the enteric diseases.

  6. Molecular characterization of viruses associated with gastrointestinal infection in HIV-positive patients

    Directory of Open Access Journals (Sweden)

    Raquel C Silva

    2010-12-01

    Full Text Available BACKGROUND: Diarrhea is a major cause of morbidity and mortality among HIV-infected patients worldwide. OBJECTIVE: We sought to determine the frequency of viral gastrointestinal infections among Brazilian HIV-infected patients with diarrhea. METHODS: A collection of 90 fecal specimens from HIV-infected individuals with diarrhea, previously tested for the presence of bacteria and parasite was analyzed by polymerase chain reaction and sequence analysis for the presence of enteric viruses such as astrovirus, norovirus, rotavirus groups A, B and C, adenovirus, herpes simplex virus, Epstein-Barr virus, cytomegalovirus, and human bocavirus. RESULTS: Twenty patients (22.2%; n = 90 were infected with parasites (11 single infections and nine coinfected with virus. Enteropathogenic bacteria were not found. Virus infections were detected in 28.9% (26/90 of the specimens. Cytomegalovirus was the most common virus detected (24.4%; 22/90. Coinfections with viruses and/or parasite were observed in 10 (11.1% samples. CONCLUSION: Gastrointestinal virus infections were more frequent than parasitic or bacterial infections in this patient population.

  7. Viral metagenomics analysis demonstrates the diversity of viral flora in piglet diarrhoeic faeces in China.

    Science.gov (United States)

    Zhang, Bin; Tang, Cheng; Yue, Hua; Ren, Yupeng; Song, Zhigang

    2014-07-01

    To investigate the diversity of viral flora, we used metagenomics to study the viral communities in a pooled faecal sample of 27 diarrhoeic piglets from intensive commercial farms in China. The 15 distinct mammalian viruses identified in the pooled diarrhoeic sample were, in order of abundance of nucleic acid sequence, Porcine epidemic diarrhea virus (PEDV), sapovirus, porcine bocavirus-4 (PBoV-4), sapelovirus, torovirus, coronavirus, PBoV-2, stool-associated single-stranded DNA virus (poSCV), astrovirus (AstV), kobuvirus, posavirus-1, porcine enterovirus-9 (PEV-9), porcine circovirus-like (po-circo-like) virus, picobirnavirus (PBV) and Torque teno sus virus 2 (TTSuV-2). The prevalence rate of each virus was verified from diarrhoeic and healthy piglets by PCR assay. A mean of 5.5 different viruses were shed in diarrhoeic piglets, and one piglet was in fact co-infected with 11 different viruses. By contrast, healthy piglets shed a mean of 3.2 different viruses. Compared with samples from healthy piglets, the co-infection of PEDV and PBoV had a high prevalence rate in diarrhoea samples, suggesting a correlation with the appearance of diarrhoea in piglets. Furthermore, we report here for the first time the presence of several recently described viruses in China, and the identification of novel genotypes. Therefore, our investigation results provide an unbiased survey of viral communities and prevalence in faecal samples of piglets. PMID:24718833

  8. Emergence of Enteric Viruses in Production Chickens Is a Concern for Avian Health

    Directory of Open Access Journals (Sweden)

    Elena Mettifogo

    2014-01-01

    Full Text Available Several viruses have been identified in recent years in the intestinal contents of chickens and turkeys with enteric problems, which have been observed in commercial farms worldwide, including Brazil. Molecular detection of these viruses in Brazil can transform to a big threat for poultry production due to risk for intestinal integrity. This disease is characterized by severely delayed growth, low uniformity, lethargy, watery diarrhea, delayed feed consumption, and a decreased conversion rate. Chicken astrovirus (CAstV, rotavirus, reovirus, chicken parvovirus (ChPV, fowl adenovirus of subgroup I (FAdV-1, and avian nephritis virus (ANV were investigated using the conventional polymerase chain reaction (PCR and the reverse transcription polymerase chain reaction (RT-PCR. In addition, the infectious bronchitis virus (IBV, which may play a role in enteric disease, was included. The viruses most frequently detected, either alone or in concomitance with other viruses, were IBV, ANV, rotavirus, and CAstV followed by parvovirus, reovirus, and adenovirus. This study demonstrates the diversity of viruses in Brazilian chicken flocks presenting enteric problems characterized by diarrhea, growth retard, loss weight, and mortality, which reflects the multicausal etiology of this disease.

  9. New viruses in veterinary medicine, detected by metagenomic approaches.

    Science.gov (United States)

    Belák, Sándor; Karlsson, Oskar E; Blomström, Anne-Lie; Berg, Mikael; Granberg, Fredrik

    2013-07-26

    In our world, which is faced today with exceptional environmental changes and dramatically intensifying globalisation, we are encountering challenges due to many new factors, including the emergence or re-emergence of novel, so far "unknown" infectious diseases. Although a broad arsenal of diagnostic methods is at our disposal, the majority of the conventional diagnostic tests is highly virus-specific or is targeted entirely towards a limited group of infectious agents. This specificity complicates or even hinders the detection of new or unexpected pathogens, such as new, emerging or re-emerging viruses or novel viral variants. The recently developed approaches of viral metagenomics provide an effective novel way to screen samples and detect viruses without previous knowledge of the infectious agent, thereby enabling a better diagnosis and disease control, in line with the "One World, One Health" principles (www.oneworldonehealth.org). Using metagenomic approaches, we have recently identified a broad variety of new viruses, such as novel bocaviruses, Torque Teno viruses, astroviruses, rotaviruses and kobuviruses in porcine disease syndromes, new virus variants in honeybee populations, as well as a range of other infectious agents in further host species. These findings indicate that the metagenomic detection of viral pathogens is becoming now a powerful, cultivation-independent, and useful novel diagnostic tool in veterinary diagnostic virology.

  10. The sensitivity and specificity of two PCR assays for detecting rabies virus%两种PCR方法检测狂犬病毒的敏感性和特异性比较

    Institute of Scientific and Technical Information of China (English)

    马莉珍; 柯雪梅; 肖建鹏; 陈清

    2011-01-01

    目的 比较Nested-PCR和SYBR Green Ⅰ Real-Time PCR两种方法检测狂犬病毒的敏感性、特异性和时效性.方法 对10倍连续稀释的狂犬病毒(疫苗株)核酸样品,采用Nested-PCR和SYBR Green Ⅰ Real-Time PCR方法进行平行检测,比较两种方法的敏感性:同时以登革热2型病毒、诺如病毒、星状病毒、EV71和乙型脑炎病毒核酸对两种方法的特异性进行评价.结果 SYBR Green Ⅰ Real-Time PCR方法可检测出2.3×106 copies/μl核酸分子,与NestedPCR方法相比,敏感度提高10倍.两种检测方法的特异性均好,与登革热2型病毒、诺如病毒、星状病毒、EV71和乙型脑炎病毒核酸均无交叉反应.SYBR Green Ⅰ Real-Time PCR方法检测花费3 h,检测时间比Nested-PCR方法节省2 h.结论 与Nested-PCR相比,SYBR Green Ⅰ Real-Time PCR是相对高效的检测狂犬病毒的方法.%Objective The aim of the study was to compare the sensitivity, specificity and time-consuming of Nested-PCR and SYBR Green I Real-Time PCR assays for detecting rabies virus (RABV). Methods A series of 10-fold dilutions of a RABV (vaccine strain) DNA was used for detection of the sensitivity of the Nested-PCR and SYBR Green I Real-Time PCR assays. EV71, Dengue type 2 virus, Norovirus, Astrovirus and Japanese encephalitis virus (JEV) were used to test the specificity of the assays. Results Sensitivity of SYBR Green I Real-Time PCR assay was 2.3×106 copies/μl which were 10 times more sensitive than that of Nested-PCR assay. There was no crossing-reaction with Dengue type 2 virus, Astrovirus,Norovirus, EV71 and JEV. The time-consuming of the SYBR Green I real-time PCR amplification was about 3 hours, 2 hours shorter than Nested-PCR. Conclusion For detection of Rabies Virus, SYBR Green I Real-Time PCR is a more sensitive and rapid assay compared with Nested-PCR.

  11. The epidemiology of acute viral gastroenteritis in hospitalized children in Cordoba city, Argentina: an insight of disease burden Epidemiologia da gastrenterite viral aguda em crianças hospitalizadas na cidade de Córdoba, Argentina: uma percepção ao impacto da doença

    Directory of Open Access Journals (Sweden)

    Miguel O. GIORDANO

    2001-08-01

    Full Text Available Information concerning the disease burden of viral gastroenteritis has important implications for the use and monitoring the impact of public health policies. The present study, carried out in Córdoba city, Argentina, documents the epidemiology of severe viral diarrhea as well as the burden of viral gastrointestinal disease in the hospital children admission. A total of 133 stools were collected from hospitalized children (Town Childhood Hospital suffering from acute diarrhea and studied for the presence of Group A rotavirus, astrovirus and adenovirus 40/41 by enzyme-immuno assay, between November 1997 and October 1998. Enteric viruses accounted for 42.1% of the total diarrheal cases analyzed. Group A rotaviruses, astroviruses, adenoviruses 40/41 and mixed infections were found in 35.3, 4.5, 1.5, and 0.8% studied specimens respectively. We estimated that 1 in 27 children in the 0-35 month-old cohort/range would be annually hospitalized for a viral gastroenteritis illness. The major impact on viral diarrhea lies on rotaviral infection, accouting for 84.0% of the viral diarrheal cases analyzed and for approximately one third of severe diarrheas requiring hospital admission in Córdoba City, Argentina.Dados a respeito do impacto das gastrenterites virais têm implicações importantes para o monitoraramento do impacto das políticas de saúde pública. O presente estudo, feito na cidade de Córdoba, Argentina, documenta a epidemiologia da diarréia viral severa como também o impacto que a mesma representa na admissão hospitalar de crianças. Pesquisou-se a presença de Rotavírus grupo A, Astrovírus e Adenovírus 40/41 por ensaio imuno-enzimático em 133 amostras de fezes obtidas durante o período de novembro de 1997 a outubro de 1998, de crianças hospitalizadas por diarréia aguda. Os virus entéricos constituíram 42,1% do total de casos de diarréia analisados. Encontraram-se Rotavírus Grupo A, Astrovírus, Adenovírus 40/41 e infec

  12. Cosavirus, Salivirus and Bufavirus in Diarrheal Tunisian Infants

    Science.gov (United States)

    Ayouni, Siwar; Estienney, Marie; Hammami, Sabeur; Neji Guediche, Mohamed; Pothier, Pierre; Aouni, Mahjoub; Belliot, Gael

    2016-01-01

    Three newly discovered viruses have been recently described in diarrheal patients: Cosavirus (CosV) and Salivirus (SalV), two picornaviruses, and Bufavirus (BuV), a parvovirus. The detection rate and the role of these viruses remain to be established in acute gastroenteritis (AGE) in diarrheal Tunisian infants. From October 2010 through March 2012, stool samples were collected from 203 children <5 years-old suffering from AGE and attending the Children’s Hospital in Monastir, Tunisia. All samples were screened for CosV, SalV and BuV as well as for norovirus (NoV) and group A rotavirus (RVA) by molecular biology. Positive samples for the three screened viruses were also tested for astrovirus, sapovirus, adenovirus, and Aichi virus, then genotyped when technically feasible. During the study period, 11 (5.4%) samples were positive for one of the three investigated viruses: 2 (1.0%) CosV-A10, 7 (3.5%) SalV-A1 and 2 (1.0%) BuV-1, whereas 71 (35.0%) children were infected with NoV and 50 (24.6%) with RVA. No mixed infections involving the three viruses were found, but multiple infections with up to 4 classic enteric viruses were found in all cases. Although these viruses are suspected to be responsible for AGE in children, our data showed that this association was uncertain since all infected children also presented infections with several enteric viruses, suggesting here potential water-borne transmission. Therefore, further studies with large cohorts of healthy and diarrheal children will be needed to evaluate their clinical role in AGE. PMID:27631733

  13. Evaluation of PCR based assays for the improvement of proportion estimation of bacterial and viral pathogens in diarrheal surveillance

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    Hongxia eGuan

    2016-03-01

    Full Text Available AbstractDiarrhea can be caused by a variety of bacterial, viral and parasitic organisms. Laboratory diagnosis is essential in the pathogen-specific burden assessment. In the pathogen spectrum monitoring in the diarrheal surveillance, culture methods are commonly used for the bacterial pathogens’ detection whereas nucleic acid based amplification, the non-cultural methods are used for the viral pathogens. Different methodology may cause the inaccurate pathogen spectrum for the bacterial pathogens because of their different culture abilities with the different media, and for the comparison of bacterial vs. viral pathogens. The application of nucleic acid-based methods in the detection of viral and bacterial pathogens will likely increase the number of confirmed positive diagnoses, and will be comparable since all pathogens will be detected based on the same nucleic acid extracts from the same sample. In this study, bacterial pathogens, including diarrheagenic Escherichia coli (DEC, Salmonella spp., Shigella spp., Vibrio parahaemolyticus and V. cholerae, were detected in 334 diarrheal samples by PCR-based methods using nucleic acid extracted from stool samples and associated enrichment cultures. A protocol was established to facilitate the consistent identification of bacterial pathogens in diarrheal patients. Five common enteric viruses were also detected by RT-PCR, including rotavirus, sapovirus, norovirus (I and II, human astrovirus, and enteric adenovirus. Higher positive rates were found for the bacterial pathogens, showing the lower proportion estimation if only using culture methods. This application will improve the quality of bacterial diarrheagenic pathogen survey, providing more accurate information pertaining to the pathogen spectrum associated with finding of food safety problems and disease burden evaluation.

  14. The structure of a rigorously conserved RNA element within the SARS virus genome.

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    Michael P Robertson

    2005-01-01

    Full Text Available We have solved the three-dimensional crystal structure of the stem-loop II motif (s2m RNA element of the SARS virus genome to 2.7-A resolution. SARS and related coronaviruses and astroviruses all possess a motif at the 3' end of their RNA genomes, called the s2m, whose pathogenic importance is inferred from its rigorous sequence conservation in an otherwise rapidly mutable RNA genome. We find that this extreme conservation is clearly explained by the requirement to form a highly structured RNA whose unique tertiary structure includes a sharp 90 degrees kink of the helix axis and several novel longer-range tertiary interactions. The tertiary base interactions create a tunnel that runs perpendicular to the main helical axis whose interior is negatively charged and binds two magnesium ions. These unusual features likely form interaction surfaces with conserved host cell components or other reactive sites required for virus function. Based on its conservation in viral pathogen genomes and its absence in the human genome, we suggest that these unusual structural features in the s2m RNA element are attractive targets for the design of anti-viral therapeutic agents. Structural genomics has sought to deduce protein function based on three-dimensional homology. Here we have extended this approach to RNA by proposing potential functions for a rigorously conserved set of RNA tertiary structural interactions that occur within the SARS RNA genome itself. Based on tertiary structural comparisons, we propose the s2m RNA binds one or more proteins possessing an oligomer-binding-like fold, and we suggest a possible mechanism for SARS viral RNA hijacking of host protein synthesis, both based upon observed s2m RNA macromolecular mimicry of a relevant ribosomal RNA fold.

  15. Novel Light-Upon-Extension Real-Time PCR Assay for Simultaneous Detection, Quantification, and Genogrouping of Group A Rotavirus▿ †

    Science.gov (United States)

    Nordgren, Johan; Bucardo, Filemón; Svensson, Lennart; Lindgren, Per-Eric

    2010-01-01

    We have developed a light-upon-extension (LUX) real-time PCR assay for detection, quantification, and genogrouping of group A rotavirus (RV), the most common cause of acute gastroenteritis in children. The LUX system uses a fluorophore attached to one primer and having a self-quenching hairpin structure, making it cost-effective and specific. We designed genogroup-specific primers having different fluorophores, making it possible to differentiate between the two main genogroups of human group A RVs. The assay was applied on clinical stool specimens from Sweden and Central America (n = 196) and compared to immunological and conventional PCR assays. The genogrouping ability was further validated against a subset of clinical specimens, which had been genogrouped using monoclonal antibodies. Our real-time PCR assay detected and quantified all positive specimens (n = 145) and exhibited higher sensitivity than immunological assays and conventional PCR. The assay exhibited a wide dynamic range, detecting from 5 to >107 genes per PCR, resulting in a theoretical lower detection limit of <10,000 viruses per gram of stool. No cross-reaction was observed with specimens containing norovirus, sapovirus, astrovirus, or adenovirus. In total, 22 (15%) of the positive clinical specimens were identified as genogroup I, 122 (84%) were identified as genogroup II, and 1 specimen was found to contain a mix of both genogroups. All genogroup I-positive specimens were associated with capsid glycoprotein 2 (G2). No significant difference in viral load was found between genogroups or geographic region. The detection and quantification, combined with the genogrouping ability, make this assay a valuable tool both for diagnostics and for molecular epidemiological investigations. PMID:20220154

  16. Novel light-upon-extension real-time PCR assay for simultaneous detection, quantification, and genogrouping of group A rotavirus.

    Science.gov (United States)

    Nordgren, Johan; Bucardo, Filemón; Svensson, Lennart; Lindgren, Per-Eric

    2010-05-01

    We have developed a light-upon-extension (LUX) real-time PCR assay for detection, quantification, and genogrouping of group A rotavirus (RV), the most common cause of acute gastroenteritis in children. The LUX system uses a fluorophore attached to one primer and having a self-quenching hairpin structure, making it cost-effective and specific. We designed genogroup-specific primers having different fluorophores, making it possible to differentiate between the two main genogroups of human group A RVs. The assay was applied on clinical stool specimens from Sweden and Central America (n=196) and compared to immunological and conventional PCR assays. The genogrouping ability was further validated against a subset of clinical specimens, which had been genogrouped using monoclonal antibodies. Our real-time PCR assay detected and quantified all positive specimens (n=145) and exhibited higher sensitivity than immunological assays and conventional PCR. The assay exhibited a wide dynamic range, detecting from 5 to >10(7) genes per PCR, resulting in a theoretical lower detection limit of <10,000 viruses per gram of stool. No cross-reaction was observed with specimens containing norovirus, sapovirus, astrovirus, or adenovirus. In total, 22 (15%) of the positive clinical specimens were identified as genogroup I, 122 (84%) were identified as genogroup II, and 1 specimen was found to contain a mix of both genogroups. All genogroup I-positive specimens were associated with capsid glycoprotein 2 (G2). No significant difference in viral load was found between genogroups or geographic region. The detection and quantification, combined with the genogrouping ability, make this assay a valuable tool both for diagnostics and for molecular epidemiological investigations.

  17. Simultaneous identification of DNA and RNA viruses present in pig faeces using process-controlled deep sequencing.

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    Jana Sachsenröder

    Full Text Available BACKGROUND: Animal faeces comprise a community of many different microorganisms including bacteria and viruses. Only scarce information is available about the diversity of viruses present in the faeces of pigs. Here we describe a protocol, which was optimized for the purification of the total fraction of viral particles from pig faeces. The genomes of the purified DNA and RNA viruses were simultaneously amplified by PCR and subjected to deep sequencing followed by bioinformatic analyses. The efficiency of the method was monitored using a process control consisting of three bacteriophages (T4, M13 and MS2 with different morphology and genome types. Defined amounts of the bacteriophages were added to the sample and their abundance was assessed by quantitative PCR during the preparation procedure. RESULTS: The procedure was applied to a pooled faecal sample of five pigs. From this sample, 69,613 sequence reads were generated. All of the added bacteriophages were identified by sequence analysis of the reads. In total, 7.7% of the reads showed significant sequence identities with published viral sequences. They mainly originated from bacteriophages (73.9% and mammalian viruses (23.9%; 0.8% of the sequences showed identities to plant viruses. The most abundant detected porcine viruses were kobuvirus, rotavirus C, astrovirus, enterovirus B, sapovirus and picobirnavirus. In addition, sequences with identities to the chimpanzee stool-associated circular ssDNA virus were identified. Whole genome analysis indicates that this virus, tentatively designated as pig stool-associated circular ssDNA virus (PigSCV, represents a novel pig virus. CONCLUSION: The established protocol enables the simultaneous detection of DNA and RNA viruses in pig faeces including the identification of so far unknown viruses. It may be applied in studies investigating aetiology, epidemiology and ecology of diseases. The implemented process control serves as quality control, ensures

  18. Diversity in the enteric viruses detected in outbreaks of gastroenteritis from Mumbai, Western India.

    Science.gov (United States)

    Chitambar, Shobha; Gopalkrishna, Varanasi; Chhabra, Preeti; Patil, Pooja; Verma, Harsha; Lahon, Anismrita; Arora, Ritu; Tatte, Vaishali; Ranshing, Sujata; Dhale, Ganesh; Kolhapure, Rajendra; Tikute, Sanjay; Kulkarni, Jagannath; Bhardwaj, Renu; Akarte, Sulbha; Pawar, Sashikant

    2012-03-01

    Faecal specimens collected from two outbreaks of acute gastroenteritis that occurred in southern Mumbai, India in March and October, 2006 were tested for seven different enteric viruses. Among the 218 specimens tested, 95 (43.6%) were positive, 73 (76.8%) for a single virus and 22 (23.2%) for multiple viruses. Single viral infections in both, March and October showed predominance of enterovirus (EV, 33.3% and 40%) and rotavirus A (RVA, 33.3% and 25%). The other viruses detected in these months were norovirus (NoV, 12.1% and 10%), rotavirus B (RVB, 12.1% and 10%), enteric adenovirus (AdV, 6.1% and 7.5%), Aichivirus (AiV, 3% and 7.5%) and human astrovirus (HAstV, 3% and 0%). Mixed viral infections were largely represented by two viruses (84.6% and 88.9%), a small proportion showed presence of three (7.7% and 11%) and four (7.7% and 0%) viruses in the two outbreaks. Genotyping of the viruses revealed predominance of RVA G2P[4], RVB G2 (Indian Bangladeshi lineage), NoV GII.4, AdV-40, HAstV-8 and AiV B types. VP1/2A junction region based genotyping showed presence of 11 different serotypes of EVs. Although no virus was detected in the tested water samples, examination of both water and sewage pipelines in gastroenteritis affected localities indicated leakages and possibility of contamination of drinking water with sewage water. Coexistence of multiple enteric viruses during the two outbreaks of gastroenteritis emphasizes the need to expand such investigations to other parts of India. PMID:22690171

  19. Detection and genetic characterization of human enteric viruses in oyster-associated gastroenteritis outbreaks between 2001 and 2012 in Osaka City, Japan.

    Science.gov (United States)

    Iritani, Nobuhiro; Kaida, Atsushi; Abe, Niichiro; Kubo, Hideyuki; Sekiguchi, Jun-Ichiro; Yamamoto, Seiji P; Goto, Kaoru; Tanaka, Tomoyuki; Noda, Mamoru

    2014-12-01

    Enteric viruses are an important cause of viral food-borne disease. Shellfish, especially oysters, are well recognized as a source of food-borne diseases, and oyster-associated gastroenteritis outbreaks have on occasion become international occurrences. In this study, 286 fecal specimens from 88 oyster-associated gastroenteritis outbreaks were examined for the presence of 10 human enteric viruses using antigenic or genetic detection methods in order to determine the prevalence of these infections. All virus-positive patients were over 18 years old. The most common enteric virus in outbreaks (96.6%) and fecal specimens (68.9%) was norovirus (NoV), indicating a high prevalence of NoV infection associated with the consumption of raw or under-cooked oysters. Five other enteric viruses, aichiviruses, astroviruses, sapoviruses, enteroviruses (EVs), and rotavirus A, were detected in 30.7% of outbreaks. EV strains were characterized into three rare genotypes, coxsackievirus (CV) A1, A19, and EV76. No reports of CVA19 or EV76 have been made since 1981 in the Infectious Agents Surveillance Report by the National Infectious Diseases Surveillance Center, Japan. Their detection suggested that rare types of EVs are circulating in human populations inconspicuously and one of their transmission modes could be the consumption of contaminated oysters. Rapid identification of pathogens is important for the development of means for control and prevention. The results of the present study will be useful to establish an efficient approach for the identification of viral pathogens in oyster-associated gastroenteritis in adults. PMID:24415518

  20. Is there still room for novel viral pathogens in pediatric respiratory tract infections?

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    Blanca Taboada

    Full Text Available Viruses are the most frequent cause of respiratory disease in children. However, despite the advanced diagnostic methods currently in use, in 20 to 50% of respiratory samples a specific pathogen cannot be detected. In this work, we used a metagenomic approach and deep sequencing to examine respiratory samples from children with lower and upper respiratory tract infections that had been previously found negative for 6 bacteria and 15 respiratory viruses by PCR. Nasal washings from 25 children (out of 250 hospitalized with a diagnosis of pneumonia and nasopharyngeal swabs from 46 outpatient children (out of 526 were studied. DNA reads for at least one virus commonly associated to respiratory infections was found in 20 of 25 hospitalized patients, while reads for pathogenic respiratory bacteria were detected in the remaining 5 children. For outpatients, all the samples were pooled into 25 DNA libraries for sequencing. In this case, in 22 of the 25 sequenced libraries at least one respiratory virus was identified, while in all other, but one, pathogenic bacteria were detected. In both patient groups reads for respiratory syncytial virus, coronavirus-OC43, and rhinovirus were identified. In addition, viruses less frequently associated to respiratory infections were also found. Saffold virus was detected in outpatient but not in hospitalized children. Anellovirus, rotavirus, and astrovirus, as well as several animal and plant viruses were detected in both groups. No novel viruses were identified. Adding up the deep sequencing results to the PCR data, 79.2% of 250 hospitalized and 76.6% of 526 ambulatory patients were positive for viruses, and all other children, but one, had pathogenic respiratory bacteria identified. These results suggest that at least in the type of populations studied and with the sampling methods used the odds of finding novel, clinically relevant viruses, in pediatric respiratory infections are low.

  1. Is There Still Room for Novel Viral Pathogens in Pediatric Respiratory Tract Infections?

    Science.gov (United States)

    Taboada, Blanca; Espinoza, Marco A.; Isa, Pavel; Aponte, Fernando E.; Arias-Ortiz, María A.; Monge-Martínez, Jesús; Rodríguez-Vázquez, Rubén; Díaz-Hernández, Fidel; Zárate-Vidal, Fernando; Wong-Chew, Rosa María; Firo-Reyes, Verónica; del Río-Almendárez, Carlos N.; Gaitán-Meza, Jesús; Villaseñor-Sierra, Alberto; Martínez-Aguilar, Gerardo; Salas-Mier, Ma. del Carmen; Noyola, Daniel E.; Pérez-Gónzalez, Luis F.; López, Susana; Santos-Preciado, José I.; Arias, Carlos F.

    2014-01-01

    Viruses are the most frequent cause of respiratory disease in children. However, despite the advanced diagnostic methods currently in use, in 20 to 50% of respiratory samples a specific pathogen cannot be detected. In this work, we used a metagenomic approach and deep sequencing to examine respiratory samples from children with lower and upper respiratory tract infections that had been previously found negative for 6 bacteria and 15 respiratory viruses by PCR. Nasal washings from 25 children (out of 250) hospitalized with a diagnosis of pneumonia and nasopharyngeal swabs from 46 outpatient children (out of 526) were studied. DNA reads for at least one virus commonly associated to respiratory infections was found in 20 of 25 hospitalized patients, while reads for pathogenic respiratory bacteria were detected in the remaining 5 children. For outpatients, all the samples were pooled into 25 DNA libraries for sequencing. In this case, in 22 of the 25 sequenced libraries at least one respiratory virus was identified, while in all other, but one, pathogenic bacteria were detected. In both patient groups reads for respiratory syncytial virus, coronavirus-OC43, and rhinovirus were identified. In addition, viruses less frequently associated to respiratory infections were also found. Saffold virus was detected in outpatient but not in hospitalized children. Anellovirus, rotavirus, and astrovirus, as well as several animal and plant viruses were detected in both groups. No novel viruses were identified. Adding up the deep sequencing results to the PCR data, 79.2% of 250 hospitalized and 76.6% of 526 ambulatory patients were positive for viruses, and all other children, but one, had pathogenic respiratory bacteria identified. These results suggest that at least in the type of populations studied and with the sampling methods used the odds of finding novel, clinically relevant viruses, in pediatric respiratory infections are low. PMID:25412469

  2. Molecular epidemiology of enteric viruses in patients with acute gastroenteritis in Aichi prefecture, Japan, 2008/09-2013/14.

    Science.gov (United States)

    Nakamura, Noriko; Kobayashi, Shinichi; Minagawa, Hiroko; Matsushita, Tadashi; Sugiura, Wataru; Iwatani, Yasumasa

    2016-07-01

    Acute gastroenteritis is a critical infectious disease that affects infants and young children throughout the world, including Japan. This retrospective study was conducted from September 2008 to August 2014 (six seasons: 2008/09-2013/14) to investigate the incidence of enteric viruses responsible for 1,871 cases of acute gastroenteritis in Aichi prefecture, Japan. Of the 1,871 cases, 1,100 enteric viruses were detected in 978 samples, of which strains from norovirus (NoV) genogroup II (60.9%) were the most commonly detected, followed by strains of rotavirus A (RVA) (23.2%), adenovirus (AdV) type 41 (8.2%), sapovirus (SaV) (3.6%), human astrovirus (HAstV) (2.8%), and NoV genogroup I (1.3%). Sequencing of the NoV genogroup II (GII) strains revealed that GII.4 was the most common genotype, although four different GII.4 variants were also identified. The most common G-genotype of RVA was G1 (63.9%), followed by G3 (27.1%), G2 (4.7%) and G9 (4.3%). Three genogroups of SaV strains were found: GI (80.0%), GII (15.0%), and GV (5.0%). HAstV strains were genotyped as HAstV-1 (80.6%), HAstV-8 (16.1%), and HAstV-3 (3.2%). These results show that NoV GII was the leading cause of sporadic acute viral gastroenteritis, although a variety of enteric viruses were detected during the six-season surveillance period. PMID:26647761

  3. A Novel Method for Multiplex Detection of Gastroenteritis-associated Viruses%建立新型的常见腹泻相关病毒的多重检测方法

    Institute of Scientific and Technical Information of China (English)

    刘艳; 胡秀梅; 马学军; 段招军; 徐子乾; 李金松; 靳淼; 程卫霞; 巩勋; 李慧莹; 杨晚竹; 杨梦婕

    2011-01-01

    利用GenomeLab(tm)GeXP遗传分析系统建立一种同时检测A组轮状病毒、诺如病毒GI、GⅡ型、札如病毒、肠道腺病毒、星状病毒、人博卡病毒Ⅱ型7种常见腹泻相关病毒的方法.对反应条件进行优化后,非同日三次重复实验表明至少在104拷贝/μL水平可同时特异地检测出7种病毒,对Enterovirus71、Human Parechovirus、PicobirnayirusⅡ阳性标本无交叉反应.本研究初步建立了一种高通量、快速的常见腹泻相关病毒的检测方法,为腹泻病原的分子诊断提供了新的方法.%To develop and optimize a simultaneous detection method of RotavirusA, Norovirus GⅠ, GⅡ,Sapovirus, human astrovirus, enteric adenoviruses and HBoV2 with GenomeLab GeXP analysis system.The sensitivity was verified to be 104 copies/μL with plasmids containing the viral targets in triplicate on different days, and no cross-reaction with enterovirus71, human Parechovirus and PicobirnavirusⅡ was observed. Finally, we successfully developed a high throughout, rapid and maneuverable multiplex RT-PCR assay for simultaneous detection of seven viruses related with viral gastroenteritis, which provide a novel method for the molecular diagnosis of diarrhea-associated virus.

  4. Nanolitre real-time PCR detection of bacterial, parasitic, and viral agents from patients with diarrhoea in Nunavut, Canada

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    David M. Goldfarb

    2013-04-01

    Full Text Available Background. Little is known about the microbiology of diarrhoeal disease in Canada's Arctic regions. There are a number of limitations of conventional microbiology testing techniques for diarrhoeal pathogens, and these may be further compromised in the Arctic, given the often long distances for specimen transport. Objective. To develop a novel multiple-target nanolitre real-time reverse transcriptase (RT-PCR platform to simultaneously test diarrhoeal specimens collected from residents of the Qikiqtani (Baffin Island Region of Nunavut, Canada, for a wide range of bacterial, parasitic and viral agents. Study design/methods. Diarrhoeal stool samples submitted for bacterial culture to Qikiqtani General Hospital in Nunavut over an 18-month period were tested with a multiple-target nanolitre real-time PCR panel for major diarrhoeal pathogens including 8 bacterial, 6 viral and 2 parasitic targets. Results. Among 86 stool specimens tested by PCR, a total of 50 pathogens were detected with 1 or more pathogens found in 40 (46.5% stool specimens. The organisms detected comprised 17 Cryptosporidium spp., 5 Clostridium difficile with toxin B, 6 Campylobacter spp., 6 Salmonella spp., 4 astroviruses, 3 noroviruses, 1 rotavirus, 1 Shigella spp. and 1 Giardia spp. The frequency of detection by PCR and bacterial culture was similar for Salmonella spp., but discrepant for Campylobacter spp., as Campylobacter was detected by culture from only 1/86 specimens. Similarly, Cryptosporidium spp. was detected in multiple samples by PCR but was not detected by microscopy or enzyme immunoassay. Conclusions. Cryptosporidium spp., Campylobacter spp. and Clostridium difficile may be relatively common but possibly under-recognised pathogens in this region. Further study is needed to determine the regional epidemiology and clinical significance of these organisms. This method appears to be a useful tool for gastrointestinal pathogen research and may also be helpful for clinical

  5. Diversity in the Enteric Viruses Detected in Outbreaks of Gastroenteritis from Mumbai, Western India

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    Renu Bhardwaj

    2012-03-01

    Full Text Available Faecal specimens collected from two outbreaks of acute gastroenteritis that occurred in southern Mumbai, India in March and October, 2006 were tested for seven different enteric viruses. Among the 218 specimens tested, 95 (43.6% were positive, 73 (76.8% for a single virus and 22 (23.2% for multiple viruses. Single viral infections in both, March and October showed predominance of enterovirus (EV, 33.3% and 40% and rotavirus A (RVA, 33.3% and 25%. The other viruses detected in these months were norovirus (NoV, 12.1% and 10%, rotavirus B (RVB, 12.1% and 10%, enteric adenovirus (AdV, 6.1% and 7.5%, Aichivirus (AiV, 3% and 7.5% and human astrovirus (HAstV, 3% and 0%. Mixed viral infections were largely represented by two viruses (84.6% and 88.9%, a small proportion showed presence of three (7.7% and 11% and four (7.7% and 0% viruses in the two outbreaks. Genotyping of the viruses revealed predominance of RVA G2P[4], RVB G2 (Indian Bangladeshi lineage, NoV GII.4, AdV-40, HAstV-8 and AiV B types. VP1/2A junction region based genotyping showed presence of 11 different serotypes of EVs. Although no virus was detected in the tested water samples, examination of both water and sewage pipelines in gastroenteritis affected localities indicated leakages and possibility of contamination of drinking water with sewage water. Coexistence of multiple enteric viruses during the two outbreaks of gastroenteritis emphasizes the need to expand such investigations to other parts of India.

  6. How long do nosocomial pathogens persist on inanimate surfaces? A systematic review

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    Schwebke Ingeborg

    2006-08-01

    Full Text Available Abstract Background Inanimate surfaces have often been described as the source for outbreaks of nosocomial infections. The aim of this review is to summarize data on the persistence of different nosocomial pathogens on inanimate surfaces. Methods The literature was systematically reviewed in MedLine without language restrictions. In addition, cited articles in a report were assessed and standard textbooks on the topic were reviewed. All reports with experimental evidence on the duration of persistence of a nosocomial pathogen on any type of surface were included. Results Most gram-positive bacteria, such as Enterococcus spp. (including VRE, Staphylococcus aureus (including MRSA, or Streptococcus pyogenes, survive for months on dry surfaces. Many gram-negative species, such as Acinetobacter spp., Escherichia coli, Klebsiella spp., Pseudomonas aeruginosa, Serratia marcescens, or Shigella spp., can also survive for months. A few others, such as Bordetella pertussis, Haemophilus influenzae, Proteus vulgaris, or Vibrio cholerae, however, persist only for days. Mycobacteria, including Mycobacterium tuberculosis, and spore-forming bacteria, including Clostridium difficile, can also survive for months on surfaces. Candida albicans as the most important nosocomial fungal pathogen can survive up to 4 months on surfaces. Persistence of other yeasts, such as Torulopsis glabrata, was described to be similar (5 months or shorter (Candida parapsilosis, 14 days. Most viruses from the respiratory tract, such as corona, coxsackie, influenza, SARS or rhino virus, can persist on surfaces for a few days. Viruses from the gastrointestinal tract, such as astrovirus, HAV, polio- or rota virus, persist for approximately 2 months. Blood-borne viruses, such as HBV or HIV, can persist for more than one week. Herpes viruses, such as CMV or HSV type 1 and 2, have been shown to persist from only a few hours up to 7 days. Conclusion The most common nosocomial pathogens may

  7. Characterization of a genetically heterogeneous porcine rotavirus C, and other viruses present in the fecal virome of a non-diarrheic Belgian piglet.

    Science.gov (United States)

    Theuns, Sebastiaan; Conceição-Neto, Nádia; Zeller, Mark; Heylen, Elisabeth; Roukaerts, Inge D M; Desmarets, Lowiese M B; Van Ranst, Marc; Nauwynck, Hans J; Matthijnssens, Jelle

    2016-09-01

    Next-generation sequencing (NGS) technologies are becoming increasingly accessible, leading to an expanded interest in the composition of the porcine enteric virome. In the present study, the fecal virome of a non-diarrheic Belgian piglet was determined. Although the virome of only a single piglet was analyzed, some interesting data were obtained, including the second complete genome of a pig group C rotavirus (RVC). This Belgian strain was only distantly related to the only other completely characterized pig RVC strain, Cowden. Its relatedness to RVC strains from other host species was also analyzed and the porcine strain found in our study was only distantly related to RVCs detected in humans and cows. The gene encoding the outer capsid protein VP7 belonged to the rare porcine G3 genotype, which might be serologically distinct from most other pig RVC strains. A putative novel RVC VP6 genotype was identified as well. A group A rotavirus strain also present in this fecal sample contained the rare pig genotype combination G11P[27], but was only partially characterized. Typical pig RVA genotypes I5, A8, and T7 were found for the viral proteins VP6, NSP1, and NSP3, respectively. Interestingly, the fecal virome of the piglet also contained an astrovirus and an enterovirus, of which the complete genomes were characterized. Results of the current study indicate that many viruses may be present simultaneously in fecal samples of non-diarrheic piglets. In this study, these viruses could not be directly associated with any disease, but still they might have had a potential subclinical impact on pig growth performance. The fast evolution of NGS will be a powerful tool for future diagnostics in veterinary practice. Its application will certainly lead to better insights into the relevance of many (sub)clinical enteric viral infections, that may have remained unnoticed using traditional diagnostic techniques. This will stimulate the development of new and durable prophylactic

  8. Avian rotavirus enteritis - an updated review.

    Science.gov (United States)

    Dhama, Kuldeep; Saminathan, Mani; Karthik, Kumaragurubaran; Tiwari, Ruchi; Shabbir, Muhammad Zubair; Kumar, Naveen; Malik, Yashpal Singh; Singh, Raj Kumar

    2015-01-01

    Rotaviruses (RVs) are among the leading causes of enteritis and diarrhea in a number of mammalian and avian species, and impose colossal loss to livestock and poultry industry globally. Subsequent to detection of rotavirus in mammalian hosts in 1973, avian rotavirus (AvRV) was first reported in turkey poults in USA during 1977 and since then RVs of group A (RVA), D (RVD), F (RVF) and G (RVG) have been identified around the globe. Besides RVA, other AvRV groups (RVD, RVF and RVG) may also contribute to disease. However, their significance has yet to be unraveled. Under field conditions, co-infection of AvRVs occurs with other infectious agents such as astroviruses, enteroviruses, reoviruses, paramyxovirus, adenovirus, Salmonella, Escherichia coli, cryptosporidium and Eimeria species prospering severity of disease outcome. Birds surviving to RV disease predominantly succumb to secondary bacterial infections, mostly E. coli and Salmonella spp. Recent developments in molecular tools including state-of-the-art diagnostics and vaccine development have led to advances in our understanding towards AvRVs. Development of new generation vaccines using immunogenic antigens of AvRV has to be explored and given due importance. Till now, no effective vaccines are available. Although specific as well as sensitive approaches are available to identify and characterize AvRVs, there is still need to have point-of-care detection assays to review disease burden, contemplate new directions for adopting vaccination and follow improvements in public health measures. This review discusses AvRVs, their epidemiology, pathology and pathogenesis, immunity, recent trends in diagnostics, vaccines, therapeutics as well as appropriate prevention and control strategies.

  9. Metagenomic analysis demonstrates the diversity of the fecal virome in asymptomatic pigs in East Africa.

    Science.gov (United States)

    Amimo, Joshua O; El Zowalaty, Mohamed E; Githae, Dedan; Wamalwa, Mark; Djikeng, Apollinaire; Nasrallah, Gheyath K

    2016-04-01

    Pigs harbor a variety of viruses that are closely related to human viruses and are suspected to have zoonotic potential. Little is known about the presence of viruses in smallholder farms where pigs are in close contact with humans and wildlife. This study provides insight into viral communities and the prevalence and characteristics of enteric viral co-infections in smallholder pigs in East Africa. Sequence-independent amplification and high-throughput sequencing were applied to the metagenomics analysis of viruses in feces collected from asymptomatic pigs. A total of 47,213 de novo-assembled contigs were constructed and compared with sequences from the GenBank database. Blastx search results revealed that 1039 contigs (>200 nt) were related to viral sequences in the GenBank database. Of the 1039 contigs, 612 were not assigned to any viral taxa because they had little similarity to known viral genomic or protein sequences, while 427 contigs had a high level of sequence similarity to known viruses and were assigned to viral taxa. The most frequent contigs related to mammalian viruses resembling members of the viral genera Astrovirus, Rotavirus, Bocavirus, Circovirus, and Kobuvirus. Other less abundant contigs were related to members of the genera Sapelovirus, Pasivirus, Posavirus, Teschovirus and Picobirnavirus. This is the first report on the diversity of the fecal virome of pig populations in East Africa. The findings of the present study help to elucidate the etiology of diarrheal diseases in pigs and identify potential zoonotic and emerging viruses in the region. Further investigations are required to compare the incidence of these viruses in healthy and diseased pigs in order to better elucidate their pathogenic role. PMID:26965436

  10. ENTEROPATHOGENS DETECTED IN A DAYCARE CENTER, SOUTHEASTERN BRAZIL: BACTERIA, VIRUS, AND PARASITE RESEARCH

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    Edna Donizetti Rossi Castro

    2015-02-01

    Full Text Available Introduction: The objective of this study was to determine the prevalence and etiological profile of enteropathogens in children from a daycare center. Methods: From October 2010 to February 2011 stool samples from 100 children enrolled in a government daycare center in the municipality of São José do Rio Preto, in the state of São Paulo, were collected and analyzed. Results: A total of 246 bacteria were isolated in 99% of the fecal samples; 129 were in the diarrheal group and 117 in the non-diarrheal group. Seventy-three strains of Escherichia coli were isolated, 19 of Enterobacter, one of Alcaligenes and one of Proteus. There were 14 cases of mixed colonization with Enterobacter and E. coli. Norovirus and Astrovirus were detected in children with clinical signs suggestive of diarrhea. These viruses were detected exclusively among children residing in urban areas. All fecal samples were negative for the presence of the rotavirus species A and C. The presence of Giardia lamblia, Entamoeba coli, Endolimax nana and hookworm was observed. A significant association was found between food consumption outside home and daycare center and the presence of intestinal parasites. Conclusions: For children of this daycare center, intestinal infection due to pathogens does not seem to have contributed to the occurrence of diarrhea or other intestinal symptoms. The observed differences may be due to the wide diversity of geographical, social and economic characteristics and the climate of Brazil, all of which have been reported as critical factors in the modulation of the frequency of different enteropathogens.

  11. Assessment of gastroenteric viruses from wastewater directly discharged into Uruguay River, Uruguay.

    Science.gov (United States)

    Victoria, M; Tort, L F L; García, M; Lizasoain, A; Maya, L; Leite, J P G; Miagostovich, M P; Cristina, J; Colina, R

    2014-06-01

    The aim of this study was to assess the viral contamination of group A rotavirus (RVA), norovirus (NoV), and human astrovirus (HAstV) in sewage directly discharged into Uruguay River and to characterize RVA genotypes circulating in Uruguay. For this purpose, sewage samples (n = 96) were collected biweekly from March 2011 to February 2012 in four Uruguayan cities: Bella Unión, Salto, Paysandú, and Fray Bentos. Each sample was concentrated by ultracentrifugation method. Qualitative and quantitative RT-PCR for RVA, NoV, and HAstV were performed. A wide dissemination of gastroenteric viruses was observed in the sewage samples analyzed with 80% of positivity, being NoV (51%) the most frequently detected followed by RVA with a frequency of 49% and HAstV with 45%. Genotypes of RVA were typed using multiplex semi-nested RT-PCR as follows: P[8] (n = 15), P[4] (n = 8), P[10] (n = 1), P[11] (n = 1), G2 (n = 29), and G3 (n = 2). The viral load ranged from 10(3) to 10(7) genomic copies/liter, and they were detected roughly with the same frequency in all participant cities. A peak of RVA and HAstV detection was observed in colder months (June to September), whereas no seasonality was observed for NoV. This study demonstrates for the first time, the high degree of gastroenteric viral contamination in the country; highlighting the importance of developing these analyses as a tool to determine the viral contamination in this hydrographic boundary region used by the local populations for recreation and consumption, establishing an elevated risk of gastroenteric diseases for human health.

  12. Factors associated with usage of antimicrobials in commercial mink (Neovison vison) production in Denmark.

    Science.gov (United States)

    Jensen, V F; Sommer, H M; Struve, T; Clausen, J; Chriél, M

    2016-04-01

    The American mink (Neovison vison) is used for commercial fur production in Denmark. In recent years, antimicrobial prescription for Danish mink has been increasing. In this study, the patterns and trends in antimicrobial use in mink were described and a multi-variable variance analysis was carried out with the objective of identifying risk factors for antimicrobial use on herd level. The study was based on register data for 2007-2012. Information on antimicrobial use was obtained from the national database VetStat, monitoring all medicinal products used for animals on prescription level. Data on microbiological feed quality was obtained from the Voluntary Feed Control under the Mink producers Organization, and data on herd size and the relation between farm and feed producer was obtained from the registers at Kopenhagen Fur, based on yearly reporting from the mink producers. Descriptive analysis showed a clear significant effect of season on antimicrobial use, with a peak in "treatment proportions", TP (defined daily doses per kg biomass-days) in May, around the time of whelping, and a high level in the following months. In autumn, a minor peak in antimicrobial use occurred throughout the study period. From 2007 to 2011, a 102% increase in annual antimicrobial TP was noted; on herd level, the increase was associated with an increasing frequency of prescription, and a decrease in the amounts prescribed in months with prescription. A binomial model showed that on herd level, the annual number of months with antimicrobial prescription was significantly (pfood quality, the feed producer, and the veterinarian. The prescription patterns varied significantly between veterinarians, and some veterinarians were associated with both larger and more frequent prescriptions of antimicrobials at herd level. Herd size is associated with different prescription patterns. Finally, infection with Pseudomonas aeruginosa, astrovirus, influenza virus and Salmonella spp. was associated

  13. Molecular epidemiological study on children under five years old with diarrhea and the long-term countermeasures for prevention and control of childhood diarrhea in Tangshan city%唐山市5岁以下儿童腹泻分子流行病学研究及长期预防控制对策

    Institute of Scientific and Technical Information of China (English)

    余亮科; 王林; 陈玉强; 高捷; 赵文喆

    2012-01-01

    Objective:To conduct molecular epidemiological study for children under five years old with diarrhea in Tangshan city, provide data for prevention and treatment of diarrhea, further put foreward long-term countermeasures for prevention and control of childhood diarrhea. Methods:The stool samples of 300 children with acute diarrhea were selected from Tangshan city randomly, after excluding 180 children with bacterial diarrhea, the other 120 children with viral diarrhea underwent rotavirus detection by colloidal gold method, RT-PCR was used to detect astrovirus, diarrheal adenovirus, and human calicivirus. Results; Among the children under five years old with viral diarrhea in Tangshan city, 16. 33% of them were infected by rotavirus, 10.33% of them were infected by astrovirus, 8. 67% of them were infected by diarrheal adenovirus, and 4. 67% of them were infected by human calicivirus. There was no statistically significant difference in the incidence of bacterial diarrhea among children in different age groups. The peak periods of childhood diarrhea induced by different viruses varied \\ the peak periods of childhood diarrhea induced by rotavirus, astrovirus, diarrheal adenovirus, and human calicivirus were 6-12 months, 12-28 months, 12-24 months, and 12-18 months, respectively. The change of season had no obvious impact on the causes of diarrhea. Conclusion:Bacterial infection was the most important cause of childhood diarrhea, but for the children with viral diarrhea, rotavirus was the main induced cause. More attention should be paid to the children during every age period to prevent and control bacterial diarrhea, childhood diarrhea induced by different viruses can be treated with corresponding measures according to different peak periods of onset age.%目的:对唐山市5岁以下儿重腹泻进行分子流行病学研究,为腹泻的防治提供数据,进而提出对儿重腹泻的长期预防控制措施.方法:随机抽取唐山市300例儿童急性腹泻的

  14. Human bocavirus in hospitalized children with acute gastroenteritis in Russia from 2010 to 2012.

    Science.gov (United States)

    Tymentsev, Alexander; Tikunov, Artem; Zhirakovskaia, Elena; Kurilschikov, Alexander; Babkin, Igor; Klemesheva, Vera; Netesov, Sergei; Tikunova, Nina

    2016-01-01

    Human bocavirus (HBoV) can cause respiratory diseases and is detectable in the stool samples of patients with gastroenteritis. To assess the prevalence of HBoV in children hospitalized with acute gastroenteritis in Novosibirsk, Russia, as well as its genetic diversity and the potential role in the etiology of gastroenteritis in this region, a total of 5502 stool samples from children hospitalized with gastroenteritis from 2010 to 2012, n=5250, and healthy children, n=252, were assayed for the presence of HBoV DNA by semi-nested PCR. The HBoV DNA was found in 1.2% of stool samples from children, with gastroenteritis varying from 0.5% in 2012 to 1.7% in 2011. The prevalence of HBoV in healthy children was 0.3%. HBoV strains were detected throughout the year with an increase in the fall-winter season. In 87% of cases, HBoV was detected in children before 1 year of age. All known HBoV genetic variants have been detected in Novosibirsk, although with different prevalences: HBoV2>HBoV1>HBoV4>HBoV3. At the beginning of 2011, HBoV2 replaced HBoV1 as the most prevalent variant. The median age of children with detected HBoV1 was 8.3months, and that with HBoV2 was 8.0 months. All HBoV-positive samples were assayed for the presence of the rotaviruses A and C, norovirus GII, astrovirus, enterovirus, adenovirus F, Salmonella spp., Campylobacter spp., Shigella spp., and EIEC. HBoV1 and HBoV2 as single agents were found in 45.8% and 60% samples, respectively, although this difference was not statistically significant. In the case of co-infections, HBoV was most frequently recorded with rotavirus A and norovirus GII. This study demonstrated that the detection rate of HBoV in stool samples from children with gastroenteritis was low, although both HBoV1 and HBoV2 could be found as the sole agents in children with gastroenteritis in Novosibirsk.

  15. Viruses of foodborne origin: a review

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    Todd EC

    2015-04-01

    Full Text Available Ewen CD Todd,1,2 Judy D Greig3 1Ewen Todd Consulting LLC, Okemos, MI, USA; 2Department of Nutrition and Food Science, Faculty of Agricultural and Food Sciences, American University of Beirut, Beirut, Lebanon; 3Division of Public Health Risk Sciences, Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, ON, Canada Abstract: Enteric viruses are major contributors to foodborne disease, and include adenovirus, astrovirus, rotavirus, sapovirus, hepatitis A and E viruses, and norovirus. From a foodborne transmission perspective, norovirus is the most important; however, hepatitis A is associated with more serious illness. Foodborne viruses are transmitted through contaminated food, but also in combination with person-to-person contact or through environmental contamination. These viruses survive well in the environment, are excreted in abundance in feces, and have a low infectious dose, all of which facilitate spread within a community. Many colonized individuals experience mild gastroenteritis lasting a few days or are asymptomatic, although viral excretion may continue over days or weeks. Severe illness tends to be restricted to the very young and elderly, especially in closed communities such as schools and homes for the aged. In the USA, norovirus is considered to be responsible for two thirds of all foodborne illnesses occurring in a wide range of institutional settings, including schools, colleges, child care centers, cruise ships, prisons, and soldiers on campaign. Norovirus outbreaks also occur at one-time events, such as banquets, wedding receptions, birthday parties, and potluck meals, and are most often introduced by infected food workers producing, preparing, or serving food, or through self-service buffets. Often the infections are introduced from the community into institutions where they can infect the majority of residents unless quickly controlled. In countries where economic assessments have been completed

  16. Characterization of a genetically heterogeneous porcine rotavirus C, and other viruses present in the fecal virome of a non-diarrheic Belgian piglet.

    Science.gov (United States)

    Theuns, Sebastiaan; Conceição-Neto, Nádia; Zeller, Mark; Heylen, Elisabeth; Roukaerts, Inge D M; Desmarets, Lowiese M B; Van Ranst, Marc; Nauwynck, Hans J; Matthijnssens, Jelle

    2016-09-01

    Next-generation sequencing (NGS) technologies are becoming increasingly accessible, leading to an expanded interest in the composition of the porcine enteric virome. In the present study, the fecal virome of a non-diarrheic Belgian piglet was determined. Although the virome of only a single piglet was analyzed, some interesting data were obtained, including the second complete genome of a pig group C rotavirus (RVC). This Belgian strain was only distantly related to the only other completely characterized pig RVC strain, Cowden. Its relatedness to RVC strains from other host species was also analyzed and the porcine strain found in our study was only distantly related to RVCs detected in humans and cows. The gene encoding the outer capsid protein VP7 belonged to the rare porcine G3 genotype, which might be serologically distinct from most other pig RVC strains. A putative novel RVC VP6 genotype was identified as well. A group A rotavirus strain also present in this fecal sample contained the rare pig genotype combination G11P[27], but was only partially characterized. Typical pig RVA genotypes I5, A8, and T7 were found for the viral proteins VP6, NSP1, and NSP3, respectively. Interestingly, the fecal virome of the piglet also contained an astrovirus and an enterovirus, of which the complete genomes were characterized. Results of the current study indicate that many viruses may be present simultaneously in fecal samples of non-diarrheic piglets. In this study, these viruses could not be directly associated with any disease, but still they might have had a potential subclinical impact on pig growth performance. The fast evolution of NGS will be a powerful tool for future diagnostics in veterinary practice. Its application will certainly lead to better insights into the relevance of many (sub)clinical enteric viral infections, that may have remained unnoticed using traditional diagnostic techniques. This will stimulate the development of new and durable prophylactic

  17. The role of human adenoviruses type 41 in acute diarrheal disease in Minas Gerais after rotavirus vaccination

    Directory of Open Access Journals (Sweden)

    Thaís Aparecida Vieira Reis

    2016-03-01

    Full Text Available Abstract Human adenovirus species F (HAdV-F type 40 and 41 are commonly associated with acute diarrheal disease (ADD across the world. Despite being the largest state in southeastern Brazil and having the second largest number of inhabitants, there is no information in the State of Minas Gerais regarding the role of HAdV-F in the etiology of ADD. This study was performed to determine the prevalence, to verify the epidemiological aspects of infection, and to characterize the strains of human adenoviruses (HAdV detected. A total of 377 diarrheal fecal samples were obtained between January 2007 and August 2011 from inpatient and outpatient children of age ranging from 0 to 12 years. All samples were previously tested for rotavirus, norovirus, and astrovirus, and 314 of 377 were negative. The viral DNA was extracted, amplified using the polymerase chain reaction and the HAdV-positive samples were sequenced and phylogenetically analyzed. Statistical analyses were performed using the Chi-square test (p < 0.05, considering two conditions: the total of samples tested (377 and the total of negative samples for the remaining viruses tested (314. The overall prevalence of HAdV was 12.47% (47/377; and in 76.60% (36/47 of the positive samples, this virus was the only infectious agent detected. The phylogenetic analysis of partial sequences of 32 positive samples revealed that they all clustered with the HAdV-F type 41. The statistical analysis showed that there was no correlation between the onset of the HAdV infection and the origin of the samples (inpatients or outpatients in the two conditions tested: the total of samples tested (p = 0.598 and the total of negative samples for the remaining viruses tested (p = 0.614. There was a significant association in the occurrence of infection in children aged 0–12 months for the condition 1 (p = 0.030 as well as condition 2 (p = 0.019. The occurrence of infections due to HAdV did not coincide with a pattern of

  18. The role of human adenoviruses type 41 in acute diarrheal disease in Minas Gerais after rotavirus vaccination

    Science.gov (United States)

    Reis, Thaís Aparecida Vieira; Assis, Andrêssa Silvino Ferreira; do Valle, Daniel Almeida; Barletta, Vívian Honorato; de Carvalho, Iná Pires; Rose, Tatiana Lundgren; Portes, Silvana Augusta Rodrigues; Leite, José Paulo Gagliardi; da Rosa e Silva, Maria Luzia

    2016-01-01

    Human adenovirus species F (HAdV-F) type 40 and 41 are commonly associated with acute diarrheal disease (ADD) across the world. Despite being the largest state in southeastern Brazil and having the second largest number of inhabitants, there is no information in the State of Minas Gerais regarding the role of HAdV-F in the etiology of ADD. This study was performed to determine the prevalence, to verify the epidemiological aspects of infection, and to characterize the strains of human adenoviruses (HAdV) detected. A total of 377 diarrheal fecal samples were obtained between January 2007 and August 2011 from inpatient and outpatient children of age ranging from 0 to 12 years. All samples were previously tested for rotavirus, norovirus, and astrovirus, and 314 of 377 were negative. The viral DNA was extracted, amplified using the polymerase chain reaction and the HAdV-positive samples were sequenced and phylogenetically analyzed. Statistical analyses were performed using the Chi-square test (p < 0.05), considering two conditions: the total of samples tested (377) and the total of negative samples for the remaining viruses tested (314). The overall prevalence of HAdV was 12.47% (47/377); and in 76.60% (36/47) of the positive samples, this virus was the only infectious agent detected. The phylogenetic analysis of partial sequences of 32 positive samples revealed that they all clustered with the HAdV-F type 41. The statistical analysis showed that there was no correlation between the onset of the HAdV infection and the origin of the samples (inpatients or outpatients) in the two conditions tested: the total of samples tested (p = 0.598) and the total of negative samples for the remaining viruses tested (p = 0.614). There was a significant association in the occurrence of infection in children aged 0–12 months for the condition 1 (p = 0.030) as well as condition 2 (p = 0.019). The occurrence of infections due to HAdV did not coincide with a pattern of seasonal

  19. 病毒性胃肠炎的病原学检测%Etiological analysis on viral gastroenteritis

    Institute of Scientific and Technical Information of China (English)

    付建光; 祁贤; 吴斌; 洪镭; 张洪英

    2012-01-01

    OBJECTIVE To understand the main reasons for cases in one hospital with the gastroenteritis symptoms so as to provide scientific references for prevention and control of enteric infectious diseases. METHODS The stools of ten patients were collected and detected by real-time PCR and sequencing for the viral detection, including rotavirus, norovirus, Sapporo virus, astrovirus, adenovirus. RESULTS Norovirus was detected in 7 out of 10 stools, with same subtype of GII.4. The results confirmed the etiology wasviral infection. CONCLUSION There is the threat of norovirus in Nanjing. Norovirus, subtype GⅡ.4, is the pathogen, resulting in the gastroenteritis in the hospital. It is the same subtype of norovirus as in other countries; anti-virus advocacy should be strengthened on health education and especially for prevention of infection.%目的 了解某医院的不明原因胃肠炎病例的病原学特点,为科学预防可能的流行病提供科学依据.方法 收集某医院2010年12月出现胃肠炎症状的10例患者的排泄物进行病原学检测,包括轮状病毒、诺如病毒、札幌病毒、星状病毒以及肠腺病毒5种肠道病毒的荧光定量PCR检测和测序分析.结果 10份粪便标本中,7例检测到诺如病毒核酸阳性,经测序分析为GⅡ.4亚型,未检测到其他病毒,确定为该病毒感染所致.结论 南京地区存在诺如病毒的威胁,导致该医院患者胃肠炎的病原是诺如病毒.与其他国家和地区一样,GⅡ.4亚型为主要感染亚型,应加强相应的抗病毒健康教育宣传,尤其是可能导致传播的预防工作.

  20. VIRAL ETIOLOGY ACUTE INTESTINAL INFECTIONS MOLECULAR MONITORING IN CHILDREN’S HOSPITAL

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    A. V. Sergeeva

    2015-01-01

    infections in patients with clinical signs of intestinal infection, and contact persons was 43.8%. The etiological structure of intestinal virus infections was presented by noroviruses (73.2% genotypes GII.1, GII.3, GII.4 Sydney 2012, rotaviruses (23.2% genotypes G4P[8] and G1-IP[8], and adenovirus (1.8% of the group F and astroviruses (1.8% genotypes 1 and 2. Among the hospitalized children were 9 cases of viral etiology acute intestinal infections importation, and 66 of cases were of nosocomial origin. Examination of the environment revealed the presence of contamination by enteric viruses in 47.8% of cases. 

  1. Assessment of gastroenteric viruses frequency in a children's day care center in Rio De Janeiro, Brazil: a fifteen year study (1994-2008.

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    Mônica Simões Rocha Ferreira

    Full Text Available This 15-year study aimed to determine the role of the main viruses responsible for acute infantile gastroenteritis cases in a day care center in the city of Rio de Janeiro, Brazil. From 1994 to 2008, 539 fecal samples were obtained from 23 outbreaks as well as sporadic cases that occurred in this period. The detection of Rotavirus group A (RVA, norovirus (NoV and astrovirus (AstV was investigated both by classical and molecular methods of viral detection. RVA was detected by enzymatic immune assay and/or polyacrylamide gel electrophoresis and genotyped by using semi-nested multiplex PCR. NoV and AstV were subsequently tested by real time PCR in all RVA-negative samples and genotyped throughout genome sequencing. Three protocols for molecular characterization of NoV nucleotide sequencing were performed with the partial nucleotide sequencing of genomic regions known as region B (polymerase gen, C and D (capsid gen.Viruses were identified in 47.7% (257/539 of the cases, and the detection rates of RVA, NoV and AstV in16.1% (87/539, 33.4% (151/452, and 6.3% (19/301, respectively. Most gastroenteritis cases were reported in autumn and winter, although NoV presented a broader monthly distribution. Viruses' detection rates were significantly higher among children aged less than 24 months old, although NoV cases were detected in all age groups. RVA genotypes as G1P[8], G9P[8], G2P[4], G3P[8] and G1+G3P[8] and RVA was no longer detected after 2005. NoV characterization revealed genotypes variability circulating in the period as GI.2, GI.3, GI.8 GII.2, GII.3, GII.4, GII.4 variants 2001 and 2006b, GII.6, GII.7, GII.12 and GII.17. AstV genotypes 1, 2, 4 and 5 were also characterized. Those data demonstrate the impact of NoV infection in cases of infantile gastroenteritis, surpassing RVA infection responsible for high morbidity rate in children under five years old.

  2. Comportamiento de la diarrea causada por virus y bacterias en regiones cercanas a la zona ecuatorial.

    Directory of Open Access Journals (Sweden)

    María Fernanda Gutiérrez

    2009-11-01

    Full Text Available INTRODUCCIÓN: La enfermedad diarreica aguda (EDA es un problema de salud a nivel mundial que afecta a la población infantil de distintas regiones. Casi todos los estudios epidemiológicos se han hecho en países con estaciones y poco se informa su comportamiento en países sin estaciones, donde la EDA es endémica con picos epidémicos. OBJETIVOS: Contribuir a conocer la conducta de EDA en Colombia y determinar si su comportamiento es diferente en niños menores de cinco años en dos regiones distintas entre sí en geografía y clima. MATERIALES Y MÉTODOS: Se hizo un estudio descriptivo en dos localidades colombianas. Una en la costa atlántica y otra en el centro del país. La muestra se obtuvo en menores de cinco años que consultaron por diarrea a centros asistenciales de cada región. Los microorganismos bacterianos se identificaron mediante pruebas bioquímicas y los virus con técnicas inmunoenzimáticas. En el análisis estadístico se siguieron un ensayo bivariado y pruebas Z de normalidad para verificar si el clima modifica el comportamiento de EDA y si se presenta de manera distinta en las dos regiones. RESULTADOS: En ambas zonas (Cartagena, Bolívar y Facatativa, Cundinamarca predominó la diarrea viral, frente a la EDA bacteriana. También en ambas el rotavirus fue prevalente. Fue mucho más baja la presencia de astrovirus y adenovirus. No hubo datos con significación estadística para demostrar que las condiciones ambientales y las propias de los niños, alteran el comportamiento de la EDA, pero sí se observó que la EDA por rotavirus se comporta de manera diferente al analizar en forma comparativa las dos regiones del estudio.

  3. Norovirus diversity in diarrheic children from an African-descendant settlement in Belem, Northern Brazil.

    Directory of Open Access Journals (Sweden)

    Glicélia Cruz Aragão

    Full Text Available Norovirus (NoV, sapovirus (SaV and human astrovirus (HAstV are viral pathogens that are associated with outbreaks and sporadic cases of gastroenteritis. However, little is known about the occurrence of these pathogens in relatively isolated communities, such as the remnants of African-descendant villages ("Quilombola". The objective of this study was the frequency determination of these viruses in children under 10 years, with and without gastroenteritis, from a "Quilombola" Community, Northern Brazil. A total of 159 stool samples were obtained from April/2008 to July/2010 and tested by an enzyme immunoassay (EIA and reverse transcription-polymerase chain reaction (RT-PCR to detect NoV, SaV and HAstV, and further molecular characterization was performed. These viruses were detected only in the diarrheic group. NoV was the most frequent viral agent detected (19.7%-16/81, followed by SaV (2.5%-2/81 and HAstV (1.2%-1/81. Of the 16 NoV-positive samples, 14 were sequenced with primers targeting the B region of the polymerase (ORF1 and the D region of the capsid (ORF2. The results showed a broad genetic diversity of NoV, with 12 strains being classified as GII-4 (5-41.7%, GII-6 (3-25%, GII-7 (2-16.7%, GII-17 (1-8.3% and GI-2 (1-8.3%, as based on the polymerase region; 12 samples were classified, based on the capsid region, as GII-4 (6-50%, being 3-2006b variant and 3-2010 variant, GII-6 (3-25%, GII-17 (2-16.7% and GII-20 (1-8.3%. One NoV-strain showed dual genotype specificity, based on the polymerase and capsid region (GII-7/GII-20. This study provides, for the first time, epidemiological and molecular information on the circulation of NoV, SaV and HAstV in African-descendant communities in Northern Brazil and identifies NoV genotypes that were different from those detected previously in studies conducted in the urban area of Belém. It remains to be determined why a broader NoV diversity was observed in such a semi-isolated community.

  4. 婴幼儿病毒感染与腹泻相关临床参数的关系分析%Analysis of relationship between viral infection and diarrhea-related clinical parameters in infants

    Institute of Scientific and Technical Information of China (English)

    施前锋; 潘新娣; 王叶萍; 邵伟芳; 钱娇赟; 孙爱华

    2015-01-01

    目的:研究婴幼儿病毒感染与腹泻相关临床参数的关系,为婴幼儿病毒性腹泻的诊治和预防提供依据。方法收集124例5岁以下腹泻患儿血液和粪便进行常规检测,采用免疫金层析技术检测粪便标本的轮状病毒,实时荧光定量PCR(RT‐PCR)检测粪便标本轮状病毒、星状病毒、腺病毒及诺如病毒的表达水平,对结果采用SPSS16.0软件进行统计分析。结果124例腹泻患儿中免疫金层析技术和 RT‐PCR检测轮状病毒阳性率分别为37.9%和46.0%;RT‐PCR检测星状病毒、腺病毒及诺如病毒感染率分别为41.10%、19.40%和15.32%;重叠感染91例,其中轮状病毒与星状病毒重叠感染28例最为常见;急性胃肠炎患儿病毒感染率明显高于胃肠功能紊乱患儿(P<0.05);病毒感染在1岁以下腹泻患儿更常见(P<0.05),病毒感染腹泻患儿粪便性状常见水样;胃肠功能紊乱患儿血液C‐反应蛋白(CRP)>10、白细胞(WBC)>10×109/L和粪便WBC阳性比例均明显高于急性胃肠炎患儿(P<0.05)。结论 RT‐PCR可以提高腹泻患儿轮状病毒检出率,轮状病毒为腹泻患儿特别是<1岁患儿急性胃肠炎的主要病毒性因素,病毒性感染引起的腹泻以水样便更常见,胃肠功能紊乱患儿血像变化比急性胃肠炎患儿明显。%OBJECTIVE To investigate the relationship between viral infection and diarrhea‐related clinical parame‐ters in infants so as to provide reference for diagnose and prevention of this disease .METHODS Blood and feces samples were collected for routine examination from 124 diarrhea children less than 5 years of age .Test of rotavir‐us (RVs) in feces samples was carried out by immuno‐gold chromatography and the expression levels of four virus (rotavirus ,astrovirus ,adenovirus ,norovirus) in the feces samples were detected by RT‐PCR .The results were

  5. Outbreaks of noroviral gastroenteritis and their molecular characteristics in China, 2006 -2007%中国2006-2007年诺如病毒胃肠炎暴发及其病原学特征分析

    Institute of Scientific and Technical Information of China (English)

    靳淼; 段招军; 孙军玲; 常昭瑞; 李慧莹; 刘娜; 章青; 崔淑娴; 张静; 王子军

    2010-01-01

    目的 了解中国2006-2007年诺如病毒胃肠炎暴发及其病毒基因型别.方法 收集2006-2007年19起胃肠炎暴发的流行病学资料以及腹泻粪便样本,用RT-PCR方法对201份粪便标本进行诺如病毒、轮状病毒、星状病毒、腺病毒和札如病毒检测,对扩增产物进行序列测定.用Clustal X 1.83和MEGA4.0生物软件对诺如病毒序列进行序列比对和系统进化分析.结果 诺如病毒是引起病毒性胃肠炎暴发的主要病原之一(12/19,63.2%).在12起诺如病毒胃肠炎暴发中,变异株GⅡ-4/2006b是引起暴发的流行优势株(11/12,91.7%),其他型别包括GⅡ-17、GⅡ-6和GⅡ-3.诺如病毒引起的疫情暴发主要集中在冬春季节(12月至4月),发生场所多样,且各年龄组人群均有发病.同时,12起诺如病毒暴发中有2起与其他腹泻病毒混合感染,且在同一起暴发中病原具有病毒多样性和基因型别多样性.结论 诺如病毒是2006-2007年引起胃肠炎暴发疫情的主要病原之一,变异株GⅡ-4/2006b为流行优势株.%Objective To acknowledge the epidemiology of gastroenteritis outbreaks caused by norobiruses and their genotypes. Methods Epidemiologic data and specimens were collected from 19 gastroenteritis outbreaks. 201 specimens were detected for norovirus, rotavirus, astrovirus,adenovirus and sapovirus by RT-PCR methods and PCR products were sequenced. Sequence alignment and phylogenetic analysis were performed by Clustal X 1.83 and MEGA 4.0 programs.Results Noroviruses were one of the most predominant pathogens causing viral gastroenteritis outbreaks ( 12 of 19 outbreaks, accounting for 63.2% ). Variant G Ⅱ -4/2006b was the predominant strain responsible for 11 of the 12 NV-associated outbreaks. Other genotypes would include G Ⅱ -17,G Ⅱ -6 and G Ⅱ -3. The NV-associated gastrocnteritis outbreaks occurred mainly in winter and spring between December 2006 and April 2007. These gastroenteritis outbreaks caused by

  6. Surveillance and analysis on diarrheal disease pathogen spectrum among children under 5 years old in Pudong New Area of Shanghai City%上海市浦东新区5岁以下儿童腹泻病病原谱监测分析

    Institute of Scientific and Technical Information of China (English)

    费怡; 孙乔; 傅益飞; 朱渭萍; 薛曹怡

    2013-01-01

    [目的]了解上海市浦东新区5岁以下儿童腹泻病的病原谱构成、病原特征,为制定预防控制措施提供依据。[方法]对2012年2月-2013年1月浦东新区人民医院、儿童医学中心2家监测点医院的619例腹泻患儿进行个案调查,同时采集粪便标本进行肠道致病菌和病毒的检测。[结果]诺如病毒、轮状病毒、肠道腺病毒、扎如病毒、星状病毒的检出率分别为11.95%、7.27%、2.91%、1.45%、0.97%;致泻性大肠埃希菌、非伤寒沙门菌、弯曲菌、嗜水气单胞菌、志贺菌、小肠结肠炎耶尔森菌的检出率分别为5.65%、2.42%、0.81%、0.65%、0.48%、0.32%。病毒检出率8月至次年的3月为27.70%,高于其他月份的18.48%(χ2=7.18,P<0.05);细菌检出率4-10月为15.34%,远高于其他月份的3.15%(χ2=31.22,P<0.05)。[结论]诺如病毒为浦东新区5岁以下儿童病毒性腹泻的最主要病原,致泻性大肠埃希菌为细菌性腹泻的最主要病原。细菌性腹泻的防控应以夏秋季为重点,病毒性腹泻应以全年为重点。%[Objective] To investigate the pathogen spectrum and characteristics of diarrheal disea-ses among children under five and to provide the basis for prevention and control measures . [ Methods] From February 2012 to January 2013, a total of 619 cases from 2 sentinel hospitals were collected for case survey .From them were collected stool specimens for detection of enteric pathogenic bacteria and virus nu-cleic acids. [Results] The virus detection rate was norovirus (11.95%), rotavirus(7.27%), enteric adenovirus(2.91%), saporovirus(1.45%) and astrovirus(0.97%).The bacteria detection rate was E. coli(5.65%), nontyphoidal salmonella (2.42%), campylobacter (0.81%), aeromonas hydrophila (0.65%),shigella(0.48%) and yersinia enterocolitica (0.32%).The virus detection rate was 27.70%from August to next March

  7. 基于LAMP的人轮状病毒检测方法及其在水环境中的应用%LAMP based method for detecting human rotavirus and its application in water samples

    Institute of Scientific and Technical Information of China (English)

    杨柏云; 韦玉梅; 杨丽; 宋涵; 杨海霞; 何晓青

    2013-01-01

    The present paper intends to introduce a method known as loop-mediated isothermal amplification, short for LAMP, for detecting rotavinis, a kind of toxic virus responsible for the acute viral gastroenteritis in the infants and young children in the worldwide sphere. As is known, after replication in the gastrointestinal tract, rotaviruses are usually excreted in large amount and then disperse into the environment water. The stability of rotaviruses in the environmental water and their resistance to the physicochemical treatment process is likely to facilitate their transmission through water. A lot of studies confirm the presence of rotaviruses in the sewage and even in the treated effluents. To combat the spread and transmission of such viruses, a. novel, rapid and sensitive technique called loop-mediated isothermal amplification(LAMP) has been developed in recent years, which attempts to use a DNA polymerase that is very active in stranding the displacement of DNA synthesis and a set of four specially designed primers that recognize a total of six distinct sequences on the targeted DNA. The LAMP method can operate in an extremely high speed. It is also cost-effective, sensitive and specific for the clinic service, and that is why it is now widely used in the area of virus detection. In the present paper, we have renovated the LAMP based-method for quick-finding human rotavinis. By means of the specific VP7-gene of human rotavirus, we have worked out a set of specific primers to amplify the special DNA sequence with the help of LAMP. In addition, we have managed to optimize the reaction conditions of LAMP.The experimental data indicate that the optimal amplification condition proves to be at 65 ℃ for 90 min with 3 mmol/L magnesium ions and 1 mol/L Be-taine. The specificity of RT - LAMP assay has been further validated by the cross-reaction with different viruses (human rotavirus, human astrovirus and human norovirus) and the constrained analysis of the amplified

  8. Comparing the multiplex RT-PCR method and liquichip technology in the detection of diarrhea-related virus%多重 RT-PCR 与液相悬浮芯片检测临床腹泻相关病毒的比较

    Institute of Scientific and Technical Information of China (English)

    罗欣; 余楠; 郭勇晖; 邓间开; 丁细霞; 王瑞莲; 富宁; 车小燕

    2015-01-01

    目的:比较实验室建立的多重RT-PCR与液相悬浮芯片对于临床腹泻相关病毒(腺病毒40/41型、诺如病毒GⅠ型和GⅡ型,星状病毒和札如病毒)的检测效能。方法多重RT-PCR方法学建立。收集2013年9月至2014年2月因腹泻至南方医科大学珠江医院就医的患者的粪便标本共107份。利用液相悬浮芯片技术和多重RT-PCR分别检测标本的腺病毒40/41型、诺如病毒GⅠ型和GⅡ型,对液相悬浮芯片未涵盖的星状病毒和札如病毒,以RT-PCR为参考,评估多重RT-PCR方法的特异度、敏感度。采用配对计数资料的Kappa系数检验,比较方法间的吻合度。多重RT-PCR和RT-PCR平行扩增10倍连续稀释的5种病毒质粒,测定多重RT-PCR的检测限。结果建立的多重RT-PCR方法与液相悬浮芯片、RT-PCR的检测一致性高,Kappa值分别为0.885和1.000,P均=0.000。以液相悬浮芯片为标准,多重RT-PCR检测敏感度为80.8%(21/26),特异度100.0%(295/295)。多重RT-PCR对5种病毒的检测限为104~106拷贝/μl。结论多重RT-PCR与液相悬浮芯片对于临床标本检测显示一致性佳,特异度和敏感度高,快速、高通量,适用于临床微生物实验室常见腹泻相关病毒的多重检测。(中华检验医学杂志,2015,38:387-391)%Objective To compare the detection efficiency between multiplex RT-PCR method and liquichip technology for screening the viral etiological agents of diarrhea.Methods The development of the multiplex RT-PCR method.A total of 107 feces samples from patients who suffered from diarrhea and attended to Zhujiang Hospital of Southern University from September 2013 to February 2014 were collected and tested in parallel by both multiplex RT-PCR and xTAG Gastrointestinal Pathogen Panel ( xTAG GPP) for Adenovirus, Norovirus genogroupⅠandⅡ, as well as by both multiplex RT-PCR and monoplex RT-PCR for Astrovirus and Sapovirus