Sapovirus

14,000,000 Leading Edge Experts on the ideXlab platform

Scan Science and Technology

Contact Leading Edge Experts & Companies

Scan Science and Technology

Contact Leading Edge Experts & Companies

The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform

Grant S Hansman - One of the best experts on this subject based on the ideXlab platform.

  • vesivirus 2117 capsids more closely resemble Sapovirus and lagovirus particles than other known vesivirus structures
    Journal of General Virology, 2017
    Co-Authors: Michaela J Conley, Ian Goodfellow, Edward Emmott, Richard J Orton, David W Taylor, Daniel Goncalves Carneiro, Grant S Hansman, Kazuyoshi Murata, David Bhella
    Abstract:

    Vesivirus 2117 is an adventitious agent that, in 2009, was identified as a contaminant of Chinese hamster ovary cells propagated in bioreactors at a pharmaceutical manufacturing plant belonging to Genzyme. The consequent interruption in supply of Fabrazyme and Cerezyme (drugs used to treat Fabry and Gaucher diseases, respectively) caused significant economic losses. Vesivirus 2117 is a member of the Caliciviridae, a family of small icosahedral viruses encoding a positive-sense RNA genome. We have used cryo-electron microscopy and three-dimensional image reconstruction to calculate a structure of vesivirus 2117 virus-like particles as well as feline calicivirus and a chimeric Sapovirus. We present a structural comparison of several members of the Caliciviridae, showing that the distal P domain of vesivirus 2117 is morphologically distinct from that seen in other known vesivirus structures. Furthermore, at intermediate resolutions, we found a high level of structural similarity between vesivirus 2117 and Caliciviridae from other genera: Sapovirus and rabbit hemorrhagic disease virus. Phylogenetic analysis confirms vesivirus 2117 as a vesivirus closely related to canine vesiviruses. We postulate that morphological differences in virion structure seen between vesivirus clades may reflect differences in receptor usage.

  • Sapovirus-like particles derived from polyprotein
    Virus Research, 2008
    Co-Authors: Grant S Hansman, Tomoichiro Oka, N. Takeda
    Abstract:

    We expressed full-length Sapovirus genome constructs in insect cells and analyzed their products. The capsid protein was cleaved from the ORF1 polyprotein from a native-like genome construct and two full-length genome constructs with mutations in an active polymerase motif, whereas the capsid protein was not cleaved from a full-length genome construct with a mutation in an active protease motif. Our results showed that the Sapovirus protease-polymerase precursor protein cleaved the capsid protein from the polyprotein at the putative conserved capsid start. Importantly, the cleaved capsid protein formed empty virus-like particles that were morphologically and antigenically similar to native Sapovirus.

  • acute gastroenteritis caused by gi 2 Sapovirus taiwan 2007
    Emerging Infectious Diseases, 2007
    Co-Authors: Tomoichiro Oka, Grant S Hansman, N. Takeda, Kazuhiko Katayama, Chihhsin Muo, Shyyuan Liang, Chinghsiang Hung, Donald Dahshyong Jiang, Jui Hsin Chang, Jyhyuan Yang
    Abstract:

    To the Editor: Sapovirus is an etiologic agent of human gastroenteritis. Although many of the previously reported cases were of mild, sporadic infections in young children (1–3), several recent Sapovirus-associated gastroenteritis outbreaks have affected adults, which suggests that the virus’s virulence, prevalence, or both, may be increasing (4–6). In this study, we describe a Sapovirus-associated outbreak of gastroenteritis that occurred during May 4–8, 2007, and involved college students in northern Taiwan. A total of 55 students had clinical symptoms of gastroenteritis, including diarrhea (45), vomiting (22), abdominal cramps (17), and fever (2). The clinical symptoms continued for up to 10 days (mean 4.7 days). Stool specimens were collected from 8 of 55 students on May 8 (Table). Initially, the specimens were screened for bacteria, rotavirus, and norovirus, but all specimens were negative for these pathogens. The 8 stool specimens were then examined by electron microscopy (EM), and 1 was positive for calicivirus-like particles. Table Clinical symptoms and laboratory diagnosis results for Sapovirus-related outbreak among college students, northern Taiwan, May 2007*† To confirm the EM results, we performed reverse transcription–PCR (RT-PCR), real-time RT-PCR, and sequence analysis as previously described (7). Briefly, purified RNA (10 μL) was reverse transcribed by using SuperScript III reverse transcriptase according to the manufacture’s instructions (Invitrogen, Carlsbad, CA, USA). PCR was carried out by using the SV-F11 and SV-R1 primer set directed against the conserved N terminal capsid region (8). The PCR products were analyzed with 2% agarose gel electrophoresis and visualized after ethidium bromide staining. The PCR-generated amplicons (≈780 bp) were excised from the gel and purified by the QIAquick gel extraction kit (QIAGEN, Hilden, Germany). Nucleotide sequences were prepared with the terminator cycle sequence kit (version 3.1) and determined with the ABI 3130 sequencer (Applied Biosystems, Foster City, CA, USA.). Nucleotide sequences were aligned by using ClustalX (www.clustal.org), and the distances were calculated by using the Kimura 2-parameter method. A phylogenetic tree was generated by the neighbor-joining method as described previously (1,8). Of the 8 specimens, 7 were positive by RT-PCR and real-time RT-PCR (Table). SaV124F, SaV1F, SaV5F, and SaV1245R primers as well as SaV124TP and SaV5TP minor-groove binding probes were used for real-time RT-PCR diagnosis, which targets the Sapovirus RdRp-capsid junction region as described (7). The number of Sapovirus cDNA copies ranged from 2.86 × 107 to 1.72 × 1010 copies/g of stool specimen; mean was 2.71 × 109 copies/g of stool specimen (Table). Sequence analysis of the 7 positive specimens showed 100% nucleotide identity (nt 5098–5878), indicating that the outbreak was caused by 1 Sapovirus strain. To better classify the Sapovirus, we reamplified the 3′ end of the genome from 1 positive specimen and sequenced ≈2,400 nt (nt 5074-3′) (Hu/SaV/9–5/Taipei/07/TW; GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"EU124657","term_id":"158929628"}}EU124657). PCR was performed with SV-F13, SV-F14, and TX30SXN primers as described (1). Database searches found a closely matching Sapovirus sequence (99%) that was detected in a patient with gastroenteritis in Japan, in 2004 (Chiba041413 strain; GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"AB258427","term_id":"118442701"}}AB258427). The next closely matching sequence was detected in an outbreak of gastroenteritis among adults in the United States in 1994 (Parkville strain; {"type":"entrez-nucleotide","attrs":{"text":"HCU73124","term_id":"1916653"}}HCU73124) (6). Phylogenetic analysis clustered these 3 Sapovirus sequences into genogroup I/genotype 2 (GI/2) (Appendix Figure). Sapovirus was reported in Japan in water samples (untreated wastewater, treated wastewater, and a river) and in clam samples intended for human consumption (1). Apart from these 2 environmental studies, little is known about reservoir of Sapovirus or its route of infection in the natural environment. The source of contamination in this current outbreak was not determined; however, none of the food handlers associated with the college reported symptoms of gastroenteritis. However, in a recent molecular epidemiologic study in Japan, a large number of symptomatic and asymptomatic food handlers were found to be infected with noroviruses (9). Several seroprevalence studies also indicated high prevalence rates of antibodies to Sapovirus in adults and children (10). All of these findings highlight the need to collect stool specimens from asymptomatic persons and indicate possible “silent” transmission through an asymptomatic route. Symptoms of Sapovirus infection are thought to be milder than symptoms of norovirus infections. However, in this study approximately one third (17) of the 55 students reported symptoms of abdominal pain and 22 (40%) reported symptoms of vomiting. Many of the earlier Sapovirus studies described Sapovirus GI/1 infections in young Japanese children (1), which indicated that infecting virus had a different genotype than the virus detected in this study (GI/2). In addition, the viral load in this study appeared to be comparatively high. These results suggest that some Sapovirus genotypes are more virulent than others. Similar findings were obtained with norovirus infections around the world; strains belonging to norovirus GII/4 were the most prevalent in many countries. Although several recombinant Sapovirus strains have been identified and found to be the cause of increased numbers of infections in some countries (1,5), they were not observed in this study. Increased Sapovirus surveillance and reporting are needed to shed some more light on this poorly understood virus.

  • recombinant Sapovirus gastroenteritis japan
    Emerging Infectious Diseases, 2007
    Co-Authors: Grant S Hansman, Tomoichiro Oka, Setsuko Ishida, Shima Yoshizumi, Masahiro Miyoshi, Tetsuya Ikeda, N. Takeda
    Abstract:

    To the Editor: Sapovirus and norovirus are causative agents of gastroenteritis in children and adults. Norovirus is the most important cause of outbreaks of gastroenteritis, whereas only a few outbreaks of Sapovirus have been reported (1,2). On the basis of complete capsid gene sequences, Sapovirus can be divided into 5 genogroups, among which GI, GII, GIV, and GV infect humans, whereas Sapovirus GIII infects porcine species. We report 2 outbreaks of gastroenteritis in Hokkaido, Japan. The first outbreak (A) occurred at a college from May 29 to June 2, 2000. A total of 12 persons (11 students and 1 teacher) reported symptoms of gastroenteritis (nausea, vomiting, stomachache, diarrhea, and fever); 11 stool specimens were collected from days 1 to 7 after onset of illness (Table). These specimens were negative for norovirus (data not shown), but 5 were positive for Sapoviruslike viruses by electron microscopy (Table). Table Analysis of 18 stool specimens for Sapovirus during 2 outbreaks of gastroenteritis, Japan* The 11 specimens were then examined for Sapovirus by using nested reverse transcription–PCR (RT-PCR) as described (3). A total of 9 (82%) of 11 specimens were positive for Sapovirus. Sequence analysis showed that these 9 viruses had 100% nucleotide identity and likely represented the same Sapovirus strain (termed Yak2 strain, GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"AB046353","term_id":"148717098","term_text":"AB046353"}}AB046353). To determine the number of cDNA copies per gram of stool, we performed real-time RT-PCR as described (4). The number of Sapovirus cDNA copies ranged from 5.36 × 105 to 7.47 × 109/g stool (median 5.49 × 109 copies/g stool) (Table). The second outbreak (B) occurred at a kindergarten from February 1 to 22, 2005. A total of 23 persons (15 children and 8 adults) reported symptoms of gastroenteritis (nausea, vomiting, stomachache, diarrhea, and fever); 7 stool specimens were collected (Table). These specimens were negative for norovirus (data not shown), but all were positive for Sapovirus by nested RT-PCR. The 7 sequences from this outbreak had 100% nucleotide identity and likely represented the same Sapovirus strain (termed Nay1 strain, GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"EF213768","term_id":"126565998","term_text":"EF213768"}}EF213768). The number of Sapovirus cDNA copies ranged from 1.14 × 109 to 5.41 × 1010/g stool (median 2.50 × 1010 copies/g stool) (Table). One positive Sapovirus specimen from each outbreak was subjected to further sequence analysis in which a single overlapping PCR fragment covering the partial polymerase gene and capsid gene was amplified. The Yak2 and Nay1 sequences shared ≈71% nucleotide identity for this fragment and likely represented different Sapovirus strains. The Yak2 sequence closely matched Sapovirus GIV Ehime1107 and SW278 sequences (GenBank accession nos. {"type":"entrez-nucleotide","attrs":{"text":"DQ058829","term_id":"70799531","term_text":"DQ058829"}}DQ058829 and {"type":"entrez-nucleotide","attrs":{"text":"AY237420","term_id":"45545440","term_text":"AY237420"}}AY237420, respectively) and had 98% and 97% nucleotide identity for the entire fragment, respectively (5). The Nay1 sequence closely matched the Sapovirus GII C12 sequence ({"type":"entrez-nucleotide","attrs":{"text":"AY603425","term_id":"51243518","term_text":"AY603425"}}AY603425) and had 91% nucleotide identity for the entire fragment. The Nay1 sequence closely matched the C12 sequence, which was detected in Osaka, Japan, in 2001 (6), whereas the Yak2 sequence closely matched the Ehime1107 sequence, which was detected in Matsuyama, Japan, in 2002 (5) and the SW278 sequence, which was detected in Sweden in 2003 (1). We recently described the C12 strain as intragenogroup recombinant Sapovirus strain (6), whereas the Ehime1107 and SW278 strains were described as intergenogroup recombinant Sapovirus strains (5). Our results indicate that recombination sites in intragenogroup and intergenogroup recombinant Sapovirus strains were at the polymerase and capsid junction (5,6). Sapovirus Sydney53 ({"type":"entrez-nucleotide","attrs":{"text":"DQ104360","term_id":"308196023","term_text":"DQ104360"}}DQ104360) and Sydney3 strains ({"type":"entrez-nucleotide","attrs":{"text":"DQ104357","term_id":"308196021","term_text":"DQ104357"}}DQ104357), which were detected in Australia from August 2001 to August 2004 (7), closely matched C12 and Ehime1107/SW278 sequences, respectively. These results showed that recombinant Sapovirus strains are stable in the environment and may be globally distributed. Our findings also suggest a changing distribution of Sapovirus-associated gastroenteritis in Hokkaido because different Sapovirus GI strains were predominant Sapovirus strains that caused causing outbreaks of gastroenteritis in Hokkaido (8,9). In a recent study, the number of norovirus cDNA copies per gram of stool specimen was analyzed and a discrepancy was found between the different norovirus genogroups (10). Chan et al. found that noroviruses GI and GII showed medians of 8.4 × 105 and 3.0 × 108 copies/g of stool specimen, respectively, and speculated that increased viral loads were caused by higher transmissibility of norovirus GII strains (10). Our results showed that Sapovirus GII Nay1 and GIV Yak2 strains showed higher viral loads than norovirus GII strains. These results suggest that a high degree of shedding of Sapovirus GII Nay1 and GIV Yak2 strains may have caused the outbreak of gastroenteritis. However, to elucidate this suggestion, further studies are needed with other Sapovirus strains.

  • human Sapovirus in clams japan
    Emerging Infectious Diseases, 2007
    Co-Authors: Grant S Hansman, Tomoichiro Oka, Reiko Okamoto, Tomoko Nishida, Schoichi Toda, Mamoru Noda, Daisuke Sano, You Ueki, Takahiro Imai, Tatsuo Omura
    Abstract:

    Human Sapovirus was detected in 4 of 57 clam packages by reverse transcription–PCR and sequence analysis. This represents the first finding of Sapovirus contamination in food. Closely matching sequences have been detected in stool specimens from patients with gastroenteritis in Japan, which indicates a possible food-to-human transmission link.

Hiroshi Ushijima - One of the best experts on this subject based on the ideXlab platform.

  • seasonal pattern and genotype distribution of Sapovirus infection in japan 2003 2009
    Epidemiology and Infection, 2012
    Co-Authors: Shuvra Kanti Dey, Outavong Phathammavong, T D Nguyen, Aksara Thongprachum, Wisoot Chanit, Shoko Okitsu, Masashi Mizuguchi, Hiroshi Ushijima
    Abstract:

    Sapovirus, a member of the family Caliciviridae, is one of the major causative agents of viral gastroenteritis affecting all age groups. A total of 3232 faecal specimens collected from infants and children with gastroenteritis in five different regions of Japan during 2003-2009 were examined for Sapovirus by reverse transcription-polymerase chain reaction. Sapoviruses were detected in 131 (4·05%) patients with the peak observed mainly in the cold season (November-March) in Japan during 2003-2009. During the last 6 years, Sapovirus GI/1 was the predominant strain in Japan followed by GIV, GII/3, GII/6, GII/2, GII/12 and GI, respectively.

  • novel recombinant Sapovirus in bangladesh
    Clinical Laboratory, 2011
    Co-Authors: Shuvra Kanti Dey, Shoko Okitsu, Masashi Mizuguchi, Hiroshi Ushijima
    Abstract:

    Background Recombination of RNA viruses plays an important part in molecular epidemiological study, virus evolution, vaccine design, and viral control programs. Sapovirus, a member of the family Caliciviridae, is one of the major causative agents of viral gastroenteritis affecting all age groups. Methods Sapovirus capsid and polymerase regions were amplified by PCR using specific primers. PCR products were sequenced directly and sequence analysis was performed using CLUSTAL X, SimPlot, and MEGA 4 software package. Results Based on the genetic analysis, a novel, naturally occurring recombinant Sapovirus strain was identified in Bangladesh. Breakpoint analysis of the recombinant Sapovirus showed that the recombination site was at the open reading frame ORF1/ORF2 overlap. Conclusions We described the genetic characterization of a novel, naturally occurring recombinant Sapovirus and provided the first evidence of recombination in Sapovirus in Bangladesh.

  • intergenogroup recombinant Sapovirus in japan 2007 2008
    Emerging Infectious Diseases, 2009
    Co-Authors: Wisoot Chanit, Aksara Thongprachum, Shoko Okitsu, Masashi Mizuguchi, Pattara Khamrin, Hiroshi Ushijima
    Abstract:

    We investigated the incidence of Sapovirus (SaV)–associated gastroenteritis in infants and children in Japan during 2007–2008 and characterized the diversity of SaV-positive strains. SaV was detected in 19 (4%) of 477 fecal specimens. The leading genogroup (79%, 15 cases) comprised intergenogroup recombinant SaVs (GII/GIV).

  • emergence of intragenotype recombinant Sapovirus in japan
    Infection Genetics and Evolution, 2007
    Co-Authors: Tung Gia Phan, Shuvra Kanti Dey, Shoko Okitsu, Pattara Khamrin, Trinh Duy Quang, Sayaka Takanashi, Niwat Maneekarn, Hiroshi Ushijima
    Abstract:

    Abstract Sapovirus is an important causative agent of sporadic cases as well as of outbreaks of acute gastroenteritis in humans worldwide. A total of 603 fecal specimens collected from July 2005 to June 2006 from children with acute gastroenteritis in five localities in Japan (Maizuru, Tokyo, Sapporo, Saga, and Osaka) were screened for Sapovirus by RT-PCR. It was found that 17 specimens were positive for Sapovirus and it represented 2.8%. Interestingly, intragenotype recombinant Sapovirus GI/1 emerged with 76.4% (13 of 17) and rapidly became the leading cause of acute gastroenteritis in Japan for the first time. The lower frequency of Sapovirus GI/2 and GI/4 (each of 11.8%), which were the second prevailing genotypes, was also detected. A novel nomenclature of Sapovirus was proposed, in which worldwide Sapovirus strains were classified into seven genogroups. Of these, novel Sapovirus genogroups VI and VII demonstrated the very low homologies, only 32.8–41.6% at the amino acid level and 43.6–49.9% at the nucleotide level, to those of Sapovirus genogroups I–V. Of note, two distinct clusters of Sapovirus were co-circulating in porcine. Interestingly, the worldwide Sapovirus strains shared the 25 nucleotide-conserved region, covering the polymerase–capsid junction which differed according to each species due to multiple nucleotide substitutions. The finding suggests that the Sapovirus recombination between human and animal hardly takes place in nature. This is also the first, to our best knowledge, demonstrating the emergence of the intragenotype recombinant Sapovirus with its causing diarrheal illness in Japan.

  • prevalence of Sapovirus infection among infants and children with acute gastroenteritis in dhaka city bangladesh during 2004 2005
    Journal of Medical Virology, 2007
    Co-Authors: Shuvra Kanti Dey, Shoko Okitsu, Tung Gia Phan, Tuan Anh Nguyen, Osamu Nishio, Abul Faiz Mohammad Salim, Fumihiro Yagyu, Hiroshi Ushijima
    Abstract:

    Sapovirus, a member of the family Caliciviridae is one of the major causative agents of viral gastroenteritis affecting all age group. Sapovirus was detected in 25 of 917 stool specimens from infants and children with acute gastroenteritis in a Children Hospital in Dhaka City, Bangladesh during 2004–2005. All fecal specimens were examined for Sapovirus by reverse transcription-polymerase chain reaction. Molecular analysis of Sapovirus was carried out by sequencing methods. Sapovirus detected in this study was clustered into only one distinct genogroup I. Sapovirus GI/1 was predominant, followed by GI/2 and accounted for 92% (23 of 25) and 8% (2 of 25), respectively. The results clearly indicated that Sapovirus infections were observed most commonly in the autumn to winter seasons (September to January) in Dhaka City. The common clinical symptoms of Sapovirus infected patients were dehydration (88%), vomiting (76%), and abdominal pain (60%). This is the first report of Sapovirus in Bangladesh. J. Med. Virol. 79:633–638, 2007. © 2007 Wiley-Liss, Inc.

N. Takeda - One of the best experts on this subject based on the ideXlab platform.

  • detection of Sapovirus in oysters
    Microbiology and Immunology, 2010
    Co-Authors: You Ueki, N. Takeda, Kazuhiko Katayama, Tomoichiro Oka, Mamoru Noda, Mika Shoji, Yoko Okimura, Yasuko Miyota, Yoshifumi Masago, Takayuki Miura
    Abstract:

    SaV sequences which are either genetically identical or similar were detected from oysters, feces from gastroenteritis patients, and domestic wastewater samples in geographically close areas. This is the first report of the detection of SaV in oysters which meet the legal requirements for raw consumption in Japan.

  • Quantitative analysis of fecal Sapovirus shedding: identification of nucleotide substitutions in the capsid protein during prolonged excretion
    Archives of Virology, 2009
    Co-Authors: Akira Iwakiri, N. Takeda, Kazuhiko Katayama, Takaji Wakita, Hidenari Ganmyo, Seigo Yamamoto, Kayoko Otao, Mieko Mikasa, Sigeko Kizoe, Tomoichiro Oka
    Abstract:

    Sapovirus (SaV) is an important pathogen causing gastroenteritis in humans. Quantitative analysis of the viral loads in feces collected from two SaV outbreaks was performed. Our results showed that SaV excretion generally decreased to an undetectable level in 2 weeks; however, some individuals excrete SaV in feces at high concentrations for 2–4 weeks after the onset of illness. In addition, we identified for the first time nucleotide changes in the capsid region during prolonged excretion.

  • detection of multiple Sapovirus genotypes and genogroups in oyster associated outbreaks
    Japanese Journal of Infectious Diseases, 2009
    Co-Authors: Reiko Nakagawaokamoto, Osamu Nishio, Mamoru Noda, Tomoko Aritanishida, Shoichi Toda, Hirotomo Kato, Hiroyuki Iwata, Miho Akiyama, Hirokazu Kimura, N. Takeda
    Abstract:

    This report describes multiple viruses in stool specimens from oyster-associated gastroenteritis. Eleven outbreaks of oyster-associated gastroenteritis were examined for enteric viruses between January 2002 and March 2006 in Japan. Multiple norovirus genotypes were detected in all outbreaks; moreover, kobuvirus, Sapovirus, and astrovirus were also detected in 6, 3, and 1 of the 11 outbreaks, respectively. Notably, multiple Sapovirus genogroups were detected in the stool specimens from subjects in two oyster-associated gastroenteritis outbreaks.

  • Sapovirus-like particles derived from polyprotein
    Virus Research, 2008
    Co-Authors: Grant S Hansman, Tomoichiro Oka, N. Takeda
    Abstract:

    We expressed full-length Sapovirus genome constructs in insect cells and analyzed their products. The capsid protein was cleaved from the ORF1 polyprotein from a native-like genome construct and two full-length genome constructs with mutations in an active polymerase motif, whereas the capsid protein was not cleaved from a full-length genome construct with a mutation in an active protease motif. Our results showed that the Sapovirus protease-polymerase precursor protein cleaved the capsid protein from the polyprotein at the putative conserved capsid start. Importantly, the cleaved capsid protein formed empty virus-like particles that were morphologically and antigenically similar to native Sapovirus.

  • acute gastroenteritis caused by gi 2 Sapovirus taiwan 2007
    Emerging Infectious Diseases, 2007
    Co-Authors: Tomoichiro Oka, Grant S Hansman, N. Takeda, Kazuhiko Katayama, Chihhsin Muo, Shyyuan Liang, Chinghsiang Hung, Donald Dahshyong Jiang, Jui Hsin Chang, Jyhyuan Yang
    Abstract:

    To the Editor: Sapovirus is an etiologic agent of human gastroenteritis. Although many of the previously reported cases were of mild, sporadic infections in young children (1–3), several recent Sapovirus-associated gastroenteritis outbreaks have affected adults, which suggests that the virus’s virulence, prevalence, or both, may be increasing (4–6). In this study, we describe a Sapovirus-associated outbreak of gastroenteritis that occurred during May 4–8, 2007, and involved college students in northern Taiwan. A total of 55 students had clinical symptoms of gastroenteritis, including diarrhea (45), vomiting (22), abdominal cramps (17), and fever (2). The clinical symptoms continued for up to 10 days (mean 4.7 days). Stool specimens were collected from 8 of 55 students on May 8 (Table). Initially, the specimens were screened for bacteria, rotavirus, and norovirus, but all specimens were negative for these pathogens. The 8 stool specimens were then examined by electron microscopy (EM), and 1 was positive for calicivirus-like particles. Table Clinical symptoms and laboratory diagnosis results for Sapovirus-related outbreak among college students, northern Taiwan, May 2007*† To confirm the EM results, we performed reverse transcription–PCR (RT-PCR), real-time RT-PCR, and sequence analysis as previously described (7). Briefly, purified RNA (10 μL) was reverse transcribed by using SuperScript III reverse transcriptase according to the manufacture’s instructions (Invitrogen, Carlsbad, CA, USA). PCR was carried out by using the SV-F11 and SV-R1 primer set directed against the conserved N terminal capsid region (8). The PCR products were analyzed with 2% agarose gel electrophoresis and visualized after ethidium bromide staining. The PCR-generated amplicons (≈780 bp) were excised from the gel and purified by the QIAquick gel extraction kit (QIAGEN, Hilden, Germany). Nucleotide sequences were prepared with the terminator cycle sequence kit (version 3.1) and determined with the ABI 3130 sequencer (Applied Biosystems, Foster City, CA, USA.). Nucleotide sequences were aligned by using ClustalX (www.clustal.org), and the distances were calculated by using the Kimura 2-parameter method. A phylogenetic tree was generated by the neighbor-joining method as described previously (1,8). Of the 8 specimens, 7 were positive by RT-PCR and real-time RT-PCR (Table). SaV124F, SaV1F, SaV5F, and SaV1245R primers as well as SaV124TP and SaV5TP minor-groove binding probes were used for real-time RT-PCR diagnosis, which targets the Sapovirus RdRp-capsid junction region as described (7). The number of Sapovirus cDNA copies ranged from 2.86 × 107 to 1.72 × 1010 copies/g of stool specimen; mean was 2.71 × 109 copies/g of stool specimen (Table). Sequence analysis of the 7 positive specimens showed 100% nucleotide identity (nt 5098–5878), indicating that the outbreak was caused by 1 Sapovirus strain. To better classify the Sapovirus, we reamplified the 3′ end of the genome from 1 positive specimen and sequenced ≈2,400 nt (nt 5074-3′) (Hu/SaV/9–5/Taipei/07/TW; GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"EU124657","term_id":"158929628"}}EU124657). PCR was performed with SV-F13, SV-F14, and TX30SXN primers as described (1). Database searches found a closely matching Sapovirus sequence (99%) that was detected in a patient with gastroenteritis in Japan, in 2004 (Chiba041413 strain; GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"AB258427","term_id":"118442701"}}AB258427). The next closely matching sequence was detected in an outbreak of gastroenteritis among adults in the United States in 1994 (Parkville strain; {"type":"entrez-nucleotide","attrs":{"text":"HCU73124","term_id":"1916653"}}HCU73124) (6). Phylogenetic analysis clustered these 3 Sapovirus sequences into genogroup I/genotype 2 (GI/2) (Appendix Figure). Sapovirus was reported in Japan in water samples (untreated wastewater, treated wastewater, and a river) and in clam samples intended for human consumption (1). Apart from these 2 environmental studies, little is known about reservoir of Sapovirus or its route of infection in the natural environment. The source of contamination in this current outbreak was not determined; however, none of the food handlers associated with the college reported symptoms of gastroenteritis. However, in a recent molecular epidemiologic study in Japan, a large number of symptomatic and asymptomatic food handlers were found to be infected with noroviruses (9). Several seroprevalence studies also indicated high prevalence rates of antibodies to Sapovirus in adults and children (10). All of these findings highlight the need to collect stool specimens from asymptomatic persons and indicate possible “silent” transmission through an asymptomatic route. Symptoms of Sapovirus infection are thought to be milder than symptoms of norovirus infections. However, in this study approximately one third (17) of the 55 students reported symptoms of abdominal pain and 22 (40%) reported symptoms of vomiting. Many of the earlier Sapovirus studies described Sapovirus GI/1 infections in young Japanese children (1), which indicated that infecting virus had a different genotype than the virus detected in this study (GI/2). In addition, the viral load in this study appeared to be comparatively high. These results suggest that some Sapovirus genotypes are more virulent than others. Similar findings were obtained with norovirus infections around the world; strains belonging to norovirus GII/4 were the most prevalent in many countries. Although several recombinant Sapovirus strains have been identified and found to be the cause of increased numbers of infections in some countries (1,5), they were not observed in this study. Increased Sapovirus surveillance and reporting are needed to shed some more light on this poorly understood virus.

Jan Vinjé - One of the best experts on this subject based on the ideXlab platform.

  • human calicivirus typing tool a web based tool for genotyping human norovirus and Sapovirus sequences
    Journal of Clinical Virology, 2021
    Co-Authors: Roman L Tatusov, Preeti Chhabra, Marta Diezvalcarce, Leslie Barclay, Jennifer L Cannon, Jan Vinjé
    Abstract:

    Abstract Background The family Caliciviridae consists of a genetically diverse group of RNA viruses that infect a wide range of host species including noroviruses and Sapoviruses which cause acute gastroenteritis in humans. Typing of these viruses relies on sequence-based approaches, and therefore there is a need for rapid and accurate web-based typing tools. Objective To develop and evaluate a web-based tool for rapid and accurate genotyping of noroviruses and Sapoviruses. Methods The Human Calicivirus Typing (HuCaT) tool uses a set of curated reference sequences that are compared to query sequences using a k-mer (DNA substring) based algorithm. Outputs include alignments and phylogenetic trees of the 12 top matching reference sequences for each query. Results The HuCaT tool was validated with a set of 1310 norovirus and 239 Sapovirus sequences covering all known human norovirus and Sapovirus genotypes. HuCaT tool assigned genotypes to all queries with 100 % accuracy and was much faster (17 s) than BLAST (150 s) or phylogenetic analyses approaches. Conclusions The web-based HuCaT tool supports rapid and accurate genotyping of human noroviruses and Sapoviruses.

  • near complete human Sapovirus genome sequences from kenya
    Microbiology Resource Announcements, 2019
    Co-Authors: Marta Diezvalcarce, Anna M Montmayeur, Roman L Tatusov, Jan Vinjé
    Abstract:

    We report five near-complete Sapovirus genome sequences, including GI.3, GII.2, and GII.6 and two novel GII.NA (not assigned) strains. These new sequences expand the collection of human Sapoviruses, allowing for a more accurate phylogenetic analysis of circulating strains and for designing broadly reactive primers for their detection and typing.

  • norovirus and Sapovirus epidemiology and strain characteristics among navajo and apache infants
    PLOS ONE, 2017
    Co-Authors: Lindsay R Grant, Umesh D Parashar, Katherine L Obrien, Robert Weatherholtz, Raymond Reid, Novalene Goklish, Mathuram Santosham, Jan Vinjé
    Abstract:

    Norovirus and Sapovirus are important causes of acute gastroenteritis (AGE) among American Indian infants. We investigated the prevalence and molecular epidemiology of norovirus and Sapovirus in American Indian infants who have historically experienced a high burden of AGE compared to other US populations. Stool samples were collected from 241 children with AGE (cases) and from 343 infants without AGE (controls) ≤9 months of age from 2002-2004. Cases experienced forceful vomiting and/or 3 or more watery or looser-than-normal stools in 24 hours. Stools were tested by real-time RT-PCR for norovirus GI, GII and GIV and Sapovirus GI, GII, GIV and GV. Positive samples were genotyped after sequencing conventional RT-PCR products. Norovirus was identified in 76 (31.5%) of the cases and 70 (20.4%) of the controls (p<0.001). GII.3 and GII.4 Farmington Hills were the most frequently identified genotypes in 14.5% and 30.3% of cases and 17.1% and 27.1% of controls, respectively. Sapovirus GI and GII genotypes were identified in 8 (3.3%) of cases and 8 (2.3%) of controls and a single GIV virus was detected in a control. The same norovirus and Sapovirus genotypes were circulating in the general U.S. population in the same time period. The high detection rate of norovirus in healthy controls suggests significant asymptomatic transmission in young infants in these communities.

  • population based incidence rates of diarrheal disease associated with norovirus Sapovirus and astrovirus in kenya
    PLOS ONE, 2016
    Co-Authors: Umesh D Parashar, Jan Vinjé, Kayoko Shioda, Leonard Cosmas, Allan Audi, Nicole Gregoricus, Joel M Montgomery, Daniel R Feikin, Robert F Breiman
    Abstract:

    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 Kenya.

  • etiology of viral gastroenteritis in children 5 years of age in the united states 2008 2009
    The Journal of Infectious Diseases, 2013
    Co-Authors: Preeti Chhabra, Hannah S Shirley, Daniel C Payne, Mary E. Wikswo, Umesh D Parashar, Peter G. Szilagyi, Mary Allen Staat, Kathryn M. Edwards, Xiaoyan Lu, Jan Vinjé
    Abstract:

    Background. Although rotavirus and norovirus cause nearly 40% of severe endemic acute gastroenteritis (AGE) in children <5 years of age in the United States, there are limited data on the etiologic role of other enteric viruses in this age group. Methods. We conducted active population-based surveillance in children presenting with AGE to hospitals, emergency departments, and primary care clinics in 3 US counties. Stool specimens from these children and from age-matched healthy controls collected between October 2008 and September 2009 were tested for enteric adenovirus, astrovirus, Sapovirus, parechovirus, bocavirus, and aichivirus. Typing was performed by sequencing and phylogenetic analysis. Results. Adenovirus, astrovirus, Sapovirus, parechovirus, bocavirus, and aichivirus were detected in the stool specimens of 11.8%, 4.9%, 5.4%, 4.8%, 1.4%, and 0.2% of patients with AGE and 1.8%, 3.0%, 4.2%, 4.4%, 2.4%, and 0% of healthy controls, respectively. Adenovirus (type 41), astrovirus (types 1, 2, 3, 4, and 8), Sapovirus (genogroups I and II), parechovirus (types 1, 3, 4, and 5), and bocavirus (types 1, 2, and 3) were found cocirculating. Conclusions. Adenovirus, astrovirus, and Sapovirus infections were detected in 22.1% of the specimens from children <5 years of age who had medical visits for AGE and tested negative for rotavirus and norovirus. No causal role for parechovirus and bocavirus was found.

Tomoichiro Oka - One of the best experts on this subject based on the ideXlab platform.

Related terms

Sapovirus - 15 days free trial to Access Experts & Abstracts