Genetic diversity and intergenogroup recombination events of sapoviruses detected from feces of pigs in Japan

Kuroda, Moegi; Masuda, Tsuneyuki; Ito, Mika; Naoi, Yuki; Doan, Yen Hai; Haga, Kei; Tsuchiaka, Shinobu; Kishimoto, Mai; Sano, Kaori; Omatsu, Tsutomu; Katayama, Yukie; Oba, Mami; Aoki, Hiroshi; Ichimaru, Toru; Sunaga, Fujiko; Mukono, Itsuro; Yamasato, Hiroshi; Shirai, Junsuke; Katayama, Kazuhiko; Mizutani, Tetsuya; Oka, Takahiro; Nagai, Makoto

doi:10.1016/j.meegid.2017.09.013

Cited by 23 publications

(41 citation statements)

References 40 publications

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“…Dual typing (ORF1-RdRp=P type, ORF2=genotype) is now used routinely in many laboratories worldwide and at least 14 GI P-types and 27 GII P-types as well as 9 GI capsid genotypes and 22 GII capsid genotypes have been described [2,19,27]. Inclusion of norovirus diagnostic testing by real-time quantitative reverse transcription PCR into clinical and public health routine in recent years [27,[37][38][39] has confirmed the importance of GI and GII noroviruses globally [13,31,33,35,37,[40][41][42][43][44]. The increasing use of pathogen genome sequencing to unravel modes of transmission, sources of outbreaks, or to study the burden of infections has led to identification of several new candidate norovirus genogroups and genotypes since the last norovirus classification update in 2013 [9,12,33,40,41,43,[45][46][47][48][49].…”

Section: Introductionmentioning

confidence: 99%

Updated classification of norovirus genogroups and genotypes

Chhabra

Graaf

Parra

et al. 2019

Journal of General Virology

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Noroviruses are genetically diverse RNA viruses associated with acute gastroenteritis in mammalian hosts. Phylogenetically, they can be segregated into different genogroups as well as P (polymerase)-groups and further into genotypes and P-types based on amino acid diversity of the complete VP1 gene and nucleotide diversity of the RNA-dependent RNA polymerase (RdRp) region of ORF1, respectively. In recent years, several new noroviruses have been reported that warrant an update of the existing classification scheme. Using previously described 2× standard deviation (sd) criteria to group sequences into separate clusters, we expanded the number of genogroups to 10 (GI-GX) and the number of genotypes to 49 (9 GI, 27 GII, 3 GIII, 2 GIV, 2 GV, 2 GVI and 1 genotype each for GVII, GVIII, GIX [formerly GII.15] and GX). Viruses for which currently only one sequence is available in public databases were classified into tentative new genogroups (GNA1 and GNA2) and genotypes (GII.NA1, GII.NA2 and GIV. NA1) with their definitive assignment awaiting additional related sequences. Based on nucleotide diversity in the RdRp region, noroviruses can be divided into 60 P-types (14 GI, 37 GII, 2 GIII, 1 GIV, 2 GV, 2 GVI, 1 GVII and 1 GX), 2 tentative P-groups and 14 tentative P-types. Future classification and nomenclature updates will be based on complete genome sequences and will be coordinated and disseminated by the international norovirus classification-working group.

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Section: Introductionmentioning

confidence: 99%

Updated classification of norovirus genogroups and genotypes

Chhabra

Graaf

Parra

et al. 2019

Journal of General Virology

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621

611

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“…Even though porcine SaV are regularly detected in porcine faeces, transmission to humans and zoonotic outbreaks have not been reported to date [53]. However, inter-genogroup recombination events of SaV in pigs have been reported and highlight the high genetic diversity and evolution rate of SaV [54].…”

Section: Sapovirusmentioning

confidence: 99%

Selected Viruses Detected on and in our Food

Bachofen

2018

Curr Clin Micro Rpt

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Purpose of Review The purpose of this review is to provide an update on recent literature and findings concerning selected foodborne viruses. Two groups of viruses were selected: (a) the most important viruses contaminating food, based on numbers of publications in the last 5 years and (b) viruses infecting sources of food that might have an impact on human health. Recent Findings Important foodborne viruses such as norovirus, hepatitis A and rotavirus are usually "only" contaminating food and are detected on the surface of foodstuffs. However, they are threats to human public health and make up for the majority of cases. In contrast, the meaning of viruses born from within the food such as natural animal and plant viruses is still in many cases unknown. An exception is Hepatitis E virus that is endemic in pigs, transmitted via pork meat and is recognised as an emerging zoonosis in industrialised countries. Summary Even though the clinical meaning of "new" foodborne viruses, often detected by next generation sequencing, still needs clarification, the method has great potential to enhance surveillance and detection particularly in view of an increasingly globalised food trade.

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“…Sapoviruses are also detected in other animals and are classified into genogroups/genotypes that are distinct from those in humans [25][26][27][28][29][30] ; an exception is the GI.1 strains detected in chimpanzees. 31 During the preparation of the manuscript, an additional strain that might belong to a new genogroup was detected in house mice.…”

Section: Reactivity Against All the 18 Human Sapovirus Genotypesmentioning

confidence: 99%

Broadly reactive real‐time reverse transcription‐polymerase chain reaction assay for the detection of human sapovirus genotypes

Oka

Iritani

Yamamoto

et al. 2018

Journal of Medical Virology

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Sapoviruses are associated with acute gastroenteritis. Human sapoviruses are classified into four distinct genogroups (GI, GII, GIV, and GV) based on their capsid gene sequences. A TaqMan probe‐based real‐time reverse transcription‐polymerase chain reaction (RT‐PCR) assay that detects the representative strains of these four genogroups is widely used for screening fecal specimens, shellfish, and environmental water samples. However, since the development of this test, more genetically diverse sapovirus strains have been reported, which are not detectable by the previously established assays. In this study, we report the development of a broader‐range sapovirus real‐time RT‐PCR assay. The assay can detect 2.5 × 107 and 2.5 × 10 1 copies of sapovirus and therefore is as sensitive as the previous test. Analysis using clinical stool specimens or synthetic DNA revealed that the new system detected strains representative of all the 18 human sapovirus genotypes: GI.1‐7, GII.1‐8, GIV.1, and GV.1, 2. No cross‐reactivity was observed against other representative common enteric viruses (norovirus, rotavirus, astrovirus, and adenovirus). This new assay will be useful as an improved, broadly reactive, and specific screening tool for human sapoviruses.

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Genetic diversity and intergenogroup recombination events of sapoviruses detected from feces of pigs in Japan

Cited by 23 publications

References 40 publications

Updated classification of norovirus genogroups and genotypes

Updated classification of norovirus genogroups and genotypes

Selected Viruses Detected on and in our Food

Broadly reactive real‐time reverse transcription‐polymerase chain reaction assay for the detection of human sapovirus genotypes

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