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      An outbreak of gastroenteritis associated with a novel GII.8 sapovirus variant-transmitted by vomit in Shenzhen, China, 2019

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          Abstract

          Background

          Human Sapoviruses (SaVs) has been reported as one of the causative agents of acute gastroenteritis (AGE) worldwide. An outbreak of SaVs affected 482 primary school students during spring activities from February 24 to March 11, 2019 in Shenzhen City, China. Our study was aimed at determining the epidemiology of the outbreak, investigating its origins, and making a clear identification of the SaVs genetic diversity.

          Methods

          Epidemiological investigation was conducted for this AGE outbreak. Stool samples were collected for laboratory tests of causative agents. Real-time reverse-transcription polymerase chain reaction (rRT-PCR) and conventional RT-PCR were used for detecting and genotyping of SaVs. The nearly complete genome of GII.8 SaV strains were amplified and sequenced by using several primer sets designed in this study. Phylogenetic analysis was performed to characterize the genome of GII.8 SaV strains.

          Results

          The single factor analysis showed that the students who were less than 1.5 m away from the vomitus in classroom or playgroundwere susceptible ( P < 0.05). Seven of 11 fecal samples from patients were positive for GII.8 SaV genotype. In this study, we obtained the genome sequence of a SaV GII.8 strain Hu/SaV/2019008Shenzhen/2019 /CHN (SZ08 ) and comprehensively analyzed the genetic diversity. The phylogenetic analysis showed that the GII.8 strain SZ08 formed an independent branch and became a novel variant of GII.8 genotype. Strain SZ08 harbored 11 specific amino acid variations compared with cluster A-D in full-length VP1.

          Conclusions

          This study identified SaVs as the causative agents for the AGE outbreak. Strain Hu SZ08 was clustered as independent branch and there was no recombination occurred in this strain SZ08. Further, it might become the predominant strain in diarrhea cases in the near future. Constant surveillance is required to monitor the emerging variants which will improve our knowledge of the evolution of SaVs among humans.

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          Comprehensive review of human sapoviruses.

          Tomoichiro Oka, Kazuhiko Katayama, Linda J. Saif … (2014)
          Sapoviruses cause acute gastroenteritis in humans and animals. They belong to the genus Sapovirus within the family Caliciviridae. They infect and cause disease in humans of all ages, in both sporadic cases and outbreaks. The clinical symptoms of sapovirus gastroenteritis are indistinguishable from those caused by noroviruses, so laboratory diagnosis is essential to identify the pathogen. Sapoviruses are highly diverse genetically and antigenically. Currently, reverse transcription-PCR (RT-PCR) assays are widely used for sapovirus detection from clinical specimens due to their high sensitivity and broad reactivity as well as the lack of sensitive assays for antigen detection or cell culture systems for the detection of infectious viruses. Sapoviruses were first discovered in 1976 by electron microscopy in diarrheic samples of humans. To date, sapoviruses have also been detected from several animals: pigs, mink, dogs, sea lions, and bats. In this review, we focus on genomic and antigenic features, molecular typing/classification, detection methods, and clinical and epidemiological profiles of human sapoviruses. Copyright © 2015, American Society for Microbiology. All Rights Reserved.
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            Broadly reactive and highly sensitive assay for Norwalk-like viruses based on real-time quantitative reverse transcription-PCR.

            T Kageyama, S Kojima, M. Shinohara … (2003)
            We have developed an assay for the detection of Norwalk-like viruses (NLVs) based on reverse transcription-PCR (RT-PCR) that is highly sensitive to a broad range of NLVs. We isolated virus from 71 NLV-positive stool specimens from 37 outbreaks of nonbacterial acute gastroenteritis and sequenced the open reading frame 1 (ORF1)-ORF2 junction region, the most conserved region of the NLV genome. The data were subjected to multiple-sequence alignment analysis and similarity plot analysis. We used the most conserved sequences that react with diverse NLVs to design primers and TaqMan probes for the respective genogroups of NLV, GI and GII, for use in a real-time quantitative RT-PCR assay. Our method detected NLV in 99% (80 of 81) of the stool specimens that were positive by electron microscopy, a better detection rate than with the two available RT-PCR methods. Furthermore, our new method also detected NLV in 20 of 28 stool specimens from the same NLV-related outbreaks that were negative for virus by electron microscopy. Our new assay is free from carryover DNA contamination and detects low copy numbers of NLV RNA. It can be used as a routine assay for diagnosis as well as for elucidation of the epidemiology of NLV infections.
            Article 0 comments Cited 106 times – based on 0 reviews     Review now
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              Rapid typing of human adenoviruses by a general PCR combined with restriction endonuclease analysis.

              M-A Allard, G Wadell, B Albinsson (2001)
              We have developed a system for rapid typing of adenoviruses (Ads) based on a combination of PCR and restriction endonuclease (RE) digestion (PCR-RE digestion). Degenerated consensus primers were designed, allowing amplification of DNA from all 51 human Ad prototype strains and altogether 44 different genome variants of Ad serotypes 1, 3, 4, 5, 7, 11, 19, 40, and 41. The 301-bp amplimer of 22 prototype strains representing all six subgenera and the genome variant was selected as a target for sequencing to look for subgenus and genome type variabilities. The sequences obtained were used to facilitate the selection of specific REs for discrimination purposes in a diagnostic assay by following the concept of cleavage or noncleavage of the 301-bp amplimer. On the basis of these results, a flowchart was constructed, allowing identification of subgenus B:2 and D serotypes and almost complete distinction of subgenus A, B:1, C, E, and F serotypes. Application of the PCR-RE digestion system to clinical samples allowed typing of 34 of 40 clinical samples positive for Ad. The genome type determined by this method was identical to that obtained by traditional RE typing of full-length Ad DNA. The remaining six samples were positive only after a nested PCR. Therefore, to reduce the risk of false-negative results, samples scored negative by the PCR-RE digestion system should be evaluated by the described nested PCR. Used in combination, the PCR-RE digestion method and the nested PCR provide a reliable and sensitive system that can easily be applied to all kinds of clinical samples when rapid identification of adenoviruses is needed.
              Article 0 comments Cited 83 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Miao Jin:
                ORCID: http://orcid.org/0000-0002-8442-5051
                jinmiao37@126.com
                Yuning Li: tiger19621962@163.com
                Journal
                Journal ID (nlm-ta): BMC Infect Dis
                Journal ID (iso-abbrev): BMC Infect Dis
                Title: BMC Infectious Diseases
                Publisher: BioMed Central (London )
                ISSN (Electronic): 1471-2334
                Publication date (Electronic): 1 December 2020
                Publication date PMC-release: 1 December 2020
                Publication date Collection: 2020
                Volume: 20
                Electronic Location Identifier: 911
                Affiliations
                [1 ]GRID grid.32566.34, ISNI 0000 0000 8571 0482, The First School of Clinical Medicine of Lanzhou University, ; Lanzhou, 730000 Gansu China
                [2 ]GRID grid.419468.6, ISNI 0000 0004 1757 8183, Department of Viral Diarrhea, NHC Key Laboratory of Medical Virology and Viral Diseases, , National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, ; 155 Changbai Rd, Chang-ping District, Beijing, 102206 China
                [3 ]Shenzhen Baoan Center for Disease Control and Prevention, Baoan District, Shenzhen, Guangdong Province China
                [4 ]Yingkou Center for Disease Control and Prevention, Yingkou, Liaoning China
                [5 ]GRID grid.412643.6, The First Hospital of Lanzhou University, ; Donggang-xi Rd, Cheng-guan District, Lanzhou, 730000 Gansu China
                [6 ]Central Hospital of Zhoukou, Zhoukou, 466000 Henan China
                Author information
                http://orcid.org/0000-0002-8442-5051
                Article
                Publisher ID: 5643
                DOI: 10.1186/s12879-020-05643-x
                PMC ID: 7706173
                PubMed ID: 33261582
                SO-VID: 0f0d0767-3367-476c-a29f-737bbf3790b8
                Copyright © © The Author(s) 2020
                License:

                Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

                History
                Date received : 4 June 2020
                Date accepted : 22 November 2020
                Funding
                Funded by: The Key Project of Science and Technology
                Award ID: No. 2018ZX10301408-001 and 2018ZX10102-001
                Categories
                Subject: Research Article
                Custom metadata
                issue-copyright-statement © The Author(s) 2020

                ScienceOpen disciplines: Infectious disease & Microbiology
                Keywords: sapoviruses,outbreak,vomit,genome,phylogenetic analysis
                Data availability:
                ScienceOpen disciplines: Infectious disease & Microbiology
                Keywords: sapoviruses, outbreak, vomit, genome, phylogenetic analysis

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