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      Gastroenteritis Outbreaks Associated with the Emergence of the New GII.4 Sydney Norovirus Variant during the Epidemic of 2012/13 in Shenzhen City, China

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          Abstract

          Noroviruses (NoVs) are the leading cause of gastroenteritis outbreaks in humans worldwide. Since late 2012, a new GII.4 variant Sydney 2012 has caused a significant increase in NoV epidemics in several countries. From November of 2012 to January of 2013, three gastroenteritis outbreaks occurred in two social welfare homes (Outbreaks A and B) and a factory (Outbreak C) in Shenzhen city of China. Feces and swabs were collected for laboratory tests for causative agents. While no bacterial pathogen was identified, all three outbreaks were caused by NoVs with detection rates of 26.2% (16/61) at Outbreak A, 35.2% (38/108) at Outbreak B), and 59.3% (16/27) at Outbreaks C. For Outbreak B, 25 of the 29 symptomatic individuals (86.2%) and 13 of the 79 asymptomatic individuals (16.5%) were found NoV-positive. For Outbreak C, an asymptomatic food handler was NoV-positive. All thirteen NoV sequences from the three outbreaks were classified into genogroup II and genotype 4 (GII.4), which we identified to be the GII.4 Sydney 2012 variant. The genome of two isolates from Outbreaks A and B were recombinant with the opening reading frame (ORF) 1 of GII.4 Osaka 2007 and ORF2 and 3 of the GII.4 New Orleans. Our study indicated that the GII.4 Sydney 2012 variant emerged and caused the outbreaks in China.

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          Norovirus illness is a global problem: emergence and spread of norovirus GII.4 variants, 2001-2007.

          J Joukje Siebenga, Harry Vennema, Du-Ping Zheng … (2009)
          Noroviruses (NoVs) are the most common cause of viral gastroenteritis. Their high incidence and importance in health care facilities result in a great impact on public health. Studies from around the world describing increasing prevalence have been difficult to compare because of differing nomenclatures for variants of the dominant genotype, GII.4. We studied the global patterns of GII.4 epidemiology in relation to its genetic diversity. Data from NoV outbreaks with dates of onset from January 2001 through March 2007 were collected from 15 institutions on 5 continents. Partial genome sequences (n=775) were collected, allowing phylogenetic comparison of data from different countries. The 15 institutions reported 3098 GII.4 outbreaks, 62% of all reported NoV outbreaks. Eight GII.4 variants were identified. Four had a global distribution--the 1996, 2002, 2004, and 2006b variants. The 2003Asia and 2006a variants caused epidemics, but they were geographically limited. Finally, the 2001 Japan and 2001 Henry variants were found across the world but at low frequencies. NoV epidemics resulted from the global spread of GII.4 strains that evolved under the influence of population immunity. Lineages show notable (and currently unexplained) differences in geographic prevalence. Establishing a global NoV network by which data on strains with the potential to cause pandemics can be rapidly exchanged may lead to improved prevention and intervention strategies.
          Article 0 comments Cited 199 times – based on 0 reviews     Review now
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            Design and evaluation of a primer pair that detects both Norwalk- and Sapporo-like caliciviruses by RT-PCR.

            X Jiang, P.W. Huang, W.M Zhong … (1999)
            A primer pair (p289/290) based on the RNA polymerase sequence of 25 prototype and currently circulating strains of human caliciviruses (HuCVs) was designed for the detection of both Norwalk-like caliciviruses (NLVs) and Sapporo-like caliciviruses (SLVs) by reverse transcription-polymerase chain reaction (RT-PCR). This primer pair produces RT-PCR products of 319 bp for NLVs and 331 bp for SLVs. The usefulness of this primer pair was shown by its detection of prototype NLVs (Norwalk, Snow Mountain, Hawaii and Mexico viruses) and SLVs (Sapporo/82, Hou/86, Hou/90 and Lon/92) and currently circulating strains of NLVs and SLVs in children and adults. This primer pair also detected more viruses in either NLV or SLV genera than previously designed primers. This primer pair is useful for broad detection of HuCVs for clinical and epidemiologic studies as well as for environmental monitoring.
            Article 0 comments Cited 113 times – based on 0 reviews     Review now
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              Recombination within the pandemic norovirus GII.4 lineage.

              John-Sebastian Eden, Megumi M. Tanaka-Arakawa, Aaron P White … (2013)
              Norovirus (NoV) is the leading cause of viral gastroenteritis globally. Since 1996, NoV variants of a single genetic lineage, GII.4, have been associated with at least six pandemics of acute gastroenteritis and caused between 62 and 80% of all NoV outbreaks. The emergence of these novel GII.4 variants has been attributed to rapid evolution and antigenic variation in response to herd immunity; however, the contribution of recombination as a mechanism facilitating emergence is increasingly evident. In this study, we sought to examine the role that intragenotype recombination has played in the emergence of GII.4 variants. Using a genome-wide approach including 25 complete genome sequences generated as part of this study, 11 breakpoints were identified within the NoV GII.4 lineage. The breakpoints were located at three recombination hot spots: near the open reading frame 1/2 (ORF1/2) and ORF2/3 overlaps, as well as within ORF2, which encodes the viral capsid, at the junction of the shell and protruding domains. Importantly, we show that recombination contributed to the emergence of the recent pandemic GII.4 variant, New Orleans 2009, and a newly identified GII.4 variant, termed Sydney 2012. Reconstructing the evolutionary history of the GII.4 lineage reveals the widespread impact of both inter- and intragenotype recombination on the emergence of many GII.4 variants. Lastly, this study highlights the many challenges in the identification of true recombination events and proposes that guidelines be applied for identifying NoV recombinants.
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                Author and article information

                Contributors
                Miren Iturriza-Gómara: Role: Editor
                Journal
                Journal ID (nlm-ta): PLoS One
                Journal ID (iso-abbrev): PLoS ONE
                Journal ID (publisher-id): plos
                Journal ID (pmc): plosone
                Title: PLoS ONE
                Publisher: Public Library of Science (San Francisco, CA USA )
                ISSN (Electronic): 1932-6203
                Publication date (Electronic): 9 November 2016
                Publication date Collection: 2016
                Volume: 11
                Issue: 11
                Electronic Location Identifier: e0165880
                Affiliations
                [1 ]Southern Medical University, Guangzhou, Guangdong, China
                [2 ]Shenzhen Center for Disease Control and Prevention, Shenzhen, China
                [3 ]Key Laboratory of Medical Virology and Viral Diseases; National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
                [4 ]Shenzhen Luohu Center for Disease Control and Prevention, Shenzhen, China
                University of Liverpool, UNITED KINGDOM
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                • Investigation: FZ HTZ ZZ LC.

                • Methodology: YQH KNC HLZ DJZ HY XJY MJ.

                • Software: MJ.

                • Writing – original draft: MJ YQH.

                • Writing – review & editing: ZJD YPZ.

                Article
                Publisher ID: PONE-D-15-05865
                DOI: 10.1371/journal.pone.0165880
                PMC ID: 5102426
                PubMed ID: 27829005
                SO-VID: 5f9a828a-4d49-47c9-9d84-86923b42a639
                Copyright © © 2016 He et al
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                Date received : 8 February 2015
                Date accepted : 19 October 2016
                Page count
                Figures: 4, Tables: 4, Pages: 13
                Funding
                Funded by: The Key Project of Science and Technology
                Award ID: 2012ZX10004215
                Award Recipient :
                Funded by: Health Industry Research
                Award ID: 201302004
                Award Recipient :
                The research was supported by The Key Project of Science and Technology (Grant No. 2012ZX10004215) funded by the Ministry of Science and Technology of China and the Health Industry Research (Grant No. 201302004) funded by National Health and Family Planning Commission of China to Miao Jin. The study was also supported by the National Natural Science foundation of China (Grant No. 81470856) to Yuanping Zhou. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Subject: Research Article
                Subject: Medicine and Health Sciences
                Subject: Gastroenterology and Hepatology
                Subject: Gastroenteritis
                Subject: People and Places
                Subject: Geographical Locations
                Subject: Asia
                Subject: China
                Subject: Biology and Life Sciences
                Subject: Physiology
                Subject: Physiological Processes
                Subject: Vomiting
                Subject: Medicine and Health Sciences
                Subject: Physiology
                Subject: Physiological Processes
                Subject: Vomiting
                Subject: Medicine and Health Sciences
                Subject: Diagnostic Medicine
                Subject: Signs and Symptoms
                Subject: Vomiting
                Subject: Medicine and Health Sciences
                Subject: Pathology and Laboratory Medicine
                Subject: Signs and Symptoms
                Subject: Vomiting
                Subject: Biology and Life Sciences
                Subject: Molecular Biology
                Subject: Molecular Biology Techniques
                Subject: Molecular Biology Assays and Analysis Techniques
                Subject: Phylogenetic Analysis
                Subject: Research and Analysis Methods
                Subject: Molecular Biology Techniques
                Subject: Molecular Biology Assays and Analysis Techniques
                Subject: Phylogenetic Analysis
                Subject: Medicine and Health Sciences
                Subject: Gastroenterology and Hepatology
                Subject: Diarrhea
                Subject: Medicine and Health Sciences
                Subject: Diagnostic Medicine
                Subject: Signs and Symptoms
                Subject: Diarrhea
                Subject: Medicine and Health Sciences
                Subject: Pathology and Laboratory Medicine
                Subject: Signs and Symptoms
                Subject: Diarrhea
                Subject: Social Sciences
                Subject: Sociology
                Subject: Social Welfare
                Subject: Medicine and Health Sciences
                Subject: Health Care
                Subject: Geriatric Care
                Subject: Biology and Life Sciences
                Subject: Microbiology
                Subject: Virology
                Subject: Viral Replication
                Subject: Viral Packaging
                Custom metadata
                Data Availability The nucleotide sequences generated in this study were deposited in GenBank under accession numbers KJ995534- KJ995550 (short sequences in capsid region) and KJ955492-KJ955493 (genome sequences). All sequnce files are available from the GenBank database under accession numbers KJ995534- KJ995550 (short sequences in capsid region) and KJ955492-KJ955493 (genome sequences).

                ScienceOpen disciplines: Uncategorized
                Data availability:
                ScienceOpen disciplines: Uncategorized

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