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      Complete Genome Sequence of a Coxsackievirus A16 Strain, Isolated from a Fatal Case in Shenzhen, Southern China, in 2014

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          Abstract

          We determined the complete genome sequence of a coxsackievirus A16 strain (CVA16/SZ29/CHN/2014) from a fatal case in Shenzhen, southern China, in 2014. The strain was assigned to subgenotype B1b based on phylogenetic analysis of the VP1 gene.

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          The largest outbreak of hand; foot and mouth disease in Singapore in 2008: the role of enterovirus 71 and coxsackievirus A strains.

          C Poh, S Quak, Ronald Yeo … (2010)
          During 2008, Singapore experienced its largest ever outbreak of hand, foot and mouth disease (HFMD), resulting in 29686 cases, including four cases of encephalitis and one fatality. A total of 51 clinical specimens from 43 patients with suspected HFMD at the National University Hospital, Singapore were collected for virus isolation and identification by reverse transcription polymerase chain reaction (RT-PCR) and sequencing. Enteroviruses were identified in 34 samples (66.7%), with 11 samples (21.6%) being positive for enterovirus 71 (EV71). Other non-EV71 enteroviruses (including coxsackievirus A4, A6, A10, and A16) were identified in 23 samples (45.1%). The most prevalent virus serotypes were CA6, CA10, and EV71. CA6 and CA10 accounted for 35.3% of all HFMD cases, which may explain the high transmissibility and low fatality that characterized this unprecedented epidemic associated with relatively mild disease. Phylogenetic analyses of 10 circulating EV71 strains indicated that they belonged to two subgenogroups, i.e., B5 (80%) and C2 (20%). The VP1 sequences of the 2008 EV71 strains also exhibited continuous mutations during the outbreak, reflecting the relatively high mutation rate of the EV71 capsid protein, which may have implications for future vaccine development. A safe and effective vaccine against EV71 is certainly warranted in view of its potential neurovirulence and its role in HFMD epidemics of recurring frequency with resultant fatalities in Asia, as well as other parts of the world. Copyright © 2010 International Society for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.
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            Complete genome sequences of all members of the species Human enterovirus A.

            K Maher, Steven M. Oberste, Mark Pallansch … (2004)
            The species Human enterovirus A (HEV-A) in the family Picornaviridae consists of coxsackieviruses (CV) A2-A8, A10, A12, A14 and A16 and enterovirus 71. Complete genome sequences for the prototype strains of the 10 serotypes whose sequences were not represented in public databases have been determined and analysed in conjunction with previously available complete sequences in GenBank. Members of HEV-A are monophyletic relative to all other human enterovirus species in all regions of the genome except in the 5' non-translated region (NTR), where they are known to cluster with members of HEV-B. The HEV-A prototype strains were about 66 to 86 % identical to one another in deduced capsid amino acid sequence. Antigenic cross-reactivity has been reported between CVA3-Olson and CVA8-Donovan, between CVA5-Swartz and CVA12-Texas-12 and between CVA16-G-10 and EV71-BrCr. Similarity plots, individual sequence comparisons and phylogenetic analyses demonstrate a high degree of capsid sequence similarity within each of these three pairs of prototype strains, providing a molecular basis for the observed antigenic relationships. In several cases, phylogenies constructed from the structural (P1) and non-structural regions of the genome (P2 and P3) are incongruent. The incongruent phylogenies and the similarity plot analyses imply that recombination has played a role in the evolution of the HEV-A prototype strains. CVA6-Gdula clearly contains sequences that are also present in CVA10-Kowalik and CVA12-Texas-12, suggesting that these three strains have a shared evolutionary history despite their lack of similarity in the capsid region.
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              Emergence, circulation, and spatiotemporal phylogenetic analysis of coxsackievirus a6- and coxsackievirus a10-associated hand, foot, and mouth disease infections from 2008 to 2012 in Shenzhen, China.

              Ting-Zhang Hu, Wen Xu, Ling Chen … (2013)
              Sporadic hand, foot, and mouth disease (HFMD) outbreaks and other infectious diseases in recent years have frequently been associated with certain human enterovirus (HEV) serotypes. This study explored the prevalences and genetic characteristics of non-HEV71 and non-coxsackievirus A16 (CV-A16) human enterovirus-associated HFMD infections in Shenzhen, China. A total of 2,411 clinical stool specimens were collected from hospital-based surveillance for HFMD from 2008 to 2012. The detection of HEV was performed by real-time reverse transcription-PCR (RT-PCR) and RT-seminested PCR, and spatiotemporal phylogenetic analysis was performed based on the VP1 genes. A total of 1,803 (74.8%) strains comprising 28 different serotypes were detected. In the past 5 years, the predominant serotypes were HEV71 (60.0%), followed by CV-A16 (21.2%) and two uncommon serotypes, CV-A6 (13.0%) and CV-A10 (3.3%). However, CV-A6 replaced CV-A16 as the second most common serotype between 2010 and 2012. As an emerging pathogen, CV-A6 became as common a causative agent of HFMD as HEV71 in Shenzhen in 2012. Phylogenetic analysis revealed that little variation occurred in the Chinese HEV71 and CV-A16 strains. The genetic characteristics of the Chinese CV-A6 and CV-A10 strains displayed geographic differences. The CV-A6 and CV-A10 strains circulating in Shenzhen likely originated in Europe. It was found that human enteroviruses have a high mutation rate due to evolutionary pressure and frequent recombination (3.2 × 10(-3) to 6.4 ×10(-3) substitutions per site per year for HEV71, CV-A6, CV-A16, and CV-A10). Since certain serotypes are potential threats to the public health, this study provides further insights into the significance of the epidemiological surveillance of HFMD.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Genome Announc
                Journal ID (iso-abbrev): Genome Announc
                Journal ID (hwp): ga
                Journal ID (pmc): ga
                Journal ID (publisher-id): GA
                Title: Genome Announcements
                Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )
                ISSN (Electronic): 2169-8287
                Publication date (Electronic): 30 April 2015
                Publication date Collection: Mar-Apr 2015
                Volume: 3
                Issue: 2
                Electronic Location Identifier: e00391-15
                Affiliations
                [a ]Major Infectious Disease Control Key Laboratory and Shenzhen Public Service Platform of Pathogenic Microorganisms Repository, Shenzhen Center for Disease Control and Prevention, Shenzhen, People’s Republic of China
                [b ]Department of Health Statistics and Epidemiology, College of Public Health, Sun Yat-sen University, Guangzhou, People’s Republic of China
                Author notes
                Address correspondence to Ya-Qing He, heyaqing1019@ 123456126.com .
                Article
                Publisher ID: genomeA00391-15
                DOI: 10.1128/genomeA.00391-15
                PMC ID: 4417703
                PubMed ID: 25931607
                SO-VID: 35631654-b8c9-4f11-bab1-a01d960928eb
                Copyright © Copyright © 2015 Chen et al.
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.

                History
                Date received : 16 March 2015
                Date accepted : 18 March 2015
                Page count
                Figures: 0, Tables: 0, Equations: 0, References: 6, Pages: 2, Words: 1034
                Categories
                Subject: Viruses
                Custom metadata
                cover-date March/April 2015
                access-type free

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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