Molecular Phylogeny of Coxsackievirus A16

Sun, Tongming; Liu, Yiming; Zhang, Yanjun; Zhou, Linfu

doi:10.1128/jcm.01330-14

Cited by 11 publications

(9 citation statements)

References 5 publications

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“…For enteroviruses, genetic recombination is a frequently phenomenon in picornaviruses which generates evolutionary diversity and also is a means to acquire new phenotypic traits which could result in the emergence of viruses with altered pathogenic potentials [14]. Phylogenetic analysis suggested that intertypic recombination event may have occurred between CA16 and EV71 genotype C, which was similar to other studies [15,16,17]. Meanwhile, similarity plot and bootscan analyses demonstrated that recombination events has possibly taken place between nucleotide 2160 and 2280, corresponding to the VP3 region.…”

Section: Discussionsupporting

confidence: 86%

Identification of a Novel Coxsackievirus A16 Strain Isolated from the Clinic HFMD Sample in Hubei Province in 2010

Xu¹

2016

ABB

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Enterovirus 71 (EV71) and Coxsackievirus A16 (CoxA16) are two major pathogens of Hand, foot and mouth disease (HFMD) that epidemic periodically among children and cause deaths occasionally. There is no effective vaccine or drug for HFMD to date. Here the whole genome of a clinic virus isolate GDV126(China Center for Type Culture Collection, CCTCC) of HFMD was sequenced in Hubei 2010. Phylogenetic analysis demonstrates that the virus belongs to CoxA16. Both phylogenetic and recombination analysis of GDV126 showed that the GDV126 was a recombinant strain of CoxA16. In addition, GDV126 had different cell tropism from EV71. This work demonstrated the genetic variations and evolution of the HFMD pathogens and implicated complication to prevent the disease.

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Section: Discussionsupporting

confidence: 86%

Identification of a Novel Coxsackievirus A16 Strain Isolated from the Clinic HFMD Sample in Hubei Province in 2010

Xu¹

2016

ABB

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“…The study expands the diversity of CV-A16 to a clade whose epidemiological origin was traced back to Peru. Earlier comparative analyses of the VP4 and VP1 protein genes suggested that CV-A16 strains circulating worldwide belonged to three genogroups, designated A, B, and C (27)(28)(29)(30)(31)(32)(33). Our study revealed the recent emergence and effective spread of a previously undescribed genogroup that we suggest be designated by the letter D. The strains of genogroup D cocirculated with those of genogroup B in France over the period studied.…”

Section: Discussionmentioning

confidence: 50%

“…The phylogenetic relationships determined with the VP1 sequences ( Fig. 2A) showed that the two CV-A16 clades (large phylogenetic groups) previously reported as genogroups A and B (27,28) had more than 23% nucleotide differences. Genogroup A was represented by a single sequence (G-10ԽSouth AfricaԽ1951), while genogroup B included multiple phylogenetic subgroups below the 10% p-distance threshold.…”

Section: Resultsmentioning

confidence: 88%

Phylogeography of Coxsackievirus A16 Reveals Global Transmission Pathways and Recent Emergence and Spread of a Recombinant Genogroup

Hassel

Mirand

Farkas

et al. 2017

J Virol

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Coxsackievirus A16 (CV-A16; ) is an enterovirus (EV) type associated with hand, foot, and mouth disease (HFMD) in children. To investigate the spatial spread of CV-A16, we used viral sequence data sampled during a prospective sentinel surveillance of HFMD in France (2010 to 2014) and phylogenetic reconstruction. A data set of 168 VP1 sequences was assembled with 416 publicly available sequences of various geographic origins. The CV-A16 sequences reported were assigned to two clades, genogroup B and a previously uncharacterized clade D. The time origins of clades B and D were assessed in 1978 (1973 to 1981) and 2004 (2001 to 2007), respectively. The shape of the global CV-A16 phylogeny indicated worldwide cocirculation of genetically distinct virus lineages over time and across geographic regions. Phylogenetic tree topologies and Bayes factor analysis indicated virus migration. Virus transportation events in clade B within Europe and Asia and between countries of the two geographic regions were assessed. The sustained transmission of clade D viruses over 4 years was analyzed at the township level in France and traced back to Peru in South America. Comparative genomics provided evidence of recombination between CV-A16 clades B and D and suggested an intertype recombinant origin for clade D. Time-resolved phylogenies and HFMD surveillance data indicated that CV-A16 persistence is sustained by continuing virus migration at different geographic scales, from community transmission to virus transportation between distant countries. The results showed a significant impact of virus movements on the epidemiological dynamics of HFMD that could have implications for disease prevention. Coxsackievirus A16 is one of the most prevalent enterovirus types in hand, foot, and mouth disease outbreaks reported in Southeast Asia. This study is based on epidemiological and viral data on HFMD caused by CV-A16 in a European country. The phylogeographic data complemented the syndromic surveillance with virus migration patterns between geographic regions in France. The results show how viral evolutionary dynamics and global virus spread interact to shape the worldwide pattern of an EV disease. CV-A16 transmission is driven by movements of infected individuals at different geographic levels: within a country (local dynamics), between neighboring countries (regional dynamics), and between distant countries (transcontinental dynamics). The results are consistent with our earlier data on EV-A71 and confirm the epidemiological interconnection of Asia and Europe with regard to EV infections.

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“…Based on the VP1 gene of the viral genome, all CV‐A16 strains are presently divided into two genotypes, A and B. The B genotypes can be further divided into the B1 and B2 subgenotypes, and subtype B1 could be further divided into clusters B1a, B1b, and B1c …”

Section: Introductionmentioning

confidence: 99%

Molecular characterization of Coxsackievirus A16 strains isolated from children with severe hand, foot, and mouth disease in Yunnan, Southwest China, during 2009‐2015

Zhang

Zhao

Zhang

et al. 2018

Journal of Medical Virology

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Coxsackievirus A16 (CV-A16) commonly causes mild symptoms, but severe diseases, such as aseptic meningitis, encephalitis, and even fatal cases, have been reported. Thirteen CV-A16 strains were isolated from patients with severe hand, foot, and mouth disease in Yunnan, Southwest China, from 2009 to 2015. Subgenotype B1a and B1b of CV-A16 were predominantly circulating the region with B1b the predominant strain in recent years. The mean rate of nucleotide substitution based on the VP1 gene sequence was 4.545 × 10 substitution per site per year from 2009 to 2015. These results may help in understanding the genetic diversity of CV-A16 and develop a CV-A16 vaccine.

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Molecular Phylogeny of Coxsackievirus A16

Cited by 11 publications

References 5 publications

Identification of a Novel Coxsackievirus A16 Strain Isolated from the Clinic HFMD Sample in Hubei Province in 2010

Identification of a Novel Coxsackievirus A16 Strain Isolated from the Clinic HFMD Sample in Hubei Province in 2010

Phylogeography of Coxsackievirus A16 Reveals Global Transmission Pathways and Recent Emergence and Spread of a Recombinant Genogroup

Molecular characterization of Coxsackievirus A16 strains isolated from children with severe hand, foot, and mouth disease in Yunnan, Southwest China, during 2009‐2015

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