Characterization of VP1 sequence of Coxsackievirus A16 isolates by Bayesian evolutionary method

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Abstract

Background: Coxsackievirus A16 (CV-A16), a major etiopathologic cause of pediatric hand, foot, and mouth disease (HFMD) worldwide, has been reported to have caused several fatalities. Revealing the evolutionary and epidemiologic dynamics of CV-A16 across time and space is central to understanding its outbreak potential. Methods: In this study, we isolated six CV-A16 strains in China's Jilin province and construct a maximum clade credibility (MCC) tree for CV-A16 VP1 gene by the Bayesian Markov Chain Monte Carlo method using 708 strains from GenBank with epidemiological information. The evolution characteristics of CV-A16 VP1 gene was also analysed dynamicly through Bayesian skyline plot. Results: All CV-A16 strains identified could be classified into five major genogroups, denoted by GI-GV. GIV and GV have co-circulated in China since 2007, and the CV-A16 epidemic strain isolated in the Jilin province, China, can be classified as GIV-3. The CV-A16 genogroups circulating recently in China have the same ancestor since 2007. The genetic diversity of the CV-A16 VP1 gene shows a continuous increase since the mid-1990s, with sharp increases in genetic diversity in 1997 and 2007 and reached peak in 2007. Very low genetic diversity existed after 2010. The CV-A16 VP1 gene evolutionary rate was 6.656E-3 substitutions per site per year. Conclusions: We predicted the dynamic phylogenetic trends, which indicate outbreak trends of CV-A16, and provide theoretical foundations for clinical prevention and treatment of HFMD which caused by a CV-A16.

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Zhao, G., Zhang, X., Wang, C., Wang, G., & Li, F. (2016). Characterization of VP1 sequence of Coxsackievirus A16 isolates by Bayesian evolutionary method. Virology Journal, 13(1). https://doi.org/10.1186/s12985-016-0578-3

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