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. 2018 Sep 20;13(9):e0204359.
doi: 10.1371/journal.pone.0204359. eCollection 2018.

Persistent circulation of genotype D coxsackievirus A2 in mainland of China since 2008

Qian Yang  1 , Xinrui Gu  1   2 , Yong Zhang  1 , Haiyan Wei  3 , Qi Li  4 , Huan Fan  5 , Yi Xu  6 , Jie Li  7 , Zhaolin Tan  8 , Yang Song  1 , Dongmei Yan  1 , Tianjiao Ji  1 , Shuangli Zhu  1 , Wenbo Xu  1   9
Affiliations

Persistent circulation of genotype D coxsackievirus A2 in mainland of China since 2008

Qian Yang et al. PLoS One. .

Abstract

Coxsackievirus A2 (CV-A2) has emerged as an important etiological agent in the hand, foot, and mouth disease and herpangina pathogen spectrum because of its high global prevalence. In the present study, we investigated the evolutionary dynamics of CV-A2 circulating in China. We analyzed a total of 163 entire VP1 sequences of CV-A2, including 74 sequences generated from the present study and 89 sequences collected from the GenBank database. Phylogenetic analysis based on the entire VP1 nucleotide sequences confirmed the persistent circulation of the predominant genotype D in mainland of China since 2008. Cluster analysis grouped the sequences into two distinct clusters, clusters 1 and 2, with most grouped under cluster 2. After 2012, cluster 1 was gradually replaced by cluster 2. Results of Bayesian Markov chain Monte Carlo analysis suggested that multiple lineages of genotype D were transmitted in mainland of China at an estimated evolutionary rate of 6.32×10(-3) substitutions per site per year, which is consistent with the global evolutionary rate of CV-A2 (5.82×10(-3) substitutions per site per year). Continuous transmission and evolution of CV-A2 resulted in the genetic polymorphism.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Temporal and geographical distribution of CV-A2 isolates in mainland of China from 2008 to 2017 based on the VP1 coding region.
Fig 2
Fig 2. Phylogenetic trees constructed based on the entire VP1 nucleotide sequences of CV-A2 strains isolated between 1947 and 2017.
The CV-A2 strains isolated in the present study are indicated by solid circles. Numbers at the nodes indicate bootstrap support for each node (percentage of 1,000 bootstrap replicates).
Fig 3
Fig 3. A Bayesian skyline plot analysis of the representative Chinese genotype D CV-A2 sequences from 2008–2017.
Ordinate: the number of effective infections at time; abscissa: time (in years). The thick solid line represents the median, and the blue area represents the 95% highest probability density (HPD) of the number of effective infections at the time estimates.
See this image and copyright information in PMC

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