Evolution, recombination and geographic spreading of global Coxsackievirus A6

Huanhuan Lu; Jinbo Xiao; Yang Song; Dongmei Yan; Shuangli Zhu; Qian Yang; Tianjiao Ji; Zhenzhi Han; Jichen Li; Ruyi Cong; Ying Liu; Haiyan Wei; Qiong Ge; Dajin Xiao; Yingying Liu; Xiaofang Zhou; Wei Huang; Hanri Zeng; Leilei Wei; Renqing Li; Likun Lv; Jun Guo; Yong Zhang

doi:10.1016/j.jcv.2024.105691

Evolution, recombination and geographic spreading of global Coxsackievirus A6

J Clin Virol. 2024 Aug:173:105691. doi: 10.1016/j.jcv.2024.105691. Epub 2024 May 11.

Authors

Huanhuan Lu¹, Jinbo Xiao¹, Yang Song¹, Dongmei Yan¹, Shuangli Zhu¹, Qian Yang¹, Tianjiao Ji¹, Zhenzhi Han², Jichen Li¹, Ruyi Cong¹, Ying Liu¹, Haiyan Wei³, Qiong Ge⁴, Dajin Xiao⁵, Yingying Liu⁶, Xiaofang Zhou⁷, Wei Huang⁸, Hanri Zeng⁹, Leilei Wei¹⁰, Renqing Li¹¹, Likun Lv¹², Jun Guo¹³, Yong Zhang¹⁴

Affiliations

¹ National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID). National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No.155 Changbai Road, Beijing 102206, PR China; National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China.
² Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing, PR China.
³ Henan Provincial Center for Disease Control and Prevention, Henan, PR China.
⁴ Zhejiang Provincial Center for Disease Control and Prevention, Zhejiang, PR China.
⁵ Jiangxi Provincial Center for Disease Control and Prevention, Jiangxi, PR China.
⁶ Hebei Provincial Center for Disease Control and Prevention, Hebei, PR China.
⁷ Yunnan Provincial Center for Disease Control and Prevention, Yunnan, PR China.
⁸ Chongqing Provincial Center for Disease Control and Prevention, Chongqing, PR China.
⁹ Guangdong Provincial Center for Disease Control and Prevention, Guangdong, PR China.
¹⁰ Jilin Provincial Center for Disease Control and Prevention, Jilin, PR China.
¹¹ Beijing Provincial Center for Disease Control and Prevention, Beijing, PR China.
¹² Tianjin Provincial Center for Disease Control and Prevention, Tianjin, PR China.
¹³ Guizhou Provincial Center for Disease Control and Prevention, Guizhou, PR China.
¹⁴ National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases (NITFID). National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No.155 Changbai Road, Beijing 102206, PR China; National Polio Laboratory, WHO WPRO Regional Polio Reference Laboratory, National Health Commission Key Laboratory for Biosafety, National Health Commission Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China. Electronic address: [email protected].

PMID: 38749308
DOI: 10.1016/j.jcv.2024.105691

Abstract

Background: The increasing incidence of hand, foot, and mouth disease (HFMD) associated with Coxsackievirus A6 (CVA6) has become a very significant public health problem. The aim of this study is to investigate the recombination, geographic transmission, and evolutionary characteristics of the global CVA6.

Methods: From 2019 to 2022, 73 full-length CVA6 sequences were obtained from HFMD patients in China and analyzed in combination with 1032 published whole genome sequences. Based on this dataset, the phylogenetic features, recombinant diversity, Bayesian phylodynamic characteristics, and key amino acid variations in CVA6 were analyzed.

Results: The four genotypes of CVA6, A, D, E, and F, are divided into 24 recombinant forms (RFs, RF-A - RF-X) based on differences in the P3 coding region. The eastern China region plays a key role in the dissemination of CVA6 in China. VP1-137 and VP1-138 are located in the DE loop on the surface of the CVA6 VP1 protein, with the former being a highly variable site and the latter having more non-synonymous substitutions.

Conclusions: Based on whole genome sequences, this study contributes to the CVA6 monitoring, early warning, and the pathogenic mechanism by studying recombination diversity, geographical transmission characteristics, and the variation of important amino acid sites.

Keywords: Coxsackievirus A6; Evolution; Geographical transmission; Hand, foot, and mouth disease; Recombination diversity.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Bayes Theorem
China / epidemiology
Enterovirus / classification
Enterovirus / genetics
Enterovirus / isolation & purification
Evolution, Molecular*
Genetic Variation
Genome, Viral
Genotype*
Hand, Foot and Mouth Disease* / epidemiology
Hand, Foot and Mouth Disease* / virology
Humans
Phylogeny*
Recombination, Genetic*
Whole Genome Sequencing