Evolution, recombination and geographic spreading of global Coxsackievirus A6

IF 4 3区医学 Q2 VIROLOGY Journal of Clinical Virology Pub Date : 2024-05-11 DOI:10.1016/j.jcv.2024.105691

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 , Yong Zhang

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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.

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全球柯萨奇病毒 A6 的进化、重组和地理分布。

背景：与柯萨奇病毒 A6（CVA6）相关的手足口病（HFMD）发病率不断上升，已成为一个非常重要的公共卫生问题。本研究旨在调查全球 CVA6 的重组、地域传播和进化特征：从 2019 年到 2022 年，从中国手足口病患者中获得了 73 个全长 CVA6 序列，并与 1032 个已发表的全基因组序列进行了结合分析。基于该数据集，分析了CVA6的系统发育特征、重组多样性、贝叶斯系统动力学特征和关键氨基酸变异：结果：根据P3编码区的差异，CVA6的A、D、E和F四种基因型被分为24种重组形式（RFs，RF-A - RF-X）。华东地区是 CVA6 在中国传播的主要地区。VP1-137和VP1-138位于CVA6 VP1蛋白表面的DE环，前者是高变异位点，后者有较多的非同义替换：本研究基于全基因组序列，通过研究重组多样性、地域传播特征和重要氨基酸位点的变异，为CVA6的监测、预警和致病机制的研究做出了贡献。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Journal of Clinical Virology 医学-病毒学

CiteScore

22.70

自引率

1.10%

发文量

149

审稿时长

24 days

期刊介绍： The Journal of Clinical Virology, an esteemed international publication, serves as the official journal for both the Pan American Society for Clinical Virology and The European Society for Clinical Virology. Dedicated to advancing the understanding of human virology in clinical settings, the Journal of Clinical Virology focuses on disseminating research papers and reviews pertaining to the clinical aspects of virology. Its scope encompasses articles discussing diagnostic methodologies and virus-induced clinical conditions, with an emphasis on practicality and relevance to clinical practice. The journal publishes on topics that include: • new diagnostic technologies • nucleic acid amplification and serologic testing • targeted and metagenomic next-generation sequencing • emerging pandemic viral threats • respiratory viruses • transplant viruses • chronic viral infections • cancer-associated viruses • gastrointestinal viruses • central nervous system viruses • one health (excludes animal health)