摘要
目的基于柯萨奇病毒A组6型(coxsackievirus group A type 6,CV-A6)VP1编码区寻找与其流行强度增加有关的关键氨基酸位点。方法对GenBank数据库中全部CV-A6 VP1编码区核苷酸序列进行筛选,获得其中的1533条序列进行比对。使用RAxML软件构建最大似然树。使用Shannon Entropy在线分析工具计算序列的氨基酸置换熵值,并用Datamonkey在线分析平台通过MEME,SLAC和FUBAR三种方法来分析正向选择位点。结果目前全球流行的CV-A6以D3基因亚型为主。在VP1编码区存在三个高度可变的氨基酸位点,分别是VP1-5、VP1-30、VP1-137。三种方法均发现VP1-5、VP1-90、VP1-137三个位点在流行中受到过正向选择的作用。结论应继续加强对D3基因亚型CV-A6的监测,D3基因亚型的CV-A6在位于DE环中的VP1-137高度可变且受到了正向选择的作用,需要加以重视,并通过进一步研究来确定它与D3亚型广泛流行的关系。
Objective To search key amino acid sites associated with increased prevalence of coxsackievirus group A type 6(CV-A6)based on the VP1 coding region.Methods All nucleotide sequences of CV-A6 VP1 coding region in GenBank database were screened and 1533 sequences were obtained for comparison.The maximum likelihood tree was constructed using RAxML software.The Shannon Entropy online analysis tool was used to calculate the amino acid substitution entropy values of the sequences,and the Datamonkey online analysis platform was used to analyze the positive selection sites by MEME,SLAC and FUBAR methods.Results At present,D3 sub-genotype of CV-A6 is dominant in the world.There are three highly variable amino acid sites in the VP1 coding region,namely VP1-5,VP1-30,and VP1-137.All three methods(MEME,SLAC and FUBAR)found that VP1-5,VP1-90 and VP1-137 were affected by positive selection in epidemics.Conclusions The surveillance for D3 sub-genotype of CV-A6 should be strengthened continuously.The D3 sub-genotype of CV-A6 is highly variable in VP1-137 located in the DE loop,and is affected by positive selection.This should be concerned and the relationship with the widespread prevalence of D3 sub-genotype should be determined in future researches.
作者
肖金波
路环环
宋洋
王东艳
严冬梅
张勇
Xiao Jinbo;Lu Huanhuan;Song Yang;Wang Dongyan;Yan Dongmei;Zhang Yong(National Institute for Viral Disease Control and Prevention,Chinese Center for Disease Control and Prevention,Key Laboratory of Biosafety,National Health Commission,Key Laboratory of Medical Viruses and Viral Diseases,National Health Commission,Beijing 102206,China;Center for Biosafety Mega-Science,Chinese Academy of Sciences,Wuhan 430000,China)
出处
《国际病毒学杂志》
2023年第2期105-109,共5页
International Journal of Virology
