手足口病相关柯萨奇病毒A组8型全基因组序列特征分析

Genetic characterization analysis of the whole genome sequence of Coxsackievirus A8 associated with hand,foot and mouth disease in China

目的研究中国2013-2018年手足口病病例分离的柯萨奇病毒A组8型(CV-A8)全基因组序列特征及对全基因组各编码区进行遗传进化分析。方法对我国不同地区手足口病患者分离的11株CV-A8的全基因组序列,采用Sequencher 5.0、MEGA 7.0等软件对获取的全基因组序列进行比对和遗传进化分析。结果序列比对显示11株CV-A8基因组长度在7393-7400 bp之间,与原型株比较,在编码区无碱基插入或缺失,在非编码区存在个别碱基的插入或缺失。11株CV-A8毒株VP1区核苷酸和氨基酸同源性分别为78.3%-98.6%和92.6%-99.7%;与CV-A8原型株的核苷酸和氨基酸序列同源性分别为78.3%-98.2%和92.6%-99.7%。对CV-A8的VP1区序列进行了系统发育分析,可将CV-A8分为5个基因型:A、B、C、D和E,本研究11株CV-A8分属于C(1株)、D(2株)、E(8株)3个基因型。11株CV-A8毒株全基因组序列核苷酸和氨基酸同源性分别为81.3%%-98.8%和95.9%-99.5%,P2区进化树图显示,本研究的8株E基因型CV-A8和CV-A4、CV-A14和CV-A16原型株进化距离最近,P3区进化树图显示,本研究8株E基因型CV-A8和CV-A5、CV-A16、CV-A14和CV-A4进化距离最近。结论本研究中11株CV-A8其衣壳区呈现基因多样性,非衣壳区呈现重组多样性,提示CV-A8正在经历变异动态变化;CV-A8有可能成为手足口病的重要病原体,因此需要进一步加强监测CV-A8。

Objective To study the genomic sequence of Coxsackievirus A8(CV-A8)associated with hand,foot and mouth disease(HFMD)from 2013 to 2018 in China and to analyze the genetic evolution of each coding region of the full-length genome.Methods The genome sequences of 11 CV-A8 strains isolated from patients with HFMD in different regions of China from 2013 to 2018 were determined.Sequence alignment and genetic evolution analysis were performed by Sequencher 5.0 and MEGA 7.0 software,etc.Results Sequence alignment showed that the genome length of 11 CV-A8 strains ranged from 7393 bp to 7400 bp.There was no base insertion or deletion in the coding region compared with the prototype strain,but there were individual base insertion or deletion in the non-coding region.The nucleotide and amino acid similarities in the VP1 region of 11 CV-A8 strains were 78.3%-98.6%and 92.6%-99.7%,respectively,and the nucleotide and amino acid sequences identities with the CV-A8 prototype strain were 78.3%-98.2%and 92.6%-99.7%,respectively.Based on the phylogenetic analysis of VP1 region sequences,the CV-A8 can be divided into five genotypes:A,B,C,D and E.The 11 CV-A8 strains in this study belonged to genotypes C(1 strain),D(2 strains)and E(8 strains).The nucleotide and amino acid similarities of 11 CV-A8 full-length genomes were 81.3%-98.8%and 95.9%-99.5%,respectively.The phylogenetic tree of the P2 region showed that the eight E genotypes CV-A8 had the closest evolutionary distance with CV-A4,CV-A14,and CV-A16.The phylogenetic tree of the P3 region showed that the eight E genotypes CV-A8 had a close evolutionary distance with CV-A5,CV-A16,CV-A14 and CV-A4.Conclusions The 11 CV-A8 stains in this study showed significant intra-genotype diversity in capsid region and recombinant diversity in non-capsid region which indicated that CV-A8 quasispecies were still undergoing dynamics variation.CV-A8 may become an important pathogen of HFMD and the monitoring of CV-A8 needs to be further strengthened.