长沙地区1株重组柯萨奇病毒A4基因型的全基因组序列分析  

Full-genome sequence analysis of a recombinant coxsackievirus A4 strain isolated in Changsha city of China

作　　者：欧新华[1] 黄政[1] 姚栋[1] 肖姗[1] 李灵之[1] 叶文[1] OU Xin-hua;HUANG Zheng;YAO Dong;XIAO Shan;LI Ling-zhi;YE Wen(Department of Microbiology Center for Disease Control and Prevention of Changsha City,Changsha,Hunan 410004,China)

机构地区：[1]湖南省长沙市疾病预防控制中心微生物检验科,湖南长沙410004

出　　处：《中国病毒病杂志》2021年第4期290-294,共5页Chinese Journal of Viral Diseases

基　　金：湖南省卫生健康委科研课题(202112061212);长沙市卫生计生委科研计划课题项目。

摘　　要：目的对湖南省长沙市手足口病患儿咽拭子中分离的1株柯萨奇病毒A组4型(coxsackievirus A4,CV-A4)毒株进行全基因组序列及分子进化特征分析。为手足口病的疫情防控提供理论数据支持。方法利用人类横纹肌肉瘤(human rhabdomyosarcoma,RD)细胞对2019年6月长沙市常规监测的手足口病病例咽拭子标本进行病毒分离,提取病毒RNA序列进行逆转录-聚合酶链反应(reverse transcription-polymerase chain reaction,RT-PCR),并利用Illumina二代测序技术对其进行全基因组序列测定,利用MEGA 6.0构建系统进化树,用BioEdit和Simplot软件进行重组和进化分析。结果手足口病患儿的咽拭子中分离的CV-A4毒株为1株重组毒株,毒株命名为S270/Changsha/CHN/2019(简称S270),序列全长为7454 bp。基于核苷酸序列的进化树结果表明,S270毒株的结构蛋白区域(P1)属于CV-A4分支,非结构蛋白区域(P2和P3)属于CV-A2分支。S270毒株与AY421762株(简称CV-A4代表株)对比,核苷酸序列P1区的同源性为85.05%;非结构蛋白P2和P3区的同源性为83.90%。全基因组氨基酸序列与CV-A4代表株的同源性为84.7%。VP1区氨基酸序列与CV-A4代表株的同源性为83.8%,氨基酸位点出现A55T和M229T两个突变。重组位点分析发现S270毒株全基因组重组位点发生在2B非结构蛋白区域,位于基因组序列位点约3849 bp位置。结论S270分离株属于CV-A4重组毒株,基因重组位点位于2B区内,属于GI基因群的GIB亚型。Objective To study the characteristics of the full-genome sequences of a coxsackievirus A4(CV-A4)strain isolated in Changsha city of China.Methods Human rhabdomyosarcoma(RD)cells were used to isolate the virus from pharyngeal swab samples collected in June 2019,extract the viral RNA sequence for reverse transcription-polymerase chain reaction(RT-PCR),determine the whole genome sequence by Illumina second-generation sequencing technology,and construct the phylogenetic tree by MEGA 6.0,BioEdit and Simplot software were used for recombination and evolutionary analysis.Results The CV-A4 strain isolated from pharyngeal swabs of children with hand,foot and mouth disease in Changsha,Hunan province in 2019 was a recombinant strain named s270/Changsha/CHN/2019(S270),with a total length of 7454 bp.The results of phylogenetic tree based on nucleotide sequence showed that the structural protein P1 region of S270 strain belonged to CV-A4 branch,and the non structural protein region(P2 and P3)belonged to CV-A2 branch.Compared with AY421762 strain,the homology of P1 region of nucleotide sequence of S270 strain was 85.05%.The homology of P2 and P3 regions was 83.90%.The homology of the whole genome amino acid sequence with the representative strain CV-A4 was 84.7%.The homology of VP1 amino acid sequence with CV-A4 was 83.8%.There were two mutations of A55 Tand M229 Tat the amino acid site.Recombination site analysis showed that the whole genome recombination site of S270 strain occurred in the 2 Bregion,which was located at about 3849 bp of the genome sequence site.Conclusions The recombinant CV-A4 strain is grouped to GIB subtype.The break-point is present at the position of 3849 bp in 2 Bregion.

关 键 词：柯萨奇病毒A4 柯萨奇病毒A2 基因重组 全基因组序列 

分 类 号：R373.9[医药卫生—病原生物学]