苏州市柯萨奇病毒A2型、A4型和A5型的全基因组序列特征分析

Analysis of complete genome sequence characteristics of coxsackievirus A2,A4 and A5 in Suzhou city

目的了解苏州市3种柯萨奇病毒(Coxsackievirus,CV)亚型(CV-A2、CV-A4和CV-A5)的基因组特征及进化趋势。方法2022年1~6月苏州市手足口病常规监测期间共采集248份样本,通过实时荧光逆转录聚合酶链反应(Real-time fluorescence-reverse transcription polymerase chain reaction,Real-time RT-PCR)对标本进行CV检测分型。利用Miseq高通量测序平台对CV阳性样本进行测序,获得CV全基因组序列,进行同源性分析。采用MEGA(Molecular Evolutionary Genetics Analysis)X构建进化树。使用SimPlot和BootScan分析毒株序列重组区域。结果苏州市2022年1~6月手足口病常规监测中发现CV-A2、CV-A4和CV-A5毒株各一株,并获得全基因组序列。CV-A2和CV-A4与目前中国流行株聚为一类,CV-A2基因组中未发现新增氨基酸位点突变;CV-A4与原型株比较在非结构区新增了多个氨基酸位点的突变;CV-A5属于C1基因亚型3谱系,CV-A5基因组在非结构蛋白区新增了多个氨基酸突变位点,并发生重组。结论苏州市CV-A2和CV-A4毒株为稳定流行株,CV-A5毒株为重组毒株。

Objective To understand the genomic characteristics and evolutionary trends of three coxsackievirus(CV)subtypes,including CV-A2,CV-A4 and CV-A5,in Suzhou city.Methods Totally 248 samples were collected during routine monitoring for hand,foot,and mouth disease in Suzhou city from January to June in 2022.The specimens were detected for CV genotypes using Real-time fluorescence-reverse transcription polymerase chain reaction(Real-time RT-PCR).The CV positive samples were sequenced using the Miseq high-throughput sequencing platform.After obtaining the whole genome sequences of CV strains,homology analysis was performed.An evolutionary tree was constructed using molecular evolutionary genetics analysis(MEGA)X.Sequence recombination regions were analyzed using SimPlot and BootScan.Results During routine monitoring for hand,foot and mouth disease in Suzhou city from January to June in 2022,one strain each of CV-A2,CV-A4,and CV-A5 viruses were identified,and their complete genomes were sequenced.CV-A2 and CV-A4 were clustered with the current prevalent strains in China,and no new amino acid site mutations were found in the whole genome of CV-A2;CV-A4 had several new amino acid site mutations in the non-structural region compared with the prototype strain;CV-A5 belonged to the C1 subgenotype 3 lineage,and the genome of CV-A5 had several new amino acid mutation sites in the non-structural protein region and underwent recombination.Conclusions The CV-A2 and CV-A4 strains are stable epidemic strains,the CV-A5 strain is recombinant strain in Suzhou city.