长沙市柯萨奇病毒A2型和A5型全基因组序列特征分析

Complete genome analysis of coxsackievirus A2 and A5 strains in Changsha

目的 了解长沙市柯萨奇病毒A2型(coxsackievirus A2, CV-A2)和A5型(coxsackievirus A5, CV-A5)的序列分子特征及进化趋势。方法 采用二代测序技术获得CV-A2和CV-A5的全基因组序列,进行同源性和进化树分析,使用SimPlot查看毒株序列重组区域。结果 获得长沙市2019年手足口病常规监测病例中CV-A2和CV-A5毒株全基因组序列。CV-A2毒株命名为S281/Changsha/CHN/2019,基因组全长7 422 bp。CV-A5毒株命名为S272/Changsha/CHN/2019,基因组全长7 425 bp。CV-A2全基因组序列与国内CV-A2毒株进行同源性分析发现,非结构蛋白区比结构蛋白区同源性低。CV-A2毒株与原型株Fleetwood(NC038306)相比同源性为79.20%,与湖北省CV-A2毒株(MN419014)同源性最高为95.60%,但非结构蛋白3C和3D区同源性最低,分别为90.51%和92.06%。进化树分析发现3C和3D区位于CV-A4分支。非结构蛋白区新增多个氨基酸突变位点,结构蛋白区氨基酸序列保守。基因重组分析发现CV-A2毒株在3C和3D区存在重组现象。对CV-A5全基因组序列分析发现,与国内CV-A5毒株相比,非结构蛋白区比结构蛋白区同源性低。全基因组序列与CV-A5原型株Swartz(AY421763)相比同源性为80.7%,与澳大利亚毒株(MH111030)相比同源性最高为97.43%,进化树分析发现与MH111030位于同一分支,证明CV-A5为输入型毒株。CV-A5毒株结构蛋白区氨基酸序列保守。结论 长沙市CV-A2毒株为重组毒株,CV-A5毒株为国外输入型。本研究可帮助了解长沙地区CV-A2和CV-A5的全基因组特征,为了解柯萨奇病毒的进化趋势及遗传特征提供理论数据,以便及时有效地阻断疾病传播。

Objective To investigate the molecular characteristic and evolutionary trends of full-genome sequences ofcoxsackievirus A2(CV-A2) and A5(CV-A5) in Changsha City.Methods The CV-A2 and CV-A5 strains were isolated anddetected from patients with hand, foot and mouth disease(HFMD) cases. The full-genome sequences of CV-A2 and CV-A5strains were obtained using NGS sequencing. Homology and phylogenetic tree analysis were performed, and the recombinationregions of the strains were examined by Sim Plot software.Results The full-genome sequences of CV-A2 and CV-A5 strainswere obtained from routine surveillance cases of HFMD in Changsha in 2019. The CV-A2 strain was named S281/Changsha/CHN/2019 with the full-genome sequence of 7 422 bp long;the CV-A5 strain was named S272/Changsha/CHN/2019 with thefull-genome sequence of 7 425 bp long. Homology analysis of the isolates by comparison with the nucleic acid sequences of CV-A2 and other CV-A2 strains in China showed that the non-structural protein region shared lower similarity than that ofstructural protein region. The CV-A2 showed 79.20% similarity with Fleetwood strain(NC038306), showed the highestsimilarity 95.60% with MN419014 strain from Hubei Province. The non-structural protein 3C and 3D region shared the lowestsimilarity with MN419014, 90.51 and 92.06%, respectively. Phylogenetic tree analysis showed that 3C and 3D regions werelocated in the CV-A4 branch. Amino acid mutation sites were found in non-structural protein region, and the amino acidsequence in structural protein region was conserved. Sim Plot analysis showed that genetic recombination was found in the 3C and 3D region of CV-A2 strains. The full-genome sequence of CV-A5 showed 80.7% similarity with the Swartz(AY421763)and 97.43% similarity with the strain(MH111030) from Australian. Homology analysis showed that the non-structural proteinregion shared lower similarity than that of structural protein region, based on full-genome of CV-A5. Phylogenetic tree analysisshowed that CV-A5 and MH111030 were in the same branch, indicating that CV-A5 strain not from local. The amino acid sequence of CV-A5 strain was conserved.ConclusionsThe CV-A2 strain in Changsha City shared genome sequenceinformation with CV-A4, and the CV-A5 strain was imported from abroad. Our findings are expected to understand themolecular and recombination characteristics of CV-A2 and CV-A5, provided the data of evolution and genetic features of thecoxsackievirus, and interrupt disease transmission in a timely and effective manner.