2015—2022年江苏省柯萨奇病毒A10型全基因组序列特征分析

Whole-genome sequence analysis of coxsackievirus A10 strains isolated in Jiangsu Province from 2015 to 2022

目的对江苏省2015—2022年柯萨奇病毒A10型(CVA10)分离株全基因组序列特征进行分析,阐明其分子流行病学特征。方法选取2015—2022年间江苏省地区流行的45株CVA10分离株进行全基因组测序,基于CVA10全基因组、VP1、P1、P2和P3区序列分别构建系统进化树,运用DNAStar、MEGA7.0和Similarity plots3.5.1等生物信息学软件对获取的全基因组序列进行比对,分析同源性、基因重组情况和主要氨基酸变异位点。结果45株CVA10分离株全基因组核苷酸和氨基酸序列同源性分别为90.3%~99.1%和97.9%~99.8%;各区段比对发现,P1区核苷酸序列同源性最高,为92.1%~100.0%;P3区段序列同源性差异较大为84.7%~100.0%,但相比于核苷酸序列的多样性,各区段氨基酸序列均较为保守。基于VP1序列的系统进化树将CVA10分为A~H共8个基因型,其中江苏与其他国内大部分流行株均属于C基因型,全基因组进化树和VP1进化树分析结果接近一致。基于基因组各区段序列的系统进化与Simplot重组分析结果显示,江苏分离株GD07/Lianyungang/2017和N180/Suqian/2016与CVA10原型株在P1区域高度匹配,而在非结构蛋白(P2、P3)、5′-UTR和3′-UTR区均观察到与其他EVA存在重组信号。而氨基酸突变位点分析结果显示,与原型株AY421767/Kowalik/2004相比,VP1区以及多个重要氨基酸位点变异频繁,这可能会使得CVA10衣壳蛋白的结构、潜在的受体结合位点产生一些难以察觉的变化。结论本研究通过探究江苏地区CVA10在基因组水平的进化方向和重组特征,及时把控基因重组和氨基酸位点突变对CVA10感染及疾病发生造成的影响,为江苏省手足口病的防控工作提供了基础资料。

Objective To analyze the whole-genome sequences of coxsackievirus A10(CVA10)strains isolated in Jiangsu Province from 2015 to 2022 and their molecular epidemiological characteristics.Methods Forty-five CVA10 isolates circulating in Jiangsu Province during 2015 to 2022 were selected for whole-genome sequencing.Phylogenetic trees were constructed based on the whole genome,VP1,P1,P2 and P3 sequences of CVA10 strains.Bioinformatics software,including DNAStar,MEGA7.0 and Similarity plots3.5.1,was used for analysis of homology,genetic recombination and major amino acid variation sites.Results The nucleotide and amino acid sequence homology of the whole-genome sequences of 45 CVA10 strains was 90.3%-99.1%and 97.9%-99.8%,respectively.The nucleotide sequence homology of P1 region was the highest(92.1%-100.0%),while the nucleotide sequence homology of P3 region ranged from 84.7%to 100.0%.In contrast to the diversity of nucleotide sequences,the amino acid sequences of each region were conserved.A phylogenetic analysis based on the complete VP1 sequences of CVA10 strains revealed eight genotypes:A-H.The CVA10 isolates in Jiangsu Province and other prevalent strains in China mainly belonged to genogroup C.Results of the phylogenetic analysis based on the whole-genome sequences and complete VP1 sequences were consistent.Phylogenetic analysis bases on different gene segments and Simplot recombination analysis revealed that Jiangsu isolates GD07/Lianyungang/2017 and N180/Suqian/2016 showed high homology with the CVA10 prototype in the P1 region,but had recombination sites with other strains of enterovirus group A in the P2,P3,5′-UTR and 3′-UTR regions.Compared with the prototype strain AY421767/Kowalik/2004,the Jiangsu isolates showed frequent variations in the VP1 region and many other major amino acid sites,which might result in some imperceptible changes in capsid structure and potential receptor-binding sites.Conclusions By analyzing the evolution and genetic recombination features of CVA10 strains at the genome level in Jiangsu Province,this study elucidated the influence of genetic recombination and amino acid site mutation on CVA10 infection,providing basic data for the prevention and control of hand-foot-mouth disease in Jiangsu Province.