2015—2022年江苏省柯萨奇病毒A组4型全基因组序列特征分析

Analysis of whole-genome sequences of coxsackievirus A4 strains isolated in Jiangsu Province from 2015 to 2022

目的回顾性分析2015—2022年江苏省柯萨奇病毒A组4型(CVA4)的分子流行病学特征及重组情况。方法收集疱疹性咽峡炎和手足口病患者咽拭子或肛拭子标本,采用荧光定量PCR检测试剂盒对CVA4进行鉴定。利用72个CVA4完整基因组序列、99个CVA4 VP1序列进行全面系统的系统发育分析,同时采用生物信息学软件DNAStar、MEGA7.0和Similarity plots3.5.1对江苏省CVA4分离株同源性、基因重组和氨基酸变异位点进行分析。结果根据现有VP1核苷酸序列CVA4被分为A、B、C和D基因型,基因型C可以进一步分为C1~C55个亚基因型,其中,C2基因型是与手足口病相关的CVA4主要亚基因型。江苏省分离株序列在P1区与CVA4原型具有较高的同源性,而在P2和P3区与其他肠道病毒A组(EV-A)流行株具有较高的同源性。重组分析表明,江苏省分离株在P2、P3和3′-UTR区与其他EV-A流行株存在3种基因重组模式,这些重组模式是CVA4在人群中持续和广泛传播过程中获得的,更利于CVA4传播。结论分析28个江苏省分离株CVA4完整基因组的系统发育和分子特征,丰富了已知CVA4基因组多样性;研究基因重组和VP1氨基酸位点突变情况、及时把控CVA4感染及疾病发生造成的影响,可更好地了解CVA4的进化关系和传播途径,从而帮助指导疾病控制和预防。

Objective To retrospectively analyze the molecular epidemiological features and genetic recombination of coxsackievirus A4(CVA4)strains isolated in Jiangsu from 2015 to 2022.Methods Throat or anal swab samples were collected from patients with herpangina or hand,foot and mouth disease(HFMD).Real-time PCR was used to detect CVA4.A comprehensive and systematic phylogenetic analysis was conducted based on 72 whole genomes and 99 VP1 sequences of CVA4 strains.Several bioinformatics software including DNAStar,MEGA7.0 and Similarity plots3.5.1 was used for analysis of homology,genetic recombination and amino acid variation sites.Results Four genotypes(A,B,C and D)and five sub-genotypes(C1-C5)of CVA4 were identified based on the VP1 nucleotide sequences.C2 was the predominant sub-genotype causing HFMD.The Jiangsu strains showed high homology with the CVA4 prototype in the P1 region,and higher identity with other strains of enterovirus group A(EV-A)in the P2 and P3 regions.Genetic recombination analysis revealed that the Jiangsu strains had three genetic recombination patterns with other EV-A epidemic strains in the P2,P3 and 3′-UTR regions.These recombination patterns took place during the sustained and widespread circulation of CVA4 in people and increased the transmissibility of CVA4.Conclusions This study analyzes the phylogenetic and molecular features of 28 whole genomes of Jiangsu CVA4 strains,which helps to better understand the genomic diversity of CVA4.By analyzing the genetic recombination and amino acid mutations in the VP1 region,this study elucidates the evolution and transmission of CVA4,which is conducive to the control and prevention of CVA4 infection.