Genetic characteristics of the whole genome sequences of coxsackievirus A6 strains in Jiangsu Province from 2013 to 2022
10.3969/j.issn.1002-2694.2023.00.143
- VernacularTitle:2013-2022年江苏省柯萨奇病毒A6型全基因组序列特征分析
- Author:
Huan FAN
1
;
Chang-Jun BAO
;
Li-Guo ZHU
;
Jian-Li HU
;
Hong JI
Author Information
1. 江苏省疾病预防控制中心急性传染病防制所,卫生部肠道病原微生物重点实验室,南京 210009
- Keywords:
hand,foot and mouth disease;
coxsackie virus A6;
genetic recombination;
genetic characteristics
- From:
Chinese Journal of Zoonoses
2023;39(12):1165-1173
- CountryChina
- Language:Chinese
-
Abstract:
This study explored the genetic characteristics of the whole genome sequences of coxsackie virus A6 strains in Jiangsu province from 2013 to 2022,and analyzed the genetic evolution of each coding region of the full-length genome.To in-vestigate why coxsackievirus A6 has replaced enterovirus A71 and coxsackievirus A16 as the most predominant etiological agent for HFMD in Jiangsu province,we selected 35 CVA6 isolates circulating in Jiangsu province during 2013-2022 for whole ge-nome sequence amplification and analysis.Sequence alignment,homology analysis,phylogenetic analysis and genetic recombi-nation were performed with the DNASTAR,MEGA7.0 and similarity plots 3.5.1 software packages.We analyzed the impor-tant amino acid sites of CV-A6 in the Pl region and 3D region.The nucleotide and amino acid similarities of 35 CV-A6 full-length genomes were 87.5％-99.6％ and 97.0％-99.8％,respectively,and the nucleotide and amino acid sequence identity with the CV-A6 prototype strain was 80.3％-81.0％ and 94.7％-95.3％,respectively.On the basis of phylogenetic analysis of VP1 region sequences,the 34 CV-A6 strains in this study belonged to the D3a genotype,and only one strain belonged to the D2 genotype.According to the phylo-genetic analysis of 3D region sequences,four recombinant forms(RFs),RF-A,RF-L,RF-K and RF-C,appeared primarily in 2013-2022 in Jiangsu province.Recombination analysis demonstrated that CVA6s,which was prevalent in Jiang-su from 2013 to 2022,had high similarity to the CVA6 prototype strain Gdula in the structured protein sequences.However,in the non-structured protein sequences and noncoding regions,similarities were higher among CVA6s and prototype strains of other EV-A types.Amino acid mutation site analysis showed that multiple amino acid sites in the Pl and 3D regions varied fre-quently with respect to the prototype strain Gdula.These differences might have resulted in small changes in the capsid struc-ture and potential receptor-binding sites.In conclusion,by analyzing the whole genome sequence of CV-A6,this study advances understanding of the gene recombination and genetic evolution relationship of CV-A6 in Jiangsu Province;in addition,it may explain possible reasons why CV-A6 has become the main pathogen of HFMD in recent years,and it provides basic data for the prevention and control of CV-A6.
