Complete genome characteristics of coxsackievirus A6 strains isolated from the Shanghai Pudong District
10.3969/j.issn.1002-2694.2025.00.144
- VernacularTitle:上海市浦东新区柯萨奇病毒A组6型全基因组序列特征分析
- Author:
Xuechun ZHANG
1
;
Yu GU
1
;
Xiao WANG
1
;
Yuqing ZHOU
1
;
Dan LIU
1
;
Bing ZHAO
1
Author Information
1. 上海市浦东新区疾病预防控制中心,上海 200136;复旦大学浦东预防医学研究院,上海 200136
- Publication Type:Journal Article
- Keywords:
hand,foot and mouth disease;
coxsackievirus A6;
gene recombination;
amino acid variation
- From:
Chinese Journal of Zoonoses
2025;41(9):917-924
- CountryChina
- Language:Chinese
-
Abstract:
This study characterized the whole-genome sequences of 45 Coxsackievirus A6(CVA6)strains isolated from Pudong District,Shanghai,during 2015-2023,to elucidate regional genetic evolution and recombination patterns.Viral genomes were ampli-fied and sequenced with Illumina MiSeq platforms,and phylogenetic analysis of the VP1 and 3D regions was conducted via MEGA 11(maximum-likelihood method,bootstrap=1 000).Nucleotide/amino acid homology and variation sites were assessed in DNAstar v7.0,and recombination events were identified with SimPlot v3.5.1 and RDP4.All isolates belonged to the D3a subtype,and exhibited intra-strain nucleotide and amino acid homologies of 88.0%-99.9%and 92.4%-100%,respectively,in contrast to lower homologies to the prototype Gdula strain(78.0%-80.5%nucleotide;94.5%-95.1%amino acid).Thirty-six mutation sites were identified in the VP1 re-gion.Recombination analysis revealed frequent cross-serotype events involving CVA4 and EV-A71,with dominant RF-A(84.5%)and minor RF-K(15.5%)patterns localized in the 3D region.This study elucidated the gene recombination and genetic evolution of CVA6 in Pudong District,Shanghai,thereby providing data support to enhance understanding of the evolutionary trends and genetic characteristics of coxsackieviruses,and offering theoretical evidence for the prevention and control of CVA6.
