Analysis of whole-genome sequences of coxsackievirus A4 strains isolated in Jiangsu Province from 2015 to 2022
10.3760/cma.j.cn112309-20230724-00012
- VernacularTitle: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
- Author:
Huan FAN
1
;
Changjun BAO
;
Liguo ZHU
;
Jianli 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;
Coxsackievirus A4;
Molecular characteristics;
Phylogenetic analysis;
Genetic recombination
- From:
Chinese Journal of Microbiology and Immunology
2024;44(3):249-258
- CountryChina
- Language:Chinese
-
Abstract:
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.
