A whole genome analysis of two coxsackievirus A2 strains isolated from patients with herpetic angina in Shanghai
10.19428/j.cnki.sjpm.2025.24306
- VernacularTitle:上海地区2株疱疹性咽峡炎柯萨奇病毒A2型株的全基因组分析
- Author:
Jingyi ZHANG
1
;
Jiayu WANG
2
;
Run LI
1
;
Fanghao FANG
1
;
Wencheng WU
1
;
Wanju ZHANG
1
;
Min CHEN
1
;
Xin CHEN
1
;
Zheng TENG
1
Author Information
1. Institute of Microbiology Laboratory, Shanghai Municipal Center for Disease Control and Prevention, Shanghai 200336, China
2. Institute of Microbiology Laboratory, Shanghai Institute of Preventive Medicine, Shanghai 200336, China
- Publication Type:Journal Article
- Keywords:
coxsackievirus A2;
herpetic angina;
whole genome analysis;
genetic characteristic
- From:
Shanghai Journal of Preventive Medicine
2025;37(3):215-221
- CountryChina
- Language:Chinese
-
Abstract:
ObjectiveTo understand the whole genome characteristics and the information for genetic evolution in the two coxsackievirus A2 (CVA2) strains isolated from patients with herpangina in Shanghai, and to provide a scientific basis for the prevention and treatment of herpetic angina. MethodsTwo CAV2 strains isolated from patients with herpetic angina in Shanghai were performed whole genome sequencing and analysis for phylogenetics, nucleotide homology, and evolution. ResultsA phylogenetic analysis of the VP1 region revealed that the two Shanghai strains both belonged to CVA2 genotype D, with the highest homology to OL357660, a strain from Yunnan. The average nucleotide identity (ANI) of the whole genome between the two Shanghai strains was 98.88%, and the ANI of the whole genome comparisons to other CVA2 genotype D strains and CVA2 genotypes A-C strains ranged from 84.64% to 97.42% and from 79.21% to 84.20%, respectively. The two Shanghai strains had low homology in the 3D region compared to the existing CVA2 strains. The phylogenetic analysis and sliding window nucleotide similarity analysis indicated that the two Shanghai strains and the Yunnan OL357660 strain might constitute a new genetic lineage. ConclusionThe two CVA2 strains isolated for the first time in Shanghai are assigned to genotype D (GenBank: PQ130039 and PQ130040), which is identical to the existing subtype prevalent in China. As represented by the Shanghai strains, a new CVA2 genetic lineage is been identified. This study has enriched the data on genetic evolution and genetic variation of CVA2 in Shanghai, indicating the requirement to strengthen surveillance for the epidemiological pattern of CVA2.
