Analysis of complete genome sequence characteristics of coxsackievirus A2, A4 and A5 in Suzhou city
10.3760/cma.j.cn112866-20240119-00011
- VernacularTitle:苏州市柯萨奇病毒A2型、A4型和A5型的全基因组序列特征分析
- Author:
Ruimin YANG
1
;
Di WANG
;
Zeyuan CHEN
;
Yang LIU
;
Haibing YANG
;
Yu XIA
Author Information
1. 南京医科大学，南京 210000
- Keywords:
Hand, food and mouth disease;
Coxsackievirus;
Whole genome sequence;
Recombination
- From:
Chinese Journal of Experimental and Clinical Virology
2024;38(2):125-130
- CountryChina
- Language:Chinese
-
Abstract:
Objective:To understand the genomic characteristics and evolutionary trends of three coxsackievirus (CV) subtypes, including CV-A2, CV-A4 and CV-A5, in Suzhou city.Methods:Totally 248 samples were collected during routine monitoring for hand, foot, and mouth disease in Suzhou city from January to June in 2022. The specimens were detected for CV genotypes using Real-time fluorescence-reverse transcription polymerase chain reaction (Real-time RT-PCR). The CV positive samples were sequenced using the Miseq high-throughput sequencing platform. After obtaining the whole genome sequences of CV strains, homology analysis was performed. An evolutionary tree was constructed using molecular evolutionary genetics analysis (MEGA) X. Sequence recombination regions were analyzed using SimPlot and BootScan.Results:During routine monitoring for hand, foot and mouth disease in Suzhou city from January to June in 2022, one strain each of CV-A2, CV-A4, and CV-A5 viruses were identified, and their complete genomes were sequenced. CV-A2 and CV-A4 were clustered with the current prevalent strains in China, and no new amino acid site mutations were found in the whole genome of CV-A2; CV-A4 had several new amino acid site mutations in the non-structural region compared with the prototype strain; CV-A5 belonged to the C1 subgenotype 3 lineage, and the genome of CV-A5 had several new amino acid mutation sites in the non-structural protein region and underwent recombination.Conclusions:The CV-A2 and CV-A4 strains are stable epidemic strains, the CV-A5 strain is recombinant strain in Suzhou city.
