Genetic characteristics and recombination analysis of hand, foot and mouth disease related coxsackievirus A5 in Fujian province from 2011 to 2020
10.3760/cma.j.cn112866-20220402-00080
- VernacularTitle:2011—2020年福建省手足口病相关柯萨奇病毒A5型基因特征及重组分析
- Author:
Wenxiang HE
1
;
Ying ZHU
;
Wei CHEN
;
Yuwei WENG
Author Information
1. 福建省疾病预防控制中心 福建省人兽共患病研究重点实验室，福州 350001
- Keywords:
Coxsackievirus A5;
Phylogenetic analysis;
Recombination
- From:
Chinese Journal of Experimental and Clinical Virology
2022;36(6):678-684
- CountryChina
- Language:Chinese
-
Abstract:
Objective:To investigate the gene characteristics and recombination of coxsackievirus A5(CV-A5)in Fujian province.Methods:The VP1 regions of CV-A5 strains from positive samples of hand, foot and mouth disease (HFMD) collected from all cities in Fujian province from 2011 to 2020 were amplified by reverse transcription nested polymerase chain reaction (RT-nPCR), then sequenced and identified the subgenotypes. CV-A5 strains were isolated in rhabdomyosarcoma (RD) cells. The isolated virus strains were sequenced by next generation sequencing to obtain the whole genome sequences. MEGA7.0 was used for phylogenetic analysis. RDP4 and SimPlot 3.5.1 softwares were used to analyze viral gene recombination.Results:Total thirty-one HFMD related CV-A5 cases were detected in Fujian province from 2011 to 2020, mainly in children aged 1 to 2 years (16/31), with a male/female ratio of 2.1∶1 (21/10), including 3 severe cases and 1 deceased case. CV-A5 subgenotyping was successful in 27 cases, all of them belonged to E1 subgenotype. The whole genome sequences of six CV-A5 strains were obtained, and the homology with the prototype strain Swartz was 81.1%-81.6%. Phylogenetic analysis results based on the sequences of whole genome, P1, P2 and P3 regions showed that the virus strain 2017FJFZ239 is a suspected recombinant strain, which was distributed in the same branch as CV-A5 reference strains (GenBank accession number: MW079817 and MN663160) in P2 and P3 regions. Analyzing with RDP4 showed that the virus strain 2017FJFZ239 had the same recombination event with CV-A5 reference strains (GenBank accession number: MW079817 and MN663160) and the potential parental sequences were CV-A2 (GenBank accession number: KX595284) and CV-A5 (GenBank accession number: KP289362). Further analyzing with SimPlot showed that the virus strain 2017FJFZ239 may recombine with CV-A2 strain (GenBank accession number: KX595284) in non-structural protein 2B, 2C and P3 regions.Conclusions:From 2011 to 2020, HFMD related CV-A5 in Fujian province belongs to E1 subgenotype, and there is a recombinant strain.
