Complete genome analysis of a coxsackievirus A4 strain isolated from a patient with severe hand, foot, and mouth disease in Yunnan, China
10.3760/cma.j.cn112866-20201126-00295
- VernacularTitle:一株分离自云南重症手足口病患者的柯萨奇病毒A组4型毒株的全基因组分析
- Author:
Changzeng FENG
1
;
Ming ZHANG
;
Danhan XU
;
Shanri CONG
;
Guangxian ZHANG
;
Chi XU
;
Zhimin LU
;
Zhaoqing YANG
;
Shaohui MA
Author Information
1. 中国医学科学院&北京协和医学院医学生物学研究所 云南省重大传染病疫苗研发重点实验室，昆明 650118
- Keywords:
Coxsackievirus A4;
Phylogenetic analysis;
Recombination analysis
- From:
Chinese Journal of Experimental and Clinical Virology
2021;35(4):395-403
- CountryChina
- Language:Chinese
-
Abstract:
Objective:To provide useful information for in-depth understanding of the epidemic and molecular evolution of Coxsackievirus A4 (CV-A4), the genetic characteristics of the complete genome and recombination events in some genome regions of CV-A4 strain isolated from a patient with severe hand, foot and mouth disease (HFMD) in Yunnan province were analyzed.Methods:The CV-A4 strain was isolated from feces using RD, KMB17 and A549 cells respectively, and the viral RNA was extracted from the supernatant with CPE. The whole VP1 and complete genome sequences of the virus were amplified by RT-PCR and sequenced through Sanger’s sequencing. Complete genome sequence and genome regions of the isolated virus were analyzed through MEGA7.0 and SimPlot 3.5.1 software.Results:The virus isolated from RD cells belonged to CV-A4 and was designated as R11-20/YN/CHN/2011 strain. This CV-A4 strain was C2 sub-genotype through phylogenetic analysis based on the VP1 sequence. CV-A4 R11-20/YN/CHN/2011 has the highest nucleotide sequence identity with 09214/SD/CHN/2009 in VP1 and CVA4/SZ/CHN/09 in the complete genome. Recombination occurred between CV-A4 R11-20/YN/CHN/2011 and EV-A71 in 3D region.Conclusions:The CV-A4 R11-20/YN/CHN/2011 strain belongs to C2 sub-genotype and recombines with EV-A71 in 3D region.
