Complete genomic analysis of Coxsackievirus B5 isolate in Qinghai province
10.3760/cma.j.cn112866-20200421-00139
- VernacularTitle:青海省一株柯萨奇病毒B5分离株全基因组分析
- Author:
Mingxu YANG
1
;
Lixia FAN
;
Huaxiang RAO
;
Juan YU
Author Information
1. 长治医学院 046000
- Keywords:
Coxsackievirus B5;
Whole genome;
Phylogenetic analysis;
Recombination analysis
- From:
Chinese Journal of Experimental and Clinical Virology
2021;35(4):441-447
- CountryChina
- Language:Chinese
-
Abstract:
Objective:To characterize the complete genome sequence of Coxsackievirus B5 (CVB5) isolate from one influenza-like case in Qinghai province in 2018.Methods:Whole genome of QH/CVB5/2018 strain was sequenced by next-generation sequencing. The genome sequence splicing, genetic evolution, gene recombination and amino acid mutation analysis were performed by using SPAdes, DNAStar 7.1, MEGA6.0, Simplot 3.5.1 and RDP4 software respectively.Results:The whole genome of QH/CVB5/2018 had 7 369 nucleotides in length, encoding a 2 185 aa polyprotein, which showed a highly homology with CVB5 isolates through BLAST analysis, with the highest homology of 96.9% in nucleotide and 99.5% in amino acid to 417/JS/CHN/2013. The phylogenetic tree, constructed on the complete VP1 region, indicated that QH/CVB5/2018 can be classified into CVB5-C genotypes. Recombination analysis indicated recombinant event appeared with beginning breakpoint at around 6114 and ending breakpoint at around 7 199, with major parent strain of CHN_SH/CVB5/2008 and minor parent strain of CHN_YN-CVB3/2009. Compared with other CVB5 isolates, amino acid substitution of 139S, 864S, 1086R, 1693C, 1814D and 1819N are specific for QH/CVB5/2018.Conclusions:QH/CVB5/2018 belongs to genotype C of Coxsackievirus B5, which possibly be a recombinant strain.
