Analysis of genetic characteristics of varicella-zoster virus in Liaoning Province based on SNP loci and phylogenetic tree
10.3760/cma.j.cn112309-20240530-00181
- VernacularTitle:基于SNP位点及系统进化树分析辽宁省水痘-带状疱疹病毒基因特征
- Author:
Wensi WANG
1
;
Yan WANG
;
Yinghui WANG
;
Xing FANG
;
Shuyi AN
;
Jinyuan GUO
;
Siping FEI
Author Information
1. 辽宁省疾病预防控制中心免疫规划所，辽宁 110172
- Publication Type:Journal Article
- Keywords:
Varicella-zoster virus;
Genotype;
Single nucleotide polymorphism;
Phylogenetic tree
- From:
Chinese Journal of Microbiology and Immunology
2024;44(12):1067-1075
- CountryChina
- Language:Chinese
-
Abstract:
Objective:To analyze the gene sequence of varicella-zoster virus (VZV) in Liaoning Province, and determine the prevailing dominant genotypes and nucleotide and amino acid variations.Methods:The open reading frames (ORFs) of 31 VZV strains from 2017 to 2020 in Liaoning Province were analyzed by PCR, including 1, 6, 12, 16, 17, 21, 22, 35, 37, 38, 50, 54, 55, 56, 60 and 66. The amplified products were sequenced, combined with single nucleotide polymorphism (SNP) and phylogenetic tree to determine the virus genotype, and the variation of nucleotides and amino acids at different sites was analyzed.Results:All 31 VZV strains in Liaoning Province were Clade 2 genotype. Compared with Clade 2 genotype reference strains, the 31 strains had nucleotide and amino acid homology of 99.6%-100.0% and 98.7%-100.0%, respectively, and the genetic distance was 0-0.002. Compared with V-Oka vaccine strain, the 31 strains all had site mutation, which led to amino acid changes, including one strain with ACCTCCCAA deletion at 541-549 sites of ORF1 and two strains with inserted CGG at the 780-781 site of ORF1; the 31 VZV strains had point mutations at 24 sites, including 15 synonymous mutations, 9 missense mutations, 20 mutations in the coding region, 4 mutations outside the coding region, 13 synonymous mutations in the coding region and 7 missense mutations in the coding region. The missense mutations in the coding region included a base mutation of C→T at site 731, a base mutation of C→T at site 790, a base mutation of C→T at site 791, a base mutation of A→G at site 17829, a base mutation of G→A at site 24567, a base mutation of T→C at site 98261, a base mutation of A→C at site 101579, which leaded to the amino acid changes of Arginine→Lysine, Arginine→Glutamine, Arginine→Glutamine, Histidine→Arginine, Arginine→Glutamine, Tyrosine→Histidine, Leucine→Arginine.Conclusions:Clade 2 genotype is the dominant genotype of VZV in Liaoning Province in recent years, and the gene sequences of VZV strains in Liaoning Province is highly conserved. Studying the characteristics of VZV gene is of great significance for studying the molecular epidemiology of VZV in Liaoning Province, and provides important scientific basis for varicella control and vaccination plan.
