| Objective To analyze the genotype and molecular characteristics of varicella-zoster Virus(VZV)in four provinces of China from 2018 to 2020,identify the vaccine strains and wild strains,analyze the g E glycoproteins,and select the wild strains of VZV for the whole base-group determination and analysis.Methods A total of 55 vesicle fluid or throat swab samples were collected from patients suspected VZV infection in Liaoning,Hubei,Chongqing and Tibet provinces from 2018 to 2020.The suspected samples were screened by real-time quantitative polymerase chain reaction,and the positive samples were analyzed by detection six Single Nucleotide Polymorphism(SNP)sites in Open Reading Frame(ORF)22 and ORF38 which to identify the genotypes of the virus strains,and then compared with the VZV strains in Gen Bank to establish the genetic relationship tree.Four SNPs on ORF38 and ORF62 were amplified to identify the vaccine strain from the wild strain.The gene sequence encoding g E glycoprotein was determined and compared with the loci of the standard reference strain DUMAS and domestic and foreign vaccine strains(Baike,Varilrix,Varilvax,Poka,and Voka)to analyze the antigen stability.A throat swab sample,which is VZV wild strain was determined and analyzed the whole genome by second generation sequencing.Results In this study,55 VZV samples were collected from four provinces in China from2018 to 2020,and 50 positive samples were detected.Of the 50 positive samples,46 were amplified and sequenced,including 30 in Liaoning Province,10 in Hubei Province,5 in Chongqing and 1 in Tibet.Compared with the standard reference strain Dumas,the VZV genotypes in the above provinces belonged to clade2 wild strain.Among them,A?G mutation occurred at position 37990 in sample 2019-LN-14,resulting in the change of glutamine to arginine.A total of 33 g E protein fragments were amplified,including 22 from Liaoning,9 from Hubei,1 from Chongqing and 1 from Tibet.Analysis of gene characteristics of g E protein fragment showed that all strains had a C?T mutation at 115926 site,resulting in the change of threonine to isoleucine.In 2019-LN-29 and 2019-LN-32 samples,A ? G mutation occurred at 116314 site,resulting in lysine to arginine;G?A mutation occurred at116775 site,resulting in glutamic acid to lysine.A?G a mutation occurred at 116446 site in2019-LN-4,resulting in the change of arginine to histidine.The whole genome of2018-CQ-14 sample detected in the second generation analysis was named SD14 strain,with a length of 125184 bp and GC content of 46.13%.Compared with 222 VZV genome sequences downloaded from Gen Bank,12 SNPs were found in SD14 genome sequence.There were three non synonymous mutations,L135 R in ORF6,K98 T in ORF37 and N47 S in ORF54.According to PROVEAN analysis,none of the three non synonymous substitutions had any effect on protein function.Conclusions In the four provinces of China from 2018 to2020,the VZV genotypes prevalent in Liaoning,Hubei,Chongqing and Tibet belong to Clade2,all of which are wild strains.No infection caused by vaccine strain was found in clinical samples from varicella or herpes zoster.The analysis of Ge protein showed that although there were some changes in amino acids,there was no specific change in virulence of the virus.In this study,we used high-throughput sequencing method to analyze the throat swab samples of a patient with systemic lupus erythematosus complicated with varicella infection.Compared with 223 VZV genomes,77 clade specific markers were identified,20 of which were specific for Clade2.This study is the first time to detect and analyze the main epidemic VZV in China,which provides a sufficient scientific basis for the follow-up development and optimization of varicella vaccine.It provides abundant background data for monitoring the spread,evolution,recombination and genetic diversity of viruses. |
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