Analysis of the whole genome characteristics of 9 hepatitis A virus strains in China
10.3760/cma.j.cn112866-20191115-00177
- VernacularTitle:9株甲型肝炎病毒流行株全基因组特征分析
- Author:
Fengxue DU
1
;
Jingyuan CAO
;
Wenting ZHOU
;
Shengli BI
Author Information
1. 中国疾病预防控制中心病毒病预防控制所，北京 102206
- Keywords:
Hepatitis A virus;
Phylogenetic analysis;
Molecular epidemiology
- From:
Chinese Journal of Experimental and Clinical Virology
2020;34(2):140-144
- CountryChina
- Language:Chinese
-
Abstract:
Objective:To analyze the characteristics of the whole genome of hepatitis A virus (HAV) strains from Nanchong, Sichuan and Hetian, Xinjiang.Methods:Serum samples of 9 patients with acute hepatitis A were selected for HAV whole genome sequencing. Among them, 3 were from the same outbreak in Nanchong, Sichuan (2006) and 6 were from Hetian, Xinjiang(2016). Nine full length HAV sequences were obtained by viral RNA extraction, reverse transcription, nested PCR and sequencing. Phylogenetic analysis, neutralizing epitope sites, recombination and natural selection analysis were also performed.Results:Genotyping of HAV VP1-2A region indicated that the 9 HAV sequences all belonged to sub-genotype IA and were divided into four different branches, with 3 Nanchong sequences and 3 Hetian sequences in the same branch. While the whole genome sequence showed that the nucleotide and amino acid homology of 3 Nanchong sequences were 99.99%~100% and 100%, respectively. The difference of nucleotides and amino acids were 0.50%~0.57% and 0.08%~0.17% between 3 Nanchong and 3 Hetian sequences, respectively. The nucleotide and amino acid identities of nine HAV genomes were 98.29%~100% and 99.62%~100%, which was closely related to hd9 in China and MNA12-001 in Mongolia (nucleotide and amino acid homology: with hd9 98.60%~99.50% and 99.75%~99.92%; and with MNA12-001 98.45%~99.32% and 99.71%~99.87%, respectively). The 9 HAV sequences did not change at the neutralizing epitope sites, and no recombination events were found. Natural selection analysis indicated that the HAV coding region was subjected to a negative selection.Conclusions:There are many HAV epidemic strains in China; the 9 HAV amino acid sequences were conserved at the major neutralizing epitope sites.
