Sequence analysis of E1/E2 gene of hepatitis C virus in Dali area

Abstract

Objective To understand the genotypes of hepatitis C virus(HCV) and the genetic evolution and molecular characteristics of the predominant genotypes (6n and 3a) currently circulating in the Dali, Yunnan province. Methods From January to May 2014, sera were collected from patients with HCV infection in the First People's Hospital of Dali.RNA was extracted from the serum samples, which were analyzed using RT-PCR with 5'UTR and E1/E2 primers. The RNA was sequenced, and sequence analysis was performed using bioinformatics software. Results Of 24 serum specimens from patients suspected of infection with HCV, 21 were confirmed positive for HCV by RT-PCR with HCV 5UTRspecific primer, of which 15 were HCV genotype 3 (4 cases of 3a and 11 cases of 3b) and 6 were HCV genotype 6 (4 cases of 6k and 2 cases of 6n). The homology of the nucleotide sequence and amino acid sequence of E1/E2 gene between isolate 4 and genotype 3a were up to 87.98%±3.07and 87.97%±2.82. The homology of the nucleotide sequence and aminoacid sequence between isolate 10 and genotype 6n were up to 90.30±1.87 and 90.54±1.53.There were 10 potential glycosylation sites on both of E1/E2 gene of two isolates HCV isolates. Only the predicted value of 5 T cell epitopes of 4 and 10 increasedor decreased because of amino acid mutations. The rest of predicted value of epitope slightly changed. Conclusion HCV genotype 3(3a and 3b) and genotype 6(6k and 6n) were the predominant genotypes or subtypes currently circulating in the Dali, Yunnan province. The virulence and immunological characteristics of HCV 3a and 6n did not change significantly. Key words: Hepatitis C; Hepatitis viruses; Genotype; Sequence analysis