The phylogenetic analysis of hepatitis C virus genotype 1b mutants in China / 中华检验医学杂志

ABSTRACT

Objectives In our studies before, we reported mutation C-T at -222 of hepatitis C virus type 1b genotyped on 5′ noncoding region (5′NCR). There was no this mutation of type 1b recorded in GenBank. Since genotypiog based on 5′NCR cannot differentiate subtypes, it is necessary to investigate whether the hepatitis C virus genotype 1b strains with mutation C-T belongs to other subtypes of genotype 1. Methods 64 HCV genotype 1b samples were amplified from 5′NCR by RT-PCR.Then the products were digested by use of BamHⅠ restriction enzymes. We randomly chose 6 samples with BamHⅠ restriction site and subjected them to amplification of 5′NCR and NS5B. The sequences of 5′NCR were analyzed. Sequences of NS5B fragments from the 6 samples were respectively subjected to phylogenetic analysis with subtypes of genotype 1 and 38 complete genomes of genotype 1b from GenBank.Results The phylogenetic analysis of 6 samples and subtypes of genotype 1 indicated that the genotypes of 6 strains with BamHⅠ restriction site in 5′NCR were type 1b, instead of subtype of type 1. Tree construction with 38 complete genomes of genotype 1b showed that the 6 mutants of genotype 1b did not belong to the same branch of the tree and there were no genetic differences between the mutants and the other strains of genotype 1b.Conclusions Our research indicated that the hepatitis C virus stains of C-T in 5′NCR were mutants of type 1b. Since the 5′NCR is a highly conserved region of HCV, the mutation might have some relationship to the long-time IFN therapy.