Phylogenetic Analysis the 5’-Noncoding Sequences of the Hepatitis C Virus Detected from the Patient with HCV Infection

Abstract

BACKGROUND/AIMS:Several strains of the hepatitis C virus exist; distinct genotypes and subtypes can be identified by sequence comparison of the viral genomes. Recent evidence that the genotype/subtype of hepatitis C virus may influence the clinical course of chronic hepatitis C and the response to interferon-alpha therapy for this disease suggests that methods to identify the genotype may become clinically useful. In the present study we evaluated a recently introduced method for identifying genotype HCV based on sequencing 5‘UTR region. METHODS: HCV-RNA was isolated from serum samples from 209 plasma patients with HCV infection, the 5’-UTR region was amplified by RT-PCR and subsequently sequenced in the 5’-noncoding by the dideoxynucleotide chain termination method. HCV-genotyping was performed by the blast search of the sequences with the HCV genotype gene bank. The phylogenetic analysis were used to differentiate the separate clusters of the identified HCV genotypes. RESULTS: The result of genotypes using blast search shows the proportions of patients with HCV subtype types 1a, 1b, 1c were 24.1%, 45%, 1.9% respectively, and other genotypes were genotype 2a 11,4% (24/209), 2b 0,48% (1/209), 2c 0,96% (2/209), 3a 0,96% (2/209) , 6a 15,68% (31/209). However, among the genotype 1, the subtypes 1a,1b and 1c are merged together demonstrated by the phylogenetic analysis. These results said that the differentiation of hepatitis C virus subtypes in genotype 1 was possibly insufficient in the phylogenetic tree analysis. CONCLUSIONS: Our results suggest that HCV 5’ NC-region genotyping methods give sufficient information for clinical purposes, but the phylogenetic tree analysis could not differentiate the separate cluster of the subtypes among type 1.