Identification of predominant hepatitis C virus genotype in Turkish population

Abstract

Hepatitis C virus (HCV) is a major cause of acute and chronic hepatitis, leading to cirrhosis and hepatocellular carcinoma. Approximately 170 millions of person are chronically infected with HCV worldwide. HCV is an enveloped positive stranded RNA virus with 9.5 kb genome. The error-prone replication of HCV leads to its highly heterogeneous nature. There are 6 main genotypes and around 70 subtypes. The genotypes and subtypes of HCV have different prevalence rates and geographical distributions. They also differ in clinical manifestations, such as response to interferon treatment and disease progression. The identification of genotype distribution is of scientific importance because of its help in understanding of epidemiology of HCV and the clinical implications of the genotypes. In a previous study, conducted in our laboratory, the predominant genotype of HCV in South and Southeast Anatolia regions of Turkey was determined as subtype 1b with 91% prevalence. Subtype 1a, 2a and 4 were also present with lower prevalences, 6.3%, 1.3%, 1.3%, respectively. The high prevalence rate of subtype 1b and limitations of genotyping from 5' UTR in discrimination between subtype 1a from subtype 1b lead to confirmation of these results from another region of HCV genome. In this study, to confirm the results of the previous study we sequenced part of NS5B region and constructed phylogenetic tree. The results of this study were in concordance with the former study, indicating the predominant genotype as subtype 1b in South and Southeast Anatolia regions of Turkey. After identification of subtype 1b as the predominant genotype, a Turkish HCV-1b isolate was sequenced. Cloning and the partial sequence of HCV-1b isolate was performed by Aslý Öztan and in this study, we obtained the complete nucleic acid sequence of a Turkish HCV-1b isolate. It comprises 9361 nucleotides, including 306 nucleotides of 5' UTR, a single long open reading frame of 9033 nucleotides, and 22 nucleotides of 3' UTR. By sequence comparisons, we characterized the Turkish HCV- 1b isolate.