Identification of hepatitis C virus genotypes and subtypes in patients from Maharashtra based on 5’UTR sequencing and analysis: a retrospective study

Abstract

The clinical importance of HCV genotypes lies in its persistence and ability to cause chronic liver disease. Knowledge of HCV genotype distribution periodically is now essential for the clinical management of infected patients. The current study was designed to genotype and subtype HCV isolates in patients from Pune, Mumbai and Nashik districts of Maharashtra, determine association of HCV genotypes between both sexes and different age groups and perform phylogenetic analysis of the study isolates. Eighty HCV RNA positive patients were genotyped and subtyped in the study. Primers targeting 5’untranslated region (UTR) were designed for both amplification and sequencing of all isolates. All HCV isolates were characterized by direct sequencing of 5’ UTR followed by analysis with NCBI genotyping tool and in-silico BLAST analysis. The results were correlated with the Los Alamos Hepatitis C sequence and immunology database’s sequence alignment tool HCVAlign and phylogenetic analysis. Most of HCV isolates in this study belonged to genotype 3(56.25%) followed by genotype 1(35%) and genotype 4(7.5%). A rare genotype 5(1.25%) was identified in one of the patients. Prevalent subtypes were: subtype 3a (42.5%), subtype 1a (21.25%) and subtype 1b (13.75%). No notable association of age and gender with respect to genotypes was observed except for genotype 1a which showed an overrepresentation in males. Compared with phylogenetic analysis, NCBI genotyping tool was simpler for genotyping and subtyping HCV isolates. The present study revealed that HCV genotypes 3 and 1 were prevalent in Pune, Mumbai and Nashik districts of Maharashtra. With rare genotype (genotype 5) being identified and due to very few genotyping studies carried out in this region, this study aims at contributing towards monitoring the distribution of HCV genotypes among studied regions of Maharashtra.