Phylogenetic Characterization of the 5′ Untranslated Region of Untypable HCV Genotypes Circulating in Pakistan

Abstract

<b><i>Introduction:</i></b> Commercial methods for HCV genotyping is challenged by the increased prevalence of untypable genotypes in Pakistan. <b><i>Objective:</i></b> The aim of the current study was to perform nucleotide sequencing of 5′ UTR region for genotyping of viral isolates circulating in Peshawar, Pakistan. <b><i>Methods:</i></b> The total number of commercially untypable samples were 94 in which 18 samples were sequenced for the characterization of 5′ UTR region. Post-sequencing analysis was performed for genotype identification (<i>n</i> = 18) and molecular phylogenetic analysis. <b><i>Results:</i></b> The current study reveals different genotypes, that is, 10/18 viral isolates were found to be genotype 3a (55.55%), 3 isolates (genotype 3b, 16.66%), 2 isolates (genotype 6h/6g, 11.11%), 2 (6g/d, 11.11%), and 1 sample (genotype 1c, 5.55%). In addition, genotype 3a is the dominant representative of HCV circulating in Pakistan and has been increasing across the country. <b><i>Conclusion:</i></b> The current study also reveals that genotype 6 (2 were genotype 6h/6g and 2 were 6g/d) is also circulating in Pakistan and not restricted to South China and Hong Kong.