Genetic Variability of Untypable Hepatitis C Virus Isolates Based on 5′-Untranslated Region

Abstract

Background: Hepatitis C virus (HCV) is a single-stranded enveloped virus with a ribonucleic acid (RNA) genome of approximately 9.6 kb that predominantly infects the liver. The main objective of the current research was to determine the unknown HCV genotypes by analyzing the 5′-untranslated region (5′-UTR) to identify different genotypes and classify them by their phylogenetic relationships. Methods: Serum samples (104) were taken from untyped chronic HCV isolates, and cDNA was synthesized using reverse transcriptase enzyme. Nested polymerase chain reaction (PCR) was used to amplify the 5′-UTR followed by agarose gel electrophoresis. The 5′-UTR amplified products were sequenced by the Sanger method. Evolutionary analysis was performed using Molecular Evolutionary Genetics Analysis Version 7 (MEGA7) software. Results: 104 untyped chronic HCV patients were studied, representing the higher frequency of males (62%). Out of the total, nine samples of 5′-UTR products were sequenced for genotype confirmation. In the phylogenetic analysis, genotype 3 was reported to be 89% (3a 77%, 3b 11%) and 11% unknown genotype. Overall, in the phylogenetic tree, the 5′-UTR sequences were successfully clustered in a clad with the reference sequences of genotype 3a, and 3b, while one sequence showed an unknown genotype. Conclusions: The study concludes that genotype 3 is predominant, and identification of genotypes by this procedure is an accurate and alternative method.