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

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.