Amino Acid Mutations in NS5B Protein among Treatment-naive Genotype 3A Infected Patients

To determine the frequency of mutations at specific amino acid positions in full length NS5B gene among chronic HCV genotype 3a infected patients of Peshawar, who had not taken any previous treatment.

Cross-sectional descriptive study.

Institute of Basic Medical Sciences, Khyber Medical University, Peshawar (IBMS, KMU) and Comsats Institute of Information Technology (CIIT), Islamabad from September 2016 to December 2017.

HCV genotype determination was carried out among 310 actively infected, treatment-naive patients, using type specific PCR-based genotyping assay. In a total of 162 (52%) HCV genotype 3a isolates, NS5B gene was amplified in 126 (78%) samples using qualitative PCR and sequencing. NS5B gene sequences were analysed for clinically relevant mutations against standard HCV 3a reference sequence (Isolate NZL1, BAA04609) using MEGA 6 software.

Analysis of HCV NS5B amino acid sequences (aa.1-591), comprising essential motif A-F revealed four novel mutations: A67V, T131I, R374H and M425L in 27 (21%) viral isolates. Mutation D/N244S and D/N310K were found in 14 (11%) of the pre-treatment isolates. Mutations at positions 282 and 316 (S282T and C316N/Y) were not identified among studied isolates.

This study reports mutations based on complete NS5B protein of HCV 3a genome that could help predict treatment response among the chronically infected with HCV genotype 3a patients of Peshawar.