CD8+ T-cell exhaustion phenotype in chronic hepatitis C virus infection is associated with epitope sequence variation

During chronic hepatitis C virus (HCV) infection CD8+ T-cells become functionally exhausted, undergoing progressive phenotypic changes, i.e., overexpression of inhibitory molecules such as PD-1 (programmed cell death protein 1) and/or Tim-3 (T-cell immunoglobulin and mucin domain-containing molecule-3). The extreme intrahost genetic diversity of HCV is a major mechanism of immune system evasion, facilitating epitope escape. The aim of the study was to determine whether T-cell exhaustion phenotype in chronic HCV infection is related to the sequence repertoire of NS3 viral immunodominant epitopes.The dataset comprises original NGS fastq reads from 90 prospective patients with chronic HCV genotype 1b infection. Amplicons of 2223 bp, encompassing the NS3/4a viral genes of hepatitis C virus, (nt 3466-5689 according to H77 reference genome, GenBank: AF009606), covering epitopes NS31073, NS31406 and NS31436 encoding regions were tagmented using Nextera XT Sample preparation Kit (Illumina). Sequencing was performed on MiSeq (Illumina) platform using MiSeq Reagent v3 kit 2x300 bp, (Illumina).