Whole-Genome Sequence Analysis of HCV identifies HLA Class I-Associated Selection Pressure at the Population Level

Introduction Antiviral CD8+T cells are a key component of the adaptive immune against hepatitis C viruses (HCV). Failure of CD8 T-cell immunity is characterized by a progressive dysfunction of T-cells and selection of escape mutations inside epitopes. Here, we applied whole-genome sequencing of HCV in a large cohort with chronic infection to study viral adaptation to immune pressure at the population level. Materials & Methods The complete HCV-genome from 1334 HLA class-I-genotyped chronic HCV-patients was sequenced using a genotype-specific tiling-PCR approach and Oxford-Nanopore-Sequencing. Consensus sequences were created by an in-house algorithm. Isolates with>90% genome coverage were defined as whole-genome sequences. HLA-associated selection pressure was detected with a Bayesian model (HAMdetector). Results Complete genomes were recovered from 81.5% (n=1,089) of samples, with amplification efficiency closely correlating with viral load. Across the complete polyprotein, we identified 148 HLA-associated mutations (HAMs) with posterior probability>0.8. Of these, 101 mapped to previously described epitopes, while 47 represent putative novel HAMs, suggesting the presence of additional, uncharacterized epitopes. HAM frequencies did not differ significantly between proteins. However, their genomic distribution varied between genotypes 1 and 3, indicating that selection pressure targets distinct sites depending on the genetic background. Conclusion Our high-throughput HCV whole-genome sequencing protocol enables comprehensive analysis of viral sequence diversity. The results demonstrate extensive CD8+ T-cell selection pressure across the entire HCV polyprotein, indicating that immune-driven adaptation shapes circulating HCV isolates at the population level. Publication History Article published online: 26 January 2026 © 2026. Thieme. All rights reserved. Georg Thieme Verlag KG Oswald-Hesse-Straße 50, 70469 Stuttgart, Germany