CD8⁺ T-cell response promotes evolution of hepatitis c virus nonstructural proteins

Background & Aims: Hepatitis C virus (HCV) acquires mutations that allow it to escape the CD8⁺ T-cell response, although the extent to which this process contributes to viral evolution at the population level is not clear. We studied viral adaptation using data from a large outbreak of HCV genotype 1b infection that occurred among women immunized with contaminated immunoglobulin from 1977 to 1978. Methods: The HCV nonstructural protein coding regions NS3-NS5B were sequenced from 78 patients, and mutations were mapped according to their location inside or outside previously described CD8 ⁺ T-cell epitopes. A statistical approach was developed to identify sites/regions under reproducible selection pressure associated with HLA class I. Results: The frequency of nonsynonymous mutations was significantly higher inside previously described CD8⁺ T-cell epitopes than outsideparticularly in NS3/4A and NS5B. We identified new regions that are under selection pressure, indicating that not all CD8⁺ T-cell epitopes have been identified; 6 new epitopes that interact with CD8⁺ T cells were identified and confirmed in vitro. In some CD8⁺ T-cell epitopes mutations were reproducibly identified in patients that shared the relevant HLA allele, indicating immune pressure at the population level. There was statistical support for selection of mutations in 18 individual epitopes. Interestingly, 14 of these were restricted by HLA-B allele. Conclusions: HLA class I-associated selection pressure on the nonstructural proteins and here predominantly on NS3/4A and NS5B promotes evolution of HCV. HLA-B alleles have a dominant effect in this selection process. Adaptation of HCV to the CD8 ⁺ T-cell response at the population level creates challenges for vaccine design.