Comprehensive determinant mapping of the hepatitis C-specific CD8 cell repertoire reveals unpredicted immune hierarchy

While CD8 cells are thought to play an important role in the control hepatitis C infection, low frequencies of virus-specific cells and high numbers of potential determinants have made it challenging to obtain direct and comprehensive data regarding fine specificity and clonal size of the CD8 cells involved. Most assays suited for measuring CD8 cell frequencies require prior knowledge of immune dominant peptides. While there are excellent algorithms for predicting MHC-peptide binding strength for particular class I alleles, it is unknown how accurate these algorithms are in predicting the actual determinant recognized in an individual coexpressing other class I alleles. We used a high throughput ELISPOT approach to test for responses to every possible 9-mer determinant within the 191 residue hepatitis C core protein in addition to 61 previously defined CD8 cell determinants. The amino acid sequence of each determinant recognized was compared with HLA-binding predictions for the expressed class I alleles. These data show feasibility for and importance of comprehensive direct ex vivo monitoring, an approach which should facilitate design of antiviral immunotherapeutic strategies.