Majority of HCV-specific T cells have only limited cross-genotype reactivity

The existence of multiple HCV genotypes characterized by marked sequence differences is a challenge for immune control. The objective of this study is a comparison of the antiviral CD8 T cell response targeting HCV genotype 1 and genotype 3 antigens to determine the extent of cross-genotype reactivity of HCV-specific T cells. We analyze a cohort of patients with past or ongoing intravenous drug use hypothesizing that multiple exposures to different genotypes may occur. Methods: HCV-specific T cells are expanded from PBMC in the presence of peptide pools covering NS3 from genotype 1 or 3. Individual reactive peptides are determined by intracellular cytokine staining of IFNg. Complete NS3 is amplified by PCR and sequenced from all viremic patients. Results: 56 subjects were analyzed; this includes 20 subjects with genotype 1 and 22 subjects with genotype 3 infection and 14 anti-HCV-positive subjects with undetectable viremia. A total of 28 distinct epitopes (37 CD8 responses) was identified, with 14 epitopes (50%) exclusively targeted in genotype 1 and 10 epitopes (35,7%) exclusively targeted in genotype 3. Only 4 CD8 epitopes (14,3%) were cross-reactive in both genotypes including two epitopes where the targeted peptide sequence is identical. Only two epitopes show cross-reactivity despite being different in both genotypes. Interestingly, we identified multiple subjects with CD8 responses consistent with exposure to both genotypes. Conclusions: The majority of HCV-specific CD8 epitopes identified in individuals with intravenous drug use have only limited cross-genotype reactivity. There is strong immunological evidence for exposure to both genotypes in this cohort.