Influence of the hepatitis C genotype on the antiviral immune response

Transmission of hepatitis C virus (HCV) is closely linked to blood-blood contact. Accordingly, in developed countries HCV is mainly acquired by people who inject drugs (PWID). Importantly, PWID living in Germany are frequently exposed to different HCV genotypes (GTs) with GT1 and GT3 being predominant. As the infecting genotype can influence the infection outcome and HCV-specific CD8+ T cells play a major role in the immune response against HCV, we wanted to investigate the influence of the viral GT on the antiviral CD8+ T cell response in more detail in highly exposed individuals. For this purpose we worked with a cohort of 363 PWID from Essen, Germany that consisted of patients that remained seronegative for HCV (11%), patients with spontaneously resolved HCV infection (25%) and chronically infected patients (33% GT1, 27% GT3 and 4% other GTs). As a first step, we examined two host genetic factors that have been implicated with affecting HCV infection outcome. Single nucleotide polymorphisms near the IFNL3 gene have been associated with spontaneous clearance and enhanced response to therapy. In our cohort the “protective” IFNL3 rs12979860 C/C GT was significantly less frequent in GT1 infected patients compared to patients with resolved HCV infection, while subjects infected with GT3 showed an intermediate GT frequency. No significant differences in the CD8+ T cell response depending on the IFNL3 GT were detected, suggesting that the protective effect mediated by the IFNL3 C/C GT is independent of the CD8+ T cell response. Next, the impact of the HLA class I genotype on infection outcome was determined. In this cohort HLA-B*08 was a risk allele for GT1 infection, whereas HLA-B*27 was protective against both GT1 and GT3 infection. This second finding was unexpected, as HLA-B*27 was so far only described to protect against GT1 due to sequence differences in the immunodominant CD8+ T cell epitope NS5B2841 between both genotypes. We therefore aimed to identify novel GT3-specific CD8+ T cell responses that might mediate the protective effect. By screening predicted HLA-B*27-binders we identified the two novel epitopes, NS2840 GRLIWWNQY and NS2942 GRWFNTYLY, with the latter one being immunodominant in GT3. The strength of the CD8+ T cell response to the immunodominant GT3-specific B*27-epitope was comparable to the response against the known GT1-specific NS5B2841 epitope. Viral sequence analysis of the NS2 epitope regions provided evidence for mutational escape in HLA-B*27-positive patients in the NS2942 epitope. In summary, different epitope repertoires could be detected in GT1 and GT3 infected patients indicating that different CD8+ T cell responses contribute to the protective effect of HLA-B*27. Genotype-specific differences in the elicited CD8+ T cell response can also play an important role in determining the outcome of HCV infection. Our group has previously shown that patients with CD8+ T cells active against both GT1 and GT3 are predominantly found in PWID with resolved infection. Here, we tested if distinct CD8+ T cell responses against different sequence variants of the same epitope can be activated in patients exposed to different genotypes. The analysis was focused on immunodominant epitopes presented by HLA class I alleles that have been described in the context of immune control of viral infections (HLA-B*13, HLA-B*15, HLA-B*27 and HLA-B*57). Distinct responses against two GT-specific variants were found for 4 out of 5 tested epitopes, while one epitope was cross-reactive between all tested GT variants. Analysis of the T cell receptor (TCR) Vβ chain repertoire confirmed in most cases that distinct CD8+ T cell populations were activated by the different variants. As a proof of principle, priming against two different GT-specific variants of the same epitope is therefore possible within one patient, suggesting that inclusion of different sequence variants of important epitopes in a prophylactic vaccine may be feasible. As a last factor influencing the outcome of HCV infection in different genotypes we looked at the deletion of HCV-specific CD8+ T cells, as a rapid loss of specific T cells is observed upon viral persistence and continuous antigen exposure. We confirmed lower frequencies of HCV-specific CD8+ T cells in chronically infected patients compared to patients with resolved infection. It was tested whether the pro-apoptotic protein Bim is involved in CD8+ T cell depletion in HCV, as it was reported that activation of T cells in the liver of mice and in human HBV infection leads to upregulation of Bim. In contrast to HBV, Bim was not differentially regulated in CD8+ T cells from patients with resolved or chronic HCV infection ex vivo. Upon antigen-specific activation Bim and CD38 were both upregulated irrespective of the disease status. Taken together, our data suggest that dysregulation of Bim does not seem to contribute to CD8+ T cell depletion during chronic HCV infection.