Anti-Hepatitis C Virus T-Cell Immunity in the Context of Multiple Exposures to the Virus

Abstract

Characterisation of Hepatitis C virus (HCV)-specific CD8+ T-cell responses in the context of multiple HCV exposures is critical to identify broadly protective immune responses necessary for an effective HCV vaccine against the different HCV genotypes. However, host and viral genetic diversity complicates vaccine development. To compensate for the observed variation in circulating autologous viruses and host molecules that restrict antigen presentation (human leucocyte antigens; HLA), this study used a reverse genomics approach that identified sites of viral adaptation to HLA-restricted T-cell immune pressure to predict genotype-specific HCV CD8+ T-cell targets. Peptides representing these putative HCV CD8+ T-cell targets, and their adapted form, were used in individualised IFN-γ ELISpot assays to screen for HCV-specific T-cell responses in 133 HCV-seropositive subjects with high-risk of multiple HCV exposures. The data obtained from this study i) confirmed that genetic studies of viral evolution is an effective approach to detect novel in vivo HCV T-cell targets, ii) showed that HCV-specific T-cell epitopes can be recognised in their adapted form and would not have been detected using wild-type peptides and iii) showed that HCV-specific T-cell (but not antibody) responses against alternate genotypes in chronic HCV-infected subjects are readily found, implying clearance of previous alternate genotype infection. In summary, HCV adaptation to HLA Class I-restricted T-cell responses plays a central role in anti-HCV immunity and multiple HCV genotype exposure is highly prevalent in at-risk exposure populations, which are important considerations for future vaccine design.

Evidence of CD4+ T cell-mediated immune pressure on the Hepatitis C virus genome

“…It is worth noting that the relatively low HCV-specific responses observed in this study were mainly from chronic infected subjects and similar to outcomes from other groups 15 , 28 . We have also observed lower responses overall for HCV antigens than for HIV antigens using the same immunological approaches for CD8 + T cell responses (median IFNγ response in ELISpot of 590 SFUs/10 6 cells with an inter-quartile range (IQR) of 280–1440 for HIV versus a median of 63 SFU/10 6 cells for HCV with an IQR of 38.5–117; including for known T cell epitopes) 8 , 9 . Other studies have also shown typically lower responses for HCV-specific T cells than for other antigen-specific T cells for HIV, CMV and EBV 15 , 25 , 29 – 34 .…”

“…As for the ICS results, we also observed IFNγ responses to both non-adapted and adapted forms of the epitopes (see Supplementary material and Supplementary Table 6 ). However, for these subjects, where CD8 + T cell epitopes in the same region(s) were known, we had previously tested the PBMCs with these known CD8 + T cell epitopes in these subjects in an earlier study and had not detected responses >25 SFU/million PBMCs 9 .…”

“…In this study, where possible, peptides containing adapted and non-adapted amino acids were compared. We, and others, have shown for HIV and HCV that amino acid adaptation to HLA class I-restricted CD8 + T cell responses can lead to escape as the peptide can no longer be presented by the relevant HLA or recognized by the TCR of the responding effector cell 8 , 9 . However, we have also shown that in many cases the peptides containing adapted amino acids are still recognized and may even elicit greater IFNγ responses than to the non-adapted form of the peptide 9 , 10 .…”

“…So far, studies on HCV have focused on viral adaptation to antigen-specific CD8 + T cell immune responses and were identified as HLA class I-associated viral polymorphisms. These putative viral adaptations were used as leads to identify novel antigen-specific CD8 + T cell epitopes 8 , 9 . These viral adaptations commonly resulted in the loss of antigen recognition (‘classical viral escape’), however alternative mechanisms of viral adaptation were also identified, including examples in which viral adaptation was associated with increased interferon gamma (IFNγ) CD8 + T cell responses 10 .…”

Primer ID Ultra-Deep Sequencing Reveals Dynamics of drug Resistance-Associated Variants in Breakthrough Hepatitis C Viruses: Relevance to Treatment Outcome and Resistance Screening

“…For example, position 48 falls at the P2 position within a well-known human leucocyte antigen (HLA)restricted HCV T-cell epitope (CINGVCWTV) for the common HLA-A2 allele; variation at the P2 position in this epitope has been identified as a putative viral adaptation to the host's immune response [34]. Furthermore, position 86 falls within another described HLA-restricted T-cell epitope (WPAPQGARSL) for the common HLA-B*07 allele [34] at the P2 position; a site known to influence HLA-peptide binding. Of note, these subjects also undertook IFN-based treatment as part of their boceprevir regimen and studies have shown IFN-a-based treatment can affect the host's immune response (reviewed in [35]).…”