Correlates of protective immunity against hepatitis C virus

Hepatitis C virus (HCV) currently infects ~185 million individuals worldwide. Despite the development of new effective antivirals against HCV, it is estimated that two million new infections occur annually, especially among marginalized populations and in developing countries. As with many chronic viral infections, the development of an effective prophylactic vaccine is hampered by the limited knowledge of determinants of a protective immune response in humans upon natural exposure to the virus. HCV represents a unique model to study protective immunity in chronic viruses, since ~30% of the patients are able to clear the primary infection spontaneously. In this thesis, we proceeded to study protective immunity against HCV in cohorts of injection drug users (IDUs) who are continuously at risk of infection and reinfection by HCV. We hypothesized that the majority of spontaneous resolvers of a primary HCV infection are protected against chronicity of infection upon re-exposure. Protective immunity would likely be associated with the highest breadth, frequency and functional avidity of HCV-specific polyfunctional CD4 and CD8 memory T cells. The protective capacity of memory T cells upon infection with novel HCV variants will depend on the diversity and flexibility of the T cell repertoire that can recognize these viral variants and/or the capacity to generate de novo T cell responses specific for these variants.  The first aim of the project was to define and dissect correlates of protective immunity conferred by HCV-specific T cells in reinfected individuals. Our results showed that protection from chronicity upon reinfection was associated with an increased magnitude and breadth of the HCV-specific polyfunctional CD4 and CD8 T-cell responses, as well as the appearance of a CD127lo tetramer+ CD8+ effector T-cell population at the peak of the response. Individuals who developed persistent viremia upon HCV reinfection demonstrated very limited or no expansion of HCV-specific T cells. Sequencing of the cytotoxic T-lymphocyte (CTL) epitopes targeted by the memory immune response in unprotected individuals revealed that the sequence of the autologous reinfecting virus was different from the reference sequence used in our immunological assays.  The second aim was to analyse the dynamics of the T-cell receptor (TCR) repertoire of HCV-specific CD8 T-cells in protected versus unprotected patients and in relation to infection with variant viral sequences. Our results demonstrate that for epitope-specific CD8 T cells a more focused TCR-repertoire of distinct clonotypes was associated with protection. These T-cell populations showed higher functional avidity and polyfunctionality compared to their counterparts in non-protected patients. The clonotypes forming the effector T-cell population during reinfection were recruited from the memory pool, rather being de novo responses generated from the naïve pool. In conclusion, our results suggest that protection from persistence upon HCV reinfection is associated with an enhanced magnitude, breadth and quality of the HCV-specific T-cell response, as well as a more focused TCR-repertoire of distinct clonotypes with high functional avidity. The degree of homology between viral strains causing the consecutive episodes of infection is a critical determinant for protection. These findings provide a first insight into the correlates of protective immunity against HCV and have important implications for the rational design of effective prophylactic vaccines against HCV and other chronic viruses.

Keyphrases: Hepatitis C Virus (HCV), Memory immune response, HCV reinfection, Protective immunity, T-cell receptor (TCR) repertoire