Characterising viral evolution and the host humoral immune response in early primary HCV infection

Transmission of hepatitis C virus (HCV) is associated with a strong genetic bottleneck with 1-3 transmitted/founder (T/F) viruses establishing infection followed by a second genetic bottleneck at ~100 days post-infection if chronicity is established. The first bottleneck is hypothesised to be driven by efficiency of cell entry, as observed in HIV. Examination of the second bottleneck has revealed T/F viruses are replaced by new variants that carry mutations within the Envelope region, suggesting that antibody responses are driving immune escape in early infection. The aim of this study was to compare, in a rare cohort of very recently HCV-infected individuals, the viral and host immune characteristics between clearers and chronic progressors. The timing and potency of the developing HCV specific antibody responses were examined between the two groups and contrasted against how the viral population was evolving phenotypically, in terms of in vitro infectivity and CD81 binding, over the course of infection.The sequence analysis of the viral quasispecies over the course of infection suggested that the developing humoral immune response targeted epitopes that overlapped with CD81 binding sites. Using HCV pseudo-particle (HCVpp) generated with autologous Envelopes, it was determined that efficient cell entry was a phenotypic trait of variants circulating early in infection, and was associated with higher binding to the host receptor, CD81.HCVpp neutralisation assays showed that early and potent neutralising antibody (nAb) responses occurred in clearer subjects prior to extinction of the T/F virus and were associated with no emergence of new viral variants, whereas in chronic progressors nAbs emerged after loss of T/F variants and after new ‘chronic variants’ had emerged. The early nAb response in clearers was associated with IgA as well as IgG1 and IgG3 responses.Finally, it was observed that when an anti-E2 IgG1 response was present, both CD81 binding and infectivity decreased. However, in the absence of humoral immune response, an increase in entry efficiency via CD81 occurred.The findings indicate that entry competent variants dominate the early phase of infection and that early nAb activity associated with both IgG3 and IgG1 subclasses appear to be essential to prevent emergence of new HCV variants and development of chronic infection. Results presented in this thesis advance our understanding of the interplay between host and viral responses, which is critical to inform vaccine design