Extra-epitopic hepatitis C virus polymorphisms confer resistance to broadly neutralizing antibodies by modulating binding to scavenger receptor B1

Broadly-neutralizing monoclonal antibodies (bNAbs) may guide vaccine development for highly variable viruses including hepatitis C virus (HCV), since they target conserved viral epitopes that could serve as vaccine antigens. However, HCV resistance to bNAbs could reduce the efficacy of a vaccine. HC33.4 and AR4A are two of the most potent anti-HCV human bNAbs characterized to date, binding to highly conserved epitopes near the amino- and carboxy-terminus of HCV envelope (E2) protein, respectively. Given their distinct epitopes, it was surprising that these bNAbs showed similar neutralization profiles across a panel of natural HCV isolates, suggesting that some viral polymorphisms may confer resistance to both bNAbs. To investigate this resistance, we developed a large, diverse panel of natural HCV envelope variants and a novel computational method to identify bNAb resistance polymorphisms in envelope proteins (E1 and E2). By measuring neutralization of a panel of HCV pseudoparticles by 10 μg/mL of each bNAb, we identified E1E2 variants with resistance to one or both bNAbs, despite 100% conservation of the AR4A binding epitope across the panel. We discovered polymorphisms outside of either binding epitope that modulate resistance to both bNAbs by altering E2 binding to the HCV co-receptor, scavenger receptor B1 (SR-B1). This study is focused on a mode of neutralization escape not addressed by conventional analysis of epitope conservation, highlighting the contribution of extra-epitopic polymorphisms to bNAb resistance and presenting a novel mechanism by which HCV might persist even in the face of an antibody response targeting multiple conserved epitopes.

Generation of an immune response that is protective against a wide variety of naturally occurring isolates is necessary for vaccines against highly variable viruses like hepatitis C virus (HCV). Two broadly neutralizing human monoclonal antibodies, HC33.4 and AR4A, neutralize multiple highly divergent HCV isolates, raising hope that a vaccine against HCV is possible. Previous reports have defined the distinct, highly conserved sites on the viral envelope proteins where these antibodies bind. However, little is known about naturally occurring variation in sensitivity of different HCV isolates to these antibodies. We developed a high throughput assay and computational algorithm to evaluate over 100 naturally occurring HCV variants for their sensitivity to these two antibodies, identifying several resistance polymorphisms to each antibody which do not fall within their mapped binding sites. Furthermore, two of these polymorphisms modulate resistance to both antibodies by enhancing or reducing envelope protein binding to HCV co-receptor scavenger receptor B1 (SR-B1). By developing this broadly applicable platform, we have shown the important neutralization resistance conferred by changes distant from antibody binding sites, presenting a potential mechanism by which HCV might persist even in the face of an antibody response targeting multiple conserved sites.