Abstract
Hepatitis C virus (HCV) exhibits significant genetic diversity and is a cause of severe liver complications. The viral envelope glycoproteins E1 and E2, key targets for neutralizing antibodies, are highly variable. To understand how host and viral genetic factors modulate antibody responses, we analyze genetic and antibody binding and neutralization data from 54 patients infected with HCV genotype 3a. We find that host polymorphisms in IFNL4 gene (IFNλ4-P70 generating haplotype) are associated with reduced antibody binding. Within the virus, variations at three specific E1/E2 amino acid positions and three N-glycosylation sites (including one site common to both analyses) significantly correlate with antibody binding and/or neutralization sensitivity. Furthermore, greater intra-patient diversity within the E2 hypervariable region 1 is associated with stronger antibody binding. These results identify specific host and viral genetic features that shape humoral immunity against HCV genotype 3a, providing insights crucial for designing broadly effective vaccines.