Interplay of Amino Acid Residues at Positions 28 and 31 in NS5A Defines Resistance Pathways in Hepatitis C Virus Genotype 2

ABSTRACT Hepatitis C virus (HCV) genotype 2 (GT2) represents approximately 9% of all viral infections globally. While treatment outcomes for GT2-infected patients have improved substantially with direct-acting antiviral agents (DAAs) compared to alpha interferon, the presence of polymorphisms in NS5A can impact the efficacy of NS5A inhibitor-containing regimens. Thus, pathways of NS5A resistance were explored in GT2 subtypes using elbasvir, an NS5A inhibitor with broad genotype activity. Resistance selection studies, resistance analysis in NS5A-inhibitor treated virologic failures, and analyses of antiviral activities in replicons bearing a panel of GT2 subtype sequences and amino acid substitutions introduced by site-directed mutagenesis were performed to define determinants of inhibitor susceptibility. Elbasvir showed differential antiviral activities in replicons bearing GT2 sequences. The 50% effective concentration (EC50) values for replicons bearing reference NS5A sequences for GT2a and GT2b were 0.003 and 3.4 nM, respectively. Studies performed with recombinant replicons demonstrated cross talk between amino acid positions 28 and 31. The combination of phenylalanine and methionine at positions 28 and 31, respectively, conferred the highest potency reduction for elbasvir in GT2a and GT2b. This combination was observed in failures seen in the C-SCAPE trial. Addition of grazoprevir, an NS3/4A protease inhibitor, to elbasvir more effectively suppressed the emergence of resistance in GT2 at modest inhibitor concentrations (3× EC90). Ruzasvir, a potent, pan-genotype NS5A inhibitor, successfully inhibited replicons bearing GT2 resistance-associated substitutions (RASs) at positions 28 and 31. The results demonstrate that cross talk between amino acids at positions 28 and 31 in NS5A modulated inhibitor potency and may impact treatment outcomes in some HCV GT2-infected patients.