Evolutionary pathways to NS5A inhibitor resistance in genotype 1 hepatitis C virus

Abstract

Direct-acting antivirals (DAAs) targeting NS5A are broadly effective against hepatitis C virus (HCV) infections, but sustained virological response rates are generally lower in patients infected with genotype (gt)-1a than gt-1b viruses. The explanation for this remains uncertain. Here, we adopted a highly accurate, ultra-deep primer ID sequencing approach to intensively study serial changes in the NS5A-coding region of HCV in gt-1a- and gt-1b-infected subjects receiving a short course of monotherapy with the NS5A inhibitor, elbasvir. Low or undetectable levels of viremia precluded on-treatment analysis in gt-1b-infected subjects, but variants with the resistance-associated substitution (RAS) Y93H in NS5A dominated rebounding virus populations following cessation of treatment. These variants persisted until the end of the study, two months later. In contrast, while Y93H emerged in multiple lineages and became dominant in subjects with gt-1a virus, these haplotypes rapidly decreased in frequency off therapy. Substitutions at Q30 and L31 emerged in distinctly independent lineages at later time points, ultimately coming to dominate the virus population off therapy. Consistent with this, cell culture studies with gt-1a and gt-1b reporter viruses and replicons demonstrated that Y93H confers a much greater loss of replicative fitness in gt-1a than gt-1b virus, and that L31M/V both compensates for the loss of fitness associated with Q30R (but not Y93H) and also boosts drug resistance. These observations show how differences in the impact of RASs on drug resistance and replicative fitness influence the evolution of gt-1a and gt-1b viruses during monotherapy with an antiviral targeting NS5A.

In Vitro Susceptibility of Hepatitis C Virus Genotype 1 through 6 Clinical Isolates to the Pangenotypic NS3/4A Inhibitor Voxilaprevir

“…Taken together, these results indicate a high contextdependence (i.e., influenced strongly by both subtype and presence of other RASs) of the effect of particular RAS on VOX susceptibility. This conclusion is consistent with previous studies of the effect of various RASs on in vitro susceptibility to VOX (15) and other DAAs (52,53).…”

Primer ID Next-Generation Sequencing for the Analysis of a Broad Spectrum Antiviral Induced Transition Mutations and Errors Rates in a Coronavirus Genome

“…We have further developed a multiplexing Primer ID approach, allowing the sequencing of multiple regions of the viral genome in a single cDNA synthesis/PCR ( This approach is ideal for studying intra-host RNA virus populations due to its ability to accurately characterize individual viral genomes. We have used this approach to determine the genetic structures of intra-host viral populations in HIV (Zhou et al, 2016;Lee et al, 2017;Dennis et al, 2018;Abrahams et al, 2019;Adewumi et al, 2020;Council et al, 2020), to study drug resistance mutations in HIV and HCV (Clutter et al, 2017;Zhou et al, 2018;Keys et al, 2015), and to detect nucleotide mutation rates in single-stranded DNA molecule after heating (Lewis et al, 2016).…”

Efetividade, segurança e dinâmica de seleção de mutações de resistência envolvendo o uso de fármacos de ação direta na infecção crônica pelo genótipo 3 do HCV

“…Os resultados não mostraram associação entre a presença isolada da A62S no baseline e a não RVS. Entretanto,JEONG et al, 2018;ZHOU et al, 2018).Ainda sobre as substituições na posição 62 da NS5A, a SAR A62T, assim como a A62S, mostrou uma alta frequência entre os não respondedores, quando analisadas as amostras do vezes o FC em relação à presença da Y93H isolada. SARs associadas à falha da terapia viral com inibidores da NS5A são desenvolvidas durante a terapia, entretanto, a pressão seletiva imposta pelos DAAs pode alterar a população de quasispecies ao selecionar substituições que circulavam em menor frequência previamente ao tratamento ou no baseline.…”