HCV genome-wide analysis for development of efficient culture systems and unravelling of antiviral resistance in genotype 4. Issue 3 (8th April 2021)

• Record Type: Journal Article
• Authors: Pham, Long V.; Pedersen, Martin Schou; Fahnøe, Ulrik; Fernandez-Antunez, Carlota; Humes, Daryl; Schønning, Kristian; Ramirez, Santseharay; Bukh, Jens
• Is Part Of: Gut. Volume 71:Issue 3(2022)
• Page Start: 627
• Page End: 642
• Publication Date: 2021-04-08
• Subjects: HCV -- drug resistance -- Hepatitis C -- genotype; Gastroenterology -- Periodicals; 616.33
• DOI: 10.1136/gutjnl-2020-323585
• Languages: English
• ISSNs: 0017-5749

Abstract

Abstract : Objective: HCV-genotype 4 infections are a major cause of liver diseases in the Middle East/Africa with certain subtypes associated with increased risk of direct-acting antiviral (DAA) treatment failures. We aimed at developing infectious genotype 4 cell culture systems to understand the evolutionary genetic landscapes of antiviral resistance, which can help preserve the future efficacy of DAA-based therapy. Design: HCV recombinants were tested in liver-derived cells. Long-term coculture with DAAs served to induce antiviral-resistance phenotypes. Next-generation sequencing (NGS) of the entire HCV-coding sequence identified mutation networks. Resistance-associated substitutions (RAS) were studied using reverse-genetics. Result: The in-vivo infectious ED43(4a) clone was adapted in Huh7.5 cells, using substitutions identified in ED43(Core-NS5A)/JFH1-chimeric viruses combined with selected NS5B-changes. NGS, and linkage analysis, permitted identification of multiple genetic branches emerging during culture adaptation, one of which had 31 substitutions leading to robust replication/propagation. Treatment of culture-adapted ED43 with nine clinically relevant protease-DAA, NS5A-DAA and NS5B-DAA led to complex dynamics of drug-target-specific RAS with coselection of genome-wide substitutions. Approved DAA combinations were efficient against the original virus, but not against variants with RAS in corresponding drug targets. However, retreatment with glecaprevir/pibrentasvir remained efficient against NS5A inhibitor and sofosbuvir resistant variants. Recombinants with specific RAS at NS3-156, NS5A-28, 30, 31 and 93 and NS5B-282 were viable, but NS3-A156M and NS5A-L30Δ (deletion) led to attenuated phenotypes. Conclusion: Rapidly emerging complex evolutionary landscapes of mutations define the persistence of HCV-RASs conferring resistance levels leading to treatment failure in genotype 4. The high barrier to resistance of glecaprevir/pibrentasvir could prevent persistence and propagation of antiviral resistance.