Characterization of multi-DAA resistance using a novel hepatitis C virus genotype 3a infectious culture system

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Background and Aims: The high HCV infection cure rates achieved with direct-acting antiviral (DAA) treatments could be compromised in the future by the emergence of antiviral resistance. Thus, it is essential to understand the viral determinants that influence DAA resistance, which is most prevalent in genotype 3. We aimed at studying how resistance to protease-, NS5A-, and NS5B-inhibitors influences the activities of glecaprevir/pibrentasvir, sofosbuvir/velpatasvir, and sofosbuvir/velpatasvir/voxilaprevir in cell culture, and how the HCV genome adapts to selective pressure by successive rounds of treatment failure. Approach and Results: A previously developed in vivo infectious cDNA clone of strain S52 (genotype 3a) was adapted to efficiently replicate and propagate in human hepatoma cells (Huh7.5) using 31 adaptive substitutions. DAA escape experiments resulted in the selection of S52 variants with decreased drug susceptibility (resistance), which was linked to the emergence of known resistance-associated substitutions (RASs). NS5A-inhibitor resistance was sufficient to promote treatment failure with double-DAA but not triple-DAA regimens. Enhanced viral fitness associated with the selection of sofosbuvir resistance accelerated escape from DAAs. After serial DAA treatment failure, HCV genetic evolution led to a complex genome-wide network of substitutions, some of which coevolved with known RASs. Conclusions: Baseline NS5A-RAS can compromise the efficacy of double-DAA pangenotypic regimens for HCV genotype 3, and enhanced viral fitness can accelerate treatment failure. Persistence of RASs after successive treatment failure is facilitated by the remarkable evolutionary capacity and plasticity of the HCV genome. Proof-of-concept for the potential development of multi-DAA resistance is shown.

OriginalsprogEngelsk
TidsskriftHepatology
Vol/bind78
Udgave nummer2
Sider (fra-til)621-636
Antal sider16
ISSN0270-9139
DOI
StatusUdgivet - 2023

Bibliografisk note

Funding Information:
This study was supported by a PhD stipend from Candys Foundation (Carlota Fernandez-Antunez) and by grants from The Region H Foundation (Santseharay Ramirez and Jens Bukh), The Lundbeck Foundation (Santseharay Ramirez and Jens Bukh), The Novo Nordisk Foundation (Jens Bukh), Independent Research Fund Denmark (DFF), Medical Sciences (Santseharay Ramirez and Jens Bukh), Innovation Fund Denmark (Infect-ERA EU, Jens Bukh), and Weimann Foundation (Ulrik Fahnøe). Jens Bukh is the recipient of the 2015 Novo Nordisk Prize and the 2022 Hagedorn Prize, and the 2019 recipient of a Distinguished Investigator grant from the Novo Nordisk Foundation.

Publisher Copyright:
© 2023 John Wiley and Sons Inc.. All rights reserved.

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