HCV genotype 1-6 NS3 residue 80 substitutions impact protease inhibitor activity and promote viral escape

Pham, Long V.; Jensen, Sanne B.; Fahnøe, Ulrik; Pedersen, Martin Schou; Tang, Qi; Ghanem, Lubna; Ramírez, Santseharay; Humes, Daryl; Serre, Stéphanie B. N.; Schønning, Kristian; Bukh, Jens; Gottwein, Judith M.

doi:10.1016/j.jhep.2018.10.031

Cited by 37 publications

(42 citation statements)

References 48 publications

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“…Although patients failing DAA combination treatment often have RASs in several drug targets, NS3P positions 156 and 168 are hotspots for PI resistance . In line with recent findings in replicons and patients, we demonstrated that 156‐RASs were essential for resistance to glecaprevir and voxilaprevir for genotype 1a (this study and Pham et al) and genotype 3a . In contrast to grazoprevir and paritaprevir, no concentration‐dependent RAS selection patterns, including RASs at other NS3P positions than at position 156, were observed for glecaprevir and voxilaprevir .…”

Section: Discussionsupporting

confidence: 91%

“…). We recently acquired the PIs glecaprevir and voxilaprevir . As previously observed, compared with grazoprevir and especially paritaprevir, these PIs showed increased efficacy against the original genotype 1‐3 viruses .…”

Section: Resultsmentioning

confidence: 78%

“…Although antiviral resistance is a severe public health concern, the understanding of underlying mechanisms is limited . A recently developed technique for NGS‐based substitution linkage and haplotype reconstruction allowed us to explore the nature and frequency of PI resistance–associated NS3P haplotypes in unprecedented detail . In addition, by analyzing viruses longitudinally during evolution under drug pressure, we suggest a strategy for genome‐wide linkage analysis and haplotype reconstruction, which was validated by subclonal analysis including ancestral reconstruction.…”

Section: Discussionmentioning

confidence: 99%

“…In vitro testing is required for characterization of RASs. In constrast to enzyme and replicon assays, infectious HCV culture systems allow investigation of the complete genome and viral life cycle, and results obtained in such systems reflect in vivo data …”

Section: Discussionmentioning

confidence: 99%

“…Briefly, 5 × 10 3 cells in 96‐well plates were infected with NS3P sequence–confirmed first‐passage virus stocks. One day after infection, PI treatment was administered using a range of noncytotoxic concentrations in triplicates . Three days following infection, immunostaining was carried out; counts of HCV infected cells from treated wells were related to means of counts from infected, nontreated wells.…”

Section: Methodsmentioning

confidence: 99%

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Evolutionary Pathways to Persistence of Highly Fit and Resistant Hepatitis C Virus Protease Inhibitor Escape Variants

Jensen¹,

Fahnøe²,

Pham³

et al. 2019

Hepatology

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Protease inhibitors (PIs) are important components of treatment regimens for patients with chronic hepatitis C virus (HCV) infection. However, emergence and persistence of antiviral resistance could reduce their efficacy. Thus, defining resistance determinants is highly relevant for efforts to control HCV. Here, we investigated patterns of PI resistance–associated substitutions (RASs) for the major HCV genotypes and viral determinants for persistence of key RASs. We identified protease position 156 as a RAS hotspot for genotype 1‐4, but not 5 and 6, escape variants by resistance profiling using PIs grazoprevir and paritaprevir in infectious cell culture systems. However, except for genotype 3, engineered 156‐RASs were not maintained. For genotypes 1 and 2, persistence of 156‐RASs depended on genome‐wide substitution networks, co‐selected under continued PI treatment and identified by next‐generation sequencing with substitution linkage and haplotype reconstruction. Persistence of A156T for genotype 1 relied on compensatory substitutions increasing replication and assembly. For genotype 2, initial selection of A156V facilitated transition to 156L, persisting without compensatory substitutions. The developed genotype 1, 2, and 3 variants with persistent 156‐RASs had exceptionally high fitness and resistance to grazoprevir, paritaprevir, glecaprevir, and voxilaprevir. A156T dominated in genotype 1 glecaprevir and voxilaprevir escape variants, and pre‐existing A156T facilitated genotype 1 escape from clinically relevant combination treatments with grazoprevir/elbasvir and glecaprevir/pibrentasvir. In genotype 1 infected patients with treatment failure and 156‐RASs, we observed genome‐wide selection of substitutions under treatment. Conclusion: Comprehensive PI resistance profiling for HCV genotypes 1‐6 revealed 156‐RASs as key determinants of high‐level resistance across clinically relevant PIs. We obtained in vitro proof of concept for persistence of highly fit genotype 1‐3 156‐variants, which might pose a threat to clinically relevant combination treatments.

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Section: Discussionsupporting

confidence: 91%

Section: Resultsmentioning

confidence: 78%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 3 more Smart Citations

Evolutionary Pathways to Persistence of Highly Fit and Resistant Hepatitis C Virus Protease Inhibitor Escape Variants

Jensen¹,

Fahnøe²,

Pham³

et al. 2019

Hepatology

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Guignardones Y–Z, Antiviral Meroterpenes from Penicillium sp. NBUF154 Associated with a Crella Sponge from the Marine Mesophotic Zone

Zou

Ding

et al. 2022

Chemistry & Biodiversity

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Guignardones Y-Z (1 -2), two new meroterpenoids, and six known metabolites involving guignardones A -H (3 -4), gyorgy-isoflavone (5), daidzein (6), blumenol A (7) and guignardianone A (8) were isolated from the fungus Penicillium sp. NBUF154, which was obtained from a 60 m deep Crella sponge. Their structures including absolute configurations were unambiguously elucidated by exhaustive spectroscopic analysis and ECD calculations. A putative biosynthetic pathway toward guignardones (1 -4) is here proposed. Biological evaluation of compounds 1-8 showed that 1 and 7 exert potent inhibitory effects towards human enterovirus 71 (EV71).

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Identification of novel neutralizing determinants for protection against HCV

et al. 2023

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Background and Aims: HCV evasion of neutralizing antibodies (nAb) results in viral persistence and poses challenges to the development of an urgently needed vaccine. N-linked glycosylation of viral envelope proteins is a key mechanism for such evasion. To facilitate rational vaccine design, we aimed to identify determinants of protection of conserved neutralizing epitopes. Approach and Results: Using a reverse evolutionary approach, we passaged genotype 1a, 1b, 2a, 3a, and 4a HCV with envelope proteins (E1 and E2) derived from chronically infected patients without selective pressure by nAb in cell culture. Compared with the original viruses, HCV recombinants, engineered to harbor substitutions identified in polyclonal cell culturepassaged viruses, showed highly increased fitness and exposure of conserved neutralizing epitopes in antigenic regions 3 and 4, associated with protection from chronic infection. Further reverse genetic studies of acquired E1/E2 substitutions identified positions 418 and 532 in the N1 and N6 glycosylation motifs, localizing to adjacent E2 areas, as key regulators of changes of the E1/E2 conformational state, which governed viral sensitivity to nAb. These effects were independent of predicted glycan occupancy. Conclusions:We show how N-linked glycosylation motifs can trigger dramatic changes in HCV sensitivity to nAb, independent of glycan occupancy.

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HCV genotype 1-6 NS3 residue 80 substitutions impact protease inhibitor activity and promote viral escape

Cited by 37 publications

References 48 publications

Evolutionary Pathways to Persistence of Highly Fit and Resistant Hepatitis C Virus Protease Inhibitor Escape Variants

Evolutionary Pathways to Persistence of Highly Fit and Resistant Hepatitis C Virus Protease Inhibitor Escape Variants

Guignardones Y–Z, Antiviral Meroterpenes from Penicillium sp. NBUF154 Associated with a Crella Sponge from the Marine Mesophotic Zone

Identification of novel neutralizing determinants for protection against HCV

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