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

Sanne Brun Jensen; Ulrik Fahnøe; Long V. Pham; Stéphanie Brigitte Nelly Serre; Qi Tang; Lubna Ghanem; Martin Schou Pedersen; Santseharay Ramirez; Daryl Humes; Anne Finne Pihl; Jonathan Filskov; Christina Søhoel Sølund; Julia Dietz; Slim Fourati; Jean Michel Pawlotsky; Christoph Sarrazin; Nina Weis; Kristian Schønning; Henrik Krarup; Jens Bukh; Judith Margarete Gottwein

doi:10.1002/hep.30647

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

Sanne Brun Jensen, Ulrik Fahnøe, Long V. Pham, Stéphanie Brigitte Nelly Serre, Qi Tang, Lubna Ghanem, Martin Schou Pedersen, Santseharay Ramirez, Daryl Humes, Anne Finne Pihl, Jonathan Filskov, Christina Søhoel Sølund, Julia Dietz, Slim Fourati, Jean Michel Pawlotsky, Christoph Sarrazin, Nina Weis, Kristian Schønning, Henrik Krarup, Jens BukhJudith Margarete Gottwein^*

^*Corresponding author for this work

Department of Clinical Medicine

12 Citations (Scopus)

19 Downloads (Pure)

Abstract

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.

Original language	English
Journal	Hepatology
Volume	70
Issue number	3
Pages (from-to)	771-787
Number of pages	17
ISSN	0270-9139
DOIs	https://doi.org/10.1002/hep.30647
Publication status	Published - Sept 2019

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Evolutionary Pathways to Persistence of Highly Fit and Resistant Hepatitis C Virus Protease Inhibitor Escape VariantsFinal published version, 2.04 MBLicence: CC BY

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Jensen, S. B., Fahnøe, U., Pham, L. V., Serre, S. B. N., Tang, Q., Ghanem, L., Pedersen, M. S., Ramirez, S., Humes, D., Pihl, A. F., Filskov, J., Sølund, C. S., Dietz, J., Fourati, S., Pawlotsky, J. M., Sarrazin, C., Weis, N., Schønning, K., Krarup, H., ... Gottwein, J. M. (2019). Evolutionary Pathways to Persistence of Highly Fit and Resistant Hepatitis C Virus Protease Inhibitor Escape Variants. Hepatology, 70(3), 771-787. https://doi.org/10.1002/hep.30647

Jensen, SB, Fahnøe, U , Pham, LV, Serre, SBN, Tang, Q, Ghanem, L, Pedersen, MS, Ramirez, S, Humes, D, Pihl, AF, Filskov, J, Sølund, CS, Dietz, J, Fourati, S, Pawlotsky, JM, Sarrazin, C, Weis, N , Schønning, K, Krarup, H, Bukh, J & Gottwein, JM 2019, 'Evolutionary Pathways to Persistence of Highly Fit and Resistant Hepatitis C Virus Protease Inhibitor Escape Variants', Hepatology, vol. 70, no. 3, pp. 771-787. https://doi.org/10.1002/hep.30647

@article{e77af09cf44f4876943b5230f5414c3c,

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

abstract = "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.",

author = "Jensen, {Sanne Brun} and Ulrik Fahn{\o}e and Pham, {Long V.} and Serre, {St{\'e}phanie Brigitte Nelly} and Qi Tang and Lubna Ghanem and Pedersen, {Martin Schou} and Santseharay Ramirez and Daryl Humes and Pihl, {Anne Finne} and Jonathan Filskov and S{\o}lund, {Christina S{\o}hoel} and Julia Dietz and Slim Fourati and Pawlotsky, {Jean Michel} and Christoph Sarrazin and Nina Weis and Kristian Sch{\o}nning and Henrik Krarup and Jens Bukh and Gottwein, {Judith Margarete}",

year = "2019",

month = sep,

doi = "10.1002/hep.30647",

language = "English",

volume = "70",

pages = "771--787",

journal = "Hepatology",

issn = "0270-9139",

publisher = "JohnWiley & Sons, Inc.",

number = "3",

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TY - JOUR

T1 - Evolutionary Pathways to Persistence of Highly Fit and Resistant Hepatitis C Virus Protease Inhibitor Escape Variants

AU - Jensen, Sanne Brun

AU - Fahnøe, Ulrik

AU - Pham, Long V.

AU - Serre, Stéphanie Brigitte Nelly

AU - Tang, Qi

AU - Ghanem, Lubna

AU - Pedersen, Martin Schou

AU - Ramirez, Santseharay

AU - Humes, Daryl

AU - Pihl, Anne Finne

AU - Filskov, Jonathan

AU - Sølund, Christina Søhoel

AU - Dietz, Julia

AU - Fourati, Slim

AU - Pawlotsky, Jean Michel

AU - Sarrazin, Christoph

AU - Weis, Nina

AU - Schønning, Kristian

AU - Krarup, Henrik

AU - Bukh, Jens

AU - Gottwein, Judith Margarete

PY - 2019/9

Y1 - 2019/9

N2 - 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.

AB - 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.

U2 - 10.1002/hep.30647

DO - 10.1002/hep.30647

M3 - Journal article

C2 - 30964552

AN - SCOPUS:85071462326

SN - 0270-9139

VL - 70

SP - 771

EP - 787

JO - Hepatology

JF - Hepatology

IS - 3

ER -

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

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