<i>In Vitro</i>
            Phenotypic Characterization of Hepatitis C Virus NS3 Protease Variants Observed in Clinical Studies of Telaprevir

Jiang, Min; Mani, Nagraj; Lin, Chao; Ardzinski, Andrzej; Nelson, Michelle; Reagan, Dugan; Bartels, Doug J.; Zhou, Yi; Nicolas, Olivier; Rao, B. Govinda; Müh, Ute; Hanzelka, Brian L.; Tigges, Ann M.; Rijnbrand, René; Kieffer, Tara L.

doi:10.1128/aac.01578-13

Cited by 26 publications

(26 citation statements)

References 50 publications

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“…Also, H77S.3 contains a reporter between p7 and NS2, both of which are important for viral assembly (12), and H77S.3 is not as well adapted to culture as the genotype 2a and 1a recombinants used in this study (20,23,71,72). Our study shows partial agreement with prior replicon studies, where A156T and A156V had a strong negative effect, while R155K, A156S, and T54A had either no effect or a moderate negative effect, on replication (34)(35)(36)(73)(74)(75)(76). Differences might be explained by the subgenomic nature of replicons and/or genotype/strain-specific differences.…”

Section: Discussionsupporting

confidence: 82%

Hepatitis C Virus Genotype 1 to 6 Protease Inhibitor Escape Variants: In Vitro Selection, Fitness, and Resistance Patterns in the Context of the Infectious Viral Life Cycle

Serre

Jensen

Ghanem

et al. 2016

Antimicrob Agents Chemother

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bHepatitis C virus (HCV) NS3 protease inhibitors (PIs) are important components of novel HCV therapy regimens. Studies of PI resistance initially focused on genotype 1. Therefore, knowledge about the determinants of PI resistance for the highly prevalent genotypes 2 to 6 remains limited. Using Huh7.5 cell culture-infectious HCV recombinants with genotype 1 to 6 NS3 protease, we identified protease positions 54, 155, and 156 as hot spots for the selection of resistance substitutions under treatment with the first licensed PIs, telaprevir and boceprevir. Treatment of a genotype 2 isolate with the newer PIs vaniprevir, faldaprevir, simeprevir, grazoprevir, paritaprevir, and deldeprevir identified positions 156 and 168 as hot spots for resistance; the Y56H substitution emerged for three newer PIs. Substitution selection also depended on the specific recombinant. The substitutions identified conferred cross-resistance to several PIs; however, most substitutions selected under telaprevir or boceprevir treatment conferred less resistance to certain newer PIs. In a single-cycle production assay, across genotypes, PI treatment primarily decreased viral replication, which was rescued by PI resistance substitutions. The substitutions identified resulted in differential effects on viral fitness, depending on the original recombinant and the substitution. Across genotypes, fitness impairment induced by resistance substitutions was due primarily to decreased replication. Most combinations of substitutions that were identified increased resistance or fitness. Combinations of resistance substitutions with fitness-compensating substitutions either rescued replication or compensated for decreased replication by increasing assembly. This comprehensive study provides insight into the selection patterns and effects of PI resistance substitutions for HCV genotypes 1 to 6 in the context of the infectious viral life cycle, which is of interest for clinical and virological HCV research. With more than 100 million chronic infections causing approximately 500,000 deaths annually, hepatitis C virus (HCV) is a major global health and economic burden (1, 2). The six epidemiologically important genotypes differ in ϳ30% of their sequence and in their sensitivity to antiviral regimens (3-6). In Europe, the Americas, Asia, and Australasia, genotypes 1, 2, and 3 are most prevalent. While genotypes 4, 5, and 6 are more restricted to specific geographical regions in Africa and Asia, they account for 20% of global HCV infections and have spread beyond these primary geographical locations (1, 2, 7).The development of directly acting antivirals (DAAs) has revolutionized HCV therapy. The main components of interferonfree regimens introduced in the clinic are inhibitors of the HCV nonstructural (NS) proteins NS3 protease (NS3P), NS5A,8,9). Even though DAA-based therapy regimens could cure most patients in clinical trials, failure rates of 5 to 10% are to be expected in real life, due primarily to the development of DAA resistance (4,8). Given the large ...

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Section: Discussionsupporting

confidence: 82%

Hepatitis C Virus Genotype 1 to 6 Protease Inhibitor Escape Variants: In Vitro Selection, Fitness, and Resistance Patterns in the Context of the Infectious Viral Life Cycle

Serre

Jensen

Ghanem

et al. 2016

Antimicrob Agents Chemother

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“…NS5B variant R422K had replication capacities of 1% and 47% in genotype 1a and genotype 1b replicons, respectively. Similarly, the NS3 variant V36MϩR155K had a lower replication capacity in the genotype 1a replicon (20%) than that previously obtained in the genotype 1b replicon (42%) (33). Furthermore, the replication capacity of the NS3 V36A, A156T, and V36AϩR155K variants obtained in genotype 1b (6% to 20%) was lower than that previously determined in a different genotype 1b replicon (16% to 104%) (33).…”

Section: Susceptibility Of Vx-222-resistant Variants To Filibuvir Andmentioning

confidence: 45%

“…The replication capacity of variant replicons was determined as previously described (33). Briefly, replicon RNA was in vitro transcribed and transfected into Huh-7-ETcured cells.…”

Section: Methodsmentioning

confidence: 99%

“…The EC 50 s of variant replicons were determined in Huh-7-ET-cured cells that were established by curing Huh-7-ET cells containing the subgenomic replicon pFK I 389 lucubi-neo/NS3-3=/5.1 (34) as described previously (33). Briefly, full-length HCV subgenomic replicon RNA was generated from linearized DNA templates using the Megascript T7 kit (Life Technologies, Grand Island, NY).…”

Section: Methodsmentioning

confidence: 99%

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Genotypic and Phenotypic Analyses of Hepatitis C Virus Variants Observed in Clinical Studies of VX-222, a Nonnucleoside NS5B Polymerase Inhibitor

Jiang

Zhang

Ardzinski

et al. 2014

Antimicrob Agents Chemother

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1 study. Variants with the substitutions L419C/I/M/P/S/V, R422K, M423I/T/V, I482L/N/T, A486S/T/V, and V494A were selected during VX-222 dosing, and their levels declined over time after the end of dosing. Phenotypic analysis of these variants was conducted using HCV replicons carrying site-directed mutations. Of the 17 variants, 14 showed reduced susceptibility to VX-222 compared with the wild type, with the L419C/S and R422K variants having higher levels of resistance (>200-fold) than the rest of the variants (6.8-to 76-fold). The M423I and A486S variants remained susceptible to VX-222. The 50% effective concentration (EC 50 ) for the L419P variant could not be obtained due to the poor replication of this replicon. The majority of the variants (15/17) were less fit than the wild type. A subset of the variants, predominately the L419S and R422K variants, were observed when the efficacy and safety of VX-222-and telaprevir-based regimens given for 12 weeks were investigated in genotype 1 HCV-infected patients in a phase 2 study. The NS3 and NS5B variants selected during the dual combination therapy showed reduced susceptibility to both telaprevir and VX-222 and had a lower replication capacity than the wild type. The phase 1b study has the ClinicalTrials.gov identifier NCT00911963, and the phase 2a study has ClinicalTrials.gov identifier NCT01080222.

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“…Second, in vitro measures of the telaprevir IC 50 and fitness for different variants observed by sequencing [18] suggested that there were five broad categories of resistance variants. These categories include: (I) low resistance, high fitness variants (e.g.…”

Section: Analysis Softwarementioning

confidence: 99%

Modeling population heterogeneity in viral dynamics for chronic hepatitis C infection: Insights from Phase 3 telaprevir clinical studies

Haseltine

Kimko

Luo

et al. 2015

J Pharmacokinet Pharmacodyn

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Viral dynamic modelling has proven useful for designing clinical studies and predicting treatment outcomes for patients infected with the hepatitis C virus. Generally these models aim to capture and predict the on-treatment viral load dynamics from a small study of individual patients. Here, we explored extending these models (1) to clinical studies with numerous patients and (2) by incorporating additional data types, including sequence data and prior response to interferon. Data from Phase 3 clinical studies of the direct-acting antiviral telaprevir (T; total daily dose of 2250 mg) combined with pegylated-interferon alfa and ribavirin (PR) were used for the analysis. The following data in the treatment-naïve population were reserved to verify the model: (1) a T/PR regimen where T was dosed every 8 h for 8 weeks (T8(q8h)/PR) and (2) a T/PR regimen where T was dosed twice daily for 12 weeks (T12(b.i.d.)/PR). The resulting model accurately predicted (1) sustained virologic response rates for both of these dosing regimens and (2) viral breakthrough characteristics of the T8(q8h)/PR regimen. Since the observed viral variants depend on the T exposure, the second verification suggested that the model was correctly sensitive to the different T regimen even though the model was developed using data from another T regimen. Furthermore, the model predicted that b.i.d. T dosing was comparable to q8h T dosing in the PR-experienced population, a comparison that has not been made in a controlled clinical study. The methods developed in this work to estimate the variability occurring below the limit of detection for the viral load were critical for making accurate predictions.

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In Vitro Phenotypic Characterization of Hepatitis C Virus NS3 Protease Variants Observed in Clinical Studies of Telaprevir

Cited by 26 publications

References 50 publications

Hepatitis C Virus Genotype 1 to 6 Protease Inhibitor Escape Variants: In Vitro Selection, Fitness, and Resistance Patterns in the Context of the Infectious Viral Life Cycle

Hepatitis C Virus Genotype 1 to 6 Protease Inhibitor Escape Variants: In Vitro Selection, Fitness, and Resistance Patterns in the Context of the Infectious Viral Life Cycle

Genotypic and Phenotypic Analyses of Hepatitis C Virus Variants Observed in Clinical Studies of VX-222, a Nonnucleoside NS5B Polymerase Inhibitor

Modeling population heterogeneity in viral dynamics for chronic hepatitis C infection: Insights from Phase 3 telaprevir clinical studies

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