Regulatory Analysis of Effects of Hepatitis C Virus NS5A Polymorphisms on Efficacy of Elbasvir and Grazoprevir

Komatsu, Takashi; Boyd, Sarita D.; Sherwat, Adam; Tracy, LaRee; Naeger, Lisa K.; O’Rear, Julian J.; Harrington, Patrick R.

doi:10.1053/j.gastro.2016.10.017

Cited by 51 publications

(61 citation statements)

References 21 publications

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“…Fourteen amino acid positions in NS3 were evaluated: 36, 54, 55, 56, 80, 107, 122, 132, 155, 156, 158, 168, 170, and 175. For NS5A, the four amino acid positions (28,30,31, and 93) most commonly seen in elbasvir resistance studies (18,20) were evaluated. As reported in Table 7, there was a high global conservation among Ն187 NS3 sequences obtained from the public databases.…”

Section: Resultsmentioning

confidence: 99%

Antiviral Activity and Resistance Analysis of NS3/4A Protease Inhibitor Grazoprevir and NS5A Inhibitor Elbasvir in Hepatitis C Virus GT4 Replicons

Asante‐Appiah

Curry

McMonagle

et al. 2017

Antimicrob Agents Chemother

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Although genotype 4 (GT4)-infected patients represent a minor overall percentage of the global hepatitis C virus (HCV)-infected population, the high prevalence of the genotype in specific geographic regions coupled with substantial sequence diversity makes it an important genotype to study for antiviral drug discovery and development. We evaluated two direct-acting antiviral agents-grazoprevir, an HCV NS3/4A protease inhibitor, and elbasvir, an HCV NS5A inhibitor-in GT4 replicons prior to clinical studies in this genotype. Following a bioinformatics analysis of available GT4 sequences, a set of replicons bearing representative GT4 clinical isolates was generated. For grazoprevir, the 50% effective concentration (EC 50 ) against the replicon bearing the reference GT4a (ED43) NS3 protease and NS4A was 0.7 nM. The median EC 50 for grazoprevir against chimeric replicons encoding NS3/4A sequences from GT4 clinical isolates was 0.2 nM (range, 0.11 to 0.33 nM; n ϭ 5). The difficulty in establishing replicons bearing NS3/4A resistance-associated substitutions was substantially overcome with the identification of a G162R adaptive substitution in NS3. Single NS3 substitutions D168A/V identified from de novo resistance selection studies reduced grazoprevir antiviral activity by 137-and 47-fold, respectively, in the background of the G162R replicon. For elbasvir, the EC 50 against the replicon bearing the reference full-length GT4a (ED43) NS5A gene was 0.0002 nM. The median EC 50 for elbasvir against chimeric replicons bearing clinical isolates from GT4 was 0.0007 nM (range, 0.0002 to 34 nM; n ϭ 14). De novo resistance selection studies in GT4 demonstrated a high propensity to suppress the emergence of amino acid substitutions that confer high-potency reductions to elbasvir. Phenotypic characterization of the NS5A amino acid substitutions identified (L30F, L30S, M31V, and Y93H) indicated that they conferred 15-, 4-, 2.5-, and 7.5-fold potency losses, respectively, to elbasvir. The activity profiles of grazoprevir and elbasvir supported the testing of the direct-acting antivirals in clinical studies.KEYWORDS HCV, genotype 4, resistance, antiviral, elbasvir, grazoprevir, NS5A, NS3/4A, antiviral agents, drug resistance mechanisms, hepatitis C virus H epatitis C virus (HCV) is a leading cause of chronic liver disease, with an estimated 170 million people infected globally (1, 2). The World Health Organization estimates that more than 350,000 people die every year from hepatitis C-related liver diseases (3). Approximately 20% of individuals chronically infected with HCV can be expected to develop liver cirrhosis and, of these, 6% will decompensate to end-stage liver disease, with an additional 4% developing hepatocellular carcinoma. A number of treatment options are now available with combinations of interferon-free direct-acting

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Section: Resultsmentioning

confidence: 99%

Antiviral Activity and Resistance Analysis of NS3/4A Protease Inhibitor Grazoprevir and NS5A Inhibitor Elbasvir in Hepatitis C Virus GT4 Replicons

Asante‐Appiah

Curry

McMonagle

et al. 2017

Antimicrob Agents Chemother

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“…Our data of prevalence of NS5A RASs to elbasvir (6.2%) contrasts with the prevalence of 12% (19/154) recently reported by Zeuzem et al . (2015) in treatment-naïve HCV-GT1a-infected patients enrolled in the phase 3 C-EDGE TN trial 3, 4 . Interestingly, when the same polymorphisms were compared between the C-EDGE TN trial and our study (with the M28V polymorphism included) a lower prevalence in the RAS analyzed in our study population was still present (8,8% vs 12%).…”

Section: Discussionmentioning

confidence: 99%

“…Elbasvir/grazoprevir combination therapy showed a high efficacy in treatment-naïve patients with chronic HCV enrolled in the phase 3 C-EDGE randomized, placebo-controlled trial 3, 4 . 95% of subjects achieved a sustained virological response at 12 weeks (SVR12), with an efficacy of 92% for genotype 1a, 99% for genotype 1b, 100% for genotype 4 and 80% for genotype 6.…”

Section: Introductionmentioning

confidence: 99%

Low frequency of NS5A relevant resistance-associated substitutions to Elbasvir among hepatitis C virus genotype 1a in Spain: a cross-sectional study

Palladino

Sánchez-Carrillo

Maté-Cano

et al. 2017

Sci Rep

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Relevant resistance-associated substitutions (RASs) to elbasvir, the new HCV NS5A inhibitor, may limit its efficacy and lead to virological failure in HCV-GT1a-infected patients. There are few data outside clinical trials evaluating their prevalence and impact of elbasvir/grazoprevir. A multicenter cross-sectional study of 617 HCV-GT1a-infected individuals attended in 84 Spanish hospitals from the 17 Autonomous Communities and two Autonomous cities was performed. HCV population sequencing was used to identify RASs to elbasvir and the mutational pattern and drug sensitivity were confirmed by geno2pheno[HCV]. Viruses bearing RASs to elbasvir were present in 6.2% of HCV-GT1a infected patients. The most common RASs were the Y93C/H/N and Q30E/H/R (2.4% and 2.3%; respectively). Only 3.4% of patients had viruses with RASs that confer reduced susceptibility to elbasvir by geno2pheno[HCV] that identified exclusively the positions Q30H/R (n = 7) and Y93C/H/N (n = 8) as single mutations and Q30H + Y93H (n = 4) and Q30R + Y93H (n = 2) as double mutations considered as RASs to elbasvir. Lower prevalence of RASs to elbasvir in our HCV-GT1a-Spanish cohort was observed than reported previously in clinical trials. This information may be essential to guiding the implementation of elbasvir/grazoprevir in Spain, expected at the beginning of 2017 and the management of GT1a-infected patients.

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“…Current recommendations of baseline HCV resistance testing, according to AASLD/IDSA and EASL guidelines 2016, are mainly aimed at treatment optimization to determine dosage regimen, treatment duration and the need to include ribavirin. NS5A-resistance analyses are recommended prior to the initial treatment with elbasvir/grazoprevir in G1a HCV-infected patients [25], and detection of Q80K polymorphism is advised before sofosbuvir/simeprevir therapy in infections with G1a HCV. In the re-treatment of patients who failed previous anti-HCV therapies, baseline resistance is recommended prior to combinations that include sofosbuvir/velpatasvir for G3, sofosbuvir/daclatasvir for Gs 1a and 3, sofosbuvir/ledipasvir for G1a, and elbasvir/grazoprevir and sofosbuvir/simeprevir for G1a and G1b [6].…”

Section: Introductionmentioning

confidence: 99%

Pipeline for specific subtype amplification and drug resistance detection in hepatitis C virus

et al. 2018

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BackgroundDespite the high sustained virological response rates achieved with current directly-acting antiviral agents (DAAs) against hepatitis C virus (HCV), around 5–10% of treated patients do not respond to current antiviral therapies, and basal resistance to DAAs is increasingly detected among treatment-naïve infected individuals. Identification of amino acid substitutions (including those in minority variants) associated with treatment failure requires analytical designs that take into account the high diversification of HCV in more than 86 subtypes according to the ICTV website (June 2017).MethodsThe methodology has involved five sequential steps: (i) to design 280 oligonucleotide primers (some including a maximum of three degenerate positions), and of which 120 were tested to amplify NS3, NS5A-, and NS5B-coding regions in a subtype-specific manner, (ii) to define a reference sequence for each subtype, (iii) to perform experimental controls to define a cut-off value for detection of minority amino acids, (iv) to establish bioinformatics’ tools to quantify amino acid replacements, and (v) to validate the procedure with patient samples.ResultsA robust ultra-deep sequencing procedure to analyze HCV circulating in serum samples from patients infected with virus that belongs to the ten most prevalent subtypes worldwide: 1a, 1b, 2a, 2b, 2c, 2j, 3a, 4d, 4e, 4f has been developed. Oligonucleotide primers are subtype-specific. A cut-off value of 1% mutant frequency has been established for individual mutations and haplotypes.ConclusionThe methodological pipeline described here is adequate to characterize in-depth mutant spectra of HCV populations, and it provides a tool to understand HCV diversification and treatment failures. The pipeline can be periodically extended in the event of HCV diversification into new genotypes or subtypes, and provides a framework applicable to other RNA viral pathogens, with potential to couple detection of drug-resistant mutations with treatment planning.Electronic supplementary materialThe online version of this article (10.1186/s12879-018-3356-6) contains supplementary material, which is available to authorized users.

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Regulatory Analysis of Effects of Hepatitis C Virus NS5A Polymorphisms on Efficacy of Elbasvir and Grazoprevir

Cited by 51 publications

References 21 publications

Antiviral Activity and Resistance Analysis of NS3/4A Protease Inhibitor Grazoprevir and NS5A Inhibitor Elbasvir in Hepatitis C Virus GT4 Replicons

Antiviral Activity and Resistance Analysis of NS3/4A Protease Inhibitor Grazoprevir and NS5A Inhibitor Elbasvir in Hepatitis C Virus GT4 Replicons

Low frequency of NS5A relevant resistance-associated substitutions to Elbasvir among hepatitis C virus genotype 1a in Spain: a cross-sectional study

Pipeline for specific subtype amplification and drug resistance detection in hepatitis C virus

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