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1
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Soni S, Singh D, Aggarwal R, Veerapu NS. Enhanced fitness of hepatitis C virus increases resistance to direct-acting antivirals. J Gen Virol 2022; 103. [PMID: 35133954 DOI: 10.1099/jgv.0.001699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Drug resistance mutations of hepatitis C virus (HCV) negatively impact viral replicative fitness. RNA viruses are known to change their replication behaviour when subjected to suboptimal selection pressure. Here, we assess whether mutation supply in HCV is sufficiently large to allow the selection of its variants during dual or triple direct-acting antiviral (DAA) treatment associated with augmented virus fitness or impairment. We engineered randomly mutagenized full-genome libraries to create a highly diverse population of replication-competent HCV variants in cell culture. These variants exhibited escape when treated with NS5A/NS5B inhibitors (daclatasvir/sofosbuvir), and relapse on treatment with a combination of NS3/NS5A/NS5B inhibitors (simeprevir or paritaprevir/daclatasvir/sofosbuvir). Analysis of the relationship between virus fitness and drug resistance of JFH1-derived NS5A-5B variants showed a significant positive correlation (P=0.003). At the earliest time points, intracellular RNA levels remain unchanged in both the subgenomic replicon and infection assays, whereas extracellular RNA levels increased upto ten-fold compared to wild-type JFH1. Beneficial substitutions hyperstimulated phosphatidylinositol 4-phosphate during DAA treatment, and showed decreased dependence on cyclophilins during cyclosporine A treatment, indicating an interplay of virus-host molecular mechanisms in beneficial substitution selection that may necessitate infectious virus production. This comprehensive study demonstrates a possible role for HCV fitness of overcoming drug-mediated selection pressure.
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Affiliation(s)
- Shalini Soni
- Virology Section, Department of Life Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh 201314, India
| | - Deepak Singh
- Virology Section, Department of Life Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh 201314, India
| | - Rakesh Aggarwal
- Gastroenterology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh 226014, India
| | - Naga Suresh Veerapu
- Virology Section, Department of Life Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh 201314, India
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2
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Pisaturo M, Starace M, Minichini C, De Pascalis S, Occhiello L, Fraia AD, Messina V, Sangiovanni V, Claar E, Coppola N. Virological patterns of hepatitis C virus patients with failure to the current-generation direct-acting antivirals. Int J Antimicrob Agents 2020; 56:106067. [PMID: 32599227 DOI: 10.1016/j.ijantimicag.2020.106067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 06/15/2020] [Accepted: 06/21/2020] [Indexed: 12/14/2022]
Abstract
There are few data on the virological characterisation of patients with failure to current-generation direct-acting antivirals (DAAs), namely elbasvir/grazoprevir, sofosbuvir/velpatasvir and glecaprevir/pibrentasvir. This study aimed to characterise virological patterns in patients with failure to current DAA regimens as well as the efficacy of re-treatment. All 61 consecutive hepatitis C virus (HCV) treatment-naïve patients with failure to current DAAs from January 2018 to February 2019 were enrolled. Sanger sequencing of NS3, NS5A and NS5B proteins was performed using homemade protocols. NS5A resistance-associated substitutions (RASs) were more frequent in the 17 patients treated with sofosbuvir/velpatasvir (89.5%) and 33 patients treated with elbasvir/grazoprevir (97%) compared with the 11 patients treated with glecaprevir/pibrentasvir (18.2%) (P = 0.002 and 0.000, respectively). NS3 RASs were more often detected in the 33 patients with failure to elbasvir/grazoprevir (30.3%) than in the 11 patients treated with glecaprevir/pibrentasvir (9.1%). NS3 RASs were also detected in 12% of sofosbuvir/velpatasvir-treated patients. NS5B RASs were infrequently identified. Of the glecaprevir/pibrentasvir-treated patients, 73% did not show RASs in any HCV regions, a prevalence higher than that observed in those treated with elbasvir/grazoprevir (0%; P < 0.05) or sofosbuvir/velpatasvir (12%; P < 0.05). Of the 61 patients, 21 (34.4%) were re-treated with sofosbuvir/velpatasvir and voxilaprevir. All patients achieved sustained virological response at 12 weeks (SVR12). To our knowledge, this is one of the first real-life studies describing patients who failed current-generation DAAs; the prevalence of RASs differed according to the DAA regimen used, and the efficacy of re-treatment was high.
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Affiliation(s)
- M Pisaturo
- Laboratory for the Identification of Prognostic Factors of Response to the Treatment Against Infectious Diseases, University of Campania 'L. Vanvitelli', Napoli, Italy
| | - M Starace
- Laboratory for the Identification of Prognostic Factors of Response to the Treatment Against Infectious Diseases, University of Campania 'L. Vanvitelli', Napoli, Italy
| | - C Minichini
- Laboratory for the Identification of Prognostic Factors of Response to the Treatment Against Infectious Diseases, University of Campania 'L. Vanvitelli', Napoli, Italy
| | - S De Pascalis
- Infectious Diseases and Viral Hepatitis, Department of Mental and Physical Health and Preventive Medicine, University of Campania 'L. Vanvitelli', Napoli, Italy
| | - L Occhiello
- Laboratory for the Identification of Prognostic Factors of Response to the Treatment Against Infectious Diseases, University of Campania 'L. Vanvitelli', Napoli, Italy
| | - A Di Fraia
- Laboratory for the Identification of Prognostic Factors of Response to the Treatment Against Infectious Diseases, University of Campania 'L. Vanvitelli', Napoli, Italy
| | - V Messina
- Infectious Diseases Unit, A.O. S Anna e S Sebastiano, Caserta, Italy
| | - V Sangiovanni
- Third Infectious Diseases Unit, AORN dei Colli, P.O. Cotugno, Naples, Italy
| | - E Claar
- Internal Medicine Unit, Evangelical Hospital Villa Betania, Naples, Italy
| | - N Coppola
- Laboratory for the Identification of Prognostic Factors of Response to the Treatment Against Infectious Diseases, University of Campania 'L. Vanvitelli', Napoli, Italy; Infectious Diseases and Viral Hepatitis, Department of Mental and Physical Health and Preventive Medicine, University of Campania 'L. Vanvitelli', Napoli, Italy.
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3
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The Evaluation of Medication Adherence in Patients Infected With HCV Receiving Protease Inhibitors: A Pilot Study. Gastroenterol Nurs 2019; 42:259-268. [PMID: 31145250 DOI: 10.1097/sga.0000000000000386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Adherence to treatment is essential for hepatitis C cure. Studies show the complexity of the treatment due to side effects, many pills, and rigor in the schedules. The aim of this study was to evaluate the adherence to treatment with protease inhibitor in patients with hepatitis C. It is a longitudinal, observational, prospective pilot study with patients with hepatitis C genotype 1. Bimonthly consultations and biweekly calls for 20 weeks were performed. Evaluation methods for adherence were Measure of Adherence to Treatment score, patient report, count pills, and sustained virological response. Twenty-two patients were enrolled. Mean age was 54.0 ± 8.72 years; 50% were men, educational level was 7.9 ± 3.89 years for the study, and intake of pills was 2.2 ± 1.60 per day. Adverse events reported were fatigue (90.9%), muscular pain (72.7%), and nausea (68.2%). In total, 71.4% of patients took 100% of medications and were classified as having a high degree of adherence to treatment. The sustained virological response was not significant in relation to the high or low adherence degree. Measure of Adherence to Treatment score is a good instrument to measure adherence to protease inhibitor treatment. The adherence of patients undergoing long-term and complex treatments improves when the multidisciplinary team follows up every 7-15 days. The patient's access to the team through additional phone calls or medical/nursing appointment is essential to improve adherence.
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4
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Costa VD, Delvaux N, Brandão-Mello CE, Nunes EP, de Sousa PSF, de Souza Rodrigues LLLX, Lampe E, do Amaral Mello FC. Prevalence of baseline NS3 resistance-associated substitutions (RASs) on treatment with protease inhibitors in patients infected with HCV genotype 1. Clin Res Hepatol Gastroenterol 2019; 43:700-706. [PMID: 30880098 DOI: 10.1016/j.clinre.2019.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 02/01/2019] [Accepted: 02/11/2019] [Indexed: 02/04/2023]
Abstract
BACKGROUND AND AIMS Treatment for hepatitis C has evolved significantly with the licensing of direct-acting antiviral drugs (DAAs). However, one of the limiting factors of the effectiveness of antiviral therapy with protease inhibitors (PIs) is the emergence of resistance caused by point mutations. The aim of this study was to determine the prevalence of resistance-associated substitutions (RASs) in HCV NS3 gene in patients infected with genotype 1 before therapy with simeprevir. METHODS A total of 73 serum samples from 15 treatment-experienced patients with boceprevir/telaprevir and 58 DAA-naïve patients were collected before therapy with DAAs simeprevir, daclatasvir and/or sofosbuvir. Presence of baseline resistance-associated substitutions (RAS) in the serine protease domain of HCV NS3 was analyzed by nucleotide sequencing followed by amino acid deduction. RESULTS Overall RAS prevalence in this study was 13.7% (10/73). RAS prevalence for HCV subtype 1b was 17.4% (4/23) while for HCV subtype 1a was 12% (6/50). Primary mutations V36M/L and R155K were observed only in HCV subtype 1a, whereas T54S and Q80K were identified only in HCV subtype 1b. RAS V36M, which is related to reduction of susceptibility to second-generation PIs, was the most frequent in the study (6.9%; 5/73). CONCLUSIONS Our results indicated that Brazilian isolates of HCV present a distinct pattern of RAS depending on the infecting viral subtype. In contrast to data from other countries, RAS Q80K prevalence in Brazil is low in HCV subtype 1a. This study improves the knowledge of genetic barrier for resistance to PIs involving RASs in chronically infected patients and its possible impact on an unsuccessful treatment outcome, information that might be crucial to upcoming decisions of incorporation of new DAAs in Brazilian guidelines of antiviral therapy against HCV infection.
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Affiliation(s)
- Vanessa Duarte Costa
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, FIOCRUZ, avenida Brasil, 4365 - Manguinhos, 21040-900, Rio de Janeiro, RJ, Brazil.
| | - Nathália Delvaux
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, FIOCRUZ, avenida Brasil, 4365 - Manguinhos, 21040-900, Rio de Janeiro, RJ, Brazil
| | - Carlos Eduardo Brandão-Mello
- Hospital Universitário Gaffrée & Guinle, UNIRIO, R. Mariz e Barros, 775 - Maracanã, 20270-001, Rio de Janeiro, RJ, Brazil
| | - Estevão Portela Nunes
- Instituto Nacional de Infectologia Evandro Chagas, INI/FIOCRUZ, avenida Brasil, 4365 - Manguinhos, 21040-360, Rio de Janeiro, RJ, Brazil
| | - Paulo Sérgio Fonseca de Sousa
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, FIOCRUZ, avenida Brasil, 4365 - Manguinhos, 21040-900, Rio de Janeiro, RJ, Brazil
| | | | - Elisabeth Lampe
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, FIOCRUZ, avenida Brasil, 4365 - Manguinhos, 21040-900, Rio de Janeiro, RJ, Brazil
| | - Francisco Campello do Amaral Mello
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz, FIOCRUZ, avenida Brasil, 4365 - Manguinhos, 21040-900, Rio de Janeiro, RJ, Brazil
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5
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Nejabat N, Hosseini SY, Sarvari J, Gorzin AA, Fattahi MR, Rasoolian M. The Investigation of Drug Resistance Substitutions in NS3 Protease Sequence of Hepatitis C Virus from Non-Responder Patients. Asian Pac J Cancer Prev 2019; 20:2311-2317. [PMID: 31450900 PMCID: PMC6852801 DOI: 10.31557/apjcp.2019.20.8.2311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Indexed: 12/25/2022] Open
Abstract
Background: Even with the fantastic successes of direct-acting antivirals (DAA) in the treatment of Hepatitis C Virus (HCV) infection, natural drug resistance remains a challenging obstacle for their impacts. The data regarding protease inhibitors (PIs) resistance in Iran population are limited. The aim of this study was to investigate the variations in NS3 protease of HCV from non-responder patients. Methods: In this cross-sectional study, 14 HCV infected patients with genotype 1(N=5) and 3(N=9) who have not responded to Interferon-related regime were enrolled from Liver Clinic, Shiraz. The NS3 protease region was amplified by Nested-PCR followed by product gel extraction. Besides, some amplified protease regions were cloned into a cloning vector to improve the sensitivity of mutation detection. Both crude and cloned sequences were then introduced into sequencing. The obtained sequences were compared with the NS3 reference sequences and analyzed by Geno2pheno available software to find possible substitutions. In the end, the phylogenetic tree was constructed. Results: Among variations responsible for PIs resistance, only one out of 14 (7%) sample who was infected with genotype 1a, harbored R117C+N174S double mutation, which causes reduced susceptibility to Telaprevir. Any another resistance mutation was not found among the studied population. The most frequent substitutions were determined as I52M(N=9), S102A(N=9), S166A(8) and V170I(8) for genotype 3a, and F147S/A(4) for genotype 1. However, some uncharacterized substitutions on scored position, including I132L(N=1), I170V(N=3) and N174S(N=2) were also determined among sequences. Phylogenetic analysis demonstrated that the protease region has enough power to correctly classify enrolled samples into relevant clusters on the tree. There were 2, 3 and 9 cases of sub-genotypes 1a, 1b, and 3a, respectively. Conclusion: A low frequency of PIs resistance mutations in our HCV infected population is a hopeful point of starting these drugs in HCV infected patients.
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Affiliation(s)
- Nargess Nejabat
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Seyed Younes Hosseini
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Jamal Sarvari
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Ali Akbar Gorzin
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Mohamad Reza Fattahi
- Gastroenterohepatology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Rasoolian
- Department of Genetics and Molcular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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6
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de Wispelaere M, Du G, Donovan KA, Zhang T, Eleuteri NA, Yuan JC, Kalabathula J, Nowak RP, Fischer ES, Gray NS, Yang PL. Small molecule degraders of the hepatitis C virus protease reduce susceptibility to resistance mutations. Nat Commun 2019; 10:3468. [PMID: 31371704 PMCID: PMC6672008 DOI: 10.1038/s41467-019-11429-w] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 07/12/2019] [Indexed: 12/15/2022] Open
Abstract
Targeted protein degradation is a promising drug development paradigm. Here we leverage this strategy to develop a new class of small molecule antivirals that induce proteasomal degradation of viral proteins. Telaprevir, a reversible-covalent inhibitor that binds to the hepatitis C virus (HCV) protease active site is conjugated to ligands that recruit the CRL4CRBN ligase complex, yielding compounds that can both inhibit and induce the degradation of the HCV NS3/4A protease. An optimized degrader, DGY-08-097, potently inhibits HCV in a cellular infection model, and we demonstrate that protein degradation contributes to its antiviral activity. Finally, we show that this new class of antiviral agents can overcome viral variants that confer resistance to traditional enzymatic inhibitors such as telaprevir. Overall, our work provides proof-of-concept that targeted protein degradation may provide a new paradigm for the development of antivirals with superior resistance profiles. Targeted protein degradation (TPD) is a promising strategy for drug development. In this proof-of-concept study, the authors use telaprevir, which binds hepatitis C virus (HCV) NS3/4A protease, to target the protease for protein degradation, and show inhibition of wildtype as well as drug resistant HCV.
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Affiliation(s)
- Mélissanne de Wispelaere
- Department of Microbiology and Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Guangyan Du
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Katherine A Donovan
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Tinghu Zhang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Nicholas A Eleuteri
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Jingting C Yuan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Joann Kalabathula
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Radosław P Nowak
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Eric S Fischer
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Nathanael S Gray
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Priscilla L Yang
- Department of Microbiology and Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA.
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7
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Raja R, Pareek A, Newar K, Dixit NM. Mutational pathway maps and founder effects define the within-host spectrum of hepatitis C virus mutants resistant to drugs. PLoS Pathog 2019; 15:e1007701. [PMID: 30934020 PMCID: PMC6459561 DOI: 10.1371/journal.ppat.1007701] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 04/11/2019] [Accepted: 03/13/2019] [Indexed: 12/11/2022] Open
Abstract
Knowledge of the within-host frequencies of resistance-associated amino acid variants (RAVs) is important to the identification of optimal drug combinations for the treatment of hepatitis C virus (HCV) infection. Multiple RAVs may exist in infected individuals, often below detection limits, at any resistance locus, defining the diversity of accessible resistance pathways. We developed a multiscale mathematical model to estimate the pre-treatment frequencies of the entire spectrum of mutants at chosen loci. Using a codon-level description of amino acids, we performed stochastic simulations of intracellular dynamics with every possible nucleotide variant as the infecting strain and estimated the relative infectivity of each variant and the resulting distribution of variants produced. We employed these quantities in a deterministic multi-strain model of extracellular dynamics and estimated mutant frequencies. Our predictions captured database frequencies of the RAV R155K, resistant to NS3/4A protease inhibitors, presenting a successful test of our formalism. We found that mutational pathway maps, interconnecting all viable mutants, and strong founder effects determined the mutant spectrum. The spectra were vastly different for HCV genotypes 1a and 1b, underlying their differential responses to drugs. Using a fitness landscape determined recently, we estimated that 13 amino acid variants, encoded by 44 codons, exist at the residue 93 of the NS5A protein, illustrating the massive diversity of accessible resistance pathways at specific loci. Accounting for this diversity, which our model enables, would help optimize drug combinations. Our model may be applied to describe the within-host evolution of other flaviviruses and inform vaccine design strategies.
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Affiliation(s)
- Rubesh Raja
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India
| | - Aditya Pareek
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India
| | - Kapil Newar
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India
| | - Narendra M. Dixit
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, India
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, India
- * E-mail:
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8
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Perpiñán E, Caro-Pérez N, García-González N, Gregori J, González P, Bartres C, Soria ME, Perales C, Lens S, Mariño Z, Londoño MC, Ariza X, Koutsoudakis G, Quer J, González-Candelas F, Forns X, Pérez-Del-Pulgar S. Hepatitis C virus early kinetics and resistance-associated substitution dynamics during antiviral therapy with direct-acting antivirals. J Viral Hepat 2018; 25:1515-1525. [PMID: 30141252 DOI: 10.1111/jvh.12986] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 06/15/2018] [Accepted: 07/31/2018] [Indexed: 12/14/2022]
Abstract
The emergence of resistance-associated substitutions (RASs) can compromise the high efficacy of direct-acting antivirals (DAAs). Little is known about RASs selection at very early time points during DAA treatment. Therefore, we analyzed the potential emergence of RASs immediately after therapy initiation. Samples of 71 patients treated with different DAAs were collected at baseline, during therapy (hours 4 and 8; days 1-7; weeks 2-4) or until target not detected. HCV-RNA levels were determined by qPCR, and RASs were detected by deep sequencing. Sixty-three (89%) patients achieved a sustained virological response (SVR), 7 (10%) relapsed, and 1 (1%) experienced a breakthrough. Almost all non-SVR (7/8, 88%) showed RASs either at baseline or relapse. High-frequency RASs detected at baseline (Y93H and L159F+C316N) remained detectable at early time points during therapy and reappeared as most prevalent substitutions at relapse. Conversely, emergent RASs at relapse (Q80R, D168E/V, R155K and L31V) were not observed during the first hours-days, before HCV-RNA became undetectable. HCV-RNA decay and genetic evolution of the quasispecies followed a similar pattern during the first hours of therapy in SVR and non-SVR patients. In conclusion, the absence of early RASs selection and the similar dynamics of HCV kinetics and quasispecies in SVR and non-SVR patients after therapy initiation suggest that RASs selection may occur at later stages in the remaining reservoir, where viral populations persist hidden at very low replication levels. Nevertheless, we cannot completely exclude very early selection, when RASs are present below the sensitivity limit of deep sequencing.
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Affiliation(s)
- Elena Perpiñán
- Liver Unit, Hospital Clínic, IDIBAPS, CIBEREHD, Universitat de Barcelona, Barcelona, Spain
| | - Noelia Caro-Pérez
- Liver Unit, Hospital Clínic, IDIBAPS, CIBEREHD, Universitat de Barcelona, Barcelona, Spain
| | - Neris García-González
- Joint Research Unit Infección y Salud Pública, FISABIO-Universitat de València, I2SysBio, CIBERESP, Valencia, Spain
| | - Josep Gregori
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d'Hebron (HUVH), CIBEREHD, Barcelona, Spain.,Roche Diagnostics SL, Sant Cugat del Vallès, Barcelona, Spain
| | - Patricia González
- Liver Unit, Hospital Clínic, IDIBAPS, CIBEREHD, Universitat de Barcelona, Barcelona, Spain
| | - Concepción Bartres
- Liver Unit, Hospital Clínic, IDIBAPS, CIBEREHD, Universitat de Barcelona, Barcelona, Spain
| | - Maria Eugenia Soria
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d'Hebron (HUVH), CIBEREHD, Barcelona, Spain
| | - Celia Perales
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d'Hebron (HUVH), CIBEREHD, Barcelona, Spain
| | - Sabela Lens
- Liver Unit, Hospital Clínic, IDIBAPS, CIBEREHD, Universitat de Barcelona, Barcelona, Spain
| | - Zoe Mariño
- Liver Unit, Hospital Clínic, IDIBAPS, CIBEREHD, Universitat de Barcelona, Barcelona, Spain
| | - María Carlota Londoño
- Liver Unit, Hospital Clínic, IDIBAPS, CIBEREHD, Universitat de Barcelona, Barcelona, Spain
| | - Xavier Ariza
- Liver Unit, Hospital Clínic, IDIBAPS, CIBEREHD, Universitat de Barcelona, Barcelona, Spain
| | - George Koutsoudakis
- Liver Unit, Hospital Clínic, IDIBAPS, CIBEREHD, Universitat de Barcelona, Barcelona, Spain
| | - Josep Quer
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d'Hebron (HUVH), CIBEREHD, Barcelona, Spain.,Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Fernando González-Candelas
- Joint Research Unit Infección y Salud Pública, FISABIO-Universitat de València, I2SysBio, CIBERESP, Valencia, Spain
| | - Xavier Forns
- Liver Unit, Hospital Clínic, IDIBAPS, CIBEREHD, Universitat de Barcelona, Barcelona, Spain
| | - Sofía Pérez-Del-Pulgar
- Liver Unit, Hospital Clínic, IDIBAPS, CIBEREHD, Universitat de Barcelona, Barcelona, Spain
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9
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Tavares RCF, de Castro Amaral Feldner AC, Pinho JRR, de Mello Malta F, Carvalho-Filho RJ, Santana RAF, de Castro VFD, Dastoli GTF, Lima JC, Ferraz MLCG. Prevalence of resistance-associated substitutions to direct-acting antiviral agents in hemodialysis and renal transplant patients infected with hepatitis C virus. Infect Drug Resist 2018; 11:1993-2000. [PMID: 30464541 PMCID: PMC6208931 DOI: 10.2147/idr.s169512] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Direct-acting antiviral agents (DAAs) permit the use of interferon (IFN)-free regimens to treat hepatitis C (HCV) in patients with chronic kidney disease (CKD) on hemo-dialysis (HD) or renal transplant (RTx) recipients, with excellent response rates and safety. However, the occurrence of basal or therapy-induced resistance-associated substitutions (RASs) to DAAs can result in treatment failure. The aim of this study was to estimate the prevalence of RASs to NS3A, NS5A and NS5B inhibitors, and particularly the Q80K polymorphism, in CKD patients on HD and RTx recipients infected with HCV. Patients and methods HD and RTx patients infected with HCV-genotype 1 (GT1) were subjected to sequencing of the NS3, NS5A and NS5B regions. Results Direct sequencing of NS3 protease, NS5A and NS5B was performed in 76 patients (HD, n=37; RTx, n=39). The overall prevalence of RASs was 38.2%, but only 5.3% of the patients had mutations in more than one region. Substitutions were detected in NS3A (17.8%), NS5A (21.9%) and NS5B (8.4%). Q80K was detected in 1.5 % of the patients. Highly inhibitory RASs were uncommon (L31M, 2.6%; L159F+C316N, 2.6%). RASs were more prevalent in HCV-GT1a (42.9%) than in HCV-GT1b (32.4%), P=0.35. RASs were detected in 52.4% of treatment-naive patients and 27.8% of peg-IFN/ribavirin-experienced patients (P=0.12). The presence of RASs was associated with time of RTx (P=0.01). Conclusion The Q80K polymorphism was uncommon in our sample of HD and RTx patients. Despite the high prevalence of naturally occurring RASs, most of the substitutions detected were associated with a low level of resistance to DAAs.
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Affiliation(s)
| | | | - João Renato Rebello Pinho
- Albert Einstein Diagnostic Medicine, Albert Einstein Hospital São Paulo, SP, Brazil.,Laboratory of Tropical Gastroenterology and Hepatology "João Alves de Queiroz and Castorina Bittencourt Alves," Institute of Tropical Medicine, Department of Gastroenterology, University of São Paulo, São Paulo, SP, Brazil
| | - Fernanda de Mello Malta
- Laboratory of Tropical Gastroenterology and Hepatology "João Alves de Queiroz and Castorina Bittencourt Alves," Institute of Tropical Medicine, Department of Gastroenterology, University of São Paulo, São Paulo, SP, Brazil
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Brandão R, Marcelino R, Gonçalves F, Diogo I, Carvalho A, Cabanas J, Costa I, Brogueira P, Ventura F, Miranda A, Mansinho K, Gomes P. Characterization of NS5A and NS5B Resistance-Associated Substitutions from Genotype 1 Hepatitis C Virus Infected Patients in a Portuguese Cohort. Viruses 2018; 10:E223. [PMID: 29701642 PMCID: PMC5977216 DOI: 10.3390/v10050223] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 04/20/2018] [Accepted: 04/22/2018] [Indexed: 02/07/2023] Open
Abstract
This study is focused on the prevalent NS5 coding region resistance-associated substitutions (RASs) in DAA-naive genotype (GT)1 HCV-infected patients and their potential impact on success rates. Plasma RNA from 81 GT1 HCV-infected patients was extracted prior to an in-house nested RT-PCR of the NS5 coding region, which is followed by Sanger population sequencing. NS5A RASs were present in 28.4% (23/81) of all GT1-infected patients with 9.9% (8/81) having the Y93C/H mutation. NS5B RASs showed a prevalence of 14.8% (12/81) and were only detected in GT1b. Overall 38.3% (31/81) of all GT1 HCV-infected patients presented baseline RASs. The obtained data supports the usefulness of resistance testing prior to treatment since a statistically significant association was found between treatment failure and the baseline presence of specific NS5 RASs known as Y93C/H (p = 0.04).
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Affiliation(s)
- Ruben Brandão
- Molecular Biology Laboratory, LMCBM, SPC, HEM-Centro Hospitalar Lisboa Ocidental, 1349-019 Lisboa, Portugal.
| | - Rute Marcelino
- Global Health and Tropical Medicine (GHTM), Unit of Medical Microbiology, Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), 1349-008 Lisboa, Portugal.
| | - Fátima Gonçalves
- Molecular Biology Laboratory, LMCBM, SPC, HEM-Centro Hospitalar Lisboa Ocidental, 1349-019 Lisboa, Portugal.
| | - Isabel Diogo
- Molecular Biology Laboratory, LMCBM, SPC, HEM-Centro Hospitalar Lisboa Ocidental, 1349-019 Lisboa, Portugal.
| | - Ana Carvalho
- Molecular Biology Laboratory, LMCBM, SPC, HEM-Centro Hospitalar Lisboa Ocidental, 1349-019 Lisboa, Portugal.
| | - Joaquim Cabanas
- Molecular Biology Laboratory, LMCBM, SPC, HEM-Centro Hospitalar Lisboa Ocidental, 1349-019 Lisboa, Portugal.
| | - Inês Costa
- Molecular Biology Laboratory, LMCBM, SPC, HEM-Centro Hospitalar Lisboa Ocidental, 1349-019 Lisboa, Portugal.
| | - Pedro Brogueira
- Serviço de Doenças Infeciosas, HEM-Centro Hospitalar Lisboa Ocidental, 1349-019 Lisboa, Portugal.
| | - Fernando Ventura
- Serviço de Doenças Infeciosas, HEM-Centro Hospitalar Lisboa Ocidental, 1349-019 Lisboa, Portugal.
| | - Ana Miranda
- Serviço de Doenças Infeciosas, HEM-Centro Hospitalar Lisboa Ocidental, 1349-019 Lisboa, Portugal.
| | - Kamal Mansinho
- Serviço de Doenças Infeciosas, HEM-Centro Hospitalar Lisboa Ocidental, 1349-019 Lisboa, Portugal.
| | - Perpétua Gomes
- Molecular Biology Laboratory, LMCBM, SPC, HEM-Centro Hospitalar Lisboa Ocidental, 1349-019 Lisboa, Portugal.
- Centro de Investigação Interdisciplinar Egas Moniz, CiiEM, ISCSEM, 2829-511 Almada, Portugal.
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Abdel-Hameed EA, Rouster SD, Boyce CL, Zhang X, Biesiada J, Medvedovic M, Sherman KE. Ultra-Deep Genomic Sequencing of HCV NS5A Resistance-Associated Substitutions in HCV/HIV Coinfected Patients. Dig Dis Sci 2018; 63:645-652. [PMID: 29330726 DOI: 10.1007/s10620-017-4895-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 12/18/2017] [Indexed: 12/09/2022]
Abstract
BACKGROUND AND AIMS The prevalence of naturally occurring HCV-NS5A resistance-associated substitutions (RAS) to DAA drugs might affect the response to treatment in HCV/HIV coinfected subjects. There are limited data on the frequency of HCV-NS5A naturally occurring drug-RAS at baseline in HCV/HIV coinfected patients when ultra-deep sequencing methodologies are applied. METHODS HCV-NS5A-RAS were evaluated among 25 subjects in each group. Patients were matched by age, gender, and hepatic fibrosis stage category to control for selection bias. RESULTS Within subtype 1a, RAS were observed in 28% of HCV monoinfected and 48% of HCV/HIV coinfected subjects. More patients in the HCV/HIV coinfected group had clinically relevant mutations to DAA directed at NS5A. CONCLUSION While the clinical significance of this observation may be limited in highly drug adherent populations, some HCV/HIV coinfected persons may be at greater risk of viral resistance if suboptimal dosing occurs.
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Affiliation(s)
- Enass A Abdel-Hameed
- University of Cincinnati College of Medicine, 231 Albert Sabin Way, Cincinnati, OH, 45267-0595, USA
| | - Susan D Rouster
- University of Cincinnati College of Medicine, 231 Albert Sabin Way, Cincinnati, OH, 45267-0595, USA
| | - Ceejay L Boyce
- University of Cincinnati College of Medicine, 231 Albert Sabin Way, Cincinnati, OH, 45267-0595, USA
| | - Xiang Zhang
- Department of Environmental Health, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Jacek Biesiada
- Department of Environmental Health, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Mario Medvedovic
- Department of Environmental Health, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Kenneth E Sherman
- University of Cincinnati College of Medicine, 231 Albert Sabin Way, Cincinnati, OH, 45267-0595, USA.
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Cabezas J, Llerena S, Puente Á, Fábrega E, Crespo J. Causes of treatment failure for hepatitis C in the era of direct-acting antiviral therapy. REVISTA ESPANOLA DE ENFERMEDADES DIGESTIVAS 2017; 108:421-30. [PMID: 26666379 DOI: 10.17235/reed.2015.3894/2015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Hepatitis C therapy in the era of the newer direct-acting antiviral agents has radically changed our treatment schemes by achieving very high rates of sustained virological response. However, treatment with direct antiviral agents fails in a subgroup of patients. This group of so-called difficult-to-treat individuals is the subject of this paper, which reviews the causes of virological failure, their clinical implications, and some final recommendations.
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Affiliation(s)
- Joaquín Cabezas
- Aparato Digestivo/Unidad de Hepatología, Hospital Universitario Marqués de Valdecilla, España
| | - Susana Llerena
- Aparato Digestivo/ Unidad de Hepatologia, Hospital Universitario Marqués de Valdecilla, España
| | - Ángela Puente
- Aparato Digestivo/Unidad de Hepatología, Hospital Universitario Marqués de Valdecilla, España
| | | | - Javier Crespo
- Servicio Aparato Digestivo, Hospital Universitario Marqués de Valdecilla, 39002
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13
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Li Z, Chen ZW, Li H, Ren H, Hu P. Prevalence of hepatitis C virus-resistant association substitutions to direct-acting antiviral agents in treatment-naïve hepatitis C genotype 1b-infected patients in western China. Infect Drug Resist 2017; 10:377-392. [PMID: 29184422 PMCID: PMC5673042 DOI: 10.2147/idr.s146595] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background Direct-acting antivirals (DAAs) against hepatitis C virus (HCV) are potent and highly efficacious. However, resistance-associated substitutions (RASs) relevant to DAAs can impair treatment effectiveness even at baseline. Moreover, the prevalence of baseline RASs in HCV genotype 1b-infected patients in western China is still unclear. Materials and methods Direct sequencing of the HCV NS3, NS5A, and NS5B regions was performed in baseline serum samples of 70 DAAs treatment-naïve HCV 1b-infected patients in western China. The sequences were analyzed with MEGA version 5.05 software. Evolutionary patterns of RASs and amino-acid covariance patterns in the NS3, NS5A, and NS5B genes were analyzed by MEGA and Cytoscape (version 3.2.1), respectively. Results The presence of at least one RAS in the NS3 region (C16S, T54S, Q80R/L, A87T, R117H, S122G, V132I, V170I) was observed in 85.48% (53 of 62) of patients, RASs in the NS5A region (L28M, R30Q, Q54H, P58S/T, Q62H/R, Y93H) were observed in 42.42% (28 of 66) of patients, and RASs in the NS5B region (N142S, A300T, C316N, A338V, S365A, L392I, M414L, I424V, A442T, V499A, S556G) were observed in 100% (44 of 44) of patients. Evolutionary patterns of RASs and amino-acid covariance patterns for the NS3, NS5A, and NS5B genes are reported. Conclusion The prevalence of RASs relevant to DAAs detected in the NS3, NS5A, and NS5B regions of HCV 1b from DAA treatment-naïve patients is high. Therefore, more attention should be paid to RASs associated with DAAs in the upcoming DAA-treatment era in China.
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Affiliation(s)
- Zhao Li
- Department of Infectious Diseases, Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Chinese Ministry of Education, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhi-Wei Chen
- Department of Infectious Diseases, Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Chinese Ministry of Education, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hu Li
- Department of Infectious Diseases, Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Chinese Ministry of Education, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hong Ren
- Department of Infectious Diseases, Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Chinese Ministry of Education, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Peng Hu
- Department of Infectious Diseases, Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Chinese Ministry of Education, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Prevalence of naturally occurring protease inhibitor resistance-associated variants in hemodialysis and renal transplant patients with hepatitis C virus infection. Eur J Gastroenterol Hepatol 2017; 29:754-758. [PMID: 28234637 DOI: 10.1097/meg.0000000000000866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Background NS3 protease inhibitors (PIs) were the first direct antiviral agents used for the treatment of hepatitis C virus. The combination of second-wave PIs with other direct antiviral agents enabled the use of interferon-free regimens for chronic kidney disease patients on dialysis and renal transplant (RTx) recipients, populations in which the use of interferon and ribavirin is limited. However, the occurrence of PI resistance-associated variants (RAVs), both baseline and induced by therapy, has resulted in the failure of many treatment strategies. Methods The aim of this study was to estimate the prevalence of PI RAVs and of the Q80K polymorphism in chronic kidney disease patients on hemodialysis and RTx recipients. Direct sequencing of the NS3 protease was performed in 67 patients (32 hemodialysis and 35 RTx).Results RAVs to PIs were detected in 18% of the patients: V55A (9%), V36L (1.5%), T54S (1.5%), S122N (1.5%), I170L (1.5%), and M175L (1.5%). Only 1.5% of the patients carried the Q80K polymorphism. The frequency of these mutations was more than two times higher in patients infected with GT1a (25%) than GT1b (9.7%) (P=0.1). The mutations were detected in 20% of treatment-naive patients and in 15.6% of peginterferon/ribavirin-experienced patients (P=0.64). Furthermore, no mutation that would confer high resistance to PIs was detected.Conclusion The Q80K polymorphism was rare in the population studied. The occurrence of RAVs was common, with predominance in GT1a. However, the variants observed were those associated with a low level of resistance to PIs, facilitating the use of these drugs in this special group of patients.
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Llerena S, Cabezas J, Iruzubieta P, Crespo J. Resistance to hepatitis C virus. Implications and therapeutic options. GASTROENTEROLOGIA Y HEPATOLOGIA 2017. [PMID: 28647053 DOI: 10.1016/j.gastrohep.2017.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
We are currently living in an unprecedented era of hepatitis C treatment with the availability of highly effective drugs yielding minimal side effects. The problem we currently face is the retreatment of patients refractory to these drugs. Although several factors can influence treatment failure, this review focuses on antiviral resistance. Resistance-associated substitutions may be identified at baseline or be treatment-emergent. The latter seem to be more clinically relevant and must be studied in the event of treatment failure (no virological response). In this article, we present the latest data from clinical trials and studies in real-life clinical practice. Finally, based on this current evidence, we propose some recommendations for the management and retreatment of these patients.
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Affiliation(s)
- Susana Llerena
- Servicio de Gastroenterología y Hepatología, Hospital Universitario Marqués de Valdecilla, Santander, Cantabria, España; Instituto de Investigación Valdecilla (IDIVAL), Santander, Cantabria, España
| | - Joaquín Cabezas
- Servicio de Gastroenterología y Hepatología, Hospital Universitario Marqués de Valdecilla, Santander, Cantabria, España; Instituto de Investigación Valdecilla (IDIVAL), Santander, Cantabria, España
| | - Paula Iruzubieta
- Servicio de Gastroenterología y Hepatología, Hospital Universitario Marqués de Valdecilla, Santander, Cantabria, España; Instituto de Investigación Valdecilla (IDIVAL), Santander, Cantabria, España
| | - Javier Crespo
- Servicio de Gastroenterología y Hepatología, Hospital Universitario Marqués de Valdecilla, Santander, Cantabria, España; Instituto de Investigación Valdecilla (IDIVAL), Santander, Cantabria, España.
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16
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Cuypers L, Libin P, Schrooten Y, Theys K, Di Maio VC, Cento V, Lunar MM, Nevens F, Poljak M, Ceccherini-Silberstein F, Nowé A, Van Laethem K, Vandamme AM. Exploring resistance pathways for first-generation NS3/4A protease inhibitors boceprevir and telaprevir using Bayesian network learning. INFECTION GENETICS AND EVOLUTION 2017; 53:15-23. [PMID: 28499845 DOI: 10.1016/j.meegid.2017.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 04/25/2017] [Accepted: 05/08/2017] [Indexed: 12/19/2022]
Abstract
Resistance-associated variants (RAVs) have been shown to influence treatment response to direct-acting antivirals (DAAs) and first generation NS3/4A protease inhibitors (PIs) in particular. Interpretation of hepatitis C virus (HCV) genotypic drug resistance remains a challenge, especially in patients who previously failed DAA therapy and need to be retreated with a second DAA based regimen. Bayesian network (BN) learning on HCV sequence data from patients treated with DAAs could provide insight in resistance pathways against PIs for HCV subtypes 1a and 1b, in a similar way as applied before for HIV. The publicly available 'Rega-BN' tool chain was developed to study associative analyses for various pathogens. Our first analysis, comparing sequences from PI-naïve and PI-experienced patients, determined that NS3 substitutions R155K and V36M arise with PI-exposure in HCV1a infected patients, and were defined as major and minor resistance-associated variants respectively. NS3 variant 174H was newly identified as potentially related to PI resistance. In a second analysis, NS3 sequences from PI-naïve patients who cleared the virus during PI therapy and from PI-naïve patients who failed PI therapy were compared, showing that NS3 baseline variant 67S predisposes to treatment-failure and variant 72I to treatment success. This approach has the potential to better characterize the role of more RAVs, if sufficient therapy annotated sequence data becomes available in curated public databases. In addition, polymorphisms present in baseline sequences that predispose patients to therapy failure can be identified using this approach.
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Affiliation(s)
- Lize Cuypers
- KU Leuven, University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Herestraat 49, box 1040, 3000 Leuven, Belgium.
| | - Pieter Libin
- KU Leuven, University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Herestraat 49, box 1040, 3000 Leuven, Belgium; Artificial Intelligence Lab, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.
| | - Yoeri Schrooten
- KU Leuven, University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Herestraat 49, box 1040, 3000 Leuven, Belgium.
| | - Kristof Theys
- KU Leuven, University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Herestraat 49, box 1040, 3000 Leuven, Belgium.
| | - Velia Chiara Di Maio
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, Italy.
| | - Valeria Cento
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, Italy.
| | - Maja M Lunar
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.
| | - Frederik Nevens
- University Hospitals Leuven, Department of Hepatology, Herestraat 49, 3000 Leuven, Belgium.
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.
| | | | - Ann Nowé
- Artificial Intelligence Lab, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.
| | - Kristel Van Laethem
- KU Leuven, University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Herestraat 49, box 1040, 3000 Leuven, Belgium.
| | - Anne-Mieke Vandamme
- KU Leuven, University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Herestraat 49, box 1040, 3000 Leuven, Belgium; Center for Global Health and Tropical Medicine, Microbiology Unit, Institute for Hygiene and Tropical Medicine, University Nova de Lisboa, Rua da Junqueira 100, 1349-008 Lisbon, Portugal.
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Yan Z, Wang Y. Viral and host factors associated with outcomes of hepatitis C virus infection (Review). Mol Med Rep 2017; 15:2909-2924. [PMID: 28339063 DOI: 10.3892/mmr.2017.6351] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 02/13/2017] [Indexed: 11/05/2022] Open
Abstract
Hepatitis C virus (HCV) infection is a major health issue globally. Owing to the progress made in host genetics and HCV molecular virology, emerging data have suggested that the natural course and treatment response in patients with HCV infection are largely determined by complex host‑viral interactions. HCV genotype is the most important viral factor predicting the response to pegylated interferon‑α plus ribavirin therapy. The subtype of HCV genotype 1 is the key viral factor that predicts the efficacy of direct‑acting antiviral therapy. HCV genome heterogeneity and baseline viral load are additionally associated with the treatment response. Multiple host genetic variants localized in genes associated with the immune response have been identified as predictors of spontaneous disease course and therapy outcome in chronic HCV. However, most findings from candidate gene association studies have not been proven universal for all investigated populations and independent studies. Previous findings in independent large genome wide association studies confirmed that interferon‑λ3 gene polymorphisms are associated with spontaneous clearance and treatment responsiveness. A polymorphism of the inosine triphosphatase gene has been identified as a protective factor against ribavirin‑induced anemia and dose reductions. Another genetic variant in the patatin‑like phospholipase domain containing 3 genes is associated with hepatic steatosis and fibrosis in patients with HCV. The present review focused on the identified viral and host factors associated with outcomes of patients with HCV, and assessed the involvement of viral and host genetics in the natural history and treatment outcomes of HCV infection. This will provide novel ideas concerning personalized prevention and individualized clinical management.
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Affiliation(s)
- Zehui Yan
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University, Shapingba, Chongqing 400038, P.R. China
| | - Yuming Wang
- Department of Infectious Diseases, Southwest Hospital, Third Military Medical University, Shapingba, Chongqing 400038, P.R. China
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18
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Li Z, Zhang Y, Liu Y, Shao X, Luo Q, Cai Q, Zhao Z. Naturally occurring drug resistance associated variants to hepatitis C virus direct-acting antiviral agents in treatment-naive HCV genotype 1b-infected patients in China. Medicine (Baltimore) 2017; 96:e6830. [PMID: 28489763 PMCID: PMC5428597 DOI: 10.1097/md.0000000000006830] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The direct-acting antiviral agents (DAAs) have drastically improved the prognosis of hepatitis C virus (HCV) patients. However, the resistance-associated variants (RAVs) to DAAs may hamper treatment. There was a lack of data on the prevalence of pre-exist RAVs in Chinese HCV-infected patients. We performed nested PCR assays on 74 HCV genotype 1b-infected patients to amplify HCV viral regions of NS3, NS5A, and NS5B to investigate the prevalence of RAVs to DAAs in treatment-naive HCV genotype1b-infected patients in China. The mutations A156S, T54S, and D168Y of the NS3/4A region were found in 18.33% (11/60), 6.67% (4/60), and 1.67% (1/60) of the successfully amplified cases. Mutations Q30R, L31M, and H58P of the NS5A region were confirmed in 57.63% (34/59), 1.69%(1/59), and 86.44% (51/59) of the cases. Mutations C316N, S365A, M414L, M423I, Y448H, I482T, I482 V, V494L, P495S, and V499A of the NS5B region were detected in 100% (60/60), 3.33% (2/60), 5.88% (3/51), 1.96% (1/51), 1.96% (1/51), 5.88% (3/51), 1.96% (1/51), 3.92% (2/51), 5.88% (3/51), and 15.69% (8/51) of cases, respectively. Naturally occurring RAVs to DAAs pre-exist in treatment-naive Chinese HCV genotype 1b-infected patients and the characteristic is different from that in Europe and the United States. Clinicians should consider RAVs upon the introduction of DAA-based antiviral therapy.
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Affiliation(s)
- Zhanyi Li
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-sen University
- Guangdong Provincial Key Laboratory of Liver Disease, Guangzhou, Guangdong, China
| | - Ying Zhang
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-sen University
- Guangdong Provincial Key Laboratory of Liver Disease, Guangzhou, Guangdong, China
| | - Ying Liu
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-sen University
- Guangdong Provincial Key Laboratory of Liver Disease, Guangzhou, Guangdong, China
| | - Xiaoqiong Shao
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-sen University
- Guangdong Provincial Key Laboratory of Liver Disease, Guangzhou, Guangdong, China
| | - QiuMin Luo
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-sen University
- Guangdong Provincial Key Laboratory of Liver Disease, Guangzhou, Guangdong, China
| | - Qingxian Cai
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-sen University
- Guangdong Provincial Key Laboratory of Liver Disease, Guangzhou, Guangdong, China
| | - Zhixin Zhao
- Department of Infectious Diseases, Third Affiliated Hospital of Sun Yat-sen University
- Guangdong Provincial Key Laboratory of Liver Disease, Guangzhou, Guangdong, China
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19
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Smith HL, Chung RT, Mantry P, Chapman W, Curry MP, Schiano TD, Boucher E, Cheslock P, Wang Y, Molrine DC. Prevention of allograft HCV recurrence with peri-transplant human monoclonal antibody MBL-HCV1 combined with a single oral direct-acting antiviral: A proof-of-concept study. J Viral Hepat 2017; 24:197-206. [PMID: 28127942 DOI: 10.1111/jvh.12632] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/17/2016] [Indexed: 12/25/2022]
Abstract
Patients with active hepatitis C virus (HCV) infection at transplantation experience rapid allograft infection, increased risk of graft failure and accelerated fibrosis. MBL-HCV1, a neutralizing human monoclonal antibody (mAb) targeting the HCV envelope, was combined with a licensed oral direct-acting antiviral (DAA) to prevent HCV recurrence post-transplant in an open-label exploratory efficacy trial. Eight subjects received MBL-HCV1 beginning on the day of transplant with telaprevir initiated between days 3 and 7 post-transplantation. Following FDA approval of sofosbuvir, two subjects received MBL-HCV1 starting on the day of transplant with sofosbuvir initiated on day 3. Combination treatment was administered for 8-12 weeks or until the stopping rule for viral rebound was met. The primary endpoint was undetectable HCV RNA at day 56 with exploratory endpoints of sustained virologic response (SVR) at 12 and 24 weeks post-treatment. Both subjects receiving mAb and sofosbuvir achieved SVR24. Four of eight subjects in the mAb and telaprevir group met the primary endpoint; one subject achieved SVR24 and three subjects relapsed 2-12 weeks post-treatment. The other four subjects experienced viral breakthrough. There were no serious adverse events related to study treatment. This proof-of-concept study demonstrates that peri-transplant immunoprophylaxis combined with a single oral direct-acting antiviral in the immediate post-transplant period can prevent HCV recurrence.
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Affiliation(s)
- H L Smith
- MassBiologics of the University of Massachusetts Medical School, Boston, MA, USA
| | - R T Chung
- Department of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - P Mantry
- Liver Institute, Methodist Dallas Medical Center, Dallas, TX, USA
| | - W Chapman
- Division of General Surgery, Washington University, St Louis, MO, USA
| | - M P Curry
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - T D Schiano
- Recanati-Miller Transplantation Institute and The Division of Liver Diseases, The Mount Sinai Medical Center, New York, NY, USA
| | - E Boucher
- MassBiologics of the University of Massachusetts Medical School, Boston, MA, USA
| | - P Cheslock
- MassBiologics of the University of Massachusetts Medical School, Boston, MA, USA
| | - Y Wang
- MassBiologics of the University of Massachusetts Medical School, Boston, MA, USA
| | - D C Molrine
- MassBiologics of the University of Massachusetts Medical School, Boston, MA, USA
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Meanwell NA. 2015 Philip S. Portoghese Medicinal Chemistry Lectureship. Curing Hepatitis C Virus Infection with Direct-Acting Antiviral Agents: The Arc of a Medicinal Chemistry Triumph. J Med Chem 2016; 59:7311-51. [PMID: 27501244 DOI: 10.1021/acs.jmedchem.6b00915] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The development of direct-acting antiviral agents that can cure a chronic hepatitis C virus (HCV) infection after 8-12 weeks of daily, well-tolerated therapy has revolutionized the treatment of this insidious disease. In this article, three of Bristol-Myers Squibb's HCV programs are summarized, each of which produced a clinical candidate: the NS3 protease inhibitor asunaprevir (64), marketed as Sunvepra, the NS5A replication complex inhibitor daclatasvir (117), marketed as Daklinza, and the allosteric NS5B polymerase inhibitor beclabuvir (142), which is in late stage clinical studies. A clinical study with 64 and 117 established for the first time that a chronic HCV infection could be cured by treatment with direct-acting antiviral agents alone in the absence of interferon. The development of small molecule HCV therapeutics, designed by medicinal chemists, has been hailed as "the arc of a medical triumph" but may equally well be described as "the arc of a medicinal chemistry triumph".
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Affiliation(s)
- Nicholas A Meanwell
- Department of Discovery Chemistry, Bristol-Myers Squibb Research & Development , Wallingford, Connecticut 06492, United States
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Esposito I, Trinks J, Soriano V. Hepatitis C virus resistance to the new direct-acting antivirals. Expert Opin Drug Metab Toxicol 2016; 12:1197-209. [PMID: 27384079 DOI: 10.1080/17425255.2016.1209484] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION The treatment of hepatitis C virus (HCV) infection has dramatically improved in recent years with the widespread use of interferon-free combination regimens. Despite the high sustained virological response (SVR) rates (over 90%) obtained with direct-acting antivirals (DAAs), drug resistance has emerged as a potential challenge. The high replication rate of HCV and the low fidelity of its RNA polymerase result in a high degree of genetic variability in the HCV population, which ultimately explains the rapid selection of drug resistance associated variants (RAVs). AREAS COVERED Results from clinical trials and real-world experience have both provided important information on the rate and clinical significance of RAVs. They can be present in treatment-naive patients as natural polymorphisms although more frequently they are selected upon treatment failure. In patients engaged in high-risk behaviors, RAVs can be transmitted. EXPERT OPINION Although DAA failures generally occur in less than 10% of treated chronic hepatitis C patients, selection of drug resistance is the rule in most cases. HCV re-treatment options are available, but first-line therapeutic strategies should be optimized to efficiently prevent DAA failure due to baseline HCV resistance. Considerable progress is being made and next-generation DAAs are coming with pangenotypic activity and higher resistance barrier.
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Affiliation(s)
- Isabella Esposito
- a Infectious Diseases Unit , IdiPAZ & La Paz University Hospital , Madrid , Spain
| | - Julieta Trinks
- b Instituto de Ciencias Básicas y Medicina Experimental (ICBME) , Instituto Universitario del Hospital Italiano de Buenos Aires , Buenos Aires , Argentina.,c Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Buenos Aires , Argentina
| | - Vicente Soriano
- a Infectious Diseases Unit , IdiPAZ & La Paz University Hospital , Madrid , Spain
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Zhou K, Liang Z, Wang C, Hu F, Ning C, Lan Y, Tang X, Tucker JD, Cai W. Natural Polymorphisms Conferring Resistance to HCV Protease and Polymerase Inhibitors in Treatment-Naïve HIV/HCV Co-Infected Patients in China. PLoS One 2016; 11:e0157438. [PMID: 27341031 PMCID: PMC4920402 DOI: 10.1371/journal.pone.0157438] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Accepted: 05/31/2016] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The advent of direct-acting agents (DAAs) has improved treatment of HCV in HIV co-infection, but may be limited by primary drug resistance. This study reports the prevalence of natural polymorphisms conferring resistance to NS3/4A protease inhibitors and NS5B polymerase inhibitors in treatment-naïve HIV/HCV co-infected individuals in China. METHODS Population based NS3/4A sequencing was completed for 778 treatment-naïve HIV/HCV co-infected patients from twelve provinces. NS3 sequences were amplified by nested PCR using in-house primers for genotypes 1-6. NS5B sequencing was completed for genotyping in 350 sequences. Resistance-associated variants (RAVs) were identified in positions associated with HCV resistance. RESULTS Overall, 72.8% (566/778) of all HCV sequences had at least one RAV associated with HCV NS3/4A protease inhibitor resistance. Variants were found in 3.6% (7/193) of genotype 1, 100% (23/23) of genotype 2, 100% (237/237) of genotype 3 and 92% (299/325) of genotype 6 sequences. The Q80K variant was present in 98.4% of genotype 6a sequences. High-level RAVs were rare, occurring in only 0.8% of patients. 93% (64/69) patients with genotype 1b also carried the C316N variant associated with NS5B low-level resistance. CONCLUSIONS The low frequency of high-level RAVs associated with primary HCV DAA resistance among all genotypes in HIV/HCV co-infected patients is encouraging. Further phenotypic studies and clinical research are needed.
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Affiliation(s)
- Kali Zhou
- Guangzhou Eighth People’s Hospital, 627 Dongfeng Dong Road, Guangzhou, Guangdong 510060, China
- University of California San Francisco, Department of Medicine, Division of Gastroenterology, 513 Parnassus Avenue, Room S-357, San Francisco, California, 94143-0538 United States of America
| | - Zhiwei Liang
- Guangzhou Eighth People’s Hospital, 627 Dongfeng Dong Road, Guangzhou, Guangdong 510060, China
| | - Charles Wang
- UNC-Project – China, Division of Infectious Diseases, Department of Medicine, UNC Chapel Hill School of Medicine, 130 Mason Farm Rd., 2nd Floor, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, 27599-3368, United States of America
- Brown University School of Medicine, Department of Medicine, Division of Gastroenterology 593 Eddy Street, APC 406, Providence, Rhode Island, 02903, United States of America
| | - Fengyu Hu
- Guangzhou Eighth People’s Hospital, 627 Dongfeng Dong Road, Guangzhou, Guangdong 510060, China
| | - Chuanyi Ning
- Guangzhou Eighth People’s Hospital, 627 Dongfeng Dong Road, Guangzhou, Guangdong 510060, China
- UNC-Project – China, Division of Infectious Diseases, Department of Medicine, UNC Chapel Hill School of Medicine, 130 Mason Farm Rd., 2nd Floor, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, 27599-3368, United States of America
| | - Yun Lan
- Guangzhou Eighth People’s Hospital, 627 Dongfeng Dong Road, Guangzhou, Guangdong 510060, China
| | - Xiaoping Tang
- Guangzhou Eighth People’s Hospital, 627 Dongfeng Dong Road, Guangzhou, Guangdong 510060, China
| | - Joseph D. Tucker
- Guangzhou Eighth People’s Hospital, 627 Dongfeng Dong Road, Guangzhou, Guangdong 510060, China
- UNC-Project – China, Division of Infectious Diseases, Department of Medicine, UNC Chapel Hill School of Medicine, 130 Mason Farm Rd., 2nd Floor, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, 27599-3368, United States of America
| | - Weiping Cai
- Guangzhou Eighth People’s Hospital, 627 Dongfeng Dong Road, Guangzhou, Guangdong 510060, China
- * E-mail:
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Mouse Systems to Model Hepatitis C Virus Treatment and Associated Resistance. Viruses 2016; 8:v8060176. [PMID: 27338446 PMCID: PMC4926196 DOI: 10.3390/v8060176] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 05/12/2016] [Accepted: 06/16/2016] [Indexed: 12/15/2022] Open
Abstract
While addition of the first-approved protease inhibitors (PIs), telaprevir and boceprevir, to pegylated interferon (PEG-IFN) and ribavirin (RBV) combination therapy significantly increased sustained virologic response (SVR) rates, PI-based triple therapy for the treatment of chronic hepatitis C virus (HCV) infection was prone to the emergence of resistant viral variants. Meanwhile, multiple direct acting antiviral agents (DAAs) targeting either the HCV NS3/4A protease, NS5A or NS5B polymerase have been approved and these have varying potencies and distinct propensities to provoke resistance. The pre-clinical in vivo assessment of drug efficacy and resistant variant emergence underwent a great evolution over the last decade. This field had long been hampered by the lack of suitable small animal models that robustly support the entire HCV life cycle. In particular, chimeric mice with humanized livers (humanized mice) and chimpanzees have been instrumental for studying HCV inhibitors and the evolution of drug resistance. In this review, we present the different in vivo HCV infection models and discuss their applicability to assess HCV therapy response and emergence of resistant variants.
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Yan XB. Anti-HCV therapy: Whether it comes into the age of DAA-based specific therapy? Shijie Huaren Xiaohua Zazhi 2016; 24:1943-1951. [DOI: 10.11569/wcjd.v24.i13.1943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Hepatitis C virus (HCV) infection is one of the main causes of chronic liver diseases. Direct-acting antiviral (DAA) agents undoubtedly bring hope for patients who cannot tolerate or are not suitable for interferon therapy. There have been six foreign guidelines for anti-HCV therapy in 2014, and in October this year, China also updated its guideline for the diagnosis and treatment of HCV infection. In this paper I review the current status and future perspectives of HCV treatment.
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Resistance to direct-acting antiviral agents: clinical utility and significance. Curr Opin HIV AIDS 2016; 10:381-9. [PMID: 26248125 DOI: 10.1097/coh.0000000000000177] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
PURPOSE OF REVIEW This article examines the dynamics and factors underlying hepatitis C virus (HCV) resistance, along with their impact on daily clinical management of HCV-infected patients. RECENT FINDINGS Across available treatment-regimens, GT-3 is the most difficult-to-cure genotype, but also genotype-1a may show lower success-rates compared with genotype-1b. Natural resistance to NS3, NS5A and NS5B inhibitors may contribute to treatment failures. The Q80K NS3-protease mutation affects sensibility to simeprevir + peg-interferon/ribavirin combinations. It reaches up to 48% prevalence in genotype-1a in some studies (but it is lower in other). Resistant variants (particularly in NS5A) developed at failure can persist, in a substantial proportion of patients, even 3 years after treatment-discontinuation, potentially affecting readministration of the same direct-acting antiviral agent (DAA)-class. This will become an issue for those patients failing all-oral regimens with multiple-resistant viruses. SUMMARY Recent data support the importance of an accurate genotype and genotype-1 subtype (1a/1b) assignment prior therapy. Resistance testing at baseline has no clear indication so far in clinical practice for all-DAA regimens selection, while it remains a valuable option at the retreatment of patients who failed DAA-containing regimens, provided that data are generated to inform treatment decisions based on the results of resistance testing. In this context, long-term RAVs persistence after failure should be taken into account.
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Patiño-Galindo JÁ, Salvatierra K, González-Candelas F, López-Labrador FX. Comprehensive Screening for Naturally Occurring Hepatitis C Virus Resistance to Direct-Acting Antivirals in the NS3, NS5A, and NS5B Genes in Worldwide Isolates of Viral Genotypes 1 to 6. Antimicrob Agents Chemother 2016; 60:2402-16. [PMID: 26856832 PMCID: PMC4808155 DOI: 10.1128/aac.02776-15] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 02/01/2016] [Indexed: 01/06/2023] Open
Abstract
There is no comprehensive study available on the natural hepatitis C virus (HCV) polymorphism in sites associated with resistance including all viral genotypes which may present variable susceptibilities to particular direct-acting antivirals (DAAs). This study aimed to analyze the frequencies, genetic barriers, and evolutionary histories of naturally occurring resistance-associated variants (RAVs) in the six main HCV genotypes. A comprehensive analysis of up to 103 RAVs was performed in 2,901, 2,216, and 1,344 HCV isolates for the NS3, NS5A, and NS5B genes, respectively. We report significant intergenotypic differences in the frequencies of natural RAVs for these three HCV genes. In addition, we found a low genetic barrier for the generation of new RAVs, irrespective of the viral genotype. Furthermore, in 1,126 HCV genomes, including sequences spanning the three genes, haplotype analysis revealed a remarkably high frequency of viruses carrying more than one natural RAV to DAAs (53% of HCV-1a, 28.5% of HCV-1b, 67.1% of HCV-6, and 100% of genotype 2, 3, 4, and 5 haplotypes). With the exception of HCV-1a, the most prevalent haplotypes showed RAVs in at least two different viral genes. Finally, evolutionary analyses revealed that, while most natural RAVs appeared recently, others have been efficiently transmitted over time and cluster in well-supported clades. In summary, and despite the observed high efficacy of DAA-based regimens, we show that naturally occurring RAVs are common in all HCV genotypes and that there is an overall low genetic barrier for the selection of resistance mutations. There is a need for natural DAA resistance profiling specific for each HCV genotype.
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Affiliation(s)
- Juan Ángel Patiño-Galindo
- Joint Unit in Infection and Health, FISABIO-Public Health/Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain CIBER-ESP (Centro de Investigación Biomédica en Epidemiología y Salud Publica), Instituto de Salud Carlos III, Madrid, Spain
| | - Karina Salvatierra
- Joint Unit in Genomics and Health, FISABIO-Public Health/Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain Virology Laboratory, Genomics and Health Area, FISABIO-Public Health, Generalitat Valenciana, Valencia, Spain
| | - Fernando González-Candelas
- Joint Unit in Infection and Health, FISABIO-Public Health/Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain CIBER-ESP (Centro de Investigación Biomédica en Epidemiología y Salud Publica), Instituto de Salud Carlos III, Madrid, Spain
| | - F Xavier López-Labrador
- Joint Unit in Infection and Health, FISABIO-Public Health/Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain Joint Unit in Genomics and Health, FISABIO-Public Health/Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain Virology Laboratory, Genomics and Health Area, FISABIO-Public Health, Generalitat Valenciana, Valencia, Spain CIBER-ESP (Centro de Investigación Biomédica en Epidemiología y Salud Publica), Instituto de Salud Carlos III, Madrid, Spain
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Liu L, Nardo D, Li E, Wang GP. CD4+ T-cell recovery with suppressive ART-induced rapid sequence evolution in hepatitis C virus envelope but not NS3. AIDS 2016; 30:691-700. [PMID: 26645605 DOI: 10.1097/qad.0000000000000997] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
OBJECTIVES CD4 T-cell depletion from HIV infection leads to a global decline in anti-hepatitis C virus (HCV) envelope neutralizing antibody (nAb) response, which may play a role in accelerating liver fibrosis. An increase in anti-HCV nAb titers has been reported during antiretroviral therapy (ART) but its impact on HCV remains poorly understood. The objective of this study is to determine the effects of ART on long-term HCV evolution. DESIGN AND METHODS We examined HCV quasispecies structure and long-term evolution in HIV/HCV coinfected patients with ART-induced CD4 T-cell recovery, and compared with patients with CD4 T-cell depletion from delayed ART. We applied a single-variant sequencing (SVS) method to construct authentic viral quasispecies and compared sequence evolution in HCV envelope, the primary target for humoral immune responses, and NS3, a target for cellular immunity, between the two cohorts. RESULTS The SVS method corrected biases known to skew the proportions of viral variants, revealing authentic HCV quasispeices structures. We observed higher rates of HCV envelope sequence evolution in patients with ART-induced CD4 T-cell recovery, compared with patients with CD4 T-cell depletion from delayed ART (P = 0.03). Evolutionary rates for NS3 were considerably lower than the rates for envelope (P < 0.01), with no significant difference observed between the two groups. CONCLUSION ART-induced CD4 T-cell recovery results in rapid sequence evolution in HCV envelope, but not in NS3. These results suggest that suppressive ART disproportionally enhances HCV-specific humoral responses more than cellular responses, resulting in rapid sequence evolution in HCV envelope but not NS3.
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Di Maio VC, Cento V, Di Paolo D, Aragri M, De Leonardis F, Tontodonati M, Micheli V, Bellocchi MC, Antonucci FP, Bertoli A, Lenci I, Milana M, Gianserra L, Melis M, Di Biagio A, Sarrecchia C, Sarmati L, Landonio S, Francioso S, Lambiase L, Nicolini LA, Marenco S, Nosotti L, Giannelli V, Siciliano M, Romagnoli D, Pellicelli A, Vecchiet J, Magni CF, Babudieri S, Mura MS, Taliani G, Mastroianni C, Vespasiani-Gentilucci U, Romano M, Morisco F, Gasbarrini A, Vullo V, Bruno S, Baiguera C, Pasquazzi C, Tisone G, Picciotto A, Andreoni M, Parruti G, Rizzardini G, Angelico M, Perno CF, Ceccherini-Silberstein F. HCV NS3 sequencing as a reliable and clinically useful tool for the assessment of genotype and resistance mutations for clinical samples with different HCV-RNA levels. J Antimicrob Chemother 2016; 71:739-750. [PMID: 26679249 DOI: 10.1093/jac/dkv403] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/29/2015] [Indexed: 01/13/2025] Open
Abstract
OBJECTIVES This study aims to evaluate the reliability and clinical utility of NS3 sequencing in hepatitis C virus (HCV) 1-infected patients who were candidates to start a PI-containing regimen. METHODS NS3 protease sequencing was performed by in-house-developed HCV-1 subtype-specific protocols. Phylogenetic analysis was used to test sequencing reliability and concordance with previous genotype/subtype assignment by commercial genotyping assays. RESULTS Five hundred and sixty-seven HCV plasma samples with quantifiable HCV-RNA from 326 HCV-infected patients were collected between 2011 and 2014. Overall, the success rate of NS3 sequencing was 88.9%. The success rate between the two subtype protocols (HCV-1a/HCV-1b) was similarly high for samples with HCV-RNA >3 log IU/mL (>92% success rate), while it was slightly lower for HCV-1a samples with HCV-RNA ≤3 log IU/mL compared with HCV-1b samples. Phylogenetic analysis confirmed the genotype/subtype given by commercial genotyping assays in 92.9% (303/326) of cases analysed. In the remaining 23 cases (7.1%), 1 was HCV-1g (previously defined as subtype 1a), 1 was HCV-4d (previously defined as genotype 1b) and 1 was HCV-1b (previously defined as genotype 2a/2c). In the other cases, NS3 sequencing precisely resolved the either previous undetermined/discordant subtype 1 or double genotype/subtype assignment by commercial genotyping assays. Resistance-associated variants (RAVs) to PI were detected in 31.0% of samples. This prevalence changed according to PI experience (17.1% in PI-naive patients versus 79.2% in boceprevir/telaprevir/simeprevir-failing patients). Among 96 patients with available virological outcome following boceprevir/telaprevir treatment, a trend of association between baseline NS3 RAVs and virological failure was observed (particularly for HCV-1a-infected patients: 3/21 failing patients versus 0/22 achieving sustained virological response; P = 0.11). CONCLUSIONS HCV-NS3 sequencing provides reliable results and at the same time gives two clinically relevant pieces of information: a correct subtype/genotype assignment and the detection of variants that may interfere with the efficacy of PI.
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Affiliation(s)
- V C Di Maio
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome, Italy
| | - V Cento
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome, Italy
| | - D Di Paolo
- Hepatology Unit, University Hospital of Rome 'Tor Vergata', Rome, Italy
| | - M Aragri
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome, Italy
| | - F De Leonardis
- Hepatology Unit, University Hospital of Rome 'Tor Vergata', Rome, Italy
| | - M Tontodonati
- Infectious Disease Unit, Pescara General Hospital, Pescara, Italy
| | - V Micheli
- Unit of Microbiology, Hospital Sacco of Milan, Milan, Italy
| | - M C Bellocchi
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome, Italy
| | - F P Antonucci
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome, Italy
| | - A Bertoli
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome, Italy
| | - I Lenci
- Hepatology Unit, University Hospital of Rome 'Tor Vergata', Rome, Italy
| | - M Milana
- Hepatology Unit, University Hospital of Rome 'Tor Vergata', Rome, Italy
| | - L Gianserra
- Infectious Diseases, Sant'Andrea Hospital-'La Sapienza' University, Rome, Italy
| | - M Melis
- Infectious Diseases Unit, Department of Clinical and Experimental Medicine, University of Sassari, Sassari, Italy
| | - A Di Biagio
- Infectious Diseases Unit, Department of Social Health (DISSAL) of the University of Genoa, IRCCS S. Martino-IST, Genova, Italy
| | - C Sarrecchia
- Infectious Disease, University Hospital of Rome 'Tor Vergata', Rome, Italy
| | - L Sarmati
- Infectious Disease, University Hospital of Rome 'Tor Vergata', Rome, Italy
| | - S Landonio
- Division of Infectious Disease, Hospital Sacco of Milan, Milan, Italy
| | - S Francioso
- Hepatology Unit, University Hospital of Rome 'Tor Vergata', Rome, Italy
| | - L Lambiase
- Infectious Diseases, Sant'Andrea Hospital-'La Sapienza' University, Rome, Italy
| | - L A Nicolini
- Infectious Diseases Unit, Department of Social Health (DISSAL) of the University of Genoa, IRCCS S. Martino-IST, Genova, Italy
| | - S Marenco
- Department of Internal Medicine, Gastroenterology Unit, University of Genova, Genova, Italy
| | - L Nosotti
- Hepatology Unit, National Institute of Health, Migration and Poverty, Rome, Italy
| | - V Giannelli
- Gastroenterology Unit, Department of Clinical Medicine, 'La Sapienza' University, Rome, Italy
| | - M Siciliano
- Gastroenterology, Catholic University of Rome, Rome, Italy
| | - D Romagnoli
- Department of Biomedical, Metabolic and Neural Sciences, NOCSAE Baggiovara, Modena, Italy
| | - A Pellicelli
- Hepatology Unit, San Camillo Forlanini Hospital, Rome, Italy
| | - J Vecchiet
- Infectious Disease Clinic, Chieti, Italy
| | - C F Magni
- Division of Infectious Disease, Hospital Sacco of Milan, Milan, Italy
| | - S Babudieri
- Infectious Diseases Unit, Department of Clinical and Experimental Medicine, University of Sassari, Sassari, Italy
| | - M S Mura
- Infectious Diseases Unit, Department of Clinical and Experimental Medicine, University of Sassari, Sassari, Italy
| | - G Taliani
- Department of Clinical Medicine, Policlinico Umberto I, 'Sapienza' University of Rome, Rome, Italy
| | - C Mastroianni
- Department of Infectious Diseases, University of Rome 'Sapienza' (Polo Pontino), Latina, Italy
| | | | - M Romano
- S. Pertini Hospital, Rome, Italy
| | - F Morisco
- Università 'Federico II', Naples, Italy
| | - A Gasbarrini
- Gastroenterology, Catholic University of Rome, Rome, Italy
| | - V Vullo
- Department of Public Health and Infectious Diseases, University of Rome 'Sapienza', Rome, Italy
| | - S Bruno
- Department of Internal Medicine, Humanitas University, Rozzano, Milan, Italy
| | - C Baiguera
- Hospital Niguarda Ca'Granda, Milan, Italy
| | - C Pasquazzi
- Infectious Diseases, Sant'Andrea Hospital-'La Sapienza' University, Rome, Italy
| | - G Tisone
- Liver Transplant Centre, Tor Vergata University, Rome, Italy
| | - A Picciotto
- Department of Internal Medicine, Gastroenterology Unit, University of Genova, Genova, Italy
| | - M Andreoni
- Infectious Disease, University Hospital of Rome 'Tor Vergata', Rome, Italy
| | - G Parruti
- Infectious Disease Unit, Pescara General Hospital, Pescara, Italy
| | - G Rizzardini
- Division of Infectious Disease, Hospital Sacco of Milan, Milan, Italy
| | - M Angelico
- Hepatology Unit, University Hospital of Rome 'Tor Vergata', Rome, Italy
| | - C F Perno
- Department of Experimental Medicine and Surgery, University of Rome 'Tor Vergata', Rome, Italy Molecular Virology Unit, University Hospital of Rome 'Tor Vergata', Rome, Italy
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Mohamed S, Bourliere M, Benali S, Oules V, Castellani P, Khiri H, Camus C, Penaranda G, Chiche L, Gonzalez D, Sayada C, Olive D, Halfon P. Clinical relevance of the HCV protease inhibitor-resistant mutant viral load assessed by ultra-deep pyrosequencing in treatment failure. J Clin Virol 2016; 78:36-43. [PMID: 26971166 DOI: 10.1016/j.jcv.2016.02.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 02/19/2016] [Accepted: 02/23/2016] [Indexed: 01/19/2023]
Abstract
BACKGROUND The detection of low frequency mutants in patients with hepatitis C virus (HCV) receiving direct-acting antivirals (DAAs) is still debated. The clinical relevance of the mutant viral load has not yet been evaluated. OBJECTIVES To assess the viral load of resistance associated variants (RAVs) in patients at different time points, including the baseline, virological failure and one year after the cessation of therapy. STUDY DESIGN The study included 22 patients who were previously treated with protease inhibitors (PI) (with telaprevir and boceprevir). For each patient, three time points were assessed using ultra-deep pyrosequencing (UDPS). RESULTS Baseline mutations were observed in 14/22 patients (64%). At virological failure, RAVs were detected in 18/22 patients (82%). Persistent RAVs were observed in four HCV GT 1a patients (18%). Persistence mutations were found only in HCV GT 1a patients. The baseline relative V36M, R155K, R155T and A156T mutation load of patients with persistent RAVs was significantly higher (P<0.001) than those of patients without persistent RAVs. CONCLUSION The UDPS follow-up analysis demonstrated that the presence of BOC or TLP-RAVs persist one year after therapy cessation only in HCV GT 1a patients. The relative mutant viral load should be considered prior to any PI based re-treatment. This concept of the baseline mutation viral load must be validated using current therapy and must be validated on a larger cohort.
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Affiliation(s)
- Sofiane Mohamed
- Laboratoire Alphabio, Marseille, France; CRCM, Immunity and Cancer, Inserm, U1068; Institut Paoli-Calmettes; Aix-Marseille Université, UM 105; CNRS, UMR7258, F-13009 Marseille, France
| | - Marc Bourliere
- Département d'hépato-gastroenterologie, Hôpital Saint Joseph, Marseille, France
| | - Souad Benali
- Département d'hépato-gastroenterologie, Hôpital Saint Joseph, Marseille, France
| | - Valerie Oules
- Département d'hépato-gastroenterologie, Hôpital Saint Joseph, Marseille, France
| | - Paul Castellani
- Département d'hépato-gastroenterologie, Hôpital Saint Joseph, Marseille, France
| | | | | | | | | | | | - Chalom Sayada
- Advanced Biological Laboratories (ABL), Luxembourg, Luxembourg
| | - Daniel Olive
- CRCM, Immunity and Cancer, Inserm, U1068; Institut Paoli-Calmettes; Aix-Marseille Université, UM 105; CNRS, UMR7258, F-13009 Marseille, France
| | - Philippe Halfon
- Laboratoire Alphabio, Marseille, France; Hôpital Européen, Marseille, France.
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Sarrazin C. The importance of resistance to direct antiviral drugs in HCV infection in clinical practice. J Hepatol 2016; 64:486-504. [PMID: 26409317 DOI: 10.1016/j.jhep.2015.09.011] [Citation(s) in RCA: 348] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 09/15/2015] [Accepted: 09/15/2015] [Indexed: 02/08/2023]
Abstract
Treatment of chronic hepatitis C virus (HCV) infection with direct-acting antiviral agents (DAA) is associated with high rates of sustained virologic response. Remaining factors associated with treatment failure include advanced stages of liver fibrosis, response to previous antiviral therapy and viral factors such as baseline viral load and suboptimal interaction of the DAA with the target based on viral variants. Heterogeneity within NS3, NS5A, and NS5B areas interacting with DAAs exist between HCV geno- and subtypes as well as HCV isolates of the same geno- and subtype and amino acid polymorphisms associated with suboptimal efficacy of DAAs are termed resistance-associated variants (RAVs). RAVs may be associated with virologic treatment failure. However, virologic treatment failure typically occurs only if other negative predictive host or viral factors are present at the same time, susceptibility to additional antiviral agents is reduced or duration of treatment is suboptimal. In this review geno- and phenotypic resistance testing as well as clinical data on the importance of RAVs for conventional triple therapies with sofosbuvir, simeprevir, and daclatasvir and available interferon-free DAA combinations are discussed.
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Affiliation(s)
- Christoph Sarrazin
- J. W. Goethe-University Hospital, Medizinische Klinik 1, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany.
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31
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Fourati S, Pawlotsky JM. Virologic Tools for HCV Drug Resistance Testing. Viruses 2015; 7:6346-59. [PMID: 26690198 PMCID: PMC4690865 DOI: 10.3390/v7122941] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 11/28/2015] [Accepted: 11/30/2015] [Indexed: 12/22/2022] Open
Abstract
Recent advances in molecular biology have led to the development of new antiviral drugs that target specific steps of the Hepatitis C Virus (HCV) lifecycle. These drugs, collectively termed direct-acting antivirals (DAAs), include non-structural (NS) HCV protein inhibitors, NS3/4A protease inhibitors, NS5B RNA-dependent RNA polymerase inhibitors (nucleotide analogues and non-nucleoside inhibitors), and NS5A inhibitors. Due to the high genetic variability of HCV, the outcome of DAA-based therapies may be altered by the selection of amino-acid substitutions located within the targeted proteins, which affect viral susceptibility to the administered compounds. At the drug developmental stage, preclinical and clinical characterization of HCV resistance to new drugs in development is mandatory. In the clinical setting, accurate diagnostic tools have become available to monitor drug resistance in patients who receive treatment with DAAs. In this review, we describe tools available to investigate drug resistance in preclinical studies, clinical trials and clinical practice.
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Affiliation(s)
- Slim Fourati
- National Reference Center for Viral Hepatitis B, C, and D; Department of Virology, Hôpital Henri Mondor, Université Paris-Est and INSERM U955, Créteil 94010, France.
| | - Jean-Michel Pawlotsky
- National Reference Center for Viral Hepatitis B, C, and D; Department of Virology, Hôpital Henri Mondor, Université Paris-Est and INSERM U955, Créteil 94010, France.
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Pérez-Del-Pulgar S, Gregori J, Rodríguez-Frías F, González P, García-Cehic D, Ramírez S, Casillas R, Domingo E, Esteban JI, Forns X, Quer J. Quasispecies dynamics in hepatitis C liver transplant recipients receiving grafts from hepatitis C virus infected donors. J Gen Virol 2015; 96:3493-3498. [PMID: 26395289 DOI: 10.1099/jgv.0.000289] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The allocation of liver grafts from hepatitis C virus (HCV)-positive donors in HCV-infected liver transplant (LT) recipients leads to infection with two different viral populations. In a previous study, we examined quasispecies dynamics during reinfection by clonal sequencing, which did not allow an accurate characterization of coexistence and competition events. To overcome this limitation, here we used deep-sequencing analysis of a fragment of the HCV NS5B gene in six HCV-infected LT recipients who received HCV-infected grafts. Successive expansions and contractions of quasispecies complexity were observed, evolving in all cases towards a more homogeneous population. The population that became dominant was the one displaying the highest mutant spectrum complexity. In four patients, coexistence of minority mutants, derived from the donor or the recipient, were detected. In conclusion, our study shows that, during reinfection with a different HCV strain in LT recipients, the viral population with the highest diversity always becomes dominant.
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Affiliation(s)
| | - Josep Gregori
- Liver Unit, Lab. Malalties Hepàtiques, Vall d'Hebron Institut de Recerca, Hospital Vall d'Hebron, CIBERehd, Universitat Autònoma de Barcelona, Barcelona, Spain
- Roche Diagnostics, Sant Cugat del Vallès, Barcelona, Spain
| | - Francisco Rodríguez-Frías
- Biochemistry Department, Vall d'Hebron Institut de Recerca, Hospital Vall d'Hebron, CIBERehd, Barcelona, Spain
| | | | - Damir García-Cehic
- Liver Unit, Lab. Malalties Hepàtiques, Vall d'Hebron Institut de Recerca, Hospital Vall d'Hebron, CIBERehd, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Rosario Casillas
- Liver Unit, Lab. Malalties Hepàtiques, Vall d'Hebron Institut de Recerca, Hospital Vall d'Hebron, CIBERehd, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Esteban Domingo
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid (CSIC-UAM), Campus de Cantoblanco, CIBERehd, Madrid, Spain
| | - Juan I Esteban
- Liver Unit, Lab. Malalties Hepàtiques, Vall d'Hebron Institut de Recerca, Hospital Vall d'Hebron, CIBERehd, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Xavier Forns
- Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, Barcelona, Spain
| | - Josep Quer
- Liver Unit, Lab. Malalties Hepàtiques, Vall d'Hebron Institut de Recerca, Hospital Vall d'Hebron, CIBERehd, Universitat Autònoma de Barcelona, Barcelona, Spain
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Hiramine S, Furusyo N, Ogawa E, Nakamuta M, Kajiwara E, Nomura H, Dohmen K, Takahashi K, Satoh T, Azuma K, Kawano A, Koyanagi T, Kotoh K, Shimoda S, Hayashi J. Importance of virological response in the early stage of telaprevir-based triple therapy for hepatitis C. World J Hepatol 2015; 7:2688-2695. [PMID: 26609346 PMCID: PMC4651913 DOI: 10.4254/wjh.v7.i26.2688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 05/03/2015] [Accepted: 09/07/2015] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the efficacy of virological response (VR) to telaprevir (TVR)-based triple therapy in predicting treatment outcome of hepatitis C.
METHODS: This prospective, multicenter study consisted of 253 Japanese patients infected with hepatitis C virus (HCV) genotype 1b. All received 12 wk of TVR in combination with 24 wk of pegylated-interferon-α (IFN-α) and ribavirin. Serum HCV RNA was tested at weeks 1, 2, 3, 4, 6, 8, 12, 16, 20, and 24. VR was defined as undetectable serum HCV RNA. Sustained virological response (SVR) was VR at 24 wk after the end of treatment and was regarded as a successful outcome.
RESULTS: Of 253 patients, 207 (81.8%) achieved SVR. The positive predictive value of VR for SVR was 100% at week 2, after which it gradually decreased, and was over 85% to week 12. The negative predictive value (NPV) gradually increased, reaching 100% at week 12. The upslope of the NPV showed a large increase from week 4 (40.6%) to week 6 (82.4%). There was a moderate concordance between the SVR and VR at week 6 (kappa coefficient = 0.44), although other VRs had poor concordance to SVR. Multiple logistic regression analysis extracted VR at week 6 (P < 0.0001, OR = 63.8) as an independent factor contributing to SVR. In addition, the interleukin-28B single nucleotide polymorphism and response to previous pegylated-IFN-α and ribavirin therapy were identified as independent factors for SVR.
CONCLUSION: VR at week 6, but not at week 4, is an efficient predictor of both SVR and non-SVR to TVR-based triple therapy.
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Itakura J, Kurosaki M, Takada H, Nakakuki N, Matsuda S, Gondou K, Asano Y, Hattori N, Itakura Y, Tamaki N, Yasui Y, Suzuki S, Hosokawa T, Tsuchiya K, Nakanishi H, Takahashi Y, Maekawa S, Enomoto N, Izumi N. Naturally occurring, resistance-associated hepatitis C virus NS5A variants are linked to interleukin-28B genotype and are sensitive to interferon-based therapy. Hepatol Res 2015; 45:E115-21. [PMID: 25564756 DOI: 10.1111/hepr.12474] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Revised: 12/10/2014] [Accepted: 12/23/2014] [Indexed: 12/15/2022]
Abstract
AIM The presence of resistance-associated variants (RAV) may attenuate the efficacy of direct-acting antivirals (DAA) in combination therapy for hepatitis C. The aim of this study was to characterize the NS3 and NS5A regions of hepatitis C virus (HCV) in naturally occurring RAV. METHODS The NS3 and NS5A regions of HCV were amplified by nested polymerase chain reaction and their nucleotide sequences were determined by direct sequencing in 493 genotype 1b patients naive to DAA-based therapies. The effect of baseline RAV on response to pegylated interferon and ribavirin therapy was analyzed in 65 patients after stratification by interleukin (IL)-28B genotype. RESULTS The incidence of RAV was 7.9% in NS3 (V36I/L, 1.2%; T54S, 2.8%; Q80K/R, 3.0%; A156S, 0.2%; and D168E/T, 2.4%) and 20.2% in NS5A (L31I/M, 2.2%; and Y93H, 19.0%). The incidence in interferon experienced and naive patients was similar. The incidence of Y93H in NS5A was significantly higher in the IL-28B TT genotype (rs8099917) than non-TT (27.1% vs 9.5%, P < 0.001). The virological response to pegylated interferon plus ribavirin therapy was not affected by the presence of RAV in IL-28B TT genotype. CONCLUSION RAV, especially Y93H in the NS5A region, were highly prevalent in DAA naive patients with genotype 1b HCV in Japan and were linked to IL-28B TT genotype. Interferon-based therapy could be an alternative for patients with RAV because these variants did not attenuate the response to that therapy. The analysis of RAV may impact the selection of the optimal treatment strategy.
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Affiliation(s)
- Jun Itakura
- Division of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo
| | - Masayuki Kurosaki
- Division of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo
| | - Hitomi Takada
- Division of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo
| | - Natsuko Nakakuki
- Division of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo
| | - Syuya Matsuda
- Division of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo
| | - Kouichi Gondou
- Division of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo
| | - Yu Asano
- Division of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo
| | - Nobuhiro Hattori
- Division of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo
| | - Yoshie Itakura
- Division of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo
| | - Nobuharu Tamaki
- Division of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo
| | - Yutaka Yasui
- Division of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo
| | - Shoko Suzuki
- Division of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo
| | - Takanori Hosokawa
- Division of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo
| | - Kaoru Tsuchiya
- Division of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo
| | - Hiroyuki Nakanishi
- Division of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo
| | - Yuka Takahashi
- Division of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo
| | - Syinya Maekawa
- First Department of Internal Medicine, University of Yamanashi, Yamanashi, Japan
| | - Nobuyuki Enomoto
- First Department of Internal Medicine, University of Yamanashi, Yamanashi, Japan
| | - Namiki Izumi
- Division of Gastroenterology and Hepatology, Musashino Red Cross Hospital, Tokyo
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35
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Cuypers L, Li G, Libin P, Piampongsant S, Vandamme AM, Theys K. Genetic Diversity and Selective Pressure in Hepatitis C Virus Genotypes 1-6: Significance for Direct-Acting Antiviral Treatment and Drug Resistance. Viruses 2015; 7:5018-39. [PMID: 26389941 PMCID: PMC4584301 DOI: 10.3390/v7092857] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/22/2015] [Accepted: 09/01/2015] [Indexed: 12/20/2022] Open
Abstract
Treatment with pan-genotypic direct-acting antivirals, targeting different viral proteins, is the best option for clearing hepatitis C virus (HCV) infection in chronically infected patients. However, the diversity of the HCV genome is a major obstacle for the development of antiviral drugs, vaccines, and genotyping assays. In this large-scale analysis, genome-wide diversity and selective pressure was mapped, focusing on positions important for treatment, drug resistance, and resistance testing. A dataset of 1415 full-genome sequences, including genotypes 1-6 from the Los Alamos database, was analyzed. In 44% of all full-genome positions, the consensus amino acid was different for at least one genotype. Focusing on positions sharing the same consensus amino acid in all genotypes revealed that only 15% was defined as pan-genotypic highly conserved (≥99% amino acid identity) and an additional 24% as pan-genotypic conserved (≥95%). Despite its large genetic diversity, across all genotypes, codon positions were rarely identified to be positively selected (0.23%-0.46%) and predominantly found to be under negative selective pressure, suggesting mainly neutral evolution. For NS3, NS5A, and NS5B, respectively, 40% (6/15), 33% (3/9), and 14% (2/14) of the resistance-related positions harbored as consensus the amino acid variant related to resistance, potentially impeding treatment. For example, the NS3 variant 80K, conferring resistance to simeprevir used for treatment of HCV1 infected patients, was present in 39.3% of the HCV1a strains and 0.25% of HCV1b strains. Both NS5A variants 28M and 30S, known to be associated with resistance to the pan-genotypic drug daclatasvir, were found in a significant proportion of HCV4 strains (10.7%). NS5B variant 556G, known to confer resistance to non-nucleoside inhibitor dasabuvir, was observed in 8.4% of the HCV1b strains. Given the large HCV genetic diversity, sequencing efforts for resistance testing purposes may need to be genotype-specific or geographically tailored.
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Affiliation(s)
- Lize Cuypers
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Minderbroedersstraat 10, Leuven 3000, Belgium.
| | - Guangdi Li
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Minderbroedersstraat 10, Leuven 3000, Belgium.
- Metabolic Syndrome Research Center, the Second Xiangya Hospital, Central South University, Changsha 410011, China.
| | - Pieter Libin
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Minderbroedersstraat 10, Leuven 3000, Belgium.
- Artificial Intelligence Lab, Vrije Universiteit Brussel, Pleinlaan 2, Brussels 1050, Belgium.
| | - Supinya Piampongsant
- Department of Electrical Engineering ESAT, STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, KU Leuven, University of Leuven, Kasteelpark Arenberg 10, Heverlee 3001, Belgium.
| | - Anne-Mieke Vandamme
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Minderbroedersstraat 10, Leuven 3000, Belgium.
- Center for Global Health and Tropical Medicine, Microbiology Unit, Institute for Hygiene and Tropical Medicine, University Nova of Lisboa, Rua da Junqueira 100, Lisbon 1349-008, Portugal.
| | - Kristof Theys
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Minderbroedersstraat 10, Leuven 3000, Belgium.
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36
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Haseltine EL, Kimko H, Luo H, Tolsma J, Bartels DJ, Kieffer TL, Garg V. Modeling population heterogeneity in viral dynamics for chronic hepatitis C infection: Insights from Phase 3 telaprevir clinical studies. J Pharmacokinet Pharmacodyn 2015; 42:681-98. [PMID: 26289844 DOI: 10.1007/s10928-015-9435-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 08/12/2015] [Indexed: 11/28/2022]
Abstract
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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Affiliation(s)
- Eric L Haseltine
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave., Boston, MA, 02210, United States.
| | - Holly Kimko
- Janssen Research & Development, Raritan, NJ, United States
| | | | | | - Doug J Bartels
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave., Boston, MA, 02210, United States
| | - Tara L Kieffer
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave., Boston, MA, 02210, United States
| | - Varun Garg
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave., Boston, MA, 02210, United States
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Predominance of hepatitis C virus Q80K among NS3 baseline-resistance-associated amino acid variants in direct-antiviral-agent-naïve patients with chronic hepatitis: single-centre experience. Arch Virol 2015; 160:2881-5. [PMID: 26249823 DOI: 10.1007/s00705-015-2563-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 08/01/2015] [Indexed: 12/22/2022]
Abstract
In the era of direct-acting antiviral agents (DAAs), hepatitis C virus (HCV) genotyping tests at baseline are controversial. The HCV NS3-Q80K polymorphism is associated with resistance to the recently approved NS3 inhibitor simeprevir (SMV) when combined with PEG-interferon and ribavirin (PEG-IFN/RBV) and alternative therapy should be considered for patients with baseline Q80K. The aim of this study was to provide an estimate of Q80K prevalence at baseline in a study group of 205 DAA-naïve patients (21% of them with HIV coinfection) using NS3 full-population direct sequencing to detect resistance-associated amino acid variants (RAVs). NS3 RAVs were identified in 56 patients (27.3%). Q80K was the most frequently reported one (41%), in both HIV/HCV-coinfected and HCV-monoinfected patients, but it was only detectable in cases of HCV-subtype 1a infection. Therefore, in clinical practice, an NS3-Q80K genotyping test prior to simeprevir plus PEG-IFN/RBV treatment is highly recommended.
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38
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Development and Validation of Two Screening Assays for the Hepatitis C Virus NS3 Q80K Polymorphism Associated with Reduced Response to Combination Treatment Regimens Containing Simeprevir. J Clin Microbiol 2015; 53:2942-50. [PMID: 26135875 DOI: 10.1128/jcm.00650-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 06/26/2015] [Indexed: 01/03/2023] Open
Abstract
Persons with hepatitis C virus (HCV) genotype 1a (GT1a) infections harboring a baseline Q80K polymorphism in nonstructural protein 3 (NS3) have a reduced virologic response to simeprevir in combination with pegylated interferon-alfa and ribavirin. We aimed to develop, validate, and freely disseminate an NS3 clinical sequencing assay to detect the Q80K polymorphism and potentially other HCV NS3 drug resistance mutations. HCV RNA was extracted from frozen plasma using a NucliSENS easyMAG automated nucleic acid extractor, amplified by nested reverse transcription-PCR, and sequenced using Sanger and/or next-generation (MiSeq) methods. Sanger chromatograms were analyzed using in-house software (RECall), and nucleotide mixtures were called automatically. MiSeq reads were iteratively mapped to the H77 reference genome, and consensus NS3 sequences were generated with nucleotides present at >20% called as mixtures. The accuracy, precision, and sensitivity for detecting the Q80K polymorphism were assessed in 70 samples previously sequenced by an external laboratory. A comparison of the sequences generated by the Sanger and MiSeq methods with those determined by an external lab revealed >98.5% nucleotide sequence concordance and zero discordant calls of the Q80K polymorphism. The results were both highly repeatable and reproducible (>99.7% nucleotide concordance and 100% Q80K concordance). The limits of detection (>2 and ∼5 log10 IU/ml for the Sanger and MiSeq assays, respectively) are sufficiently low to allow genotyping in nearly all chronically infected treatment-naive persons. No systematic bias in the under- or overamplification of minority variants was observed. Coinfection with other viruses (e.g., HIV and hepatitis B virus [HBV]) did not affect the assay results. The two independent HCV NS3 sequencing assays with the automated analysis procedures described here are useful tools to screen for the Q80K polymorphism and other HCV protease inhibitor drug resistance mutations.
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39
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Hajji H, Aherfi S, Motte A, Ravaux I, Mokhtari S, Ruiz JM, Poizot-Martin I, Tourres C, Tivoli N, Gérolami R, Tamalet C, Colson P. Diversity of 1,213 hepatitis C virus NS3 protease sequences from a clinical virology laboratory database in Marseille university hospitals, southeastern France. J Med Virol 2015; 87:1921-33. [PMID: 25959702 DOI: 10.1002/jmv.24261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2015] [Indexed: 12/21/2022]
Abstract
Infection with hepatitis C virus (HCV) represents a major public health concern worldwide. Recent therapeutic advances have been considerable, HCV genotype continuing to guide therapeutic management. Since 2008, HCV genotyping in our clinical microbiology laboratory at university hospitals of Marseille, Southeastern France, has been based on NS3 protease gene population sequencing, to allow concurrent HCV genotype and protease inhibitor (PI) genotypic resistance determinations. We aimed, first, to analyze the genetic diversity of HCV NS3 protease obtained from blood samples collected between 2003 and 2013 from patients monitored at university hospitals of Marseille and detect possible atypical sequences; and, second, to identify NS3 protease amino acid patterns associated with decreased susceptibility to HCV PIs. A total of 1,213 HCV NS3 protease sequences were available in our laboratory sequence database. We implemented a strategy based on bioinformatic tools to determine whether HCV sequences are representative of our local HCV genetic diversity, or divergent. In our 2003-2012 HCV NS3 protease sequence database, we delineated 32 clusters representative of the majority HCV genetic diversity, and 61 divergent sequences. Five of these divergent sequences showed less than 85% nucleotide identity with their top GenBank hit. In addition, among the 294 sequences obtained in 2013, three were divergent relative to these 32 previously delineated clusters. Finally, we detected both natural and on-treatment genotypic resistance to HCV NS3 PIs, including a substantial prevalence of Q80K substitutions associated with decreased susceptibility to simeprevir, a second generation PI.
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Affiliation(s)
- Hind Hajji
- Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Marseille, France
| | - Sarah Aherfi
- Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Marseille, France.,Aix-Marseille University, URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, Facultés de Médecine et de Pharmacie, Marseille, France
| | - Anne Motte
- Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Marseille, France
| | - Isabelle Ravaux
- IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Service de Maladies Infectieuses, Centre Hospitalo-Universitaire Conception, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Saadia Mokhtari
- IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Service de Maladies Infectieuses, Centre Hospitalo-Universitaire Nord, Marseille, France
| | - Jean-Marie Ruiz
- Assistance Publique-Hôpitaux de Marseille, Hôpitaux Sud, Service de Médecine en milieu pénitentiaire, Centre pénitentiaire de Marseille, Marseille, France
| | - Isabelle Poizot-Martin
- AP-HM Sainte-Marguerite, Service d'Immuno-hématologie clinique, Marseille, France.,Aix-Marseille University, INSERM, UMR 912 (SESSTIM), Marseille, France
| | - Christian Tourres
- Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Marseille, France
| | - Natacha Tivoli
- Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Marseille, France
| | - René Gérolami
- Service d'Hépato-Gastro-Entérologie, Centre Hospitalo-Universitaire Conception, Marseille, France
| | - Catherine Tamalet
- Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Marseille, France.,Aix-Marseille University, URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, Facultés de Médecine et de Pharmacie, Marseille, France
| | - Philippe Colson
- Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Marseille, France.,Aix-Marseille University, URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, Facultés de Médecine et de Pharmacie, Marseille, France
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Naturally Occurring Resistance-Associated Variants of Hepatitis C Virus Protease Inhibitors in Poor Responders to Pegylated Interferon-Ribavirin. J Clin Microbiol 2015; 53:2195-202. [PMID: 25926499 DOI: 10.1128/jcm.03633-14] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 04/23/2015] [Indexed: 11/20/2022] Open
Abstract
The pretherapeutic presence of protease inhibitor (PI) resistance-associated variants (RAVs) has not been shown to be predictive of triple-therapy outcomes in treatment-naive patients. However, they may influence the outcome in patients with less effective pegylated interferon (pegIFN)-ribavirin (RBV) backbones. Using hepatitis C virus (HCV) population sequence analysis, we retrospectively investigated the prevalence of baseline nonstructural 3 (NS3) RAVs in a multicenter cohort of poor IFN-RBV responders (i.e., prior null responders or patients with a viral load decrease of <1 log IU/ml during the pegIFN-RBV lead-in phase). The impact of the presence of these RAVs on the outcome of triple therapy was studied. Among 282 patients, the prevalances (95% confidence intervals) of baseline RAVs ranged from 5.7% (3.3% to 9.0%) to 22.0% (17.3% to 27.3%), depending to the algorithm used. Among mutations conferring a >3-fold shift in 50% inhibitory concentration (IC50) for telaprevir or boceprevir, T54S was the most frequently detected mutation (3.9%), followed by A156T, R155K (0.7%), V36M, and V55A (0.35%). Mutations were more frequently found in patients infected with genotype 1a (7.5 to 23.6%) than 1b (3.3 to 19.8%) (P = 0.03). No other sociodemographic or viroclinical characteristic was significantly associated with a higher prevalence of RAVs. No obvious effect of baseline RAVs on viral load was observed. In this cohort of poor responders to IFN-RBV, no link was found with a sustained virological response to triple therapy, regardless of the algorithm used for the detection of mutations. Based on a cross-study comparison, baseline RAVs are not more frequent in poor IFN-RBV responders than in treatment-naive patients and, even in these difficult-to-treat patients, this study demonstrates no impact on treatment outcome, arguing against resistance analysis prior to treatment.
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Barth H. Hepatitis C virus: Is it time to say goodbye yet? Perspectives and challenges for the next decade. World J Hepatol 2015; 7:725-737. [PMID: 25914773 PMCID: PMC4404378 DOI: 10.4254/wjh.v7.i5.725] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 12/22/2014] [Accepted: 01/20/2015] [Indexed: 02/06/2023] Open
Abstract
The majority of individuals exposed to hepatitis C virus (HCV) establish a persistent infection, which is a leading cause of chronic liver disease, cirrhosis and hepatocellular carcinoma. Major progress has been made during the past twenty-five years in understanding the HCV life cycle and immune responses against HCV infection. Increasing evidence indicates that host genetic factors can significantly influence the outcome of HCV infection and the response to interferon alpha-based antiviral therapy. The arrival of highly effective and convenient treatment regimens for patients chronically infected with HCV has improved prospects for the eradication of HCV worldwide. Clinical trials are evaluating the best anti-viral drug combination, treatment doses and duration. The new treatments are better-tolerated and have shown success rates of more than 95%. However, the recent breakthrough in HCV treatment raises new questions and challenges, including the identification of HCV-infected patients and to link them to appropriate health care, the high pricing of HCV drugs, the emergence of drug resistance or naturally occurring polymorphism in HCV sequences which can compromise HCV treatment response. Finally, we still do not have a vaccine against HCV. In this concise review, we will highlight the progress made in understanding HCV infection and therapy. We will focus on the most significant unsolved problems and the key future challenges in the management of HCV infection.
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Shepherd SJ, Abdelrahman T, MacLean AR, Thomson EC, Aitken C, Gunson RN. Prevalence of HCV NS3 pre-treatment resistance associated amino acid variants within a Scottish cohort. J Clin Virol 2015; 65:50-3. [PMID: 25766988 PMCID: PMC4728298 DOI: 10.1016/j.jcv.2015.02.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 02/04/2015] [Accepted: 02/06/2015] [Indexed: 12/22/2022]
Abstract
BACKGROUND Protease inhibitors (PI) including boceprevir, telaprevir and simeprevir have revolutionised HCV genotype 1 treatment since their introduction. A number of pre-treatment resistance associated amino acid variants (RAVs) and polymorphisms have been associated with reduced response to treatment. OBJECTIVES We measured the prevalence of RAVs/polymorphisms in a PI treatment-naïve HCV genotype 1 Scottish cohort using Sanger sequencing. STUDY DESIGN Chronically infected, treatment-naïve, HCV genotype 1 patients (n = 146) attending NHS Greater Glasgow and Clyde clinics were investigated for RAVs/polymorphisms to the PIs boceprevir, telaprevir and simeprevir. The NS3/4A region was amplified by nested polymerase chain reaction. The 1.4 kb amplified product was sequenced using an ABI 3710XL DNA sequencer. Sequence analysis was performed using web-based ReCall (beta 2.10). Amino acid positions 36, 41, 43, 54, 55, 80, 109, 122, 155, 156, 168 and 170 were analysed for RAVs/polymorphisms. RESULTS Overall, 23.29% (34/146) of patients had an RAV or polymorphism detected. Overall, 13.69% (20/146) of patients had HCV virus that contained the Q8 K polymorphism. Other RAVs detected were: V36 M 0.70% (1/146), V36L 0.70% (1/146), T54S 6.85% (10/146), V55A 3.42% (5/146) and V/I170A 0.68% (1/146). Four patients had dual combinations of mutations (T54S+V36L; T54S+V55A and 2 patients with T54S+Q80K). CONCLUSIONS Q80K was the most prevalent baseline polymorphism detected in the Scottish cohort. Simeprevir treatment is not recommended in patients infected with the Q80K genotype 1a variant. This highlights the need for baseline sequencing prior to administration of this drug in this population.
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Affiliation(s)
- Samantha J Shepherd
- West of Scotland Specialist Virology Centre, Level 5, New Lister Building, 10-16 Alexandra Parade, Glasgow G31 2ER, United Kingdom.
| | - Tamer Abdelrahman
- MRC-University of Glasgow Centre for Virus Research, Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, United Kingdom
| | - Alasdair R MacLean
- West of Scotland Specialist Virology Centre, Level 5, New Lister Building, 10-16 Alexandra Parade, Glasgow G31 2ER, United Kingdom
| | - Emma C Thomson
- MRC-University of Glasgow Centre for Virus Research, Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, United Kingdom
| | - Celia Aitken
- West of Scotland Specialist Virology Centre, Level 5, New Lister Building, 10-16 Alexandra Parade, Glasgow G31 2ER, United Kingdom
| | - Rory N Gunson
- West of Scotland Specialist Virology Centre, Level 5, New Lister Building, 10-16 Alexandra Parade, Glasgow G31 2ER, United Kingdom
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Klibanov OM, Gale SE, Santevecchi B. Ombitasvir/paritaprevir/ritonavir and dasabuvir tablets for hepatitis C virus genotype 1 infection. Ann Pharmacother 2015; 49:566-81. [PMID: 25680759 DOI: 10.1177/1060028015570729] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
OBJECTIVE To review the data with ombitasvir/paritaprevir/ritonavir and dasabuvir for the treatment of chronic hepatitis C virus (HCV) genotype 1 infection. DATA SOURCES Phase I, II, and III trials and review articles were identified through MEDLINE (1996-January 2015) and PubMed (1996-January 2015), conference abstracts, and US national clinical trials registry, using the keywords NS3/4A protease inhibitor, NS5A inhibitor, NS5B polymerase inhibitor, ABT-450, ABT-267, ABT-333, paritaprevir, ombitasvir, and dasabuvir. STUDY SELECTION AND DATA EXTRACTION Preclinical, phase I, II, and III studies describing pharmacology, pharmacokinetics, efficacy, safety, and tolerability were identified. DATA SYNTHESIS Noncirrhotic patients with HCV genotype 1b experienced sustained virological response 12 weeks after completion of therapy (SVR12) rates of 96% to 100% when ombitasvir/paritaprevir/ritonavir and dasabuvir were administered for 12 weeks, regardless of inclusion of ribavirin. SVR12 rates of 95% to 97% were seen in noncirrhotic patients with HCV genotype 1a infection who received ombitasvir/paritaprevir/ritonavir and dasabuvir with ribavirin for 12 weeks. Patients with Child-Pugh Class A cirrhosis also experienced high SVR12 rates (91.8%) when ombitasvir/paritaprevir/ritonavir and dasabuvir were administered with ribavirin for 12 weeks. Cirrhotic patients with HCV genotype 1a and a history of prior null response to peginterferon/ribavirin have higher SVR12 rates when ombitasvir/paritaprevir/ritonavir and dasabuvir and ribavirin are administered for 24 instead of 12 weeks (94.2% vs 88.6%). Adverse events are typically mild, most commonly consisting of fatigue, headache, nausea, and diarrhea. CONCLUSION The regimen consisting of ombitasvir/paritaprevir/ritonavir and dasabuvir is highly efficacious in the treatment of HCV genotype 1 infection, with minimal adverse events. It is expected to play an important role in the armamentarium of novel agents that have a high chance of curing HCV infection.
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Affiliation(s)
| | - Stormi E Gale
- Wingate University School of Pharmacy, Wingate, NC, USA
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Larrat S, Kulkarni O, Claude JB, Beugnot R, Blum MGB, Fusillier K, Lupo J, Tremeaux P, Plages A, Marlu A, Duborjal H, Signori-Schmuck A, Francois O, Zarski JP, Morand P, Leroy V. Ultradeep pyrosequencing of NS3 to predict response to triple therapy with protease inhibitors in previously treated chronic hepatitis C patients. J Clin Microbiol 2015; 53:389-97. [PMID: 25411182 PMCID: PMC4298514 DOI: 10.1128/jcm.02547-14] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 10/28/2014] [Indexed: 01/04/2023] Open
Abstract
Despite the gain in sustained virological responses (SVR) provided by protease inhibitors (PIs), failures still occur. The aim of this study was to determine if a baseline analysis of the NS3 region using ultradeep pyrosequencing (UDPS) can help to predict an SVR. Serum samples from 40 patients with previously nonresponding genotype 1 chronic hepatitis C who were retreated with triple therapy, including a PI, were analyzed. Baseline UDPS of the NS3 gene was performed on plasma and peripheral blood mononuclear cells (PBMC). Mutations conferring resistance to PIs were sought. The overall diversity of the quasispecies was evaluated by calculating the Shannon entropy (SE). Resistance mutations were found in plasma and PBMC but were not discriminating enough to predict an SVR. NS3 quasispecies heterogeneity was significantly lower at baseline in patients achieving an SVR than in those not achieving an SVR (SE of 26.98 ± 16.64 × 10(-3) versus 44.93 ± 19.58 × 10(-3), P = 0.0047). With multivariate analysis, the independent predictors of an SVR were fibrosis of stage F ≤2 (odds ratio [OR], 13.3; 95% confidence interval [CI], 1.25 to 141.096; P < 0.03) and SE below the median (OR, 5.4; 95% CI, 1.22 to 23.87; P < 0.03). More than the presence of minor mutations at the baseline in plasma or in PBMC, the NS3 viral heterogeneity determined by UDPS is an independent factor for an SVR in previously treated patients receiving triple therapy that includes a PI.
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Affiliation(s)
- Sylvie Larrat
- Laboratoire de Virologie, Département des Agents Infectieux, Pôle Biologie, Centre Hospitalier Universitaire Grenoble, CS10217, Grenoble, France Unit of Virus Host Cell Interactions UMI 3265 UJF-EMBL-CNRS, BP 181, Grenoble, France
| | - Om Kulkarni
- Laboratoire TIMC-IMAG/University of Grenoble Alpes/CNRS/UMR 5525, Grenoble, France
| | | | - Réjane Beugnot
- Laboratoire de Virologie, Département des Agents Infectieux, Pôle Biologie, Centre Hospitalier Universitaire Grenoble, CS10217, Grenoble, France
| | - Michaël G B Blum
- Laboratoire TIMC-IMAG/University of Grenoble Alpes/CNRS/UMR 5525, Grenoble, France
| | - Katia Fusillier
- Laboratoire de Virologie, Département des Agents Infectieux, Pôle Biologie, Centre Hospitalier Universitaire Grenoble, CS10217, Grenoble, France
| | - Julien Lupo
- Laboratoire de Virologie, Département des Agents Infectieux, Pôle Biologie, Centre Hospitalier Universitaire Grenoble, CS10217, Grenoble, France Unit of Virus Host Cell Interactions UMI 3265 UJF-EMBL-CNRS, BP 181, Grenoble, France
| | - Pauline Tremeaux
- Laboratoire de Virologie, Département des Agents Infectieux, Pôle Biologie, Centre Hospitalier Universitaire Grenoble, CS10217, Grenoble, France Unit of Virus Host Cell Interactions UMI 3265 UJF-EMBL-CNRS, BP 181, Grenoble, France
| | - Agnès Plages
- Clinique Universitaire d'Hépato-gastroentérologie, Pôle Digidune, Centre Hospitalier Universitaire Grenoble, CS10217, Grenoble, France
| | - Alice Marlu
- Clinique Universitaire d'Hépato-gastroentérologie, Pôle Digidune, Centre Hospitalier Universitaire Grenoble, CS10217, Grenoble, France
| | | | - Anne Signori-Schmuck
- Laboratoire de Virologie, Département des Agents Infectieux, Pôle Biologie, Centre Hospitalier Universitaire Grenoble, CS10217, Grenoble, France
| | - Olivier Francois
- Laboratoire TIMC-IMAG/University of Grenoble Alpes/CNRS/UMR 5525, Grenoble, France
| | - Jean-Pierre Zarski
- Clinique Universitaire d'Hépato-gastroentérologie, Pôle Digidune, Centre Hospitalier Universitaire Grenoble, CS10217, Grenoble, France Unité INSERM/University Grenoble Alpes U823, IAPC Institut Albert Bonniot, Grenoble, France
| | - Patrice Morand
- Laboratoire de Virologie, Département des Agents Infectieux, Pôle Biologie, Centre Hospitalier Universitaire Grenoble, CS10217, Grenoble, France Unit of Virus Host Cell Interactions UMI 3265 UJF-EMBL-CNRS, BP 181, Grenoble, France
| | - Vincent Leroy
- Clinique Universitaire d'Hépato-gastroentérologie, Pôle Digidune, Centre Hospitalier Universitaire Grenoble, CS10217, Grenoble, France Unité INSERM/University Grenoble Alpes U823, IAPC Institut Albert Bonniot, Grenoble, France
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Cento V, Di Paolo D, Di Carlo D, Micheli V, Tontodonati M, De Leonardis F, Aragri M, Antonucci FP, Di Maio VC, Mancon A, Lenci I, Manunta A, Taliani G, Di Biagio A, Nicolini LA, Nosotti L, Sarrecchia C, Siciliano M, Landonio S, Pellicelli A, Gasbarrini A, Vecchiet J, Magni CF, Babudieri S, Mura MS, Andreoni M, Parruti G, Rizzardini G, Angelico M, Perno CF, Ceccherini-Silberstein F. Hepatitis C virus RNA levels at week-2 of telaprevir/boceprevir administration are predictive of virological outcome. Dig Liver Dis 2015; 47:157-63. [PMID: 25544656 DOI: 10.1016/j.dld.2014.11.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 11/12/2014] [Accepted: 11/18/2014] [Indexed: 12/11/2022]
Abstract
BACKGROUND Triple therapy with telaprevir/boceprevir + pegylated-interferon+ribavirin can achieve excellent antiviral efficacy, but it can be burdened with resistance development at failure. AIMS To evaluate kinetics of hepatitis C virus (HCV) RNA decay and early resistance development, in order to promptly identify patients at highest risk of failure to first generation protease inhibitors. METHODS HCV-RNA was prospectively quantified in 158 patients receiving pegylated-interferon+ribavirin+telaprevir (N = 114) or+boceprevir (N = 44), at early time-points and during per protocol follow-up. Drug resistance was contextually evaluated by population sequencing. RESULTS HCV-RNA at week-2 was significantly higher in patients experiencing virological failure to triple-therapy than in patients with sustained viral response (2.3 [1.9-2.8] versus 1.2 [0.3-1.7]log IU/mL, p < 0.001). A 100 IU/mL cut-off value for week-2 HCV-RNA had the highest sensitivity (86%) in predicting virological success. Indeed, 23/23 (100%) patients with undetectable HCV-RNA reached success, versus 26/34 (76.5%) patients with HCV-RNA<100 IU/mL, and only 11/31 (35.5%) with HCV-RNA > 100 IU/mL (p < 0.001). Furthermore, differently from failing patients, none of the patient with undetectable HCV-RNA at week-2 had baseline/early resistance. CONCLUSIONS With triple therapy based on first generation protease inhibitors, suboptimal HCV-RNA decay at week-2 combined with early detection of resistance can help identifying patients with higher risk of virological failure, thus requiring a closer monitoring during therapy.
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Affiliation(s)
- Valeria Cento
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, Italy
| | - Daniele Di Paolo
- Hepatology Unit, University Hospital of Rome "Tor Vergata", Rome, Italy
| | - Domenico Di Carlo
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, Italy
| | | | - Monica Tontodonati
- Infectious Disease Clinic, Chieti, Italy; Infectious Disease Unit, Pescara General Hospital, Pescara, Italy
| | | | - Marianna Aragri
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, Italy
| | | | - Velia Chiara Di Maio
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, Italy
| | | | - Ilaria Lenci
- Hepatology Unit, University Hospital of Rome "Tor Vergata", Rome, Italy
| | - Alessandra Manunta
- Infectious Diseases Unit, Department of Clinical and Experimental Medicine, University of Sassari, Italy
| | | | | | | | - Lorenzo Nosotti
- Hepatology Unit, National Institute of Health, Migration and Poverty, Rome, Italy
| | - Cesare Sarrecchia
- Infectious Disease, University Hospital of Rome "Tor Vergata", Rome, Italy
| | | | - Simona Landonio
- Division of Infectious Disease, Hospital Sacco of Milan, Milan, Italy
| | | | | | | | | | - Sergio Babudieri
- Infectious Diseases Unit, Department of Clinical and Experimental Medicine, University of Sassari, Italy
| | - Maria Stella Mura
- Infectious Diseases Unit, Department of Clinical and Experimental Medicine, University of Sassari, Italy
| | - Massimo Andreoni
- Infectious Disease, University Hospital of Rome "Tor Vergata", Rome, Italy
| | - Giustino Parruti
- Infectious Disease Unit, Pescara General Hospital, Pescara, Italy
| | | | - Mario Angelico
- Hepatology Unit, University Hospital of Rome "Tor Vergata", Rome, Italy
| | - Carlo Federico Perno
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", Rome, Italy
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No correspondence between resistance mutations in the HCV-NS3 protease at baseline and early telaprevir-based triple therapy. BBA CLINICAL 2015; 3:146-51. [PMID: 26674563 PMCID: PMC4661554 DOI: 10.1016/j.bbacli.2015.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 01/23/2015] [Accepted: 01/26/2015] [Indexed: 02/06/2023]
Abstract
Direct-acting antiviral (DAA)-based therapy is the new standard treatment for chronic hepatitis C virus (HCV) infection. However, protease inhibitor (PI)-resistant viral variants have been often described. This study aimed to examine HCV-NS3 protease variants at baseline and at 4 weeks under triple therapy. To this end, we analyzed the presence of variants in HCV-NS3 protease region from peripheral blood samples of 16 patients infected with HCV-1 at baseline and at 4 weeks of combined therapy with telaprevir, pegylated interferon, and ribavirin, using next-generation sequencing. Several variants with synonymous and non-synonymous amino acid substitutions were detected at both time points. Variants detected at low frequency corresponded to 74% (HCV-1a) and 35% (HCV-1b) of non-synonymous substitutions. We found nine PI-resistance-associated variants (V36A, T54S, V55I, Q80K, Q80R, V107I, I132V, D168E, M175L) in HCV-NS3 of 10 patients. There was no correspondence of resistance-associated variant profile between baseline and at 4 weeks. Moreover, these resistance variants at baseline and short-term treatment are not good predictors of outcome under triple therapy. Our study also shows a large number of others minor and major non-synonymous variants in HCV-NS3 early in telaprevir-based therapy that can be important for further drug resistance association studies with newly developed PI agents.
HCV-NS3 protease variants were analyzed at baseline and 4 weeks of triple therapy. Synonymous and non-synonymous variants, even at low frequency, were detected. Nine PI resistance mutations were identified in 10/16 patients in both time points. There was no correspondence between resistance mutation at baseline and 4 weeks. We provide a comprehensive databank of non-synonymous variants in HCV-NS3.
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May S, Ngui SL, Collins S, Lattimore S, Ramsay M, Tedder RS, Ijaz S. Molecular epidemiology of newly acquired hepatitis C infections in England 2008-2011: genotype, phylogeny and mutation analysis. J Clin Virol 2014; 64:6-11. [PMID: 25728071 DOI: 10.1016/j.jcv.2014.12.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 12/19/2014] [Accepted: 12/23/2014] [Indexed: 10/24/2022]
Abstract
BACKGROUND Analysis of laboratory testing data collected through the Sentinel Surveillance programme has provided a method for identifying individuals who have recently acquired their hepatitis C virus (HCV) infection. Access to samples from these individuals provided a rare opportunity to undertake molecular characterization studies. OBJECTIVES To describe the epidemiology and genetic diversity of hepatitis C in recent seroconverter infections and to predict how this will impact on HCV treatment and control. STUDY DESIGN One hundred and forty seven samples were available from individuals, identified to have recently acquired their HCV infection. Genotype determination with additional phylogenetic analysis was carried out on NS5B sequences. Analysis across the NS3 region investigated the presence of antiviral resistance mutations. Where possible, molecular data was linked to demographic and risk/behavioural factor information. RESULTS The majority of new infections occurred in males with a mean age of 37 years. The most commonly observed genotypes were 1a (49%) and 3a (42%) and injecting drug use (58%) was the most common risk factor. Genotype distribution differed between persons who inject drugs and those with other risk factors suggesting two possible epidemics. Phylogenetic analysis indicated possible transmission networks within specific risk groups. Amino acid changes associated with antiviral resistance were noted in the NS3 region in some samples. CONCLUSIONS Continued surveillance of linked molecular, virological, demographic and epidemiological information on recently acquired infections will contribute to understanding the on-going HCV epidemic in England.
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Affiliation(s)
- Shoshanna May
- Blood Borne Virus Unit, Microbiology Service - Colindale, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Siew Lin Ngui
- Blood Borne Virus Unit, Microbiology Service - Colindale, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Sarah Collins
- Immunisation, Hepatitis and Blood Safety Department, Centre for Infectious Disease Surveillance and Control, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Sam Lattimore
- Immunisation, Hepatitis and Blood Safety Department, Centre for Infectious Disease Surveillance and Control, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Mary Ramsay
- Immunisation, Hepatitis and Blood Safety Department, Centre for Infectious Disease Surveillance and Control, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK
| | - Richard S Tedder
- Blood Borne Virus Unit, Microbiology Service - Colindale, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK; Division of Infection and Immunity, University College London, Gower Street, London WC1E 6BT, UK; Transfusion Microbiology, NHS Blood and Transplant, Colindale Avenue, London, NW9 5BG, UK
| | - Samreen Ijaz
- Blood Borne Virus Unit, Microbiology Service - Colindale, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK.
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McCormick AL, Moynihan L, Macartney MJ, Garcia-Diaz A, Smith C, Johnson MA, Rodger AJ, Bhagani S, Haque T, Webster DP. Baseline drug resistance mutations are detectable in HCV genes NS3 and NS5A but not NS5B in acute and chronic HIV-coinfected patients. Antivir Ther 2014; 20:361-3. [PMID: 25279548 DOI: 10.3851/imp2871] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2014] [Indexed: 10/24/2022]
Affiliation(s)
- Adele L McCormick
- Department of Virology, Royal Free London NHS Foundation Trust, London, UK.
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Liu G, Cai Q, Li Z, Shao X, Luo Q, Zhang X, Zhao Z. Effect of drug resistance mutations on antiviral agents in HCV patients. Antivir Ther 2014; 21:369-75. [PMID: 25222865 DOI: 10.3851/imp2852] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2014] [Indexed: 10/24/2022]
Abstract
BACKGROUND Gene polymorphism of HCV is an important cause of drug resistance to direct-acting antivirals (DAAs). METHODS Nested PCR assays were performed to amplify the HCV viral regions of NS3, NS5A and NS5B. RESULTS Major resistant mutation A156S was found in 18.33% of patients with HCV-1b and 64.28% of patients with HCV-2a. HCV-6a patients had a Q80K mutation rate of 95.45%, while the mutation rate of V170I was up to 100%. Mutation frequency varied with the different genotypes of HCV. The proportion of four resistance mutations (M36L, Q80K, A156S, V170I) in different groups were statistically significant (P<0.05). Resistant mutation Q30R was detected in 116 (72.5%) samples with HCV-1b and -6a, L31M was found in 16 patients, including 12 with HCV-2a and 4 with HCV-6a, H58P was discovered in 42.5% (68/160) of patients with the genotypes Q30R, L31M and H58P; Y93C was found in 9individuals with only HCV-2a. In HCV NS5B sequences, only a few resistant variants were detected, including C316N and S282T. CONCLUSIONS Naturally occurring dominant resistance mutations to HCV DAAs pre-existed in treatment-naive patients in China. Mutation frequency and characteristics varied with the HCV genotype.
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Affiliation(s)
- Grey Liu
- The Department of Infectious Disease, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
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Applegate TL, Gaudieri S, Plauzolles A, Chopra A, Grebely J, Lucas M, Hellard M, Luciani F, Dore GJ, Matthews GV. Naturally occurring dominant drug resistance mutations occur infrequently in the setting of recently acquired hepatitis C. Antivir Ther 2014; 20:199-208. [PMID: 25105742 DOI: 10.3851/imp2821] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2014] [Indexed: 12/13/2022]
Abstract
BACKGROUND Direct-acting antivirals (DAAs) are predicted to transform hepatitis C therapy, yet little is known about the prevalence of naturally occurring resistance mutations in recently acquired HCV. This study aimed to determine the prevalence and frequency of drug resistance mutations in the viral quasispecies among HIV-positive and -negative individuals with recent HCV. METHODS The NS3 protease, NS5A and NS5B polymerase genes were amplified from 50 genotype 1a participants of the Australian Trial in Acute Hepatitis C. Amino acid variations at sites known to be associated with possible drug resistance were analysed by ultra-deep pyrosequencing. RESULTS A total of 12% of individuals harboured dominant resistance mutations, while 36% demonstrated non-dominant resistant variants below that detectable by bulk sequencing (that is, <20%) but above a threshold of 1%. Resistance variants (<1%) were observed at most sites associated with DAA resistance from all classes, with the exception of sofosbuvir. CONCLUSIONS Dominant resistant mutations were uncommonly observed in the setting of recent HCV. However, low-level mutations to all DAA classes were observed by deep sequencing at the majority of sites and in most individuals. The significance of these variants and impact on future treatment options remains to be determined. Clinicaltrials.gov NCT00192569.
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