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Molecular Epidemiology and Baseline Resistance of Hepatitis C Virus to Direct Acting Antivirals in Croatia. Pathogens 2022; 11:pathogens11070808. [PMID: 35890052 PMCID: PMC9323280 DOI: 10.3390/pathogens11070808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/15/2022] [Accepted: 07/18/2022] [Indexed: 02/04/2023] Open
Abstract
Molecular epidemiology of hepatitis C virus (HCV) is exceptionally complex due to the highly diverse HCV genome. Genetic diversity, transmission dynamics, and epidemic history of the most common HCV genotypes were inferred by population sequencing of the HCV NS3, NS5A, and NS5B region followed by phylogenetic and phylodynamic analysis. The results of this research suggest high overall prevalence of baseline NS3 resistance associate substitutions (RAS) (33.0%), moderate prevalence of NS5A RAS (13.7%), and low prevalence of nucleoside inhibitor NS5B RAS (8.3%). Prevalence of RAS significantly differed according to HCV genotype, with the highest prevalence of baseline resistance to NS3 inhibitors and NS5A inhibitors observed in HCV subtype 1a (68.8%) and subtype 1b (21.3%), respectively. Phylogenetic tree reconstructions showed two distinct clades within the subtype 1a, clade I (62.4%) and clade II (37.6%). NS3 RAS were preferentially associated with clade I. Phylogenetic analysis demonstrated that 27 (9.0%) HCV sequences had a presumed epidemiological link with another sequence and classified into 13 transmission pairs or clusters which were predominantly comprised of subtype 3a viruses and commonly detected among intravenous drug users (IDU). Phylodynamic analyses highlighted an exponential increase in subtype 1a and 3a effective population size in the late 20th century, which is a period associated with an explosive increase in the number of IDU in Croatia.
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Tisthammer KH, Solis C, Orcales F, Nzerem M, Winstead R, Dong W, Joy JB, Pennings PS. Assessing in vivo mutation frequencies and creating a high-resolution genome-wide map of fitness costs of Hepatitis C virus. PLoS Genet 2022; 18:e1010179. [PMID: 35500034 PMCID: PMC9113599 DOI: 10.1371/journal.pgen.1010179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 05/17/2022] [Accepted: 03/30/2022] [Indexed: 11/18/2022] Open
Abstract
Like many viruses, Hepatitis C Virus (HCV) has a high mutation rate, which helps the virus adapt quickly, but mutations come with fitness costs. Fitness costs can be studied by different approaches, such as experimental or frequency-based approaches. The frequency-based approach is particularly useful to estimate in vivo fitness costs, but this approach works best with deep sequencing data from many hosts are. In this study, we applied the frequency-based approach to a large dataset of 195 patients and estimated the fitness costs of mutations at 7957 sites along the HCV genome. We used beta regression and random forest models to better understand how different factors influenced fitness costs. Our results revealed that costs of nonsynonymous mutations were three times higher than those of synonymous mutations, and mutations at nucleotides A or T had higher costs than those at C or G. Genome location had a modest effect, with lower costs for mutations in HVR1 and higher costs for mutations in Core and NS5B. Resistance mutations were, on average, costlier than other mutations. Our results show that in vivo fitness costs of mutations can be site and virus specific, reinforcing the utility of constructing in vivo fitness cost maps of viral genomes.
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Affiliation(s)
- Kaho H. Tisthammer
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
- * E-mail:
| | - Caroline Solis
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Faye Orcales
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Madu Nzerem
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Ryan Winstead
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Weiyan Dong
- BC Centre for Excellence in HIV/AIDS, Vancouver, British Colombia, Canada
| | - Jeffrey B. Joy
- BC Centre for Excellence in HIV/AIDS, Vancouver, British Colombia, Canada
- Division of Infectious Diseases, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Bioinformatics Programme, University of British Columbia, Vancouver, British Colombia, Canada
| | - Pleuni S. Pennings
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
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Akiyama MJ, Riback L, Reeves JD, Lie YS, Agyemang L, Norton BL, Arnsten JH, Litwin AH. Hepatitis C Resistance-Associated Substitutions Among People Who Inject Drugs Treated With Direct-Acting Antiviral-Containing Regimens. Open Forum Infect Dis 2021; 8:ofab474. [PMID: 34692891 PMCID: PMC8530260 DOI: 10.1093/ofid/ofab474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/17/2021] [Indexed: 12/09/2022] Open
Abstract
BACKGROUND Resistance-associated substitutions (RASs) to HCV direct-acting antivirals (DAAs) can contribute to virologic failure and limit retreatment options. People who inject drugs (PWID) are at highest risk for transmission of resistant virus. We report on RASs at baseline and after virologic failure in DAA-naive and protease inhibitor-experienced PWID. METHODS We sequenced the NS3/4A, NS5A, and NS5B regions from 150 PWID with genotype 1 (GT1) viruses; 128 (85.3%) GT1a, 22 (14.7%) GT1b. RESULTS Among the 139 (92.7%) DAA-naive PWID, 85 of 139 (61.2%) had baseline RASs-67 of 139 (48.2%) in NS3 (predominantly Q80K/L); 25 of 139 (18.0%) in NS5A; and 8 of 139 (5.8%) in NS5B. Of the 11 protease inhibitor-experienced participants, 9 had baseline NS3 RASs (V36L N = 1, Q80K N = 9) and 4 had baseline NS5A RASs (M28V N = 2, H58P N = 1, A92T N = 1). Among the 11 participants who had posttreatment samples with detectable virus (7 treatment failures, 1 late relapse, 3 reinfections), 1 sofosbuvir/ledipasvir failure had a baseline H58P. Two sofosbuvir/ledipasvir-treated participants developed new NS5A mutations (Q30H, Y93H, L31M/V). Otherwise, no RASs were detected. CONCLUSIONS Our results demonstrate RAS prevalence among DAA-naive PWID is comparable to that in the general population. Only 2 of 150 (1.3%) in our longitudinal cohort developed treatment-emergent RASs. Concern for transmission of resistant virus may therefore be minimal.
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Affiliation(s)
- Matthew J Akiyama
- Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NEW YORK, USA
| | - Lindsey Riback
- Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NEW YORK, USA
| | | | - Yolanda S Lie
- Monogram Biosciences, LabCorp, South San Francisco, California, USA
| | - Linda Agyemang
- Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NEW YORK, USA
| | - Brianna L Norton
- Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NEW YORK, USA
| | - Julia H Arnsten
- Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NEW YORK, USA
| | - Alain H Litwin
- Prisma Health, Greenville, South Carolina, USA
- University of South Carolina School of Medicine, Greenville, South Carolina, USA
- Clemson University, Clemson, South Carolina, USA
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Dultz G, Srikakulam SK, Konetschnik M, Shimakami T, Doncheva NT, Dietz J, Sarrazin C, Biondi RM, Zeuzem S, Tampé R, Kalinina OV, Welsch C. Epistatic interactions promote persistence of NS3-Q80K in HCV infection by compensating for protein folding instability. J Biol Chem 2021; 297:101031. [PMID: 34339738 PMCID: PMC8405986 DOI: 10.1016/j.jbc.2021.101031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 11/28/2022] Open
Abstract
The Q80K polymorphism in the NS3-4A protease of the hepatitis C virus is associated with treatment failure of direct-acting antiviral agents. This polymorphism is highly prevalent in genotype 1a infections and stably transmitted between hosts. Here, we investigated the underlying molecular mechanisms of evolutionarily conserved coevolving amino acids in NS3-Q80K and revealed potential implications of epistatic interactions in immune escape and variants persistence. Using purified protein, we characterized the impact of epistatic amino acid substitutions on the physicochemical properties and peptide cleavage kinetics of the NS3-Q80K protease. We found that Q80K destabilized the protease protein fold (p < 0.0001). Although NS3-Q80K showed reduced peptide substrate turnover (p < 0.0002), replicative fitness in an H77S.3 cell culture model of infection was not significantly inferior to the WT virus. Epistatic substitutions at residues 91 and 174 in NS3-Q80K stabilized the protein fold (p < 0.0001) and leveraged the WT protease stability. However, changes in protease stability inversely correlated with enzymatic activity. In infectious cell culture, these secondary substitutions were not associated with a gain of replicative fitness in NS3-Q80K variants. Using molecular dynamics, we observed that the total number of residue contacts in NS3-Q80K mutants correlated with protein folding stability. Changes in the number of contacts reflected the compensatory effect on protein folding instability by epistatic substitutions. In summary, epistatic substitutions in NS3-Q80K contribute to viral fitness by mechanisms not directly related to RNA replication. By compensating for protein-folding instability, epistatic interactions likely protect NS3-Q80K variants from immune cell recognition.
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Affiliation(s)
- Georg Dultz
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Sanjay K Srikakulam
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University Campus, Saarbrücken, Germany; Graduate School of Computer Science, Saarland University, Saarbrücken, Germany; Interdisciplinary Graduate School of Natural Product Research, Saarland University, Saarbrücken, Germany
| | - Michael Konetschnik
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Tetsuro Shimakami
- Department of Gastroenterology, Kanazawa University Hospital, Kanazawa, Japan
| | - Nadezhda T Doncheva
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Julia Dietz
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Christoph Sarrazin
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Ricardo M Biondi
- Molecular Targeting, Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Stefan Zeuzem
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt am Main, Germany; University Center for Infectious Diseases, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Olga V Kalinina
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research, Saarland University Campus, Saarbrücken, Germany; Medical Faculty, Saarland University, Homburg, Germany; Center for Bioinformatics, Saarland Informatics Campus, Saarbrücken, Germany
| | - Christoph Welsch
- Department of Internal Medicine 1, Goethe University Hospital Frankfurt, Frankfurt am Main, Germany; University Center for Infectious Diseases, University Hospital Frankfurt, Frankfurt am Main, Germany.
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Frías M, Rivero-Juárez A, Machuca I, Camacho Á, Rivero A. The outlook for precision medicine for the treatment of chronic hepatitis C infection: challenges and opportunities. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2020. [DOI: 10.1080/23808993.2020.1764346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Mario Frías
- Clinical Virology and Zoonoses, Hospital Universitario Reina Sofía de Córdoba. Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC), Universidad de Córdoba, Spain
| | - Antonio Rivero-Juárez
- Clinical Virology and Zoonoses, Hospital Universitario Reina Sofía de Córdoba. Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC), Universidad de Córdoba, Spain
| | - Isabel Machuca
- Clinical Virology and Zoonoses, Hospital Universitario Reina Sofía de Córdoba. Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC), Universidad de Córdoba, Spain
| | - Ángela Camacho
- Clinical Virology and Zoonoses, Hospital Universitario Reina Sofía de Córdoba. Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC), Universidad de Córdoba, Spain
| | - Antonio Rivero
- Clinical Virology and Zoonoses, Hospital Universitario Reina Sofía de Córdoba. Instituto Maimonides de Investigación Biomédica de Córdoba (IMIBIC), Universidad de Córdoba, Spain
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Peres-da-Silva A, Antunes D, Quintanilha Torres AL, Caffarena ER, Lampe E. Effects of the Q80K Polymorphism on the Physicochemical Properties of Hepatitis C Virus Subtype 1a NS3 Protease. Viruses 2019; 11:E691. [PMID: 31366046 PMCID: PMC6723822 DOI: 10.3390/v11080691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/04/2019] [Accepted: 06/13/2019] [Indexed: 02/07/2023] Open
Abstract
Hepatitis C virus genotype 1a (HCV-1a) comprises clades I and II. The Q80K polymorphism is found predominantly in clade I but rarely in clade II. Here, we investigated whether natural polymorphisms in HCV-1a clade II entailed structural protein changes when occurrence of the Q80K variant was simulated. Based on HCV-1a clade I and II protein sequences, the structure of the HCV-1a Q80K mutant NS3-4A was obtained by comparative modeling. Its physicochemical properties were studied by molecular dynamics simulations and network analysis. Results demonstrate that, in the presence of the K80 variant, clade II protease polymorphisms A91 and S/G174 led to variations in hydrogen bond occupancies. Structural analyses revealed differences in (i) flexibility of the H57 catalytic residue on the NS3 protease and (ii) correlations between amino acids on the NS3 protease and the NS4A cofactor. The latter indicated possible destabilization of interactions, resulting in increased separation of these proteins. The present findings describe how the relationships between different HCV-1a NS3 protease amino acid residues could affect the appearance of viral variants and the existence of distinct genetic barriers to HCV-1a isolates.
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Affiliation(s)
- Allan Peres-da-Silva
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz/FIOCRUZ, Rio de Janeiro, RJ 21040-900, Brazil.
| | - Deborah Antunes
- Programa de Computação Científica, Instituto Oswaldo Cruz/FIOCRUZ, Rio de Janeiro, RJ 21040-900, Brazil
| | - André Luiz Quintanilha Torres
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz/FIOCRUZ, Rio de Janeiro, RJ 21040-900, Brazil
- Laboratório de Bioinformática, Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro/UFRJ, Rio de Janeiro, RJ 21941-909, Brazil
| | - Ernesto Raul Caffarena
- Programa de Computação Científica, Instituto Oswaldo Cruz/FIOCRUZ, Rio de Janeiro, RJ 21040-900, Brazil
| | - Elisabeth Lampe
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz/FIOCRUZ, Rio de Janeiro, RJ 21040-900, Brazil
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Abstract
The comparative study of homologous proteins can provide abundant information about the functional and structural constraints on protein evolution. For example, an amino acid substitution that is deleterious may become permissive in the presence of another substitution at a second site of the protein. A popular approach for detecting coevolving residues is by looking for correlated substitution events on branches of the molecular phylogeny relating the protein-coding sequences. Here we describe a machine learning method (Bayesian graphical models) implemented in the open-source phylogenetic software package HyPhy, http://hyphy.org , for extracting a network of coevolving residues from a sequence alignment.
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Esposito I, Marciano S, Haddad L, Galdame O, Franco A, Gadano A, Flichman D, Trinks J. Prevalence and Factors Related to Natural Resistance-Associated Substitutions to Direct-Acting Antivirals in Patients with Genotype 1 Hepatitis C Virus Infection. Viruses 2018; 11:E3. [PMID: 30577623 PMCID: PMC6356817 DOI: 10.3390/v11010003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 12/14/2018] [Accepted: 12/19/2018] [Indexed: 02/06/2023] Open
Abstract
This study aimed to assess the prevalence of natural resistance-associated substitutions (RASs) to NS3, NS5A and NS5B inhibitors in 86 genotype 1 Hepatitis C Virus (HCV)-infected patients from Buenos Aires, Argentina, and to determine their effect on therapy outcome. Additionally, virological, clinical and host genetic factors were explored as predictors of the presence of baseline RASs. NS3 RASs (39.2%) were more prevalent than NS5A RASs (25%) and NS5B RASs (8.9%). In the three regions, the frequencies of RASs were significantly higher in HCV-1b than in HCV-1a. The prevalence of Y93H, L159F and Q80K were 1.3%, 6.3% and 2.5%, respectively. IFNL3 CC genotype was identified as an independent predictor of the presence of baseline RASs in NS5A and NS3 genes (p = 0.0005 and p = 0.01, respectively). Sustained virologic response was achieved by 93.3% of the patients after receiving direct-acting antivirals (DAAs), although 48.7% of them showed baseline RASs related to the DAA-regimen. Notably, the prevalence of clinically relevant RASs in the three genes was lower than that observed around the world. The baseline presence of RASs in both subtypes did not appear to affect therapy outcome. These results support the need to evaluate resistance patterns in each particular country since RASs´ prevalence significantly vary worldwide.
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Affiliation(s)
- Isabella Esposito
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), CONICET, Instituto Universitario del Hospital Italiano (IUHI), Hospital Italiano (HIBA), C1199ACL Buenos Aires, Argentina.
| | - Sebastián Marciano
- Sección de Hepatología, Servicio de Clínica Médica, Hospital Italiano de Buenos Aires, C1199ABB Buenos Aires, Argentina.
- Departamento de Investigación, Hospital Italiano de Buenos Aires, C1199ABB Buenos Aires, Argentina.
| | - Leila Haddad
- Sección de Hepatología, Servicio de Clínica Médica, Hospital Italiano de Buenos Aires, C1199ABB Buenos Aires, Argentina.
| | - Omar Galdame
- Sección de Hepatología, Servicio de Clínica Médica, Hospital Italiano de Buenos Aires, C1199ABB Buenos Aires, Argentina.
| | - Alejandra Franco
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), CONICET, Instituto Universitario del Hospital Italiano (IUHI), Hospital Italiano (HIBA), C1199ACL Buenos Aires, Argentina.
| | - Adrián Gadano
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), CONICET, Instituto Universitario del Hospital Italiano (IUHI), Hospital Italiano (HIBA), C1199ACL Buenos Aires, Argentina.
- Sección de Hepatología, Servicio de Clínica Médica, Hospital Italiano de Buenos Aires, C1199ABB Buenos Aires, Argentina.
- Departamento de Investigación, Hospital Italiano de Buenos Aires, C1199ABB Buenos Aires, Argentina.
| | - Diego Flichman
- Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, C1113AAD Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1425FQB Buenos Aires, Argentina.
| | - Julieta Trinks
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), CONICET, Instituto Universitario del Hospital Italiano (IUHI), Hospital Italiano (HIBA), C1199ACL Buenos Aires, Argentina.
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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: 1.0] [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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Schnell G, Krishnan P, Tripathi R, Beyer J, Reisch T, Irvin M, Dekhtyar T, Lu L, Ng TI, Xie W, Pilot-Matias T, Collins C. Hepatitis C virus genetic diversity by geographic region within genotype 1-6 subtypes among patients treated with glecaprevir and pibrentasvir. PLoS One 2018; 13:e0205186. [PMID: 30286205 PMCID: PMC6171933 DOI: 10.1371/journal.pone.0205186] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 09/20/2018] [Indexed: 12/24/2022] Open
Abstract
Hepatitis C virus (HCV) is genetically diverse and includes 7 genotypes and 67 confirmed subtypes, and the global distribution of each HCV genotype (GT) varies by geographic region. In this report, we utilized a large dataset of NS3/4A and NS5A sequences isolated from 2348 HCV GT1-6-infected patients treated with the regimen containing glecaprevir/pibrentasvir (GLE/PIB) to assess genetic diversity within HCV subtypes by geographic region using phylogenetic analyses, and evaluated the prevalence of baseline amino acid polymorphisms in NS3 and NS5A by region/country and phylogenetic cluster. Among 2348 NS3/4A and NS5A sequences, phylogenetic analysis identified 6 genotypes and 44 subtypes, including 3 GT1, 8 GT2, 3 GT3, 13 GT4, 1 GT5, and 16 GT6 subtypes. Phylogenetic analysis of HCV subtype 1a confirmed the presence of two clades, which differed by geographic region distribution and NS3 Q80K prevalence. We detected phylogenetic clustering by country in HCV subtypes 1a, 1b, 2a, 2b, and 5a, suggesting that genetically distinct virus lineages are circulating in different countries. In addition, two clades were detected in HCV GT4a and GT6e, and NS5A amino acid polymorphisms were differentially distributed between the 2 clades in each subtype. The prevalence of NS3 and NS5A baseline polymorphisms varied substantially by genotype and subtype; therefore, we also determined the activity of GLE or PIB against replicons containing NS3/4A or NS5A from HCV GT1-6 clinical samples representing 6 genotypes and 21 subtypes overall. GLE and PIB retained activity against the majority of HCV replicons containing NS3/4A or NS5A from HCV GT1-6 clinical samples, with a median EC50 of 0.29 nM for GLE and 1.1 pM for PIB in a transient replicon assay. The data presented in this report expands the available data on HCV epidemiology, subtype diversity by geographic region, and NS3 and NS5A baseline polymorphism prevalence.
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Affiliation(s)
- Gretja Schnell
- Research & Development, AbbVie Inc., North Chicago, Illinois, United States of America
| | - Preethi Krishnan
- Research & Development, AbbVie Inc., North Chicago, Illinois, United States of America
| | - Rakesh Tripathi
- Research & Development, AbbVie Inc., North Chicago, Illinois, United States of America
| | - Jill Beyer
- Research & Development, AbbVie Inc., North Chicago, Illinois, United States of America
| | - Thomas Reisch
- Research & Development, AbbVie Inc., North Chicago, Illinois, United States of America
| | - Michelle Irvin
- Research & Development, AbbVie Inc., North Chicago, Illinois, United States of America
| | - Tatyana Dekhtyar
- Research & Development, AbbVie Inc., North Chicago, Illinois, United States of America
| | - Liangjun Lu
- Research & Development, AbbVie Inc., North Chicago, Illinois, United States of America
| | - Teresa I. Ng
- Research & Development, AbbVie Inc., North Chicago, Illinois, United States of America
| | - Wangang Xie
- Research & Development, AbbVie Inc., North Chicago, Illinois, United States of America
| | - Tami Pilot-Matias
- Research & Development, AbbVie Inc., North Chicago, Illinois, United States of America
| | - Christine Collins
- Research & Development, AbbVie Inc., North Chicago, Illinois, United States of America
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11
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Knops E, Sierra S, Kalaghatgi P, Heger E, Kaiser R, Kalinina OV. Epistatic Interactions in NS5A of Hepatitis C Virus Suggest Drug Resistance Mechanisms. Genes (Basel) 2018; 9:E343. [PMID: 29986475 PMCID: PMC6071292 DOI: 10.3390/genes9070343] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 06/29/2018] [Indexed: 02/06/2023] Open
Abstract
Hepatitis C virus (HCV) causes a major health burden and can be effectively treated by direct-acting antivirals (DAAs). The non-structural protein 5A (NS5A), which plays a role in the viral genome replication, is one of the DAAs’ targets. Resistance-associated viruses (RAVs) harbouring NS5A resistance-associated mutations (RAMs) have been described at baseline and after therapy failure. A mutation from glutamine to arginine at position 30 (Q30R) is a characteristic RAM for the HCV sub/genotype (GT) 1a, but arginine corresponds to the wild type in the GT-1b; still, GT-1b strains are susceptible to NS5A-inhibitors. In this study, we show that GT-1b strains with R30Q often display other specific NS5A substitutions, particularly in positions 24 and 34. We demonstrate that in GT-1b secondary substitutions usually happen after initial R30Q development in the phylogeny, and that the chemical properties of the corresponding amino acids serve to restore the positive charge in this region, acting as compensatory mutations. These findings may have implications for RAVs treatment.
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Affiliation(s)
- Elena Knops
- Institute of Virology, University of Cologne, 50935 Cologne, Germany.
| | - Saleta Sierra
- Institute of Virology, University of Cologne, 50935 Cologne, Germany.
- German Center for Infection Research (DZIF)-Cologne-Bonn Partner Site, 50935 Cologne, Germany.
| | - Prabhav Kalaghatgi
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123 Saarbrücken, Germany.
- German Center for Infection Research (DZIF)-Saarbrücken Partner Site, 66123 Saarbrücken, Germany.
| | - Eva Heger
- Institute of Virology, University of Cologne, 50935 Cologne, Germany.
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, 50935 Cologne, Germany.
- German Center for Infection Research (DZIF)-Cologne-Bonn Partner Site, 50935 Cologne, Germany.
| | - Olga V Kalinina
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123 Saarbrücken, Germany.
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12
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Moreira RC, de Torres Santos AP, Lisboa-Neto G, Mendes-Corrêa MCJ, Lemos MF, Malta FM, Santana RAF, Dastoli GTF, de Castro VFD, Pinho JRR. Prevalence of naturally occurring amino acid substitutions associated with resistance to hepatitis C virus NS3/NS4A protease inhibitors in São Paulo state. Arch Virol 2018; 163:2757-2764. [PMID: 29961118 DOI: 10.1007/s00705-018-3920-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 04/12/2018] [Indexed: 02/07/2023]
Abstract
Hepatitis C (HCV)-infected patients are treated with direct-acting antiviral agents (DAAs) in highly effective, well-tolerated, all-oral regimens. However, naturally occurring resistance-associated amino acid substitutions (RASs) may be selected during treatment. This study aimed to screen naturally occurring RASs NS3/NS4A inhibitors (PIs). Samples were obtained from DAA naïve patients, living in São Paulo state, Brazil. Screening for RASs in the HCV NS3 region was conducted in 859 samples from HCV-infected patients, of which 425 and 434 samples were subtype 1a and 1b, respectively. HCV-RNA was extracted, amplified, and sequenced. The overall prevalence of RASs to HCV PIs was 9.4%. The following RASs were observed in HCV-1a subtype infected patients: V36L (2.6%), T54S (1.6%), V55I/A (1.2% / 8.9%, respectively), Q80K (2.1%), R155K (0.5%), and D168E (0.2%); and in HCV-1b infected patients: V36L (0.7%), T54A/S (0.2% and 0.5%, respectively), V55A (0.5%), Q80K (0.2%), D168E (1.6%), and M175L (0.5%). HCV 1a infected subjects had higher serum viral load than that seen in patients infected with HCV 1b. There was no difference between the proportions of NS3 RASs with regards to geographic distribution within the investigated areas. These findings should be supported by additional studies in Brazil to help in the formation of local clinical guidelines for managing hepatitis C.
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Affiliation(s)
- Regina Célia Moreira
- Laboratory of Viral Hepatitis, Virology Center, Instituto Adolfo Lutz, Avenida Dr. Arnaldo, 355, Cerqueira César, São Paulo, SP, CEP 01246-902, Brazil.
| | - Ana Paula de Torres Santos
- Laboratory of Viral Hepatitis, Virology Center, Instituto Adolfo Lutz, Avenida Dr. Arnaldo, 355, Cerqueira César, São Paulo, SP, CEP 01246-902, Brazil.,Divisão de Laboratório Central, Laboratório de Imunologia, Faculdade de Medicina, Hospital das Clínicas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Gaspar Lisboa-Neto
- Department of Infectious Diseases, School of Medicine, University of São Paulo, São Paulo, SP, Brazil
| | | | - Marcilio Figueiredo Lemos
- Laboratory of Viral Hepatitis, Virology Center, Instituto Adolfo Lutz, Avenida Dr. Arnaldo, 355, Cerqueira César, São Paulo, SP, CEP 01246-902, Brazil
| | - Fernanda Mello Malta
- Laboratory of Tropical Gastroenterology and Hepatology "João de Queiroz and Castorina Bettencourt Alves"-LIM 07-Institute of Tropical Medicine Department of Gastroenterology, School of Medicine, University of São Paulo, São Paulo, SP, Brazil
| | | | | | | | - João Renato Rebello Pinho
- Laboratory of Tropical Gastroenterology and Hepatology "João de Queiroz and Castorina Bettencourt Alves"-LIM 07-Institute of Tropical Medicine Department of Gastroenterology, School of Medicine, University of São Paulo, São Paulo, SP, Brazil.,Albert Einstein Medicina Diagnóstica, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
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13
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Abstract
PURPOSE OF REVIEW This review provides an overview of HCV resistance-associated substitutions (RASs) with a focus on NS3 protease and NS5A inhibitor resistance. Treatment approaches for managing resistance are also covered including the use of newly approved therapies with improved resistance profiles. RECENT FINDINGS HCV RASs are frequently selected if the patient is not cured during treatment; NS5A RASs persist for prolonged periods of time (years) after treatment failure and may adversely impact retreatment responses. Newly approved regimens with improved potency and resistance profiles are less impacted by resistance and provide the best retreatment options for patients who previously failed DAA therapy. The clinical impact of HCV RASs has been lessened significantly with the introduction of new DAA treatment regimens. Routine testing for resistance is unlikely to impact retreatment approaches if newer regimens are accessible. Knowledge of factors, such as the presence of cirrhosis and prior treatment regimens, remain as the key to optimizing retreatment approaches.
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Affiliation(s)
- David L Wyles
- Division of Infectious Diseases, Denver Health Medical Center, 660 Bannock St, MC 4000, Denver, CO, 80204, USA.
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14
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Jones BR, Howe AYM, Harrigan PR, Joy JB. The global origins of resistance-associated variants in the non-structural proteins 5A and 5B of the hepatitis C virus. Virus Evol 2018; 4:vex041. [PMID: 29362671 PMCID: PMC5769712 DOI: 10.1093/ve/vex041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
New, costly, fast acting, therapies targeting the non-structural proteins 5A and 5B (NS5A and NS5B) regions of the hepatitis C virus (HCV) genome are curative in the majority of cases. Variants with certain mutations in the NS5A and NS5B regions of HCV have been shown to reduce susceptibility to direct-acting NS5A and NS5B therapy and are found in treatment naïve patients. Despite this, the ease with which these variants evolve is poorly known, as are their evolutionary and geographic origins. To address this crucial gap we inferred the evolutionary and geographic origins of resistance-associated variants (RAVs) in the HCV NS5A and NS5B regions of subtypes 1a, 1b, and 3a sequences available from global databases. We found that RAVs in the NS5A region of HCV, when prevalent, were widely dispersed throughout the phylogenetic tree of HCV with multiple independent origins and that these variants are globally distributed. In contrast, most of the NS5B C316N variants came from one of two clades in the phylogenetic tree of HCV subtype 1b. The presence of serine (S) at codon 218 of HCV NS5B appears to facilitate the evolution of the C316N RAV. Other NS5B RAVs did not arise very frequently in our data set, except for S556G in subtype 1b and with respect to geography NS5B RAVs were also globally distributed. The inferred distribution of RAVs in the NS5A region and frequency of their origin suggest a low fitness barrier without the need for co-evolution of compensatory mutations. A low fitness barrier may allow rapid selection of de novo resistance to NS5A inhibitors during therapy.
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Affiliation(s)
- Bradley R Jones
- Laboratory Program, BC Centre for Excellence in HIV/AIDS, 608—1081 Burrard Street, Vancouver, BC, Canada V6Z 1Y6
| | - Anita Y M Howe
- Laboratory Program, BC Centre for Excellence in HIV/AIDS, 608—1081 Burrard Street, Vancouver, BC, Canada V6Z 1Y6
| | - P Richard Harrigan
- Laboratory Program, BC Centre for Excellence in HIV/AIDS, 608—1081 Burrard Street, Vancouver, BC, Canada V6Z 1Y6
- Department of Medicine, University of British Columbia, 2775 Laurel Street, Vancouver, BC, Canada V5Z 1M9
| | - Jeffrey B Joy
- Laboratory Program, BC Centre for Excellence in HIV/AIDS, 608—1081 Burrard Street, Vancouver, BC, Canada V6Z 1Y6
- Department of Medicine, University of British Columbia, 2775 Laurel Street, Vancouver, BC, Canada V5Z 1M9
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15
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Martínez AP, Culasso ACA, Pérez PS, Romano V, Campos RH, Ridruejo E, García G, Di Lello FA. Polymorphisms associated with resistance to protease inhibitors in naïve patients infected with hepatitis C virus genotype 1 in Argentina: Low prevalence of Q80K. Virus Res 2017; 240:140-146. [PMID: 28837817 DOI: 10.1016/j.virusres.2017.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 08/16/2017] [Accepted: 08/16/2017] [Indexed: 12/26/2022]
Abstract
Incorporation of direct acting antivirals (DAA) in the treatment of Hepatitis C Virus (HCV) significantly increases sustained virologic response rates. However, despite the greater potency offered by these antivirals, drug resistance plays a key role in patients with failure to DAA. Nevertheless, there is no information about the prevalence of resistance-associated substitutions (RASs) in Argentina. The aim of this study was to analyze HCV variants resistant to protease inhibitors (PI) in naïve patients infected with HCV genotype 1 from Argentina. In this retrospective cross-sectional study, 103 patients infected with HCV-1 were included. Eighteen positions related with RASs were analyzed by Sanger at baseline and phylogenetic analysis was performed to determine the diversification of this samples. The analyzed RASs were present in 38 out of 103 patients (36.9%) infected with HCV-1. Patients infected with subtype HCV-1b had higher prevalence of baseline RASs than patients infected with HCV-1a [51.6% vs. 12.8%, respectively (p<0.001)]. The Q80K polymorphism was not found in HCV-1a samples, even when 51% of them belonged to cluster 1, which is associated with a high frequency of Q80K. Phylogenetic analysis showed that Argentinean samples were intermingled with sequences from other geographic regions. RASs to PI were highly prevalent and subtype dependent in treatment-naïve Argentinean patients. Surprisingly, Q80K polymorphism was not detected in our study population. The phylogenetic analysis showed no relationship between our samples and other samples from Brazil which also present a low prevalence of Q80K. This study supports the need for surveillance of resistance in patients who will be treated with DAA in each particular country since the observed RASs have very different prevalence worldwide.
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Affiliation(s)
- Alfredo P Martínez
- Virology Section, Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno "CEMIC", Ciudad Autónoma de Buenos Aires, C1425ASG Buenos Aires, Argentina
| | - Andrés C A Culasso
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología y Biotecnología, Cátedra de Virología, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Paula S Pérez
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología y Biotecnología, Cátedra de Virología, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Vanesa Romano
- Virology Section, Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno "CEMIC", Ciudad Autónoma de Buenos Aires, C1425ASG Buenos Aires, Argentina
| | - Rodolfo H Campos
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología y Biotecnología, Cátedra de Virología, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Ezequiel Ridruejo
- Hepatology Section, Department of Medicine, Centro de Educación Médica e Investigaciones Clínicas Norberto Quirno "CEMIC", Ciudad Autónoma de Buenos Aires, C1425ASG Buenos Aires, Argentina
| | - Gabriel García
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología y Biotecnología, Cátedra de Virología, Buenos Aires, Argentina
| | - Federico A Di Lello
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología y Biotecnología, Cátedra de Virología, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
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16
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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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17
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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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18
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High Prevalence of Q80K Among NS3 Resistance-Associated Substitutions in Subtype 1a Patients with Chronic Hepatitis C Prior to Treatment with Direct Acting Antivirals: The Croatian Data. HEPATITIS MONTHLY 2017. [DOI: 10.5812/hepatmon.45543] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
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19
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Implications of hepatitis C virus subtype 1a migration patterns for virus genetic sequencing policies in Italy. BMC Evol Biol 2017; 17:70. [PMID: 28270091 PMCID: PMC5341469 DOI: 10.1186/s12862-017-0913-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 02/14/2017] [Indexed: 02/06/2023] Open
Abstract
Background In-depth phylogeographic analysis can reveal migration patterns relevant for public health planning. Here, as a model, we focused on the provenance, in the current Italian HCV subtype 1a epidemic, of the NS3 resistance-associated variant (RAV) Q80K, known to interfere with the action of NS3/4A protease inhibitor simeprevir. HCV1a migration patterns were analysed using Bayesian phylodynamic tools, capitalising on newly generated and publicly available time and geo-referenced NS3 encoding virus genetic sequence data. Results Our results showed that both immigration and local circulation fuel the current Italian HCV1a epidemic. The United States and European continental lineages dominate import into Italy, with the latter taking the lead from the 1970s onwards. Since similar migration patterns were found for Q80K and other lineages, no clear differentiation of the risk for failing simeprevir can be made between patients based on their migration and travel history. Importantly, since HCV only occasionally recombines, these results are readily transferable to the genetic sequencing policy concerning NS5A RAVs. Conclusions The patient migration and travel history cannot be used to target only part of the HCV1a infected population for drug resistance testing before start of antiviral therapy. Consequently, it may be cost-effective to expand genotyping efforts to all HCV1a infected patients eligible for simeprevir-based therapies. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0913-3) contains supplementary material, which is available to authorized users.
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20
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Abdel-hameed EA, Rouster SD, Zhang X, Chen J, Medvedovic M, Goodman ZD, Sherman KE. Characterization of HCV NS3 Protease Variants in HCV/HIV-Coinfected Patients by Ultra-Deep Sequence Analysis: Relationship with Hepatic Fibrosis. J Acquir Immune Defic Syndr 2017; 74:353-358. [PMID: 27898525 PMCID: PMC5303138 DOI: 10.1097/qai.0000000000001256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND Treatment of HCV/HIV coinfection is now largely based on utilization of direct acting agents. Pretreatment viral resistant-associated variants (RAVs) and host liver condition may affect the sustained virological response. In this study, we explored relative prevalence of protease resistance-associated mutations, the evolution of those RAVs after 12 weeks of pegylated interferon alfa exposure, and the role hepatic fibrosis might have on RAV display. METHODS Thirty nonresponder HCV/HIV-coinfected subjects were evaluated before and after 12 weeks of PegIFN treatment. Ultra-deep sequence analysis of NS3 RAVs was performed. Hepatic fibrosis was determined by sensitive computer-assisted histomorphometry determination. RESULTS At baseline, protease inhibitor RAVs were present in 73.3% of patients and expanded to 83.3% of patients after 12 weeks of PegIFN exposure. Q80K showed the highest prevalence before and after treatment at 46.7% and 56.7%, respectively. The presence of Q80K is positively correlated with percent collagen content of the liver tissue. CONCLUSIONS Key RAVs for HCV protease inhibitors are present in a major portion of the HCV/HIV-coinfected population before therapy. Some variants get selected after exposure. Correlation of Q80K with collagen content of the liver suggests that compartmentalization within the liver may contribute to persistence of mutations less fit than wildtype.
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Affiliation(s)
| | - Susan D. Rouster
- University of Cincinnati College of Medicine, Cincinnati, OH
45267
| | - Xiang Zhang
- University of Cincinnati, Department of Environmental Health,
Cincinnati, OH 45267
| | - Jing Chen
- University of Cincinnati, Department of Environmental Health,
Cincinnati, OH 45267
| | - Mario Medvedovic
- University of Cincinnati, Department of Environmental Health,
Cincinnati, OH 45267
| | - Zachary D. Goodman
- Center for Liver Diseases, Inova Fairfax Hospital, Falls Church, VA
22042
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21
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Eltahla AA, Leung P, Pirozyan MR, Rodrigo C, Grebely J, Applegate T, Maher L, Luciani F, Lloyd AR, Bull RA. Dynamic evolution of hepatitis C virus resistance-associated substitutions in the absence of antiviral treatment. Sci Rep 2017; 7:41719. [PMID: 28139734 PMCID: PMC5282498 DOI: 10.1038/srep41719] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 12/28/2016] [Indexed: 01/01/2023] Open
Abstract
Resistance against new hepatitis C virus (HCV) antivirals is an area of increasing interest. Resistance-associated substitutions (RASs) have been identified in treatment-naïve individuals, but pressures driving treatment-independent RAS emergence are poorly understood. We analysed the longitudinal evolution of RASs in twelve participants with early acute HCV infections. Full-genome deep sequences were analysed for changes in RAS frequency within NS3, NS5A and NS5B-coding regions over the course of the infection. Emergence of RASs relevant only to the polymerase non-nucleoside inhibitors (NNI) was detected, and these lay within CD8+ T-cell epitopes. Conversely, the loss of NNI RASs over time appeared likely to be driven by viral fitness constraints. These results highlight the importance of monitoring CD8+ T cell epitope-associated RASs in populations with dominant HLA types.
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Affiliation(s)
- Auda A. Eltahla
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW 2052, Australia
| | - Preston Leung
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW 2052, Australia
| | - Mehdi R. Pirozyan
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW 2052, Australia
| | - Chaturaka Rodrigo
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW 2052, Australia
| | - Jason Grebely
- The Kirby Institute, UNSW Australia, Sydney, NSW 2052, Australia
| | - Tanya Applegate
- The Kirby Institute, UNSW Australia, Sydney, NSW 2052, Australia
| | - Lisa Maher
- The Kirby Institute, UNSW Australia, Sydney, NSW 2052, Australia
| | - Fabio Luciani
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW 2052, Australia
| | - Andrew R. Lloyd
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW 2052, Australia
| | - Rowena A. Bull
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW 2052, Australia
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22
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Gozlan Y, Ben-Ari Z, Moscona R, Shirazi R, Rakovsky A, Kabat A, Veizman E, Berdichevski T, Weiss P, Cohen-Ezra O, Lurie Y, Gafanovich I, Braun M, Cohen-Naftaly M, Shlomai A, Shibolet O, Zigmond E, Zuckerman E, Carmiel-Haggai M, Nimer A, Hazzan R, Maor Y, Kitay-Cohen Y, Shemer-Avni Y, Kra-Oz Z, Schreiber L, Peleg O, Sierra S, Harrigan PR, Mendelson E, Mor O. HCV genotype-1 subtypes and resistance-associated substitutions in drug-naive and in direct-acting antiviral treatment failure patients. Antivir Ther 2017; 22:431-441. [PMID: 28067632 DOI: 10.3851/imp3123] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2016] [Indexed: 10/20/2022]
Abstract
BACKGROUND Direct-acting antiviral (DAA) treatment regimens and response rates of patients with HCV genotype-1 (GT1) are currently considered subtype-dependent. Identification of clinically relevant resistance-associated substitutions (RASs) in the NS3 and NS5A proteins at baseline and in DAA failures, may also impact clinical decisions. METHODS In a multicentre cohort study (n=308), NS3 or NS5B sequencing (n=248) was used to discriminate between GT1 subtypes. The correlation between baseline NS3 and NS5A RASs on the 12-week sustained virological response (SVR12) rates of 160 of the patients treated with second-generation DAAs was also assessed. Post-treatment resistance analysis was performed on samples from 58 patients exhibiting DAA virological failure. RESULTS GT1a, GT1b and GT1d subtypes were identified in 23.0%, 75.4% and 1.2% of tested samples. GT1b was most prevalent (97.7%, 128/131) among patients born in the former Soviet Union. The Q80K NS3 RAS was identified in 17.5% (10/57) of the GT1a carriers, most of whom were Israeli-born. NS3 and NS5A baseline RASs showed a negligible correlation with SVR12 rates. Treatment-emergent RASs were observed among 8.9% (4/45) and 76.9% (10/13) of first- and second-generation DAA failures, respectively, with D168V/E (NS3), Y93H and L31M (NS5A) being the most prevalent mutations. CONCLUSIONS NS3 sequencing analysis can successfully discriminate between GT1 subtypes and identify NS3 amino acid substitutions. While pre-treatment NS3 and NS5A RASs marginally affect second-generation DAA SVR12 rates, post-treatment resistance analysis should be considered prior to re-therapy.
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Affiliation(s)
- Yael Gozlan
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
| | - Ziv Ben-Ari
- Liver Disease Center, Sheba Medical Center, Ramat-Gan, Israel.,The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Roy Moscona
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
| | - Rachel Shirazi
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
| | - Aviya Rakovsky
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
| | - Arij Kabat
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
| | - Ella Veizman
- Liver Disease Center, Sheba Medical Center, Ramat-Gan, Israel
| | | | - Peretz Weiss
- Liver Disease Center, Sheba Medical Center, Ramat-Gan, Israel
| | | | - Yoav Lurie
- Liver Unit, Shaare Zedek Medical Center, Jerusalem, Israel
| | | | - Marius Braun
- The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Liver Institute, Rabin Medical Center, Petah-Tikva, Israel
| | - Michal Cohen-Naftaly
- The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Liver Institute, Rabin Medical Center, Petah-Tikva, Israel
| | - Amir Shlomai
- The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Liver Institute, Rabin Medical Center, Petah-Tikva, Israel
| | - Oren Shibolet
- The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Gastroenterology, Tel-Aviv Medical Center, Tel Aviv, Israel
| | - Ehud Zigmond
- The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Gastroenterology, Tel-Aviv Medical Center, Tel Aviv, Israel
| | | | - Michal Carmiel-Haggai
- Liver Unit, Galilee Medical Center, Naharya, Israel.,Faculty of Medicine in the Galilee, Bar-Ilan University, Ramat-Gan, Israel
| | - Assy Nimer
- Faculty of Medicine in the Galilee, Bar-Ilan University, Ramat-Gan, Israel.,Internal Medicine Department, Galilee Medical Center, Naharya, Israel
| | - Rawi Hazzan
- Liver Unit, Haemek Medical Center, Afula, Israel
| | - Yaakov Maor
- Division of Gastroenterology, Kaplan Health Sciences Centre, Department of Medicine, Faculty of Medicine, Hebrew University, Rehovot, Israel
| | - Yona Kitay-Cohen
- Gastroenterology and Hepatology Institute, Meir Medical Center, Kfar Saba, Israel
| | | | - Zipi Kra-Oz
- Virology Laboratory, Rambam Medical Center, Haifa, Israel
| | | | | | - Saleta Sierra
- Institute of Virology, University of Cologne, Cologne, Germany
| | | | - Ella Mendelson
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel.,School of Public Health, Tel Aviv University, Tel Aviv, Israel
| | - Orna Mor
- Central Virology Laboratory, Ministry of Health, Sheba Medical Center, Ramat-Gan, Israel
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The hepatitis C virus nonstructural protein 3 Q80K polymorphism is frequently detected and transmitted among HIV-infected MSM in the Netherlands. AIDS 2017; 31:105-112. [PMID: 27898592 DOI: 10.1097/qad.0000000000001263] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
OBJECTIVES The Q80K polymorphism is a naturally occurring resistance-associated variant in the hepatitis C virus (HCV) nonstructural protein 3 (NS3) region and is likely transmissible between hosts. This study describes the Q80K origin and prevalence among HCV risk groups in the Netherlands and examines whether Q80K is linked to specific transmission networks. DESIGN AND METHODS Stored blood samples from HCV genotype 1a-infected patients were used for PCR and sequencing to reconstruct the NS3 maximum likelihood phylogeny. The most recent common ancestor was estimated with a coalescent-based model within a Bayesian statistical framework. RESULTS Study participants (n = 150) were either MSM (39%), people who inject drugs (17%), or patients with other (15%) or unknown/unreported (29%) risk behavior. Overall 45% was coinfected with HIV. Q80K was present in 36% (95% confidence interval 28-44%) of patients throughout the sample collection period (2000-2015) and was most prevalent in MSM (52%, 95% confidence interval 38-65%). Five MSM-specific transmission clusters were identified, of which three exclusively contained sequences with Q80K. The HCV-1a most recent common ancestor in the Netherlands was estimated in 1914 (95% higher posterior density 1879-1944) and Q80K originated in 1957 (95% higher posterior density 1942-1970) within HCV-1a clade I. All Q80K lineages could be traced back to this single origin. CONCLUSION Q80K is a highly stable and transmissible resistance-associated variant and was present in a large part of Dutch HIV-coinfected MSM. The introduction and expansion of Q80K variants in this key population suggest a founder effect, potentially jeopardizing future treatment with simeprevir.
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Wilson EM, Rosenthal ES, Kattakuzhy S, Tang L, Kottilil S. Clinical Laboratory Testing in the Era of Directly Acting Antiviral Therapies for Hepatitis C. Clin Microbiol Rev 2017; 30:23-42. [PMID: 27795306 PMCID: PMC5217793 DOI: 10.1128/cmr.00037-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Directly acting antiviral (DAA) combination therapies for chronic hepatitis C virus (HCV) infection are highly effective, but treatment decisions remain complex. Laboratory testing is important to evaluate a range of viral, host, and pharmacological factors when considering HCV treatment, and patients must be monitored during and after therapy for safety and to assess the viral response. In this review, we discuss the laboratory tests relevant for the treatment of HCV infection in the era of DAA therapy, grouped according to viral and host factors.
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Affiliation(s)
- Eleanor M Wilson
- Institute of Human Virology, University of Maryland School of Medicine, University of Maryland, Baltimore, Maryland, USA
- Critical Care Medicine Department of the NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Elana S Rosenthal
- Critical Care Medicine Department of the NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Sarah Kattakuzhy
- Institute of Human Virology, University of Maryland School of Medicine, University of Maryland, Baltimore, Maryland, USA
- Critical Care Medicine Department of the NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Lydia Tang
- Institute of Human Virology, University of Maryland School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Shyam Kottilil
- Institute of Human Virology, University of Maryland School of Medicine, University of Maryland, Baltimore, Maryland, USA
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
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25
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Chen Q, Belmonte I, Buti M, Nieto L, Garcia-Cehic D, Gregori J, Perales C, Ordeig L, Llorens M, Soria ME, Esteban R, Esteban JI, Rodriguez-Frias F, Quer J. New real-time-PCR method to identify single point mutations in hepatitis C virus. World J Gastroenterol 2016; 22:9604-9612. [PMID: 27920481 PMCID: PMC5116604 DOI: 10.3748/wjg.v22.i43.9604] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 08/25/2016] [Accepted: 10/10/2016] [Indexed: 02/07/2023] Open
Abstract
AIM To develop a fast, low-cost diagnostic strategy to identify single point mutations in highly variable genomes such as hepatitis C virus (HCV).
METHODS In patients with HCV infection, resistance-associated amino acid substitutions within the viral quasispecies prior to therapy can confer decreased susceptibility to direct-acting antiviral agents and lead to treatment failure and virological relapse. One such naturally occurring mutation is the Q80K substitution in the HCV-NS3 protease gene, which confers resistance to PI inhibitors, particularly simeprevir. Low-cost, highly sensitive techniques enabling routine detection of these single point mutations would be useful to identify patients at a risk of treatment failure. LightCycler methods, based on real-time PCR with sequence-specific probe hybridization, have been implemented in most diagnostic laboratories. However, this technique cannot identify single point mutations in highly variable genetic environments, such as the HCV genome. To circumvent this problem, we developed a new method to homogenize all nucleotides present in a region except the point mutation of interest.
RESULTS Using nucleotide-specific probes Q, K, and R substitutions at position 80 were clearly identified at a sensitivity of 10% (mutations present at a frequency of at least 10% were detected). The technique was successfully applied to identify the Q80K substitution in 240 HCV G1 serum samples, with performance comparable to that of direct Sanger sequencing, the current standard procedure for this purpose. The new method was then validated in a Catalonian population of 202 HCV G1-infected individuals. Q80K was detected in 14.6% of G1a patients and 0% of G1b in our setting.
CONCLUSION A fast, low-cost diagnostic strategy based on real-time PCR and fluorescence resonance energy transfer probe melting curve analysis has been successfully developed to identify single point mutations in highly variable genomes such as hepatitis C virus. This technique can be adapted to detect any single point mutation in highly variable genomes.
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26
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Jimenez-Sousa MÁ, Gutiérrez-Rivas M, Álvaro-Meca A, García-Álvarez M, Harrigan PR, Fedele CG, Briz V, Vázquez-Morón S, Resino S. NS3 Resistance-Associated Variants (RAVs) in Patients Infected with HCV Genotype 1a in Spain. PLoS One 2016; 11:e0163197. [PMID: 27685471 PMCID: PMC5042525 DOI: 10.1371/journal.pone.0163197] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 09/06/2016] [Indexed: 02/08/2023] Open
Abstract
Background Resistance-associated variants have been related to treatment failure of hepatitis C virus (HCV) therapy with direct-acting antiviral drugs. The aim of our study was to analyze the prevalence of clinically relevant resistance-associated variants within NS3 in patients infected with HCV genotype 1a (GT1a) in Spain. Methods We performed a cross-sectional study on 2568 patients from 115 hospitals throughout Spain (2014–2015). The viral NS3 protease gene was amplified by nested polymerase chain reaction and sequenced by Sanger sequencing using an ABI PRISM 377 DNA sequencer. Additionally, clade information for genotype 1a was obtained by using the software geno2pheno (http://hcv.geno2pheno.org/). Results In total, 875 out of 2568 samples were from human immunodeficiency virus (HIV)/HCV-coinfected patients. Q80K was the main RAV found in our patients (11.1%) and the rest of the resistance-associated variants had a lower frequency, including S122G (6.23%), T54S (3.47%), V55A (2.61%), and V55I (2.15%), which were among the most frequent after Q80K. Overall, 286 samples had the Q80K polymorphism (11.1%) and 614 (23.9%) were GT1a clade I. HIV/HCV-coinfected patients had a higher frequency of Q80K and GT1a clade I than HCV-monoinfected patients (12.9% vs. 9.6% [p = 0.012] and 28.5% vs. 21.4% [p<0.001], respectively). Both the prevalence of Q80K and GT1a clade I were not uniform throughout the country (p<0.001), which ranged from 7.3%-22.2% and 15.7%-42.5%, respectively. The frequency of the Q80K polymorphism was far higher in patients infected with GT1a clade I than in patients infected with GT1a clade II (41.5% vs. 1.6%; p<0.001). Conclusions The prevalence of most resistance-associated variants in NS3 was low in patients infected with HCV GT1a in Spain, except for Q80K (11.1%), which was also notably higher in HIV/HCV-coinfected patients. The vast majority of Q80K polymorphisms were detected in GT1a clade I.
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Affiliation(s)
- María Ángeles Jimenez-Sousa
- Viral Infection and Immunity Unit, National Centre for Microbiology. Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Mónica Gutiérrez-Rivas
- Viral Infection and Immunity Unit, National Centre for Microbiology. Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Alejandro Álvaro-Meca
- Preventive Medicine and Public Health Unit, Faculty of Health Sciences, Rey Juan Carlos College, Alcorcón, Madrid, Spain
| | - Mónica García-Álvarez
- Viral Infection and Immunity Unit, National Centre for Microbiology. Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | | | - Cesare Giovanni Fedele
- Diagnostic Approach Area, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Verónica Briz
- Viral Infection and Immunity Unit, National Centre for Microbiology. Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Sonia Vázquez-Morón
- Viral Infection and Immunity Unit, National Centre for Microbiology. Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- * E-mail: (SVM); (SR)
| | - Salvador Resino
- Viral Infection and Immunity Unit, National Centre for Microbiology. Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- * E-mail: (SVM); (SR)
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Cuypers L, Li G, Neumann-Haefelin C, Piampongsant S, Libin P, Van Laethem K, Vandamme AM, Theys K. Mapping the genomic diversity of HCV subtypes 1a and 1b: Implications of structural and immunological constraints for vaccine and drug development. Virus Evol 2016; 2:vew024. [PMID: 27774307 PMCID: PMC5072459 DOI: 10.1093/ve/vew024] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Despite significant progress in hepatitis C (HCV) treatment, global viral eradication remains a challenge. An in-depth map of its genome diversity within the context of structural and immunological constraints could contribute to the design of pan-genotypic antivirals and preventive vaccines. For such analyses, extensive information is only available for the highly prevalent HCV genotypes (GT) 1a and 1b. Using 647 GT1a and 408 GT1b full-genome sequences obtained from the Los Alamos database, we found that respectively 3 per cent and 82 per cent of all codon positions are under positive and negative selective pressure, suggesting variation mainly accumulates due to random genetic drift. An association between conservation and both structured RNA and secondary protein structures confirmed the important role of structural elements at nucleotide and at amino acid level. Remarkably, CD8+ T-cell epitopes in HCV GT1a were significantly more conserved, while at the same time containing more sites under positive selection. Similarly, CD4+ T-cell epitopes were significantly more conserved in both HCV subtypes, but under less positive selective pressure in GT1b and more negative selective pressure in GT1a. In contrast, B-cell epitopes in both subtypes were less conserved and under less stringent negative selection. These findings argue against immune selective pressure as the main force of between-host diversifying evolution. Despite its high variability, HCV is under strict evolutionary constraints, most probably to keep its genes and proteins functional during the replication cycle. These are encouraging findings for vaccine and drug design, which could consider these newly established genetic diversity profiles.
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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, 3000 Leuven, Belgium
| | - Guangdi Li
- KU Leuven, University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Minderbroedersstraat 10, 3000 Leuven, Belgium; Metabolic Syndrome Research Center, Key Laboratory of Diabetes Immunology, Ministry of Education, National Clinical Research Center for Metabolic Diseases, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Christoph Neumann-Haefelin
- Department of Medicine II, Freiburg University Medical Center, University of Freiburg, Freiburg, Germany
| | - Supinya Piampongsant
- KU Leuven, University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Minderbroedersstraat 10, 3000 Leuven, Belgium; Department of Electrical Engineering ESAT, STADIUS Center for Dynamical Systems, Signal Processing and Data Analytics, KU Leuven, University of Leuven, Kasteelpark Arenberg 10, B-3001 Heverlee, Belgium
| | - Pieter Libin
- Artificial Intelligence Lab, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; KU Leuven, University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Kristel Van Laethem
- KU Leuven, University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Minderbroedersstraat 10, 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, Minderbroedersstraat 10, 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, 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, 3000 Leuven, Belgium
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In-depth phylogenetic analysis of hepatitis C virus subtype 1a and occurrence of 80K and associated polymorphisms in the NS3 protease. Sci Rep 2016; 6:31780. [PMID: 27531254 PMCID: PMC4987637 DOI: 10.1038/srep31780] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/26/2016] [Indexed: 01/08/2023] Open
Abstract
HCV genetic diversity is high and impacts disease progression, treatment and drug resistance. HCV subtype 1a is divided in two clades (I and II), and the 80 K natural polymorphism in the viral NS3 protease is prevalent in clade I. Paradoxically, countries dominated by this clade have contrasting frequencies of 80 K. Over 2,000 HCV 1a NS3 sequences were retrieved from public databases representing Europe, Oceania and the Americas. Sequences were aligned with HCV reference sequences and subjected to phylogenetic analysis to investigate the relative presence of different subtype 1a clades and NS3 protease mutations. HCV-1a sequences split into clades I and II. Clade I was further structured into three subclades, IA to C. Sub-clade IA prevailed in the U.S., while subclade IC was major in Brazil. The NS3 80 K polymorphism was associated with subclade IA, but nearly absent in subclades IB and IC, a pattern similarly seen for the 91S/T compensatory mutation. Three HCV-1a-I sub-clades have been identified, with different frequencies in distinct regions. The 80 K and 91A/S mutations were associated with subclade IA, which provide an explanation for the disparities seen in simeprevir resistance profiles of countries dominated by HCV 1a-I, like the U.S. and Brazil.
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Jiménez-Pérez M, González-Grande R, España Contreras P, Pinazo Martínez I, de la Cruz Lombardo J, Olmedo Martín R. Treatment of chronic hepatitis C with direct-acting antivirals: The role of resistance. World J Gastroenterol 2016; 22:6573-81. [PMID: 27547001 PMCID: PMC4970473 DOI: 10.3748/wjg.v22.i29.6573] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 05/25/2016] [Accepted: 06/15/2016] [Indexed: 02/06/2023] Open
Abstract
The use of direct-acting antivirals (DAAs) to treat chronic hepatitis C has resulted in a significant increase in rates of sustained viral response (around 90%-95%) as compared with the standard treatment of peginterferon/ribavirin. Despite this, however, the rates of therapeutic failure in daily clinical practice range from 10%-15%. Most of these cases are due to the presence of resistant viral variants, resulting from mutations produced by substitutions of amino acids in the viral target protein that reduce viral sensitivity to DAAs, thus limiting the efficacy of these drugs. The high genetic diversity of hepatitis C virus has resulted in the existence of resistance-associated variants (RAVs), sometimes even before starting treatment with DAAs, though generally at low levels. These pre-existing RAVs do not appear to impact on the sustained viral response, whereas those that appear after DAA therapy could well be determinant in virological failure with future treatments. As well as the presence of RAVs, virological failure to treatment with DAAs is generally associated with other factors related with a poor response, such as the degree of fibrosis, the response to previous therapy, the viral load or the viral genotype. Nonetheless, viral breakthrough and relapse can still occur in the absence of detectable RAVs and after the use of highly effective DAAs, so that the true clinical impact of the presence of RAVs in therapeutic failure remains to be determined.
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Benítez-Gutiérrez L, Barreiro P, Labarga P, de Mendoza C, Fernandez-Montero JV, Arias A, Peña JM, Soriano V. Prevention and management of treatment failure to new oral hepatitis C drugs. Expert Opin Pharmacother 2016; 17:1215-23. [PMID: 27149603 DOI: 10.1080/14656566.2016.1182156] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Chronic hepatitis C virus (HCV) infection has become a curable disease. Sustained virologic response rates above 90% have been achieved with recommended direct-acting antiviral (DAA) combinations in most registration trials. However, outcomes in real-world patients are lower. In patients experiencing DAA failure, resistance-associated variants (RAVs) are almost universally selected. At this time it is unclear when and how to re-treat hepatitis C in patients with prior DAA failure. AREAS COVERED The rate of DAA failure and predictors of lack of treatment response using distinct DAA combinations are analyzed. We discuss the management of HCV treatment failure and the impact of RAVs on re-treatment strategies. EXPERT OPINION Failure to DAA combinations occurs more often in chronic hepatitis C patients with baseline predictors of poor response, such as those with RAVs, genotypes 3 or 1a, advanced liver cirrhosis, elevated serum HCV-RNA and perhaps HIV coinfection. Impaired antiviral efficacy is more frequent when multiple factors are present. On-treatment predictors of DAA failure are poor drug adherence and development of side effects. Extending the length of therapy, adding ribavirin and/or using DAA from other drug families may allow successful re-treatment of most prior DAA failures.
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Affiliation(s)
- Laura Benítez-Gutiérrez
- a Department of Internal Medicine , Puerta de Hierro Research Institute & University Hospital , Majadahonda , Spain
| | - Pablo Barreiro
- b Infectious Diseases Unit , La Paz University Hospital , Madrid , Spain
| | - Pablo Labarga
- c Department of Internal Medicine , La Milagrosa Clinic , Madrid , Spain
| | - Carmen de Mendoza
- a Department of Internal Medicine , Puerta de Hierro Research Institute & University Hospital , Majadahonda , Spain
| | - José V Fernandez-Montero
- d Department of Infectious Diseases , University Hospital Crosshouse , Kilmarnock , Scotland , United Kingdom
| | - Ana Arias
- a Department of Internal Medicine , Puerta de Hierro Research Institute & University Hospital , Majadahonda , Spain
| | - José M Peña
- b Infectious Diseases Unit , La Paz University Hospital , Madrid , Spain
| | - Vicente Soriano
- b Infectious Diseases Unit , La Paz University Hospital , Madrid , Spain
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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: 5.3] [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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Vicenti I, Falasca F, Sticchi L, Bruzzone B, Turriziani O, Zazzi M. Evaluation of a commercial real-time PCR kit for the detection of the Q80K polymorphism in plasma from HCV genotype 1a infected patients. J Clin Virol 2016; 76:20-3. [PMID: 26802683 DOI: 10.1016/j.jcv.2016.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 12/18/2015] [Accepted: 01/08/2016] [Indexed: 01/14/2023]
Abstract
BACKGROUND Screening of the natural HCV NS3 polymorphism Q80K is required prior to simeprevir administration due to the reduced susceptibility of genotype 1 viruses carrying this amino acid variant. A simple, rapid and robust test for Q80K screening would be advisable in routine diagnostic laboratories. OBJECTIVES The aim of this study was to evaluate a commercial NS3 Q80K real-time PCR kit (Q80K Polymorphism Kit, Clonit srl, Milan, Italy). STUDY DESIGN Forty-three plasma samples obtained from untreated HCV genotype 1a-infected patients and previously sequenced at a reference laboratory, were sent to two public clinical virology laboratories for blinded Q80K screening with the kit under evaluation. The sample panel included 25 cases with the wild type 80Q, 17 with the mutant 80K and 1 with the mutant 80L. RESULTS Laboratory 1 identified 22/25 (88.0%) 80Q and 17/17 (100.0%) 80K cases. Laboratory 2 identified 23/25 (92.0%) 80Q and 16/17 (94.2%) 80K cases. All of the unidentified cases were scored as negative, with no mutant/wild type miscalling. The 80L variant was scored as indeterminate by Laboratory 1 and as negative by Laboratory 2. Overall, sensitivity and specificity for detection of 80K were 97.1% (95% C.I., 82.9-99.8%) and 100.0% (90.2-100.0%), respectively. However, the system did not provide any result for 6/84 cases (7.1% failure rate), not including the 80L variant which is not expected to be detected as stated in the kit package insert. Global inter-laboratory concordance was 93.0%. CONCLUSIONS Despite good specificity, this Q80K detection system needs improvements in amplification success rate and robustness.
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Affiliation(s)
- Ilaria Vicenti
- Department of Medical Biotechnology, University of Siena, Viale Bracci n.16, 53100 Siena, Italy.
| | - Francesca Falasca
- Department of Molecular Medicine, Sapienza University of Rome, Italy.
| | - Laura Sticchi
- Hygiene Unit, IRCCS AOU San Martino-IST, Genoa, Italy; Department of Health Sciences, University of Genoa, Genoa, Italy.
| | | | | | - Maurizio Zazzi
- Department of Medical Biotechnology, University of Siena, Viale Bracci n.16, 53100 Siena, Italy.
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Analysis of Hepatitis C Virus Genotype 1b Resistance Variants in Japanese Patients Treated with Paritaprevir-Ritonavir and Ombitasvir. Antimicrob Agents Chemother 2015; 60:1106-13. [PMID: 26643326 PMCID: PMC4750684 DOI: 10.1128/aac.02606-15] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 12/02/2015] [Indexed: 02/06/2023] Open
Abstract
Treatment of HCV genotype 1b (GT1b)-infected Japanese patients with paritaprevir (NS3/4A inhibitor boosted with ritonavir) and ombitasvir (NS5A inhibitor) in studies M12-536 and GIFT-I demonstrated high sustained virologic response (SVR) rates. The virologic failure rate was 3% (13/436) across the two studies. Analyses were conducted to evaluate the impact of baseline resistance-associated variants (RAVs) on treatment outcome and the emergence and persistence of RAVs in patients experiencing virologic failure. Baseline paritaprevir resistance-conferring variants in NS3 were infrequent, while Y93H in NS5A was the most prevalent ombitasvir resistance-conferring variant at baseline. A comparison of baseline prevalence of polymorphisms in Japanese and western patients showed that Q80L and S122G in NS3 and L28M, R30Q, and Y93H in NS5A were significantly more prevalent in Japanese patients. In the GIFT-I study, the prevalence of Y93H in NS5A varied between 13% and 21% depending on the deep-sequencing detection threshold. Among patients with Y93H comprising <1%, 1 to 40%, or >40% of their preexisting viral population, the 24-week SVR (SVR24) rates were >99% (276/277), 93% (38/41), and 76% (25/33), respectively, indicating that the prevalence of Y93H within a patient's viral population is a good predictor of treatment response. The predominant RAVs at the time of virologic failure were D168A/V in NS3 and Y93H alone or in combination with other variants in NS5A. While levels of NS3 RAVs declined over time, NS5A RAVs persisted through posttreatment week 48. Results from these analyses are informative in understanding the resistance profile of an ombitasvir- plus paritaprevir/ritonavir-based regimen in Japanese GT1b-infected patients.
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Buti M, Riveiro-Barciela M, Esteban R. Management of direct-acting antiviral agent failures. J Hepatol 2015; 63:1511-22. [PMID: 26299621 DOI: 10.1016/j.jhep.2015.08.010] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/10/2015] [Accepted: 08/11/2015] [Indexed: 12/12/2022]
Abstract
Failure to respond to the approved combinations of multiple direct-acting antiviral agents is relatively low in hepatitis C virus treatment registration studies, with rates of 1% to 7%, depending on the patients' baseline characteristics. In real life, failure is slightly higher, likely because of lower compliance. Treatment failures are usually related to relapse and less often to on-treatment viral breakthrough. Hepatitis C drug-resistant variants are detected in most patients who do not achieve viral eradication. The risk of developing these variants depends on host- and virus-related factors, the properties of the drugs used, and the treatment strategies applied. Patients who carry resistance-associated variants may not obtain benefits from treatment and are at risk of disease progression and transmission of the variants. Whether hepatitis C resistance-associated variants persist depends on their type: NS3-4A variants often disappear gradually after therapy is stopped, whereas NS5A variants tend to persist for more than 2 years. The best way to prevent emergence of resistant variants is to eliminate the virus at the first treatment using highly potent antivirals with genetic barriers to resistance. In patients failing first-generation protease inhibitors, combination therapies with sofosbuvir and NS5 inhibitors have proven effective. Some salvage regimens can be shortened to 12 weeks by addition of ribavirin. The optimal treatment for patients who fail an NS5A inhibitor and those with multidrug-resistant variants remains to be defined, and research efforts should continue to focus on treatment for these patients.
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Affiliation(s)
- Maria Buti
- Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d'Hebron and Universitat Autònoma de Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain.
| | - Mar Riveiro-Barciela
- Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d'Hebron and Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Rafael Esteban
- Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d'Hebron and Universitat Autònoma de Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
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Perales C, Quer J, Gregori J, Esteban JI, Domingo E. Resistance of Hepatitis C Virus to Inhibitors: Complexity and Clinical Implications. Viruses 2015; 7:5746-66. [PMID: 26561827 PMCID: PMC4664975 DOI: 10.3390/v7112902] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 10/23/2015] [Accepted: 10/26/2015] [Indexed: 12/20/2022] Open
Abstract
Selection of inhibitor-resistant viral mutants is universal for viruses that display quasi-species dynamics, and hepatitis C virus (HCV) is no exception. Here we review recent results on drug resistance in HCV, with emphasis on resistance to the newly-developed, directly-acting antiviral agents, as they are increasingly employed in the clinic. We put the experimental observations in the context of quasi-species dynamics, in particular what the genetic and phenotypic barriers to resistance mean in terms of exploration of sequence space while HCV replicates in the liver of infected patients or in cell culture. Strategies to diminish the probability of viral breakthrough during treatment are briefly outlined.
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Affiliation(s)
- Celia Perales
- Liver Unit, Internal Medicine, Laboratory of Malalties Hepàtiques, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain.
- Centro de Biologia Molecular "Severo Ochoa" (CSIC-UAM), Cantoblanco, 28049 Madrid, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 08035 Barcelona, Spain.
| | - Josep Quer
- Liver Unit, Internal Medicine, Laboratory of Malalties Hepàtiques, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 08035 Barcelona, Spain.
- Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.
| | - Josep Gregori
- Liver Unit, Internal Medicine, Laboratory of Malalties Hepàtiques, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 08035 Barcelona, Spain.
- Roche Diagnostics SL, 08174 Sant Cugat del Vallès, Spain.
| | - Juan Ignacio Esteban
- Liver Unit, Internal Medicine, Laboratory of Malalties Hepàtiques, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 08035 Barcelona, Spain.
- Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.
| | - Esteban Domingo
- Centro de Biologia Molecular "Severo Ochoa" (CSIC-UAM), Cantoblanco, 28049 Madrid, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 08035 Barcelona, Spain.
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Beloukas A, King S, Childs K, Papadimitropoulos A, Hopkins M, Atkins M, Agarwal K, Nelson M, Geretti A. Detection of the NS3 Q80K polymorphism by Sanger and deep sequencing in hepatitis C virus genotype 1a strains in the UK. Clin Microbiol Infect 2015; 21:1033-9. [DOI: 10.1016/j.cmi.2015.07.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/14/2015] [Accepted: 07/19/2015] [Indexed: 01/27/2023]
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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: 1.2] [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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Resistance analysis of baseline and treatment-emergent variants in hepatitis C virus genotype 1 in the AVIATOR study with paritaprevir-ritonavir, ombitasvir, and dasabuvir. Antimicrob Agents Chemother 2015; 59:5445-54. [PMID: 26100711 PMCID: PMC4538512 DOI: 10.1128/aac.00998-15] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Accepted: 06/16/2015] [Indexed: 12/14/2022] Open
Abstract
AVIATOR, a phase 2 clinical trial, evaluated ritonavir-boosted paritaprevir (a protease inhibitor), ombitasvir (an NS5A inhibitor), and dasabuvir (a nonnucleoside polymerase inhibitor) (the three-drug [3D] regimen) with or without ribavirin (RBV) for 8, 12, or 24 weeks in 406 HCV genotype 1 (GT1)-infected patients. The rate of sustained virologic response 24 weeks after treatment ranged from 88% to 100% across the arms of the 3D regimen with or without RBV; 20 GT1a-infected patients and 1 GT1b-infected patient experienced virologic failure (5.2%). Baseline resistance-conferring variants in NS3 were rare. M28V in GT1a and Y93H in GT1b were the most prevalent preexisting variants in NS5A, and C316N in GT1b and S556G in both GT1a and GT1b were the most prevalent variants in NS5B. Interestingly, all the GT1a sequences encoding M28V in NS5A were from the United States, while GT1b sequences encoding C316N and S556G in NS5B were predominant in the European Union. Variants preexisting at baseline had no significant impact on treatment outcome. The most prevalent treatment-emergent resistance-associated variants (RAVs) in GT1a were R155K and D168V in NS3, M28T and Q30R in NS5A, and S556G in NS5B. The single GT1b-infected patient experiencing virologic failure had no RAVs in any target. A paritaprevir-ritonavir dose of 150/100 mg was more efficacious in suppressing R155K in NS3 than a 100/100-mg dose. In patients who failed after receiving 12 or more weeks of treatment, RAVs were selected in all 3 targets, while most patients who relapsed after 8 weeks of treatment did so without any detectable RAVs. Results from this study guided the selection of the optimal treatment regimen, treatment duration, and paritaprevir dose for further development of the 3D regimen. (This study has been registered at ClinicalTrials.gov under registration number NCT01464827.)
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De Luca A, Di Giambenedetto S, Lo Presti A, Sierra S, Prosperi M, Cella E, Giovanetti M, Torti C, Caudai C, Vicenti I, Saladini F, Almi P, Grima P, Blanc P, Fabbiani M, Rossetti B, Gagliardini R, Kaiser R, Ciccozzi M, Zazzi M. Two Distinct Hepatitis C Virus Genotype 1a Clades Have Different Geographical Distribution and Association With Natural Resistance to NS3 Protease Inhibitors. Open Forum Infect Dis 2015; 2:ofv043. [PMID: 26213689 PMCID: PMC4511743 DOI: 10.1093/ofid/ofv043] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 03/26/2015] [Indexed: 12/18/2022] Open
Abstract
Background. Hepatitis C virus (HCV) genotype 1 is the most prevalent worldwide. Subtype 1a, compared with 1b, shows lower response rates and higher propensity to select for drug resistance to NS3 and selected NS5A and nonnucleoside NS5B inhibitors. Two distinct clades of subtype 1a have been described. Methods. Using Bayesian methodology, we performed a time-scaled phylogeny reconstruction of clade separation and characterized the geographic distribution, phylodynamics, and association with natural resistance variants of NS3 sequences from 362 patients carrying subtype 1a HCV. Results. All sequences segregated in 2 clearly distinct clades. Clade I showed an earlier origin from the common ancestor compared with clade II. Clade I virus was more prevalent in non-European countries, represented mostly by United States, compared with European (75.7% vs 49.3%; P < .001). The prevalence of the natural NS3 variant Q80K, associated with resistance to the macrocyclic protease inhibitor simeprevir, was detected in 51.6% of clade I and 0% of clade II (P < .001); clade I showed a lower genetic barrier for Q80K, whereas no sign of selective pressure at any protease inhibitor resistance-associated codon was detected. Conclusions. Hepatitis C virus subtype 1a clades have a clearly different distribution in Europe and the United States, and the natural resistance mutation Q80K is exclusively associated with clade I.
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Affiliation(s)
- Andrea De Luca
- Unità Operativa ComplessaMalattie Infettive Universitarie, Siena University Hospital, Italy
- Institute of Clinical Infectious Diseases, Catholic University, Roma, Italy
| | | | | | - Saleta Sierra
- Partner Site of the German Center for Infection Research Deutsches Zentrum für Infektionsforschung; Institute of Virology, University of Cologne, Germany
| | - Mattia Prosperi
- Department of Epidemiology, University of Florida, Gainesville
| | - Eleonora Cella
- Department of Infectious Diseases, National Institute of Health, Roma, Italy
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Italy
| | - Marta Giovanetti
- Department of Infectious Diseases, National Institute of Health, Roma, Italy
- Department of Biology, University of Rome “Tor Vergata”, Italy
| | - Carlo Torti
- University of Brescia, Italy
- Unit of Infectious Diseases, University “Magna Graecia”, Catanzaro, Italy
| | - Cinzia Caudai
- Department of Medical Biotechnologies, University of Siena, Italy
| | - Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, Italy
| | | | - Paolo Almi
- Unità Operativa Complessa Malattie Infettive ed Epatologia, Siena University Hospital, Italy
| | - Pierfrancesco Grima
- Infectious Diseases Unit, S. Caterina Novella Hospital, Galatina, Lecce, Italy
| | - Pierluigi Blanc
- Unità Operativa Malattie InfettiveOspedale Santa Maria Annunziata Azienda Sanitaria Locale 10, Firenze, Italy
| | | | - Barbara Rossetti
- Unità Operativa ComplessaMalattie Infettive Universitarie, Siena University Hospital, Italy
| | | | - Rolf Kaiser
- Partner Site of the German Center for Infection Research Deutsches Zentrum für Infektionsforschung; Institute of Virology, University of Cologne, Germany
| | - Massimo Ciccozzi
- Department of Infectious Diseases, National Institute of Health, Roma, Italy
- University Campus-Biomedico, Rome, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Italy
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Sarrazin C, Lathouwers E, Peeters M, Daems B, Buelens A, Witek J, Wyckmans Y, Fevery B, Verbinnen T, Ghys A, Schlag M, Baldini A, De Meyer S, Lenz O. Prevalence of the hepatitis C virus NS3 polymorphism Q80K in genotype 1 patients in the European region. Antiviral Res 2015; 116:10-6. [PMID: 25614456 DOI: 10.1016/j.antiviral.2015.01.003] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 12/19/2014] [Accepted: 01/11/2015] [Indexed: 12/12/2022]
Abstract
Hepatitis C virus (HCV) NS3 polymorphism Q80K is mainly found in patients with HCV genotype (G) 1a, and has been associated with a reduced treatment response to simeprevir with pegylated interferon (P) and ribavirin (R). Prevalence of Q80K among G1 patients may vary geographically. Q80K prevalence in the North-American G1 population in a recent study was 34%. We conducted a post hoc meta-analysis of Q80K polymorphism prevalence among HCV G1-infected patients enrolled in simeprevir and telaprevir Phase II/III studies. Baseline HCV NS3/4A protease sequences were analysed by population sequencing to determine Q80K prevalence. Overall, of 3349 patients from 25 countries in the European region analysed, 35.8%, 63.8% and 0.3% of patients had G1a, G1b and other/unknown HCV G1 subtypes, respectively. Q80K was detected at baseline in 7.5% of HCV G1 patients overall. Examination by subtype showed that 19.8%, 0.5% and 18.2% of patients with G1a, G1b and other/unknown HCV G1 subtypes had the Q80K polymorphism, respectively. Among countries in the European region with sequencing data available for either ⩾20 patients with G1a and/or ⩾40 G1 patients overall, the Q80K prevalence in G1 ranged from 0% in Bulgaria to 18.2% in the UK. Q80K prevalence also varied within G1a across different countries. HCV subtype 1a was correctly determined in 99% of patients by the LiPA v2 assay. A low overall prevalence of Q80K was observed in HCV G1-infected patients in the European region, compared with North America. However, the prevalence varied by country, due to differing ratios of G1a/G1b and differing Q80K prevalence within the G1a populations.
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Affiliation(s)
- Christoph Sarrazin
- Johann Wolfgang Goethe University Hospital, Medical Department 1, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany.
| | - Erkki Lathouwers
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium.
| | - Monika Peeters
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium.
| | - Bjorn Daems
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium.
| | - Annemie Buelens
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium.
| | - James Witek
- Janssen Research & Development LLC, 1125 Trenton Harbourton Rd, Titusville, NJ 08560, United States.
| | - Yves Wyckmans
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium.
| | - Bart Fevery
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium.
| | - Thierry Verbinnen
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium.
| | - Anne Ghys
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium.
| | - Michael Schlag
- Janssen-Cilag, Vorgartenstraße 206B, 1020 Vienna, Austria.
| | - Alessandra Baldini
- Janssen Cilag, 1 Rue Camille Desmoulins, 92130 Issy-les-Moulineaux, France.
| | - Sandra De Meyer
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium.
| | - Oliver Lenz
- Janssen Infectious Diseases BVBA, Turnhoutseweg 30, 2340 Beerse, Belgium.
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