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Li Z, Chen ZW, Li H, Ren H, Hu P. Prevalence of hepatitis C virus-resistant association substitutions to direct-acting antiviral agents in treatment-naïve hepatitis C genotype 1b-infected patients in western China. Infect Drug Resist 2017; 10:377-392. [PMID: 29184422 PMCID: PMC5673042 DOI: 10.2147/idr.s146595] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background Direct-acting antivirals (DAAs) against hepatitis C virus (HCV) are potent and highly efficacious. However, resistance-associated substitutions (RASs) relevant to DAAs can impair treatment effectiveness even at baseline. Moreover, the prevalence of baseline RASs in HCV genotype 1b-infected patients in western China is still unclear. Materials and methods Direct sequencing of the HCV NS3, NS5A, and NS5B regions was performed in baseline serum samples of 70 DAAs treatment-naïve HCV 1b-infected patients in western China. The sequences were analyzed with MEGA version 5.05 software. Evolutionary patterns of RASs and amino-acid covariance patterns in the NS3, NS5A, and NS5B genes were analyzed by MEGA and Cytoscape (version 3.2.1), respectively. Results The presence of at least one RAS in the NS3 region (C16S, T54S, Q80R/L, A87T, R117H, S122G, V132I, V170I) was observed in 85.48% (53 of 62) of patients, RASs in the NS5A region (L28M, R30Q, Q54H, P58S/T, Q62H/R, Y93H) were observed in 42.42% (28 of 66) of patients, and RASs in the NS5B region (N142S, A300T, C316N, A338V, S365A, L392I, M414L, I424V, A442T, V499A, S556G) were observed in 100% (44 of 44) of patients. Evolutionary patterns of RASs and amino-acid covariance patterns for the NS3, NS5A, and NS5B genes are reported. Conclusion The prevalence of RASs relevant to DAAs detected in the NS3, NS5A, and NS5B regions of HCV 1b from DAA treatment-naïve patients is high. Therefore, more attention should be paid to RASs associated with DAAs in the upcoming DAA-treatment era in China.
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Affiliation(s)
- Zhao Li
- Department of Infectious Diseases, Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Chinese Ministry of Education, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhi-Wei Chen
- Department of Infectious Diseases, Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Chinese Ministry of Education, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hu Li
- Department of Infectious Diseases, Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Chinese Ministry of Education, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hong Ren
- Department of Infectious Diseases, Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Chinese Ministry of Education, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Peng Hu
- Department of Infectious Diseases, Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases, Chinese Ministry of Education, Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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A Novel Inhibitor IDPP Interferes with Entry and Egress of HCV by Targeting Glycoprotein E1 in a Genotype-Specific Manner. Sci Rep 2017; 7:44676. [PMID: 28333153 PMCID: PMC5363083 DOI: 10.1038/srep44676] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/13/2017] [Indexed: 02/08/2023] Open
Abstract
Despite recent advances in curing chronic hepatitis C (CHC), the high economic burden to therapy, viral drug resistance, difficult to treat hepatitis C virus (HCV) genotypes and patient groups are still of concern. To address this unmet medical needs, we devised strategies to identify novel viral interventions through target-free high-throughput screening of small molecules utilizing a phenotypic-based HCV infection assay. Thereby, a very potent (EC50 46 ± 26 pM) iminodipyridinopyrimidine (IDPP) drug candidate was selected, and confirmed in primary human hepatocytes (EC50 0.5 nM). IDPP mainly targets a post-attachment step of HCV without affecting endosomal acidification, prevents the secretion of infectious particles and viral cell-to-cell spread. The putative molecular target of IDPP is glycoprotein E1, as revealed by selection for viral drug resistance (Gly-257-Arg). IDPP was synergistic in combination with FDA-approved HCV drugs and inhibited pre-existing resistant HCV strains induced by today's therapies. Interestingly, IDPP exclusively inhibited HCV genotype 2. However, we identified the genotype-specificity determining region in E1 and generated HCV genotype 1 susceptible to IDPP by changing one amino acid in E1 (Gln-257-Gly). Together, our results indicate an opportunity to provide an alternative treatment option for CHC and will shed light on the poorly understood function of HCV glycoprotein E1.
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Zhou K, Liang Z, Wang C, Hu F, Ning C, Lan Y, Tang X, Tucker JD, Cai W. Natural Polymorphisms Conferring Resistance to HCV Protease and Polymerase Inhibitors in Treatment-Naïve HIV/HCV Co-Infected Patients in China. PLoS One 2016; 11:e0157438. [PMID: 27341031 PMCID: PMC4920402 DOI: 10.1371/journal.pone.0157438] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Accepted: 05/31/2016] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The advent of direct-acting agents (DAAs) has improved treatment of HCV in HIV co-infection, but may be limited by primary drug resistance. This study reports the prevalence of natural polymorphisms conferring resistance to NS3/4A protease inhibitors and NS5B polymerase inhibitors in treatment-naïve HIV/HCV co-infected individuals in China. METHODS Population based NS3/4A sequencing was completed for 778 treatment-naïve HIV/HCV co-infected patients from twelve provinces. NS3 sequences were amplified by nested PCR using in-house primers for genotypes 1-6. NS5B sequencing was completed for genotyping in 350 sequences. Resistance-associated variants (RAVs) were identified in positions associated with HCV resistance. RESULTS Overall, 72.8% (566/778) of all HCV sequences had at least one RAV associated with HCV NS3/4A protease inhibitor resistance. Variants were found in 3.6% (7/193) of genotype 1, 100% (23/23) of genotype 2, 100% (237/237) of genotype 3 and 92% (299/325) of genotype 6 sequences. The Q80K variant was present in 98.4% of genotype 6a sequences. High-level RAVs were rare, occurring in only 0.8% of patients. 93% (64/69) patients with genotype 1b also carried the C316N variant associated with NS5B low-level resistance. CONCLUSIONS The low frequency of high-level RAVs associated with primary HCV DAA resistance among all genotypes in HIV/HCV co-infected patients is encouraging. Further phenotypic studies and clinical research are needed.
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Affiliation(s)
- Kali Zhou
- Guangzhou Eighth People’s Hospital, 627 Dongfeng Dong Road, Guangzhou, Guangdong 510060, China
- University of California San Francisco, Department of Medicine, Division of Gastroenterology, 513 Parnassus Avenue, Room S-357, San Francisco, California, 94143-0538 United States of America
| | - Zhiwei Liang
- Guangzhou Eighth People’s Hospital, 627 Dongfeng Dong Road, Guangzhou, Guangdong 510060, China
| | - Charles Wang
- UNC-Project – China, Division of Infectious Diseases, Department of Medicine, UNC Chapel Hill School of Medicine, 130 Mason Farm Rd., 2nd Floor, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, 27599-3368, United States of America
- Brown University School of Medicine, Department of Medicine, Division of Gastroenterology 593 Eddy Street, APC 406, Providence, Rhode Island, 02903, United States of America
| | - Fengyu Hu
- Guangzhou Eighth People’s Hospital, 627 Dongfeng Dong Road, Guangzhou, Guangdong 510060, China
| | - Chuanyi Ning
- Guangzhou Eighth People’s Hospital, 627 Dongfeng Dong Road, Guangzhou, Guangdong 510060, China
- UNC-Project – China, Division of Infectious Diseases, Department of Medicine, UNC Chapel Hill School of Medicine, 130 Mason Farm Rd., 2nd Floor, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, 27599-3368, United States of America
| | - Yun Lan
- Guangzhou Eighth People’s Hospital, 627 Dongfeng Dong Road, Guangzhou, Guangdong 510060, China
| | - Xiaoping Tang
- Guangzhou Eighth People’s Hospital, 627 Dongfeng Dong Road, Guangzhou, Guangdong 510060, China
| | - Joseph D. Tucker
- Guangzhou Eighth People’s Hospital, 627 Dongfeng Dong Road, Guangzhou, Guangdong 510060, China
- UNC-Project – China, Division of Infectious Diseases, Department of Medicine, UNC Chapel Hill School of Medicine, 130 Mason Farm Rd., 2nd Floor, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, 27599-3368, United States of America
| | - Weiping Cai
- Guangzhou Eighth People’s Hospital, 627 Dongfeng Dong Road, Guangzhou, Guangdong 510060, China
- * E-mail:
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Practices of Sequencing Quality Assurance. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch53] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Trends in Antiviral Strategies. VIRUS AS POPULATIONS 2016. [PMCID: PMC7149557 DOI: 10.1016/b978-0-12-800837-9.00009-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Viral populations are true moving targets regarding the genomic sequences to be targeted in antiviral designs. Experts from different fields have expressed the need of new paradigms for antiviral interventions and viral disease control. This chapter reviews several strategies that aim at counteracting the adaptive capacity of viral quasispecies. The proposed designs are based on combinations of different antiviral drugs and immune modulators, or in the administration of virus-specific mutagenic agents, in an approach termed lethal mutagenesis of viruses. It consists of decreasing viral fitness by an excess of mutations that render viral proteins sub-optimal or non-functional. Viral extinction by lethal mutagenesis involves several sequential, overlapping steps that recapitulate the major concepts of intra-population interactions and genetic information stability discussed in preceding chapters. Despite the magnitude of the challenge, the chapter closes with some optimistic prospects for an effective control of viruses displaying error-prone replication, based on the combined targeting of replication fidelity and the induction of the innate immune response.
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Fourati S, Pawlotsky JM. Virologic Tools for HCV Drug Resistance Testing. Viruses 2015; 7:6346-59. [PMID: 26690198 PMCID: PMC4690865 DOI: 10.3390/v7122941] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 11/28/2015] [Accepted: 11/30/2015] [Indexed: 12/22/2022] Open
Abstract
Recent advances in molecular biology have led to the development of new antiviral drugs that target specific steps of the Hepatitis C Virus (HCV) lifecycle. These drugs, collectively termed direct-acting antivirals (DAAs), include non-structural (NS) HCV protein inhibitors, NS3/4A protease inhibitors, NS5B RNA-dependent RNA polymerase inhibitors (nucleotide analogues and non-nucleoside inhibitors), and NS5A inhibitors. Due to the high genetic variability of HCV, the outcome of DAA-based therapies may be altered by the selection of amino-acid substitutions located within the targeted proteins, which affect viral susceptibility to the administered compounds. At the drug developmental stage, preclinical and clinical characterization of HCV resistance to new drugs in development is mandatory. In the clinical setting, accurate diagnostic tools have become available to monitor drug resistance in patients who receive treatment with DAAs. In this review, we describe tools available to investigate drug resistance in preclinical studies, clinical trials and clinical practice.
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Affiliation(s)
- Slim Fourati
- National Reference Center for Viral Hepatitis B, C, and D; Department of Virology, Hôpital Henri Mondor, Université Paris-Est and INSERM U955, Créteil 94010, France.
| | - Jean-Michel Pawlotsky
- National Reference Center for Viral Hepatitis B, C, and D; Department of Virology, Hôpital Henri Mondor, Université Paris-Est and INSERM U955, Créteil 94010, France.
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Lontok E, Harrington P, Howe A, Kieffer T, Lennerstrand J, Lenz O, McPhee F, Mo H, Parkin N, Pilot-Matias T, Miller V. Hepatitis C virus drug resistance-associated substitutions: State of the art summary. Hepatology 2015; 62:1623-32. [PMID: 26095927 DOI: 10.1002/hep.27934] [Citation(s) in RCA: 247] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 06/06/2015] [Indexed: 12/12/2022]
Abstract
UNLABELLED Hepatitis C virus (HCV) drug development has resulted in treatment regimens composed of interferon-free, all-oral combinations of direct-acting antivirals. While the new regimens are potent and highly efficacious, the full clinical impact of HCV drug resistance, its implications for retreatment, and the potential role of baseline resistance testing remain critical research and clinical questions. In this report, we discuss the viral proteins targeted by HCV direct-acting antivirals and summarize clinically relevant resistance data for compounds that have been approved or are currently in phase 3 clinical trials. CONCLUSION This report provides a comprehensive, systematic review of all resistance information available from sponsors' trials as a tool to inform the HCV drug development field.
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Affiliation(s)
- Erik Lontok
- Forum for Collaborative HIV Research, University of California at Berkeley, Washington, DC
| | - Patrick Harrington
- Center for Drug Evaluation and Research, Office of Antimicrobial Products, Division of Antiviral Products, US Food and Drug Administration, Silver Spring, MD
| | - Anita Howe
- Merck Research Laboratories, West Point, PA
| | | | | | - Oliver Lenz
- Janssen Infectious Diseases, Beerse, Belgium
| | - Fiona McPhee
- Bristol-Myers Squibb Research and Development, Wallingford, CT
| | | | | | | | - Veronica Miller
- Forum for Collaborative HIV Research, University of California at Berkeley, Washington, DC
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Wells JT, Landaverde C, Gutierrez J, Lawitz E. Management of patients with hepatitis C virus resistance-associated variants to NS5A inhibitors: Where are we now? Clin Liver Dis (Hoboken) 2015; 6:82-85. [PMID: 31040995 PMCID: PMC6490661 DOI: 10.1002/cld.507] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 08/23/2015] [Accepted: 08/29/2015] [Indexed: 02/04/2023] Open
Affiliation(s)
- Jennifer T. Wells
- The Texas Liver Institute/University of Texas Health Science CenterSan AntonioTX
| | - Carmen Landaverde
- The Texas Liver Institute/University of Texas Health Science CenterSan AntonioTX
| | - Julio Gutierrez
- The Texas Liver Institute/University of Texas Health Science CenterSan AntonioTX
| | - Eric Lawitz
- The Texas Liver Institute/University of Texas Health Science CenterSan AntonioTX
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Chatel-Chaix L, Bartenschlager R. A monocytic detour to replicate patient-derived hepatitis C virus in hepatoma cells and its use for phenotypic analyses. Hepatology 2015; 61:1112-4. [PMID: 25418558 DOI: 10.1002/hep.27614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Affiliation(s)
- Laurent Chatel-Chaix
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
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Quiñones-Mateu ME, Avila S, Reyes-Teran G, Martinez MA. Deep sequencing: becoming a critical tool in clinical virology. J Clin Virol 2014; 61:9-19. [PMID: 24998424 DOI: 10.1016/j.jcv.2014.06.013] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/12/2014] [Accepted: 06/14/2014] [Indexed: 02/07/2023]
Abstract
Population (Sanger) sequencing has been the standard method in basic and clinical DNA sequencing for almost 40 years; however, next-generation (deep) sequencing methodologies are now revolutionizing the field of genomics, and clinical virology is no exception. Deep sequencing is highly efficient, producing an enormous amount of information at low cost in a relatively short period of time. High-throughput sequencing techniques have enabled significant contributions to multiples areas in virology, including virus discovery and metagenomics (viromes), molecular epidemiology, pathogenesis, and studies of how viruses to escape the host immune system and antiviral pressures. In addition, new and more affordable deep sequencing-based assays are now being implemented in clinical laboratories. Here, we review the use of the current deep sequencing platforms in virology, focusing on three of the most studied viruses: human immunodeficiency virus (HIV), hepatitis C virus (HCV), and influenza virus.
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Affiliation(s)
- Miguel E Quiñones-Mateu
- University Hospital Translational Laboratory, University Hospitals Case Medical Center, Cleveland, OH, USA; Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Santiago Avila
- Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico; Centro de Investigaciones en Enfermedades Infecciosas, Mexico City, Mexico
| | - Gustavo Reyes-Teran
- Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico; Centro de Investigaciones en Enfermedades Infecciosas, Mexico City, Mexico
| | - Miguel A Martinez
- Fundació irsicaixa, Universitat Autònoma de Barcelona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
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Babcock GJ, Iyer S, Smith HL, Wang Y, Rowley K, Ambrosino DM, Zamore PD, Pierce BG, Molrine DC, Weng Z. High-throughput sequencing analysis of post-liver transplantation HCV E2 glycoprotein evolution in the presence and absence of neutralizing monoclonal antibody. PLoS One 2014; 9:e100325. [PMID: 24956119 PMCID: PMC4067308 DOI: 10.1371/journal.pone.0100325] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 05/22/2014] [Indexed: 02/07/2023] Open
Abstract
Chronic hepatitis C virus (HCV) infection is the most common cause of end-stage liver disease, often leading to liver transplantation, in which case circulating virions typically infect the transplanted liver within hours and viral concentrations can quickly exceed pre-transplant levels. MBL-HCV1 is a fully human monoclonal antibody recognizing a linear epitope of the HCV E2 envelope glycoprotein (amino acids 412–423). The ability of MBL-HCV1 to prevent HCV recurrence after liver transplantation was investigated in a phase 2 randomized clinical trial evaluating six MBL-HCV1-treated subjects and five placebo-treated subjects. MBL-HCV1 treatment significantly delayed time to viral rebound compared with placebo treatment. Here we report results from high-throughput sequencing on the serum of each of the eleven enrolled subjects prior to liver transplantation and after viral rebound. We further sequenced the sera of the MBL-HCV1-treated subjects at various interim time points to study the evolution of antibody-resistant viral variants. We detected mutations at one of two positions within the antibody epitope—mutations of N at position 415 to D, K or S, or mutation of N at position 417 to S. It has been previously reported that N415 is not glycosylated in the wild-type E2 protein, but N417S can lead to glycosylation at position 415. Thus N415 is a key position for antibody recognition and the only routes we identified for viral escape, within the constraints of HCV fitness in vivo, involve mutating or glycosylating this position. Evaluation of mutations along the entire E1 and E2 proteins revealed additional positions that changed moderately before and after MBL-HCV1 treatment for subsets of the six subjects, yet underscored the relative importance of position 415 in MBL-HCV1 resistance.
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Affiliation(s)
- Gregory J. Babcock
- MassBiologics, University of Massachusetts Medical School, Boston, Massachusetts, United States of America
| | - Sowmya Iyer
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Heidi L. Smith
- MassBiologics, University of Massachusetts Medical School, Boston, Massachusetts, United States of America
| | - Yang Wang
- MassBiologics, University of Massachusetts Medical School, Boston, Massachusetts, United States of America
| | - Kirk Rowley
- MassBiologics, University of Massachusetts Medical School, Boston, Massachusetts, United States of America
| | - Donna M. Ambrosino
- MassBiologics, University of Massachusetts Medical School, Boston, Massachusetts, United States of America
| | - Phillip D. Zamore
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Brian G. Pierce
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Deborah C. Molrine
- MassBiologics, University of Massachusetts Medical School, Boston, Massachusetts, United States of America
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail:
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Accelerating Drug Development Through Collaboration: The Hepatitis C Drug Development Advisory Group. Clin Pharmacol Ther 2014; 96:162-5. [DOI: 10.1038/clpt.2014.113] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Accepted: 05/19/2014] [Indexed: 01/12/2023]
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Amplification and sequencing of the hepatitis C virus NS3/4A protease and the NS5B polymerase regions for genotypic resistance detection of clinical isolates of subtypes 1a and 1b. Methods Mol Biol 2014; 1030:137-49. [PMID: 23821266 DOI: 10.1007/978-1-62703-484-5_12] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Genotypic testing based on subtype-specific amplification and population Sanger sequencing for two nonstructural (NS) protein-coding regions, the NS3/4A protease and the NS5B polymerase, of the hepatitis C virus (HCV) genome is described here. The protocols include the molecular steps for RNA extraction, one-step RT-PCR followed by inner PCR and population Sanger sequencing, to obtain the sequence information of the target regions from the clinical isolates of HCV subtypes 1a and 1b, which can be used to detect any sequence change in the viral genome as for example caused by the development of drug resistance in these two common viral targets.
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Resistance to HCV nucleoside analogue inhibitors of hepatitis C virus RNA-dependent RNA polymerase. Curr Opin Virol 2013; 3:508-13. [DOI: 10.1016/j.coviro.2013.08.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Revised: 08/12/2013] [Accepted: 08/20/2013] [Indexed: 11/20/2022]
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16
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Ortega-Prieto AM, Sheldon J, Grande-Pérez A, Tejero H, Gregori J, Quer J, Esteban JI, Domingo E, Perales C. Extinction of hepatitis C virus by ribavirin in hepatoma cells involves lethal mutagenesis. PLoS One 2013; 8:e71039. [PMID: 23976977 PMCID: PMC3745404 DOI: 10.1371/journal.pone.0071039] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 06/26/2013] [Indexed: 12/14/2022] Open
Abstract
Lethal mutagenesis, or virus extinction produced by enhanced mutation rates, is under investigation as an antiviral strategy that aims at counteracting the adaptive capacity of viral quasispecies, and avoiding selection of antiviral-escape mutants. To explore lethal mutagenesis of hepatitis C virus (HCV), it is important to establish whether ribavirin, the purine nucleoside analogue used in anti-HCV therapy, acts as a mutagenic agent during virus replication in cell culture. Here we report the effect of ribavirin during serial passages of HCV in human hepatoma Huh-7.5 cells, regarding viral progeny production and complexity of mutant spectra. Ribavirin produced an increase of mutant spectrum complexity and of the transition types associated with ribavirin mutagenesis, resulting in HCV extinction. Ribavirin-mediated depletion of intracellular GTP was not the major contributory factor to mutagenesis since mycophenolic acid evoked a similar decrease in GTP without an increase in mutant spectrum complexity. The intracellular concentration of the other nucleoside-triphosphates was elevated as a result of ribavirin treatment. Mycophenolic acid extinguished HCV without an intervening mutagenic activity. Ribavirin-mediated, but not mycophenolic acid-mediated, extinction of HCV occurred via a decrease of specific infectivity, a feature typical of lethal mutagenesis. We discuss some possibilities to explain disparate results on ribavirin mutagenesis of HCV.
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Affiliation(s)
- Ana M Ortega-Prieto
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
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Viral resistance in hepatitis C virus genotype 1-infected patients receiving the NS3 protease inhibitor Faldaprevir (BI 201335) in a phase 1b multiple-rising-dose study. Antimicrob Agents Chemother 2013; 57:4928-36. [PMID: 23877706 DOI: 10.1128/aac.00822-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Faldaprevir (BI 201335) is a selective NS3/4A protease inhibitor under development for the treatment of chronic hepatitis C virus (HCV) infection. NS3/4A genotyping and NS3 protease phenotyping analyses were performed to monitor the emergence of resistance in patients with HCV genotype 1 infection receiving faldaprevir alone or combined with pegylated interferon alfa 2a and ribavirin (PegIFN-RBV) during a phase 1b study. Among all baseline variants, a maximum 7-fold reduction in in vitro sensitivity to faldaprevir was observed for a rare NS3 (V/I)170T polymorphism. During faldaprevir monotherapy in treatment-naive patients, virologic breakthrough was common (77%, 20/26) and was associated with the emergence of resistance mutations predominantly carrying NS3 substitutions R155K in GT1a and D168V in GT1b. D168V conferred a greater reduction in faldaprevir sensitivity (1,800-fold) than R155K (330-fold); however, D168V was generally less fit than R155K in the absence of selective drug pressure. Treatment-experienced patients treated with faldaprevir-PegIFN-RBV triple therapy showed higher viral load reductions, lower rates of breakthrough (8%, 5/62), and less frequent emergence of resistance-associated variants compared with faldaprevir monotherapy. (This study has been registered at ClinicalTrials.gov under registration no. NCT00793793.).
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Implications of baseline polymorphisms for potential resistance to NS3 protease inhibitors in Hepatitis C virus genotypes 1a, 2b and 3a. Antiviral Res 2013; 99:12-7. [DOI: 10.1016/j.antiviral.2013.04.018] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 04/12/2013] [Accepted: 04/23/2013] [Indexed: 02/07/2023]
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Response of hepatitis C virus to long-term passage in the presence of alpha interferon: multiple mutations and a common phenotype. J Virol 2013; 87:7593-607. [PMID: 23637397 DOI: 10.1128/jvi.02824-12] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Cell culture-produced hepatitis C virus (HCV) has been subjected to up to 100 serial passages in human hepatoma cells in the absence or presence of different doses of alpha interferon (IFN-α). Virus survival, genetic changes, fitness levels, and phenotypic traits have been examined. While high initial IFN-α doses (increasing from 1 to 4 IU/ml) did not allow HCV survival beyond passage 40, a gradual exposure (from 0.25 to 10 IU/ml) allowed the virus to survive for at least 100 passages. The virus passaged in the presence of IFN-α acquired IFN-α resistance as evidenced by enhanced progeny production and viral protein expression in an IFN-α environment. A partial IFN-α resistance was also noted in populations passaged in the absence of IFN-α. All lineages acquired adaptative mutations, and multiple, nonsynonymous mutations scattered throughout the genome were present in IFN-α-selected populations. Comparison of consensus sequences indicates a dominance of synonymous versus nonsynonymous substitutions. IFN-α-resistant populations displayed decreased sensitivity to a combination of IFN-α and ribavirin. A phenotypic trait common to all assayed viral populations is the ability to increase shutoff host cell protein synthesis, accentuated in infections with IFN-α-selected populations carried out in the presence of IFN-α. The trait was associated with enhanced phosphorylation of protein kinase R (PKR) and eIF2α, although other contributing factors are likely. The results suggest that multiple, independent mutational pathways can confer IFN-α resistance to HCV and might explain why no unified picture has been obtained regarding IFN-α resistance in vivo.
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Zhang EZ, Bartels DJ, Frantz JD, Seepersaud S, Lippke JA, Shames B, Zhou Y, Lin C, Kwong A, Kieffer TL. Development of a sensitive RT-PCR method for amplifying and sequencing near full-length HCV genotype 1 RNA from patient samples. Virol J 2013; 10:53. [PMID: 23402332 PMCID: PMC3575352 DOI: 10.1186/1743-422x-10-53] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 02/07/2013] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Direct-acting antiviral (DAAs) agents for hepatitis C virus (HCV) span a variety of targets, including proteins encoded by the NS3/4A, NS4B, NS5A, and NS5B genes. Treatment with DAAs has been shown to select variants with sequence changes in the HCV genome encoding amino acids that may confer resistance to the treatment. In order to assess these effects in patients, a Reverse Transcription Polymerase Chain Reaction (RT-PCR) method was developed to sequence these regions of HCV from patient plasma. METHODS A method was developed to amplify and sequence genotype 1 HCV RNA from patient plasma. Optimization of HCV RNA isolation, cDNA synthesis, and nested PCR steps were performed. The optimization of HCV RNA isolation, design of RT-PCR primers, optimization of RT-PCR amplification conditions and reagents, and the evaluation of the RT-PCR method performance is described. RESULTS The optimized method is able to successfully, accurately, and reproducibly amplify near full-length genotype 1 HCV RNA containing a wide range of concentrations (103 to 108 IU/mL) with a success rate of 97%. The lower limit of detection was determined to be 1000 IU/mL HCV RNA. CONCLUSIONS This assay allows viral sequencing of all regions targeted by the most common DAAs currently in development, as well as the possibility to determine linkage between variants conferring resistance to multiple DAAs used in combination therapy.
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Affiliation(s)
- Eileen Z Zhang
- Vertex Pharmaceuticals Incorporated, 130 Waverly Street, Cambridge, MA 02139-4242, USA
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21
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Fantin YS, Neverov AD, Favorov AV, Alvarez-Figueroa MV, Braslavskaya SI, Gordukova MA, Karandashova IV, Kuleshov KV, Myznikova AI, Polishchuk MS, Reshetov DA, Voiciehovskaya YA, Mironov AA, Chulanov VP. Base-calling algorithm with vocabulary (BCV) method for analyzing population sequencing chromatograms. PLoS One 2013; 8:e54835. [PMID: 23382983 PMCID: PMC3557274 DOI: 10.1371/journal.pone.0054835] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2012] [Accepted: 12/19/2012] [Indexed: 02/01/2023] Open
Abstract
Sanger sequencing is a common method of reading DNA sequences. It is less expensive than high-throughput methods, and it is appropriate for numerous applications including molecular diagnostics. However, sequencing mixtures of similar DNA of pathogens with this method is challenging. This is important because most clinical samples contain such mixtures, rather than pure single strains. The traditional solution is to sequence selected clones of PCR products, a complicated, time-consuming, and expensive procedure. Here, we propose the base-calling with vocabulary (BCV) method that computationally deciphers Sanger chromatograms obtained from mixed DNA samples. The inputs to the BCV algorithm are a chromatogram and a dictionary of sequences that are similar to those we expect to obtain. We apply the base-calling function on a test dataset of chromatograms without ambiguous positions, as well as one with 3-14% sequence degeneracy. Furthermore, we use BCV to assemble a consensus sequence for an HIV genome fragment in a sample containing a mixture of viral DNA variants and to determine the positions of the indels. Finally, we detect drug-resistant Mycobacterium tuberculosis strains carrying frameshift mutations mixed with wild-type bacteria in the pncA gene, and roughly characterize bacterial communities in clinical samples by direct 16S rRNA sequencing.
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Affiliation(s)
- Yuri S. Fantin
- Federal State Institution of Science Central Research Institute of Epidemiology, Moscow, Russia
| | - Alexey D. Neverov
- Federal State Institution of Science Central Research Institute of Epidemiology, Moscow, Russia
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Alexander V. Favorov
- Department of Oncology, Division of Biostatistics and Bioinformatics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- State Research Institute of Genetics and Selection of Industrial Microorganisms GosNIIGenetika, Moscow, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Maria A. Gordukova
- Federal State Institution of Science Central Research Institute of Epidemiology, Moscow, Russia
| | - Inga V. Karandashova
- Federal State Institution of Science Central Research Institute of Epidemiology, Moscow, Russia
| | - Konstantin V. Kuleshov
- Federal State Institution of Science Central Research Institute of Epidemiology, Moscow, Russia
| | - Anna I. Myznikova
- Federal State Institution of Science Central Research Institute of Epidemiology, Moscow, Russia
| | - Maya S. Polishchuk
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Moscow, Russia
- Department of Statistics, University of California, Berkeley, California, United States of America
| | - Denis A. Reshetov
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Yana A. Voiciehovskaya
- Federal State Institution of Science Central Research Institute of Epidemiology, Moscow, Russia
| | - Andrei A. Mironov
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Institute for Information Transmission Problems (the Kharkevich Institute), Moscow, Russia
| | - Vladimir P. Chulanov
- Federal State Institution of Science Central Research Institute of Epidemiology, Moscow, Russia
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22
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Gregori J, Esteban JI, Cubero M, Garcia-Cehic D, Perales C, Casillas R, Alvarez-Tejado M, Rodríguez-Frías F, Guardia J, Domingo E, Quer J. Ultra-deep pyrosequencing (UDPS) data treatment to study amplicon HCV minor variants. PLoS One 2013; 8:e83361. [PMID: 24391758 PMCID: PMC3877031 DOI: 10.1371/journal.pone.0083361] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 11/08/2013] [Indexed: 02/07/2023] Open
Abstract
We have investigated the reliability and reproducibility of HCV viral quasispecies quantification by ultra-deep pyrosequencing (UDPS) methods. Our study has been divided in two parts. First of all, by UDPS sequencing of clone mixes samples we have established the global noise level of UDPS and fine tuned a data treatment workflow previously optimized for HBV sequence analysis. Secondly, we have studied the reproducibility of the methodology by comparing 5 amplicons from two patient samples on three massive sequencing platforms (FLX+, FLX and Junior) after applying the error filters developed from the clonal/control study. After noise filtering the UDPS results, the three replicates showed the same 12 polymorphic sites above 0.7%, with a mean CV of 4.86%. Two polymorphic sites below 0.6% were identified by two replicates and one replicate respectively. A total of 25, 23 and 26 haplotypes were detected by GS-Junior, GS-FLX and GS-FLX+. The observed CVs for the normalized Shannon entropy (Sn), the mutation frequency (Mf), and the nucleotidic diversity (Pi) were 1.46%, 3.96% and 3.78%. The mean absolute difference in the two patients (5 amplicons each), in the GS-FLX and GS-FLX+, were 1.46%, 3.96% and 3.78% for Sn, Mf and Pi. No false polymorphic site was observed above 0.5%. Our results indicate that UDPS is an optimal alternative to molecular cloning for quantitative study of HCV viral quasispecies populations, both in complexity and composition. We propose an UDPS data treatment workflow for amplicons from the RNA viral quasispecies which, at a sequencing depth of at least 10,000 reads per strand, enables to obtain sequences and frequencies of consensus haplotypes above 0.5% abundance with no erroneous mutations, with high confidence, resistant mutants as minor variants at the level of 1%, with high confidence that variants are not missed, and highly confident measures of quasispecies complexity.
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Affiliation(s)
- Josep Gregori
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain ; Roche Diagnostics SL, Sant Cugat del Vallès, Spain
| | - Juan I Esteban
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain ; CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain ; Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - María Cubero
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain ; CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Damir Garcia-Cehic
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain ; CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Celia Perales
- CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain ; Centro de Biología Molecular Severo Ochoa (CBM), UAM, Madrid, Spain
| | - Rosario Casillas
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain ; Biochemistry Unit, HUVH, Barcelona, Spain
| | | | - Francisco Rodríguez-Frías
- CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain ; Universitat Autònoma de Barcelona, Bellaterra, Spain ; Biochemistry Unit, HUVH, Barcelona, Spain
| | - Jaume Guardia
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain ; CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain ; Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Esteban Domingo
- CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain ; Centro de Biología Molecular Severo Ochoa (CBM), UAM, Madrid, Spain
| | - Josep Quer
- Liver Unit, Internal Medicine, Lab. Malalties Hepàtiques, Vall d'Hebron Institut Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Barcelona, Spain ; CIBER de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain ; Universitat Autònoma de Barcelona, Bellaterra, Spain
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Torti C, Zazzi M, Abenavoli L, Trapasso F, Cesario F, Corigliano D, Cosco L, Costa C, Curia RL, De Rosa M, Foti G, Giraldi C, Leone R, Liberto MC, Lucchino D, Marascio N, Masciari R, Matera G, Pisani V, Serrao N, Surace L, Zicca E, Castelli F, Ciccozzi M, Puoti M, Focà A. Future research and collaboration: the "SINERGIE" project on HCV (South Italian Network for Rational Guidelines and International Epidemiology). BMC Infect Dis 2012; 12 Suppl 2:S9. [PMID: 23173812 PMCID: PMC3495626 DOI: 10.1186/1471-2334-12-s2-s9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The SINERGIE (South Italian Network for Rational Guidelines and International Epidemiology) project is intended to set up a collaborative network comprising virologists, clinicians and public health officials dealing with patients affected by HCV disease in the Calabria Region. A prospective observational data-base of HCV infection will be developed and used for studies on HCV natural history, response to treatment, pharmaco-economics, disease complications, and HCV epidemiology (including phylogenetic analysis). With this approach, we aim at improving the identification and care of patients, focusing on upcoming research questions. The final objective is to assist in improving care delivery and inform Public Health Authorities on how to optimize resource allocation in this area.
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Affiliation(s)
- C Torti
- Unit of Infectious Diseases, University Magna Graecia, Catanzaro, Italy.
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24
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Abstract
The recent development of small molecule compounds that directly inhibit the viral life cycle represents a major milestone for the treatment of chronic hepatitis C virus (HCV) infection. These new drugs that are collectively termed direct-acting antivirals (DAA) include a range of inhibitors of the non-structural (NS) 3/4A protease, NS5B polymerase and NS5A protein. Two NS3/4A protease inhibitors (boceprevir and telaprevir) in combination with pegylated interferon and ribavirin have now been approved for the treatment of chronic HCV genotype 1 infection and cure rates could be increased by 20-30%. However, the majority of DAAs is still in early clinical development. The rapid replication rate of HCV, along with the error-prone polymerase activity leads to a high genetic diversity among HCV virions that includes mutants with reduced susceptibility to DAA-therapy. These resistance-associated variants often occur at very low frequencies. However, during DAA-based treatment, rapid selection of resistance mutations may occur, eventually leading to viral break-through. A number of variants with different levels of resistance have been described in vitro and in vivo for virtually all DAAs. We review the parameters that determine DAA resistance as well as the clinical implications of resistance testing. In addition, the most recent literature and conference data on resistance profiles of DAAs in clinical development and future strategies to avoid the emergence of viral resistance are also discussed.
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Affiliation(s)
- Johannes Vermehren
- Medizinische Klinik 1, Klinikum der J. W. Goethe-Universität, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
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25
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Abstract
Evolution of RNA viruses occurs through disequilibria of collections of closely related mutant spectra or mutant clouds termed viral quasispecies. Here we review the origin of the quasispecies concept and some biological implications of quasispecies dynamics. Two main aspects are addressed: (i) mutant clouds as reservoirs of phenotypic variants for virus adaptability and (ii) the internal interactions that are established within mutant spectra that render a virus ensemble the unit of selection. The understanding of viruses as quasispecies has led to new antiviral designs, such as lethal mutagenesis, whose aim is to drive viruses toward low fitness values with limited chances of fitness recovery. The impact of quasispecies for three salient human pathogens, human immunodeficiency virus and the hepatitis B and C viruses, is reviewed, with emphasis on antiviral treatment strategies. Finally, extensions of quasispecies to nonviral systems are briefly mentioned to emphasize the broad applicability of quasispecies theory.
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Affiliation(s)
- Esteban Domingo
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), C/ Nicolás Cabrera, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain.
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26
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Fusco DN, Chung RT. Novel Therapies for Hepatitis C: Insights from the Structure of the Virus. Annu Rev Med 2012; 63:373-387. [DOI: 10.1146/annurev-med-042010-085715] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
For the first time since the discovery of the hepatitis C virus (HCV), therapeutic options for hepatitis C have expanded. Several agents directly effective against HCV are now in development, including both direct-acting antiviral agents (DAAs) and host cofactor inhibitors. DAAs have been developed to inhibit several HCV proteins, including the NS3/4A serine protease, the NS5B RNA polymerase, NS5A, and NS4B. Host cofactor inhibitors include, but are not limited to, cyclophilin inhibitors, miR122 antagonists, and statins. Development of these agents represents a major advance in HCV therapeutics. This review provides a guide to HCV drugs in various stages of development, including an introduction to their mechanism of action, state of clinical development, efficacy, and side effects.
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Affiliation(s)
- Dahlene N. Fusco
- Gastroenterology Division, Massachusetts General Hospital, Boston, Massachusetts 02114;,
| | - Raymond T. Chung
- Gastroenterology Division, Massachusetts General Hospital, Boston, Massachusetts 02114;,
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27
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Vicenti I, Rosi A, Saladini F, Meini G, Pippi F, Rossetti B, Sidella L, Di Giambenedetto S, Almi P, De Luca A, Caudai C, Zazzi M. Naturally occurring hepatitis C virus (HCV) NS3/4A protease inhibitor resistance-related mutations in HCV genotype 1-infected subjects in Italy. J Antimicrob Chemother 2012; 67:984-7. [PMID: 22258932 DOI: 10.1093/jac/dkr581] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVES To assess the prevalence of hepatitis C virus (HCV) NS3/4A protease inhibitor (PI) resistance mutations in HCV genotype 1-infected PI-naive individuals in Italy. PATIENTS AND METHODS One hundred and twelve patients infected with HCV genotype 1a or 1b (based on Versant HCV Genotype 2.0 or 5'UTR/core sequencing) and never treated with any HCV PI were evaluated. The whole NS3 region was analysed by population sequencing and mutations related to resistance to linear and macrocyclic PIs were recorded. RESULTS Forty-six HCV-monoinfected and 66 HCV/HIV-coinfected subjects were studied. Complete NS3 sequence information was obtained for 109 (97.3%) samples: 67 subtype 1a and 42 subtype 1b. Subtype assignment by NS3 sequencing was concordant in 100.0% and 83.9% of cases with the original 5'UTR sequencing and Versant result, respectively. At least one mutation related to PI resistance was detected in 21 (19.3%) isolates. However, 11 of these had only Q80K, expected to confer resistance to one investigational macrocyclic compound, and were detected only in subtype 1a. Boceprevir and telaprevir resistance-related mutations were detected in 10 (9.2%) isolates and included V36L, T54S and V55A. Only one isolate harboured two mutations (V36L and T54S). There was no association between HCV PI resistance and HIV coinfection or exposure to HIV PIs. CONCLUSIONS A minority of untreated HCV genotype 1 patients in Italy harbour a virus population carrying HCV PI resistance-related mutations. The clinical implications of this finding warrant further analysis.
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Affiliation(s)
- Ilaria Vicenti
- Department of Biotechnology, University of Siena, Siena, Italy
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Canestaro WJ, Martell LA, Wassman ER, Schatzberg R. Healthcare payers: a gate or translational bridge to personalized medicine? Per Med 2012; 9:73-84. [DOI: 10.2217/pme.11.77] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Healthcare payers represent stakeholders who can act as either a bridge or a gate to the translation of personalized medicine into routine clinical practice. To date, the slow realization of the promise of personalized medicine has been partly attributable to the lack of clear evidence supporting the clinical utility of genetic and genomic tests and the lag in development of clinical guidelines for the use and interpretation of tests. These factors, along with a paucity of clear guidance from healthcare payers and clinical experience with genomic tests, serve as impediments to timely and consistent reimbursement decisions. The design of alternative strategies for collaborative evidence-generation, clinical decision support and educational initiatives for healthcare providers, patients and the payers themselves are critical needs to achieve the full benefit of personalized medicine in day-to-day healthcare settings.
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Affiliation(s)
| | - Lori A Martell
- Generation Health, 130 Turner St, Suite 205, Waltham, MA 02453, USA
| | - E Robert Wassman
- Generation Health, 130 Turner St, Suite 205, Waltham, MA 02453, USA
| | - Rick Schatzberg
- Generation Health, 130 Turner St, Suite 205, Waltham, MA 02453, USA
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Lim SR, Qin X, Susser S, Nicholas JB, Lange C, Herrmann E, Hong J, Arfsten A, Hooi L, Bradford W, Nájera I, Smith P, Zeuzem S, Kossen K, Sarrazin C, Seiwert SD. Virologic escape during danoprevir (ITMN-191/RG7227) monotherapy is hepatitis C virus subtype dependent and associated with R155K substitution. Antimicrob Agents Chemother 2012; 56:271-9. [PMID: 22064535 PMCID: PMC3256012 DOI: 10.1128/aac.05636-11] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 10/26/2011] [Indexed: 01/03/2023] Open
Abstract
Danoprevir is a hepatitis C virus (HCV) NS3/4A protease inhibitor that promotes multi-log(10) reductions in HCV RNA when administered as a 14-day monotherapy to patients with genotype 1 chronic HCV. Of these patients, 14/37 experienced a continuous decline in HCV RNA, 13/37 a plateau, and 10/37 a rebound. The rebound and continuous-decline groups experienced similar median declines in HCV RNA through day 7, but their results diverged notably at day 14. Plateau group patients experienced a lesser, but sustained, median HCV RNA decline. Baseline danoprevir susceptibility was similar across response groups but was reduced significantly at day 14 in the rebound group. Viral rebound in genotype 1b was uncommon (found in 2/23 patients). Population-based sequence analysis of NS3 and NS4A identified treatment-emergent substitutions at four amino acid positions in the protease domain of NS3 (positions 71, 155, 168, and 170), but only two (155 and 168) were in close proximity to the danoprevir binding site and carried substitutions that impacted danoprevir potency. R155K was the predominant route to reduced danoprevir susceptibility and was observed in virus isolated from all 10 rebound, 2/13 plateau, and 1/14 continuous-decline patients. Virus in one rebound patient additionally carried partial R155Q and D168E substitutions. Treatment-emergent substitutions in plateau patients were less frequently observed and more variable. Single-rebound patients carried virus with R155Q, D168V, or D168T. Clonal sequence analysis and drug susceptibility testing indicated that only a single patient displayed multiple resistance pathways. These data indicate the ascendant importance of R155K for viral escape during danoprevir treatment and may have implications for the clinical use of this agent.
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