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Comas I, Cancino-Muñoz I, Mariner-Llicer C, Goig GA, Ruiz-Hueso P, Francés-Cuesta C, García-González N, González-Candelas F. Use of next generation sequencing technologies for the diagnosis and epidemiology of infectious diseases. Enferm Infecc Microbiol Clin 2021; 38 Suppl 1:32-38. [PMID: 32111363 DOI: 10.1016/j.eimc.2020.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
For the first time, next generation sequencing technologies provide access to genomic information at a price and scale that allow their implementation in routine clinical practice and epidemiology. While there are still many obstacles to their implementation, there are also multiple examples of their major advantages compared with previous methods. Their main advantage is that a single determination allows epidemiological information on the causative microorganism to be obtained simultaneously, as well as its resistance profile, although these advantages vary according to the pathogen under study. This review discusses several examples of the clinical and epidemiological use of next generation sequencing applied to complete genomes and microbiomes and reflects on its future in clinical practice.
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Affiliation(s)
- Iñaki Comas
- Instituto de Biomedicina de Valencia, IBV-CSIC, Valencia, España; CIBER en Epidemiología y Salud Pública, Valencia, España.
| | | | | | - Galo A Goig
- Instituto de Biomedicina de Valencia, IBV-CSIC, Valencia, España
| | - Paula Ruiz-Hueso
- Unidad Mixta "Infección y Salud Pública" FISABIO-Universitat de València, Instituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-UV), Valencia, España
| | - Carlos Francés-Cuesta
- Unidad Mixta "Infección y Salud Pública" FISABIO-Universitat de València, Instituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-UV), Valencia, España
| | - Neris García-González
- Unidad Mixta "Infección y Salud Pública" FISABIO-Universitat de València, Instituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-UV), Valencia, España
| | - Fernando González-Candelas
- CIBER en Epidemiología y Salud Pública, Valencia, España; Unidad Mixta "Infección y Salud Pública" FISABIO-Universitat de València, Instituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-UV), Valencia, España
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Tsai MC, Hung CH, Lu SN, Wang JH, Chen CH, Kee KM, Chang KC, Chao TL, Hu TH. The incidence of resistance-associated variants to NS5A in HCV subtypes 1a and 1b in Taiwan. Biomed J 2020; 44:S126-S131. [PMID: 35123932 PMCID: PMC9038949 DOI: 10.1016/j.bj.2020.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 01/01/2020] [Accepted: 08/06/2020] [Indexed: 11/23/2022] Open
Abstract
Background Resistance-associated variants (RAVs) to direct-antiviral agents (DAAs) may hamper treatment. There was a lack of data on the natural prevalence of RAVs in Taiwanese HCV-infected patients. We investigated the real-life presence of RAVs in the nonstructural 5A (NS5A) region in HCV genotype 1a and 1b in chronically infected individuals in Taiwan. Methods In this single-center cohort study, nested polymerase chain reaction and direct sequencing analysis was used to determine the frequency of RAVs in the HCV NS5A region in patients with HCV genotype 1a (n = 55) and 1b (n = 525). Results In genotype 1a strains, the incidence of RAVs was 16.4% (9/55) in the NS5A region (M28V/T, n = 6, 10.9%; Q30L, n = 1, 1.8%; Y93N/H, n = 3, 5.5%). In genotype 1b, the incidence of RAVs was 17.5% (92/525) in the NS5A region (L31I/M/V, n = 7, 1.3%; Y93 H/S, n = 87, 16.5%). Patients with RAVs had significantly higher HCV RNA levels (6.1 ± 0.7 vs 5.9 ± 0.8 log IU/mL, p = 0.001) and lower rGT levels (28.9 ± 18.9 vs. 42.9 ± 57.0 U/L, p = 0.001) compared to those without RAVs. Multivariate analysis identified HCV RNA levels (odds ratio = 1.145, 95% CI: 1.060–1.237, p = 0.001) and rGT (OR = 0.989, 95% CI: 0.978–0.999, p = 0.035) as risk factors that are associated with the presence of RAVs. Importantly, there is no association between the presence of RAVs and no SVR (3.8% in patients with RAVs, 15.9% in patients without RAVs, p = 0.32). Conclusion RAVs, especially M28V and Y93H in the NS5A region, were highly prevalent in patients with genotype 1a and 1b HCV, respectively, in Taiwan, and they were linked to high HCV RNA levels and low rGT levels. Before using the NS5A inhibitors, the presence of mutated HCV variants should be taken into consideration.
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Sasaki R, Meyer K, Moriyama M, Kato N, Yokosuka O, Ray RB, Aurora R, Ray R, Kanda T. Rapid hepatitis C virus clearance by antivirals correlates with immune status of infected patients. J Med Virol 2019; 91:411-418. [PMID: 30192392 DOI: 10.1002/jmv.25310] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 09/04/2018] [Indexed: 12/12/2022]
Abstract
Altered immune parameters associated with hepatitis C virus (HCV) genotype 1b infection and their correlation with virus eradication in direct-acting antivirals (DAA)-treated patients were examined. Thirty-one HCV-infected patients were treated with DAAs for 12 weeks. Pre-DAA-treatment and post-DAA-treatment sera were analyzed for cytokines/chemokines using MILLIPLEX MAP. Serum complement level and antibody neutralization activity were measured separately. Sera from 11 spontaneously cleared HCV subjects were included for comparison. Rapid virological responders (RVR) or end-of-treatment responders (EOTR) were defined as patients with HCV RNA negative at week 4 or positive at week 4 and negative at week 12, respectively. HCV RNA eradication and a decrease in liver fibrosis-related cytokines after treatment were observed when compared with pretreatment sera from RVR and EOTR. In pretreatment sera, interferons and T-helper 1 or 2 cell-associated cytokines/chemokines were significantly higher among RVR as compared with EOTR. Furthermore, serum complement and virus neutralizing antibody levels were higher in pretreatment RVR sera. Eradication of HCV RNA by DAA decreased liver fibrosis-related cytokines. Pretreatment sera from RVR displayed an enhanced cytokine/chemokine, complement and virus neutralizing antibody response as compared with EOTR sera. Our results suggested that enhanced host immune status may play an additive role on HCV RNA clearance by DAA.
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Affiliation(s)
- Reina Sasaki
- Department of Pathology, Saint Louis University, St Louis, Missouri
- Department of Internal Medicine, Saint Louis University, St Louis, Missouri
| | - Keith Meyer
- Department of Internal Medicine, Saint Louis University, St Louis, Missouri
| | - Mitsuhiko Moriyama
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, Tokyo, Japan
| | - Naoya Kato
- Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Osamu Yokosuka
- Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Ratna B Ray
- Department of Pathology, Saint Louis University, St Louis, Missouri
- Department of Internal Medicine, Saint Louis University, St Louis, Missouri
| | - Rajeev Aurora
- Department of Molecular Microbiology and Immunology, Saint Louis University, St Louis, Missouri
| | - Ranjit Ray
- Department of Internal Medicine, Saint Louis University, St Louis, Missouri
- Department of Molecular Microbiology and Immunology, Saint Louis University, St Louis, Missouri
| | - Tatsuo Kanda
- Division of Gastroenterology and Hepatology, Department of Medicine, Nihon University School of Medicine, Tokyo, Japan
- Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, Chiba, Japan
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Leung P, Eltahla AA, Lloyd AR, Bull RA, Luciani F. Understanding the complex evolution of rapidly mutating viruses with deep sequencing: Beyond the analysis of viral diversity. Virus Res 2016; 239:43-54. [PMID: 27888126 DOI: 10.1016/j.virusres.2016.10.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/24/2016] [Accepted: 10/25/2016] [Indexed: 12/24/2022]
Abstract
With the advent of affordable deep sequencing technologies, detection of low frequency variants within genetically diverse viral populations can now be achieved with unprecedented depth and efficiency. The high-resolution data provided by next generation sequencing technologies is currently recognised as the gold standard in estimation of viral diversity. In the analysis of rapidly mutating viruses, longitudinal deep sequencing datasets from viral genomes during individual infection episodes, as well as at the epidemiological level during outbreaks, now allow for more sophisticated analyses such as statistical estimates of the impact of complex mutation patterns on the evolution of the viral populations both within and between hosts. These analyses are revealing more accurate descriptions of the evolutionary dynamics that underpin the rapid adaptation of these viruses to the host response, and to drug therapies. This review assesses recent developments in methods and provide informative research examples using deep sequencing data generated from rapidly mutating viruses infecting humans, particularly hepatitis C virus (HCV), human immunodeficiency virus (HIV), Ebola virus and influenza virus, to understand the evolution of viral genomes and to explore the relationship between viral mutations and the host adaptive immune response. Finally, we discuss limitations in current technologies, and future directions that take advantage of publically available large deep sequencing datasets.
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Affiliation(s)
- Preston Leung
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW 2052, Australia; The Kirby Institute, UNSW Australia, Sydney, NSW 2052, Australia
| | - Auda A Eltahla
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW 2052, Australia; The Kirby Institute, UNSW Australia, Sydney, NSW 2052, Australia
| | - Andrew R Lloyd
- The Kirby Institute, UNSW Australia, Sydney, NSW 2052, Australia
| | - Rowena A Bull
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW 2052, Australia; The Kirby Institute, UNSW Australia, Sydney, NSW 2052, Australia
| | - Fabio Luciani
- School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, NSW 2052, Australia; The Kirby Institute, UNSW Australia, Sydney, NSW 2052, Australia.
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Mouse Systems to Model Hepatitis C Virus Treatment and Associated Resistance. Viruses 2016; 8:v8060176. [PMID: 27338446 PMCID: PMC4926196 DOI: 10.3390/v8060176] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 05/12/2016] [Accepted: 06/16/2016] [Indexed: 12/15/2022] Open
Abstract
While addition of the first-approved protease inhibitors (PIs), telaprevir and boceprevir, to pegylated interferon (PEG-IFN) and ribavirin (RBV) combination therapy significantly increased sustained virologic response (SVR) rates, PI-based triple therapy for the treatment of chronic hepatitis C virus (HCV) infection was prone to the emergence of resistant viral variants. Meanwhile, multiple direct acting antiviral agents (DAAs) targeting either the HCV NS3/4A protease, NS5A or NS5B polymerase have been approved and these have varying potencies and distinct propensities to provoke resistance. The pre-clinical in vivo assessment of drug efficacy and resistant variant emergence underwent a great evolution over the last decade. This field had long been hampered by the lack of suitable small animal models that robustly support the entire HCV life cycle. In particular, chimeric mice with humanized livers (humanized mice) and chimpanzees have been instrumental for studying HCV inhibitors and the evolution of drug resistance. In this review, we present the different in vivo HCV infection models and discuss their applicability to assess HCV therapy response and emergence of resistant variants.
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Chayama K, Imamura M, Hayes CN. Hepatitis C virus treatment update - A new era of all-oral HCV treatment. ADVANCES IN DIGESTIVE MEDICINE 2016. [DOI: 10.1016/j.aidm.2016.03.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Kwo PY, Badshah MB. Treatment of HCV in Patients who Failed First-Generation PI Therapy: a Review of Current Literature. Curr Gastroenterol Rep 2016; 17:462. [PMID: 26342813 DOI: 10.1007/s11894-015-0462-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The addition of the first direct-acting antiviral agents, the NS3 protease inhibitors boceprevir or telaprevir, to peg interferon and ribavirin was a major advance in the treatment of genotype 1 hepatitis C individuals with sustained virological response (SVR) rates of 63-75 %. Those who did not achieve SVR had high rates of resistance-associated variants against NS3 protease domain. Retreatment options for those who have failed first-generation protease inhibitors generally are guided by retreatment with direct-acting antiviral agents from other classes. Phase 2 and phase 3 data have demonstrated that retreatment with 12-24 weeks of a NS5B inhibitor (sofosbuvir) in combination with a NS5a inhibitor (daclatasvir or ledipasvir) with or without ribavirin can achieve SVR at high rates comparable to treatment-naive individuals.
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Affiliation(s)
- Paul Y Kwo
- Department of Medicine, Division of Gastroenterology/Hepatology, Indiana University School of Medicine, 975 W. Walnut, IB 327, Indianapolis, IN, 46202-5121, USA,
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Sede MM, Laufer NL, Quarleri J. Previous failure of interferon-based therapy does not alter the frequency of HCV NS3 protease or NS5B polymerase inhibitor resistance-associated variants: longitudinal analysis in HCV/HIV co-infected patients. Int J Antimicrob Agents 2015; 46:219-24. [PMID: 26100213 DOI: 10.1016/j.ijantimicag.2015.04.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 04/09/2015] [Accepted: 04/25/2015] [Indexed: 11/29/2022]
Abstract
Since 2011, treatment of chronic hepatitis C virus (HCV) includes direct-acting antivirals (DAAs) in addition to pegylated interferon-α (peg-IFN) and ribavirin (RBV). IFN-based treatment induces strong cytotoxic T-lymphocyte activity directed to the protease- and polymerase-derived epitopes. This enhanced immunological pressure could favour the emergence of viral epitope variants able to evade immune surveillance and, when resistance-associated variants (RAVs) are implicated, could also be co-selected as a hitchhiking effect. This study analysed the dynamics of the frequency of protease and polymerase inhibitor RAVs that could affect future HCV treatment in human immunodeficiency virus (HIV) co-infected patients on stable antiretroviral therapy with previous IFN-based treatment failure. HCV genotype 1a RNA was extracted from plasma samples of 18 patients prior to and during (24h and 4, 12, 24 and 48 weeks) therapy with peg-IFN+RBV. Next-generation sequencing was performed on HCV-RNA populations using NS3 and NS5B PCR-amplified coding regions. Two measures of genetic diversity were used to compare virus populations: average pairwise nucleotide diversity (π) and Tajima's D statistic. Several protease and polymerase RAVs were detected in all subjects at very low frequencies (<5%), and in most cases their presence was not constant during follow-up. Only samples from two patients for each region exhibited Q80R/K/L and A421V as highly predominant variants. No significant differences were observed among sampling times for either π or D values. In conclusion, previous therapy and failure of peg-IFN+RBV were not associated with an increase in DAA-targeting NS3 or NS5B RAVs that naturally exist in HIV co-infected subjects.
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Affiliation(s)
- Mariano M Sede
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Universidad de Buenos Aires, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Natalia L Laufer
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Universidad de Buenos Aires, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Jorge Quarleri
- Instituto de Investigaciones Biomédicas en Retrovirus y SIDA (INBIRS), Universidad de Buenos Aires, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.
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Ogishi M, Yotsuyanagi H, Tsutsumi T, Gatanaga H, Ode H, Sugiura W, Moriya K, Oka S, Kimura S, Koike K. Deconvoluting the composition of low-frequency hepatitis C viral quasispecies: comparison of genotypes and NS3 resistance-associated variants between HCV/HIV coinfected hemophiliacs and HCV monoinfected patients in Japan. PLoS One 2015; 10:e0119145. [PMID: 25748426 PMCID: PMC4351984 DOI: 10.1371/journal.pone.0119145] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 01/09/2015] [Indexed: 12/16/2022] Open
Abstract
Pre-existing low-frequency resistance-associated variants (RAVs) may jeopardize successful sustained virological responses (SVR) to HCV treatment with direct-acting antivirals (DAAs). However, the potential impact of low-frequency (∼0.1%) mutations, concatenated mutations (haplotypes), and their association with genotypes (Gts) on the treatment outcome has not yet been elucidated, most probably owing to the difficulty in detecting pre-existing minor haplotypes with sufficient length and accuracy. Herein, we characterize a methodological framework based on Illumina MiSeq next-generation sequencing (NGS) coupled with bioinformatics of quasispecies reconstruction (QSR) to realize highly accurate variant calling and genotype-haplotype detection. The core-to-NS3 protease coding sequences in 10 HCV monoinfected patients, 5 of whom had a history of blood transfusion, and 11 HCV/HIV coinfected patients with hemophilia, were studied. Simulation experiments showed that, for minor variants constituting more than 1%, our framework achieved a positive predictive value (PPV) of 100% and sensitivities of 91.7–100% for genotyping and 80.6% for RAV screening. Genotyping analysis indicated the prevalence of dominant Gt1a infection in coinfected patients (6/11 vs 0/10, p = 0.01). For clinical samples, minor genotype overlapping infection was prevalent in HCV/HIV coinfected hemophiliacs (10/11) and patients who experienced whole-blood transfusion (4/5) but none in patients without exposure to blood (0/5). As for RAV screening, the Q80K/R and S122K/R variants were particularly prevalent among minor RAVs observed, detected in 12/21 and 6/21 cases, respectively. Q80K was detected only in coinfected patients, whereas Q80R was predominantly detected in monoinfected patients (1/11 vs 7/10, p < 0.01). Multivariate interdependence analysis revealed the previously unrecognized prevalence of Gt1b-Q80K, in HCV/HIV coinfected hemophiliacs [Odds ratio = 13.4 (3.48–51.9), p < 0.01]. Our study revealed the distinct characteristics of viral quasispecies between the subgroups specified above and the feasibility of NGS and QSR-based genetic deconvolution of pre-existing minor Gts, RAVs, and their interrelationships.
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Affiliation(s)
- Masato Ogishi
- Department of Internal Medicine, Graduate School of Medicine, University of Tokyo, Bunkyo, Tokyo, Japan
| | - Hiroshi Yotsuyanagi
- Department of Internal Medicine, Graduate School of Medicine, University of Tokyo, Bunkyo, Tokyo, Japan
- * E-mail:
| | - Takeya Tsutsumi
- Department of Internal Medicine, Graduate School of Medicine, University of Tokyo, Bunkyo, Tokyo, Japan
| | - Hiroyuki Gatanaga
- AIDS Clinical Center, National Center for Global Health and Medicine, Shinjuku, Tokyo, Japan
| | - Hirotaka Ode
- Department of Infectious Diseases and Immunology, Clinical Research Center, Nagoya Medical Center, Nagoya, Japan
| | - Wataru Sugiura
- Department of Infectious Diseases and Immunology, Clinical Research Center, Nagoya Medical Center, Nagoya, Japan
| | - Kyoji Moriya
- Department of Internal Medicine, Graduate School of Medicine, University of Tokyo, Bunkyo, Tokyo, Japan
| | - Shinichi Oka
- AIDS Clinical Center, National Center for Global Health and Medicine, Shinjuku, Tokyo, Japan
| | - Satoshi Kimura
- Director, Tokyo Teishin Hospital, Tokyo, Japan; President, Tokyo Health Care University, Tokyo, Japan
| | - Kazuhiko Koike
- Department of Internal Medicine, Graduate School of Medicine, University of Tokyo, Bunkyo, Tokyo, Japan
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Barakat KH, Anwar-Mohamed A, Tuszynski JA, Robins MJ, Tyrrell DL, Houghton M. A Refined Model of the HCV NS5A protein bound to daclatasvir explains drug-resistant mutations and activity against divergent genotypes. J Chem Inf Model 2014; 55:362-73. [PMID: 24730573 DOI: 10.1021/ci400631n] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Many direct-acting antiviral agents (DAAs) that selectively block hepatitis C virus (HCV) replication are currently under development. Among these agents is Daclatasvir, a first-in-class inhibitor targeting the NS5A viral protein. Although Daclatasvir is the most potent HCV antiviral molecule yet developed, its binding location and mode of binding remain unknown. The drug exhibits a low barrier to resistance mutations, particularly in genotype 1 viruses, but its efficacy against other genotypes is unclear. Using state-of-the-art modeling techniques combined with the massive computational power of Blue Gene/Q, we identified the atomic interactions of Daclatasvir within NS5A for different HCV genotypes and for several reported resistant mutations. The proposed model is the first to reveal the detailed binding mode of Daclatasvir. It also provides a tool to facilitate design of second generation drugs, which may confer less resistance and/or broader activity against HCV.
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Affiliation(s)
- Khaled H Barakat
- Li Ka Shing Institute of Virology, University of Alberta , Edmonton, Alberta Canada
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Nakamoto S, Kanda T, Wu S, Shirasawa H, Yokosuka O. Hepatitis C virus NS5A inhibitors and drug resistance mutations. World J Gastroenterol 2014; 20:2902-2912. [PMID: 24659881 PMCID: PMC3961994 DOI: 10.3748/wjg.v20.i11.2902] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 10/23/2013] [Accepted: 01/15/2014] [Indexed: 02/06/2023] Open
Abstract
Some direct-acting antiviral agents for hepatitis C virus (HCV), such as telaprevir and boceprevir have been available since 2011. It was reported that HCV NS5A is associated with interferon signaling related to HCV replication and hepatocarcinogenesis. HCV NS5A inhibitors efficiently inhibited HCV replication in vitro. Human studies showed that dual, triple and quad regimens with HCV NS5A inhibitors, such as daclatasvir and ledipasvir, in combination with other direct-acting antiviral agents against other regions of HCV with or without peginterferon/ribavirin, could efficiently inhibit HCV replication according to HCV genotypes. These combinations might be a powerful tool for “difficult-to-treat” HCV-infected patients. “First generation” HCV NS5A inhibitors such as daclatasvir, ledipasvir and ABT-267, which are now in phase III clinical trials, could result in resistance mutations. “Second generation” NS5A inhibitors such as GS-5816, ACH-3102, and MK-8742, have displayed improvements in the genetic barrier while maintaining potency. HCV NS5A inhibitors are safe at low concentrations, which make them attractive for use despite low genetic barriers, although, in fact, HCV NS5A inhibitors should be used with HCV NS3/4A inhibitors, HCV NS5B inhibitors or peginterferon plus ribavirin. This review article describes HCV NS5A inhibitor resistance mutations and recommends that HCV NS5A inhibitors be used in combination regimens potent enough to prevent the emergence of resistant variants.
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Wu S, Kanda T, Nakamoto S, Imazeki F, Yokosuka O. Hepatitis C virus protease inhibitor-resistance mutations: Our experience and review. World J Gastroenterol 2013; 19:8940-8948. [PMID: 24379619 PMCID: PMC3870547 DOI: 10.3748/wjg.v19.i47.8940] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Accepted: 12/04/2013] [Indexed: 02/06/2023] Open
Abstract
Direct-acting antiviral agents (DAAs) for hepatitis C virus (HCV) infection are one of the major advances in its medical treatment. The HCV protease inhibitors boceprevir and telaprevir were the first approved DAAs in the United States, Europe, and Japan. When combined with peginterferon plus ribavirin, these agents increase sustained virologic response rates to 70%-80% in treatment-naïve patients and previous-treatment relapsers with chronic HCV genotype 1 infection. Without peginterferon plus ribavirin, DAA mono-therapies increased DAA-resistance mutations. Several new DAAs for HCV are now in clinical development and are likely to be approved in the near future. However, it has been reported that the use of these drugs also led to the emergence of DAA-resistance mutations in certain cases. Furthermore, these mutations exhibit cross-resistance to multiple drugs. The prevalence of DAA-resistance mutations in HCV-infected patients who were not treated with DAAs is unknown, and it is as yet uncertain whether such variants are sensitive to DAAs. We performed a population sequence analysis to assess the frequency of such variants in the sera of HCV genotype 1-infected patients not treated with HCV protease inhibitors. Here, we reviewed the literature on resistance variants of HCV protease inhibitors in treatment naïve patients with chronic HCV genotype 1, as well as our experience.
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Jackowiak P, Kuls K, Budzko L, Mania A, Figlerowicz M, Figlerowicz M. Phylogeny and molecular evolution of the hepatitis C virus. INFECTION GENETICS AND EVOLUTION 2013; 21:67-82. [PMID: 24200590 DOI: 10.1016/j.meegid.2013.10.021] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 10/24/2013] [Accepted: 10/26/2013] [Indexed: 12/14/2022]
Abstract
The hepatitis C virus (HCV) is a globally prevalent human pathogen that causes persistent liver infections in most infected individuals. HCV is classified into seven phylogenetically distinct genotypes, which have different geographical distributions and levels of genetic diversity. Some of these genotypes are endemic and highly divergent, whereas others disseminate rapidly on an epidemic scale but display lower variability. HCV phylogeny has an important impact on disease epidemiology and clinical practice because the viral genotype may determine the pathogenesis and severity of the resultant chronic liver disease. In addition, there is a clear association between the HCV genotype and its susceptibility to antiviral treatment. Similarly to other RNA viruses, in a single host, HCV exists as a combination of related but genetically different variants. The whole formation is the actual target of selection exerted by a host organism and antiviral therapeutics. The genetic structure of the viral population is largely shaped by mutations that are constantly introduced during an error-prone replication. However, it appears that genetic recombination may also contribute to this process. This heterogeneous collection of variants has a significant ability to evolve towards the fitness optimum. Interestingly, negative selection, which restricts diversity, emerges as an essential force that drives HCV evolution. It is becoming clear that HCV evolves to become stably adapted to the host environment. In this article we review the HCV phylogeny and molecular evolution in the context of host-virus interactions.
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Affiliation(s)
- Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Karolina Kuls
- Department of Infectious Diseases and Child Neurology, Karol Marcinkowski University of Medical Sciences, Szpitalna 27/33, 60-572 Poznan, Poland
| | - Lucyna Budzko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Anna Mania
- Department of Infectious Diseases and Child Neurology, Karol Marcinkowski University of Medical Sciences, Szpitalna 27/33, 60-572 Poznan, Poland
| | - Magdalena Figlerowicz
- Department of Infectious Diseases and Child Neurology, Karol Marcinkowski University of Medical Sciences, Szpitalna 27/33, 60-572 Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; Institute of Computing Science, Poznan University of Technology, Piotrowo 3A, 60-965 Poznan, Poland.
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