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Ong AT, Tay E, Dwyer DE, George J, Douglas MW. Pre-treatment antiviral resistance in Australians with chronic hepatitis C: prevalence of NS3 and NS5A resistance data in the state of New South Wales. Antivir Ther 2020; 24:281-290. [PMID: 31085813 DOI: 10.3851/imp3317] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2019] [Indexed: 10/26/2022]
Abstract
BACKGROUND Direct-acting antivirals (DAAs) have revolutionized HCV treatment, but the impact of antiviral resistance at a population level is still not clear. The majority of patients who fail DAA therapy develop resistance-associated substitutions (RASs), which can impact re-treatment. There is potential for resistance prevalence to rise in the community with treatment scale up, due to transmission of resistant virus. Monitoring for increasing antiviral resistance requires a reliable baseline, yet there are few published data on the prevalence of HCV resistance in Australia. The aim of this study was to determine the prevalence of RASs among untreated Australians with HCV genotype-1a infection, to inform ongoing surveillance. METHODS A cross-sectional study was performed at a single large university hospital pathology laboratory in Australia. Archived blood samples referred for HCV genotype testing were analysed. All patients were naive to DAAs. The prevalence of RASs in the HCV NS3 and NS5A regions was determined using Sanger based population sequencing. RESULTS Of 379 samples tested, 34% contained DAA-resistant virus: 24% had resistance to NS3 protease inhibitors, 12% had NS5A inhibitor resistance and 4% of patients had resistance to both drug classes. Clinically relevant RASs conferring resistance against NS5A inhibitors ledipasvir, daclatasvir and elbasvir were detected in 5.8% of samples. CONCLUSIONS This is the largest study of HCV antiviral drug resistance in Australia, which differs from resistance prevalence in the USA. The results provide valuable data on the baseline prevalence of HCV resistance, which can be used in the future to monitor for increasing antiviral resistance.
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Affiliation(s)
- Adrian Tl Ong
- Storr Liver Centre, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Sydney, Australia.,Centre for Infectious Diseases and Microbiology, Westmead Hospital, Sydney, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, Australia
| | - Enoch Tay
- Storr Liver Centre, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Sydney, Australia
| | - Dominic E Dwyer
- Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Sydney, Australia
| | - Jacob George
- Storr Liver Centre, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Sydney, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, Australia
| | - Mark W Douglas
- Storr Liver Centre, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Sydney, Australia.,Centre for Infectious Diseases and Microbiology, Westmead Hospital, Sydney, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, Australia
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2
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B cell immunodominance in primary hepatitis C virus infection. J Hepatol 2020; 72:670-679. [PMID: 31785346 DOI: 10.1016/j.jhep.2019.11.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 11/12/2019] [Accepted: 11/15/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS Neutralising antibodies (NAbs) play a key role in clearance of HCV. NAbs have been isolated and mapped to several domains on the HCV envelope proteins. However, the immunodominance of these epitopes in HCV infection remains unknown, hindering efforts to elicit optimal epitope-specific responses. Furthermore, it remains unclear which epitope-specific responses are associated with broad NAb (bNAb) activity in primary HCV infection. The aim of this study was to define B cell immunodominance in primary HCV, and its implications on neutralisation breadth and clearance. METHODS Using samples from 168 patients with primary HCV infection, the antibody responses targeted 2 immunodominant domains, termed domains B and C. Genotype 1 and 3 infections were associated with responses targeted towards different bNAb domains. RESULTS No epitopes were uniquely targeted by clearers compared to those who developed chronic infection. Samples with bNAb activity were enriched for multi-specific responses directed towards the epitopes antigenic region 3, antigenic region 4, and domain D, and did not target non-neutralising domains. CONCLUSIONS This study outlines for the first time a clear NAb immunodominance profile in primary HCV infection, and indicates that it is influenced by the infecting virus. It also highlights the need for a vaccination strategy to induce multi-specific responses that do not target non-neutralising domains. LAY SUMMARY Neutralising antibodies will likely form a key component of a protective hepatitis C virus vaccine. In this work we characterise the predominant neutralising and non-neutralising antibody (epitope) targets in acute hepatitis C virus infection. We have defined the natural hierarchy of epitope immunodominance, and demonstrated that viral genotype can impact on this hierarchy. Our findings highlight key epitopes that are associated with broadly neutralising antibodies, and the deleterious impact of mounting a response towards some of these domains on neutralising breadth. These findings should guide future efforts to design immunogens aimed at generating neutralising antibodies with a vaccine candidate.
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3
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A Prospective Italian Study on Baseline NS3 and NS5A Resistance to Direct-Acting Antivirals in a Real-World Setting of HIV-1/HCV Coinfected Patients and Association with Treatment Outcome. Viruses 2020; 12:v12030269. [PMID: 32121164 PMCID: PMC7150799 DOI: 10.3390/v12030269] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/24/2020] [Accepted: 02/26/2020] [Indexed: 12/28/2022] Open
Abstract
We prospectively evaluated the frequency of natural resistance-associated substitutions (RASs) in the NS3 and NS5A regions according to different HCV genotypes and their possible effect on treatment outcome in HIV-1/HCV patients treated with direct-acting antivirals (DAAs). Baseline RASs in the NS3 and NS5A domains were investigated in 62 HIV-1/HCV patients treated with DAAs: 23 patients harbored HCV-GT1a, 26 harbored GT3a, and 13 harbored GT4d. A higher occurrence of RASs was found in the NS3 domain within GT1a (13/23) than GT3a (0/26) or GT4d (2/13). With regard to treatment outcome, NS3 RASs were detected in 14/56 patients with sustained virological response (SVR) and in 1/6 non-responder (NR) patients. Occurrence of RASs of NS5A domain was lower in SVR (4/56, had RASs) than in NR (3/6, had RASs). Evaluation of RASs at baseline instead of at virological failure, especially in the NS5A domain, could positively influence the choice of new DAA combinations for the treatment of HIV-1/HCV patients.
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4
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Rodrigo C, Leung P, Lloyd AR, Bull RA, Luciani F, Grebely J, Dore GJ, Applegate T, Page K, Bruneau J, Cox AL, Osburn W, Kim AY, Shoukry NH, Lauer GM, Maher L, Schinkel J, Prins M, Hellard M, Eltahla AA. Genomic variability of within-host hepatitis C variants in acute infection. J Viral Hepat 2019; 26:476-484. [PMID: 30578702 PMCID: PMC6417964 DOI: 10.1111/jvh.13051] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 11/26/2018] [Indexed: 01/04/2023]
Abstract
Interactions between the host immune system and the viral variants determine persistence of hepatitis C virus (HCV) infection after the acute phase of infection. This study describes the genetic variability of within-host HCV viral variants in acute infection and correlates it with host- and virus-related traits and infection outcome. Next generation sequence data (Illumina, MiSeq platform) of viral genomes from 116 incident acute infections (within 180 days of infection) were analysed to determine all the single nucleotide polymorphism (SNP) frequencies above a threshold of 0.1%. The variability of the SNPs for the full open reading frame of the genome as well as for each protein coding region were compared using mean standardized Shannon entropy (SE) values calculated separately for synonymous and nonsynonymous mutations. The envelope glycoproteins regions (E1 and E2) had the highest SE values (indicating greater variability) followed by the NS5B region. Nonsynonymous mutations rather than synonymous mutations were the main contributors to genomic variability in acute infection. The mean difference of Shannon entropy was also compared between subjects after categorizing the samples according to host and virus-related traits. Host IFNL3 allele CC polymorphism at rs12979860 (vs others) and viral genotype 1a (vs 3a) were associated with higher genomic variability across the viral open reading frame. Time since infection, host gender or continent of origin was not associated with the viral genomic variability. Viral genomic variability did not predict spontaneous clearance.
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Affiliation(s)
| | | | | | - Rowena A. Bull
- School of Medical Sciences, UNSW, NSW, Australia
- The Kirby Institute, UNSW Sydney, NSW, Australia
| | - Fabio Luciani
- School of Medical Sciences, UNSW, NSW, Australia
- The Kirby Institute, UNSW Sydney, NSW, Australia
| | | | | | | | - Kimberly Page
- University of New Mexico, Albuquerque, New Mexico, USA
| | - Julie Bruneau
- Centre de Recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
| | - Andrea L. Cox
- Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | | | | | - Naglaa H. Shoukry
- Centre de Recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
| | | | - Lisa Maher
- The Kirby Institute, UNSW Sydney, NSW, Australia
| | - Janke Schinkel
- Academic Medical Center, Amsterdam, The Netherlands
- GGD Public Health Service of Amsterdam
| | - Maria Prins
- Academic Medical Center, Amsterdam, The Netherlands
- GGD Public Health Service of Amsterdam
| | - Margaret Hellard
- Burnet Institute, Melbourne, VIC, Australia
- Monash University, Australia
- Alfred Hospital, Melbourne, Australia
- Doherty Institute and Melbourne School of Population and Global Health, University of Melbourne
| | - Auda A. Eltahla
- School of Medical Sciences, UNSW, NSW, Australia
- University of New Mexico, Albuquerque, New Mexico, USA
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5
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Huang W, Wang M, Gong Q, Yu D, Chen P, Lin J, Han Y, Su Y, Qu L, Zhang X. Comparison of Naturally Occurring Resistance-Associated Substitutions Between 2008 and 2016 in Chinese Patients with Chronic Hepatitis C Virus Infection. Microb Drug Resist 2019; 25:944-950. [PMID: 30702389 DOI: 10.1089/mdr.2018.0360] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Aims: The presence of pre-existing hepatitis C virus (HCV) resistance-associated substitutions (RASs) could attenuate viral susceptibility to direct-acting antiviral agents. The aim of this study was to better understand the differences among HCV RASs over time. We compared the prevalence and characteristics of naturally occurring HCV RASs in the NS3, NS5A, and NS5B genes between 2008 and 2016 in Chinese patients chronically infected with HCV genotypes (GT) 1b, 2a, 3a, 3b, and 6a. Methods: HCV RNA was extracted after serum samples were collected from 242 patients at treatment baseline, including 120 samples in 2008 and 122 samples in 2016. Reverse transcription and nested PCR were performed, and the PCR products of the NS3, NS5A, and NS5B regions were sequenced using the Sanger sequencing method. Finally, RASs were identified from the different viral strains. Results: In GT1b, the overall frequency of NS5A RASs in 2016 was significantly higher than that in 2008 (42.0% vs. 18.4%; p = 0.002). Among NS5A RASs, the most frequently detected RAS was Y93H (5.3% in 2008 vs. 15.9% in 2016; p = 0.035), which confers medium- to high-level resistance to the NS5A inhibitors: daclatasvir (DCV), ledipasvir (LDV), ombitasvir (OMV), and elbasvir. The frequency of NS5A L28 (low-level resistance to DCV/LDV/OMV) in 2016 was also higher than that in 2008 (11.6% vs. 1.3%; p = 0.027). In addition, the highest frequency of clinically relevant NS3 RASs was S122G/A/T (69.7% in 2008 and 72.5% in 2016) in HCV GT1b isolates, which had medium-level resistance to simeprevir and asunaprevir, followed by Y56F (7.9% in 2008 and 14.5% in 2016), which confers resistance to paritaprevir. Although NS5B C316N had the highest substitution rate in GT1b (80.2% in 2008 and 91.3% in 2016), it was associated with low-level resistance to sofosbuvir and dasabuvir. However, HCV RASs were rarely detectable at baseline in other genotypes or subtypes except GT1b in this study. Conclusion: The frequency of NS5A RASs in 2016 was significantly higher than that in 2008, especially at the L28 and Y93 substitution positions, which may be due to their better fitness compared with wild-type viruses.
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Affiliation(s)
- Wei Huang
- 1 Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Mingjie Wang
- 1 Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Qiming Gong
- 2 Department of Infectious Diseases, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Demin Yu
- 1 Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Peizhan Chen
- 3 Translational Medicine Research Center, Ruijin Hospital North, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Junyu Lin
- 1 Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Yue Han
- 1 Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
| | - Yu Su
- 4 Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Fu Dan University, Shanghai, China
| | - Lihong Qu
- 5 Department of Infectious Diseases, East Hospital, Tongji University, Shanghai, China
| | - Xinxin Zhang
- 1 Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai, China
- 3 Translational Medicine Research Center, Ruijin Hospital North, Shanghai Jiaotong University, School of Medicine, Shanghai, China
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6
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Rodrigo C, Luciani F. Dynamic interactions between RNA viruses and human hosts unravelled by a decade of next generation sequencing. Biochim Biophys Acta Gen Subj 2018; 1863:511-519. [PMID: 30528489 DOI: 10.1016/j.bbagen.2018.12.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 11/27/2018] [Accepted: 12/04/2018] [Indexed: 01/15/2023]
Abstract
BACKGROUND Next generation sequencing (NGS) methods have significantly contributed to a paradigm shift in genomic research for nearly a decade now. These methods have been useful in studying the dynamic interactions between RNA viruses and human hosts. SCOPE OF THE REVIEW In this review, we summarise and discuss key applications of NGS in studying the host - pathogen interactions in RNA viral infections of humans with examples. MAJOR CONCLUSIONS Use of NGS to study globally relevant RNA viral infections have revolutionized our understanding of the within host and between host evolution of these viruses. These methods have also been useful in clinical decision-making and in guiding biomedical research on vaccine design. GENERAL SIGNIFICANCE NGS has been instrumental in viral genomic studies in resolving within-host viral genomic variants and the distribution of nucleotide polymorphisms along the full-length of viral genomes in a high throughput, cost effective manner. In the future, novel advances such as long read, single molecule sequencing of viral genomes and simultaneous sequencing of host and pathogens may become the standard of practice in research and clinical settings. This will also bring on new challenges in big data analysis.
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Affiliation(s)
- Chaturaka Rodrigo
- School of Medical Sciences and Kirby Institute for Infection and Immunity, UNSW Australia, 2052, NSW, Australia
| | - Fabio Luciani
- School of Medical Sciences and Kirby Institute for Infection and Immunity, UNSW Australia, 2052, NSW, Australia.
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7
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Ashraf MU, Iman K, Khalid MF, Salman HM, Shafi T, Rafi M, Javaid N, Hussain R, Ahmad F, Shahzad-Ul-Hussan S, Mirza S, Shafiq M, Afzal S, Hamera S, Anwar S, Qazi R, Idrees M, Qureshi SA, Chaudhary SU. Evolution of efficacious pangenotypic hepatitis C virus therapies. Med Res Rev 2018; 39:1091-1136. [PMID: 30506705 DOI: 10.1002/med.21554] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 10/11/2018] [Accepted: 10/11/2018] [Indexed: 12/12/2022]
Abstract
Hepatitis C compromises the quality of life of more than 350 million individuals worldwide. Over the last decade, therapeutic regimens for treating hepatitis C virus (HCV) infections have undergone rapid advancements. Initially, structure-based drug design was used to develop molecules that inhibit viral enzymes. Subsequently, establishment of cell-based replicon systems enabled investigations into various stages of HCV life cycle including its entry, replication, translation, and assembly, as well as role of host proteins. Collectively, these approaches have facilitated identification of important molecules that are deemed essential for HCV life cycle. The expanded set of putative virus and host-encoded targets has brought us one step closer to developing robust strategies for efficacious, pangenotypic, and well-tolerated medicines against HCV. Herein, we provide an overview of the development of various classes of virus and host-directed therapies that are currently in use along with others that are undergoing clinical evaluation.
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Affiliation(s)
- Muhammad Usman Ashraf
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan.,Virology Laboratory, Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Kanzal Iman
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Muhammad Farhan Khalid
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan.,Department of Biomedical Engineering, University of Engineering and Technology, Lahore, Pakistan
| | - Hafiz Muhammad Salman
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan.,Plant Biotechnology Laboratory, Institute of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Talha Shafi
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Momal Rafi
- Department of Statistics, University of Gujrat, Gujrat, Pakistan
| | - Nida Javaid
- Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Rashid Hussain
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Fayyaz Ahmad
- Department of Statistics, University of Gujrat, Gujrat, Pakistan
| | | | - Shaper Mirza
- Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Muhammad Shafiq
- Plant Biotechnology Laboratory, Institute of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Samia Afzal
- Virology Laboratory, Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Sadia Hamera
- Department of Plant Genetics, Institute of Life Sciences, University of Rostock, Germany
| | - Saima Anwar
- Department of Biomedical Engineering, University of Engineering and Technology, Lahore, Pakistan
| | - Romena Qazi
- Department of Pathology, Shaukat Khanum Memorial Cancer Hospital & Research Centre, Lahore, Pakistan
| | - Muhammad Idrees
- Virology Laboratory, Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.,Hazara University, Mansehra, Pakistan
| | - Sohail A Qureshi
- Institute of Integrative Biosciences, CECOS-University of Information Technology and Emerging Sciences, Peshawar, Pakistan
| | - Safee Ullah Chaudhary
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
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8
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Bertoli A, Sorbo MC, Aragri M, Lenci I, Teti E, Polilli E, Di Maio VC, Gianserra L, Biliotti E, Masetti C, Magni CF, Babudieri S, Nicolini LA, Milana M, Cacciatore P, Sarmati L, Pellicelli A, Paolucci S, Craxì A, Morisco F, Palitti VP, Siciliano M, Coppola N, Iapadre N, Puoti M, Rizzardini G, Taliani G, Pasquazzi C, Andreoni M, Parruti G, Angelico M, Perno CF, Cento V, Ceccherini-Silberstein F. Prevalence of Single and Multiple Natural NS3, NS5A and NS5B Resistance-Associated Substitutions in Hepatitis C Virus Genotypes 1-4 in Italy. Sci Rep 2018; 8:8988. [PMID: 29895871 PMCID: PMC5997636 DOI: 10.1038/s41598-018-26862-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 05/16/2018] [Indexed: 12/15/2022] Open
Abstract
Natural resistance-associated substitutions (RASs) are reported with highly variable prevalence across different HCV genotypes (GTs). Frequency of natural RASs in a large Italian real-life cohort of patients infected with the 4 main HCV-GTs was investigated. NS3, NS5A and NS5B sequences were analysed in 1445 HCV-infected DAA-naïve patients. Sanger-sequencing was performed by home-made protocols on 464 GT1a, 585 GT1b, 92 GT2c, 199 GT3a, 16 GT4a and 99 GT4d samples. Overall, 20.7% (301/1455) of patients showed natural RASs, and the prevalence of multiclass-resistance was 7.3% (29/372 patients analysed). NS3-RASs were particularly common in GT1a and GT1b (45.2-10.8%, respectively), mainly due to 80K presence in GT1a (17%). Almost all GTs showed high prevalence of NS5A-RASs (range: 10.2-45.4%), and especially of 93H (5.1%). NS5A-RASs with fold-change >100x were detected in 6.8% GT1a (30H/R-31M-93C/H), 10.3% GT1b (31V-93H), 28.4% GT2c (28C-31M-93H), 8.5% GT3a (30K-93H), 45.5% GT4a (28M-30R-93H) and 3.8% GT4d (28V-30S-93H). Sofosbuvir RAS 282T was never detected, while the 159F and 316N RASs were found in GT1b (13.4-19.1%, respectively). Natural RASs are common in Italian patients infected with HCV-GTs 1-4. High prevalence of clinically-relevant RASs (such as Y93H) supports the appropriateness of HCV resistance-test to properly guide DAA-based therapy.
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Affiliation(s)
- Ada Bertoli
- Department Experimental Medicine and Surgery, University of Rome "Tor Vergata", 00133, Rome, Italy
| | - Maria Chiara Sorbo
- Department Experimental Medicine and Surgery, University of Rome "Tor Vergata", 00133, Rome, Italy
| | - Marianna Aragri
- Department Experimental Medicine and Surgery, University of Rome "Tor Vergata", 00133, Rome, Italy
| | - Ilaria Lenci
- Hepatology Unit, University Hospital of Rome "Tor Vergata", 00133, Rome, Italy
| | - Elisabetta Teti
- Infectious Diseases Unit, University Hospital of Rome "Tor Vergata", 00133, Rome, Italy
| | - Ennio Polilli
- Infectious Diseases Unit, Pescara General Hospital, 65124, Pescara, Italy
| | - Velia Chiara Di Maio
- Department Experimental Medicine and Surgery, University of Rome "Tor Vergata", 00133, Rome, Italy
| | - Laura Gianserra
- Infectious Diseases Unit, Sant'Andrea Hospital - "Sapienza" University, 00189, Rome, Italy
| | - Elisa Biliotti
- Tropical Diseases, Umberto I Hospital -"Sapienza" University, 00161, Rome, Italy
| | - Chiara Masetti
- Hepatology Unit, University Hospital of Rome "Tor Vergata", 00133, Rome, Italy
| | - Carlo F Magni
- 1st Division of Infectious Diseases, ASST Fatebenefratelli Sacco, 20157, Milan, Italy
| | - Sergio Babudieri
- Clinical and Experimental Medicine, University of Sassari, 07100, Sassari, Italy
| | - Laura A Nicolini
- Infectious Diseases Unit, IRCCS AOU San Martino - IST, 16132, Genoa, Italy
| | - Martina Milana
- Hepatology Unit, University Hospital of Rome "Tor Vergata", 00133, Rome, Italy
| | | | - Loredana Sarmati
- Infectious Diseases Unit, University Hospital of Rome "Tor Vergata", 00133, Rome, Italy
| | | | - Stefania Paolucci
- Molecular Virology, Fondazione IRCCS Policlinico San Matteo, 27100, Pavia, Italy
| | - Antonio Craxì
- Gastroenterology, "P. Giaccone" University Hospital, 90127, Palermo, Italy
| | - Filomena Morisco
- Gastroenterology, "Federico II" University, 80131, Naples, Italy
| | | | | | - Nicola Coppola
- Infectious Diseases Unit, "L. Vanvitelli" University of Campania, 80138, Naples, Italy
| | - Nerio Iapadre
- Infectious Diseases Unit, S. Salvatore Hospital, 67100, L'Aquila, Italy
| | - Massimo Puoti
- Infectious Diseases Unit, Niguarda Ca' Granda Hospital, 20162, Milan, Italy
| | - Giuliano Rizzardini
- 1st Division of Infectious Diseases, ASST Fatebenefratelli Sacco, 20157, Milan, Italy
| | - Gloria Taliani
- Tropical Diseases, Umberto I Hospital -"Sapienza" University, 00161, Rome, Italy
| | - Caterina Pasquazzi
- Infectious Diseases Unit, Sant'Andrea Hospital - "Sapienza" University, 00189, Rome, Italy
| | - Massimo Andreoni
- Infectious Diseases Unit, University Hospital of Rome "Tor Vergata", 00133, Rome, Italy
| | - Giustino Parruti
- Infectious Diseases Unit, Pescara General Hospital, 65124, Pescara, Italy
| | - Mario Angelico
- Hepatology Unit, University Hospital of Rome "Tor Vergata", 00133, Rome, Italy
| | | | - Valeria Cento
- Department Experimental Medicine and Surgery, University of Rome "Tor Vergata", 00133, Rome, Italy.
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9
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Jagjit Singh GK, Kaye S, Abbott JC, Boesecke C, Rockstroh J, McClure MO, Nelson M. Use of next-generation sequencing in the CHAT study (acute HCV in HIV): effect of baseline resistance-associated NS3 variants on treatment failure. HIV CLINICAL TRIALS 2018; 19:46-51. [PMID: 29493385 DOI: 10.1080/15284336.2018.1439714] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Background The epidemic of acute HCV infection among HIV-infected men who have sex with men (MSM) is ongoing. Transmission of drug-resistant variants (DRVs) after HCV treatment failure could pose a major threat to the effectiveness of future therapies. We determined the baseline prevalence of pre-existing DRVs in the HCV NS3 protease gene and their effects on the addition of telaprevir (TVR) to standard pegylated interferon and ribavirin (PEG-IFN/RBV) for acute HCV infection in individuals enrolled in a multicentre randomized controlled trial (2013 and 2014). Methods The HCV NS3 viral protease was analyzed using Sanger and next-generation sequencing (NGS) for DRVs at baseline (n = 31), and at viral breakthrough following TVR-based treatment (n = 3) or PEG-IFN/RBV alone (n = 2). Results Sequence analysis indicated that all individuals were infected with HCV genotype 1a. Complete (100%) concordance was seen between Sanger and NGS for high levels of mutant viral populations. The simeprevir-associated Q80K variant was present at high frequency in the German samples (7/11-64%) and infrequently in the UK samples (1/20-5%). In the three TVR-based treatment failures, V36M/l and R155K/T emerged, but not R155G which was detectable at low levels in two individuals at baseline. Failure rate at week 24 was 26.7% (with baseline DRVs) vs. 6.3% (without baseline DRVs), p = 0.17). Comparison of sequences pre- and post-therapy in 5 who failed therapy revealed the emergence of not previously described variants V193G, E176K, P189S (on TVR), and V181S in one instance each. Conclusion The presence of baseline DRVs for the NS3 protease gene of HCV genotype 1a did not appear to predict treatment failure in our patient cohort. Where detected, Q80K was present at high levels (>98%), but had no effect on outcomes and remained high after failure.
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Affiliation(s)
- Gurmit Kaur Jagjit Singh
- a Department of HIV and Sexual Health , Chelsea and Westminster Hospital NHS Foundation Trust , London , UK
| | - Steve Kaye
- b Division of Infectious Diseases , Imperial College London , London , UK
| | - James C Abbott
- c Department of Surgery and Cancer , Imperial College London , London , UK
| | | | - Juergen Rockstroh
- d Department of Medicine , Bonn University Hospital , Bonn , Germany
| | - Myra O McClure
- b Division of Infectious Diseases , Imperial College London , London , UK
| | - Mark Nelson
- a Department of HIV and Sexual Health , Chelsea and Westminster Hospital NHS Foundation Trust , London , UK.,b Division of Infectious Diseases , Imperial College London , London , UK
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10
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Carrasco I, Arias A, Benítez-Gutiérrez L, Lledó G, Requena S, Cuesta M, Cuervas-Mons V, de Mendoza C. Baseline NS5A resistance associated substitutions may impair DAA response in real-world hepatitis C patients. J Med Virol 2017; 90:532-536. [PMID: 28990680 DOI: 10.1002/jmv.24971] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/05/2017] [Indexed: 12/24/2022]
Abstract
Oral DAA have demonstrated high efficacy as treatment of hepatitis C. However, the presence of resistance-associated substitutions (RAS) at baseline has occasionally been associated with impaired treatment response. Herein, we examined the impact of baseline RAS at the HCV NS5A gene region on treatment response in a real-life setting. All hepatitis C patients treated with DAA including NS5A inhibitors at our institution were retrospectively examined. The virus NS5A gene was analyzed using population sequencing at baseline and after 24 weeks of completing therapy in all patients that failed. All changes recorded at positions 28, 29, 30, 31, 32, 58, 62, 92, and 93 were considered. A total of 166 patients were analyzed. HCV genotypes were as follows: G1a (31.9%), G1b (48.2%), G3 (10.2%), and G4 (9.6%). Overall, 69 (41.6%) patients were coinfected with HIV and 46.7% had advanced liver fibrosis (Metavir F3-F4). Sixty (36.1%) patients had at least one RAS at baseline, including M28A/G/T (5), Q30X (12), L31I/F/M/V (6), T58P/S (25), Q/E62D (1), A92 K (7), and Y93C/H (15). Overall, 4.8% had two or more RAS, being more frequent in G4 (12.5%) followed by G1b (6.3%) and G1a (1.9%). Of 10 (6%) patients that failed DAA therapy, five had baseline NS5A RAS. No association was found for specific baseline RAS, although changes at position 30 were more frequent in failures than cures (22.2% vs 6.4%, P = 0.074). Moreover, the presence of two or more RAS at baseline was more frequent in failures (HR: 7.2; P = 0.029). Upon failure, six patients showed emerging RAS, including Q30C/H/R (3), L31M (1), and Y93C/H (2). Baseline NS5A RAS are frequently seen in DAA-naïve HCV patients. Two or more baseline NS5A RAS were found in nearly 5% and were significantly associated to DAA failure. Therefore, baseline NS5A testing should be considered when HCV treatment is planned with NS5A inhibitors.
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Affiliation(s)
- Itzíar Carrasco
- Internal Medicine Department, Puerta de Hierro Research Institute and University Hospital, Madrid, Spain
| | - Ana Arias
- Internal Medicine Department, Puerta de Hierro Research Institute and University Hospital, Madrid, Spain
| | - Laura Benítez-Gutiérrez
- Internal Medicine Department, Puerta de Hierro Research Institute and University Hospital, Madrid, Spain
| | - Gemma Lledó
- Internal Medicine Department, Puerta de Hierro Research Institute and University Hospital, Madrid, Spain
| | - Silvia Requena
- Internal Medicine Department, Puerta de Hierro Research Institute and University Hospital, Madrid, Spain
| | - Miriam Cuesta
- Internal Medicine Department, Puerta de Hierro Research Institute and University Hospital, Madrid, Spain
| | - Valentín Cuervas-Mons
- Internal Medicine Department, Puerta de Hierro Research Institute and University Hospital, Madrid, Spain
| | - Carmen de Mendoza
- Internal Medicine Department, Puerta de Hierro Research Institute and University Hospital, Madrid, Spain
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11
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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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