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Parczewski M, Janczewska E, Pisula A, Dybowska D, Łojewski W, Witor A, Wawrzynowicz-Syczewska M, Socha Ł, Krygier R, Knysz B, Musialik J, Urbańska A, Scheibe K, Jaroszewicz J. HCV resistance-associated substitutions following direct-acting antiviral therapy failure - Real-life data from Poland. INFECTION GENETICS AND EVOLUTION 2021; 93:104949. [PMID: 34087494 DOI: 10.1016/j.meegid.2021.104949] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/27/2021] [Accepted: 05/30/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND This study analysed the NS3 and NS5A mutation frequencies, persistence and drug susceptibility in a cohort of real-life patients, with failed hepatitis C virus (HCV) therapy following directly acting antiviral (DAA) treatment. METHODS NS3/NS5A Sanger sequences from 105 patients infected with HCV genotype (G) 1a (6,5.7%), G1b (94,89.5%), G3a (4,3.8%), and G4 (1,1.0%) post DAA treatment failure were analysed. NS3 and NS5A resistance-associated substitutions (RASs) were identified using the geno2pheno algorithm and associated with clinical variables. Time trends were examined using logistic regression. RESULTS NS5A RAS were found in 87.9% of sequences derived from patients exposed to this class of agents, whereas NS3 RAS was found in 59.1% of HCV protease-exposed subjects. The frequency of the NS3 RAS increased with fibrosis stage, from 40.0% among F0/F1 individuals to 81.8% among patients with liver cirrhosis (F4, p = 0.094). NS5A mutation frequencies were 7.6% for 28A/V/M, 10.6% for 30 K/Q/R, 42.4% for 31I/F/M/V, and 75.8% for 93H. For NS3, the most common RASs were 56F-23.7%, 168A/E/I/Y/T/V-14.0%, and 117H-5.4%. Susceptibility to glecaprevir/pibrentasvir, velpatasvir/voxlaprevir, and elbasvir/grazoprevir was retained in 92.9%, 43.4%, and, 25.3% of patients, respectively. The frequency of NS3 RAS decreased with time elapsed from failure to sampling (p = 0.034 for trend). NS5A RAS frequency remained stable over the 24-months. CONCLUSIONS Following DAA treatment failure, NS5A and NS3 RASs were common with increasing frequency among patients with advanced liver disease. In most cases, despite the presence of RASs, susceptibility to DAA combinations with higher genetic barrier was retained.
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Affiliation(s)
- Miłosz Parczewski
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland.
| | - Ewa Janczewska
- Department of Basic Medical Sciences, The School of Health Sciences in Bytom, Medical University of Silesia, Bytom, Poland
| | | | - Dorota Dybowska
- Department of Infectious Diseases and Hepatology, Ludwik Rydygier Collegium Medicum, Bydgoszcz Faculty of Medicine, Nicolaus Copernicus University, Toruń, Poland
| | - Władysław Łojewski
- Department of Infectious Diseases, Regional Hospital in Zielona Góra, Zielona Góra, Poland
| | - Adam Witor
- Hospital for Infectious Diseases, Chorzów, Poland
| | - Marta Wawrzynowicz-Syczewska
- Department of Infectious Diseases, Hepatology and Liver Transplantation, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Łukasz Socha
- Department of Infectious Diseases, Hepatology and Liver Transplantation, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Rafał Krygier
- Outpatients Hepatology Department, State University of Applied Sciences, Konin, Poland
| | - Brygida Knysz
- Department of Infectious Diseases, Liver Diseases and Acquired Immune Deficiencies, Wrocław Medical University, Wrocław, Poland
| | - Joanna Musialik
- Department of Nephrology, Transplantation and Internal Medicine, Medical University of Silesia in Katowice, Katowice, Poland
| | - Anna Urbańska
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Kaja Scheibe
- Department of Infectious, Tropical Diseases and Immune Deficiency, Pomeranian Medical University in Szczecin, Szczecin, Poland
| | - Jerzy Jaroszewicz
- Department of Infectious Diseases and Hepatology, Medical University of Silesia, Katowice, Poland
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Sagnelli E, Starace M, Minichini C, Pisaturo M, Macera M, Sagnelli C, Coppola N. Resistance detection and re-treatment options in hepatitis C virus-related chronic liver diseases after DAA-treatment failure. Infection 2018; 46:761-783. [DOI: 10.1007/s15010-018-1188-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 07/30/2018] [Indexed: 12/12/2022]
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State of the Art, Unresolved Issues, and Future Research Directions in the Fight against Hepatitis C Virus: Perspectives for Screening, Diagnostics of Resistances, and Immunization. J Immunol Res 2016; 2016:1412840. [PMID: 27843956 PMCID: PMC5098088 DOI: 10.1155/2016/1412840] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/09/2016] [Accepted: 09/20/2016] [Indexed: 12/13/2022] Open
Abstract
Hepatitis C virus (HCV) still represents a major public health threat, with a dramatic burden from both epidemiological and clinical points of view. New generation of direct-acting antiviral agents (DAAs) has been recently introduced in clinical practice promising to cure HCV and to overcome the issues related to the interferon-based therapies. However, the emergence of drug resistance and the suboptimal activity of DAAs therapies against diverse HCV genotypes have been observed, determining treatment failure and hampering an effective control of HCV spread worldwide. Moreover, these treatments remain poorly accessible, particularly in low-income countries. Finally, effective screening strategy is crucial to early identifying and treating all HCV chronically infected patients. For all these reasons, even though new drugs may contribute to impacting HCV spread worldwide a preventive HCV vaccine remains a cornerstone in the road to significantly reduce the HCV spread globally, with the ultimate goal of its eradication. Advances in molecular vaccinology, together with a strong financial, political, and societal support, will enable reaching this fundamental success in the coming years. In this comprehensive review, the state of the art about these major topics in the fight against HCV and the future of research in these fields are discussed.
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Minosse C, Giombini E, Bartolini B, Capobianchi MR, Garbuglia AR. Ultra-Deep Sequencing Characterization of HCV Samples with Equivocal Typing Results Determined with a Commercial Assay. Int J Mol Sci 2016; 17:E1679. [PMID: 27739414 PMCID: PMC5085712 DOI: 10.3390/ijms17101679] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 09/13/2016] [Accepted: 09/23/2016] [Indexed: 01/18/2023] Open
Abstract
Hepatitis C virus (HCV) is classified into seven phylogenetically distinct genotypes, which are further subdivided into related subtypes. Accurate assignment of genotype/subtype is mandatory in the era of directly acting antivirals. Several molecular methods are available for HCV genotyping; however, a relevant number of samples with indeterminate, mixed, or unspecified subtype results, or even with misclassified genotypes, may occur. Using NS5B direct (DS) and ultra-deep pyrosequencing (UDPS), we have tested 43 samples, which resulted in genotype 1 unsubtyped (n = 17), mixed infection (n = 17), or indeterminate (n = 9) with the Abbott RealTime HCV Genotype II assay. Genotype 1 was confirmed in 14/17 samples (82%): eight resulted in subtype 1b, and five resulted in subtype 1a with both DS and UDPS, while one was classified as subtype 1e by DS and mixed infection (1e + 1a) by UDPS. Three of seventeen genotype 1 samples resulted in genotype 3h with both sequencing approaches. Only one mixed infection was confirmed by UDPS (4d + 1a), while in 88% of cases a single component of the mixture was detected (five genotype 1a, four genotype 1b, two genotype 3a, two genotype 4m, and two genotype 4d); 44% of indeterminate samples resulted genotype 2c by both DS and UDPS, 22% resulted genotype 3a; one indeterminate sample by Abbott resulted in genotype 4d, one resulted in genotype 6n, and one was classified as subtype 3a by DS, and resulted mixed infection (3a + 3h) by UDPS. The concordance between DS and UDPS was 94%, 88%, and 89% for genotype 1, co-infection, and indeterminate results, respectively. UDPS should be considered very useful to resolve ambiguous HCV genotyping results.
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Affiliation(s)
- Claudia Minosse
- Laboratory of Virology, National Institute for Infectious Diseases "Lazzaro Spallanzani"-IRCCS, Via Portuense 292, Rome 00149, Italy.
| | - Emanuela Giombini
- Laboratory of Virology, National Institute for Infectious Diseases "Lazzaro Spallanzani"-IRCCS, Via Portuense 292, Rome 00149, Italy.
| | - Barbara Bartolini
- Laboratory of Virology, National Institute for Infectious Diseases "Lazzaro Spallanzani"-IRCCS, Via Portuense 292, Rome 00149, Italy.
| | - Maria R Capobianchi
- Laboratory of Virology, National Institute for Infectious Diseases "Lazzaro Spallanzani"-IRCCS, Via Portuense 292, Rome 00149, Italy.
| | - Anna R Garbuglia
- Laboratory of Virology, National Institute for Infectious Diseases "Lazzaro Spallanzani"-IRCCS, Via Portuense 292, Rome 00149, Italy.
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Dustin LB, Bartolini B, Capobianchi MR, Pistello M. Hepatitis C virus: life cycle in cells, infection and host response, and analysis of molecular markers influencing the outcome of infection and response to therapy. Clin Microbiol Infect 2016; 22:826-832. [PMID: 27592089 PMCID: PMC5627509 DOI: 10.1016/j.cmi.2016.08.025] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 08/16/2016] [Accepted: 08/25/2016] [Indexed: 12/13/2022]
Abstract
Hepatitis C virus (HCV) is a major global health burden accounting for around 170 million chronic infections worldwide. Since its discovery, which dates back to about 30 years ago, many details of the viral genome organization and the astonishing genetic diversity have been unveiled but, owing to the difficulty of culturing HCV in vitro and obtaining fully susceptible yet immunocompetent in vivo models, we are still a long way from the full comprehension of viral life cycle, host cell pathways facilitating or counteracting infection, pathogenetic mechanisms in vivo, and host defences. Here, we illustrate the viral life cycle into cells, describe the interplay between immune and genetic host factors shaping the course of infection, and provide details of the molecular approaches currently used to genotype, monitor replication in vivo, and study the emergence of drug-resistant viral variants.
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Affiliation(s)
- L B Dustin
- Kennedy Institute for Rheumatology and Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - B Bartolini
- Laboratory of Virology, National Institute for Infectious Diseases "Lazzaro Spallanzani" IRCCS, Rome, Italy
| | - M R Capobianchi
- Laboratory of Virology, National Institute for Infectious Diseases "Lazzaro Spallanzani" IRCCS, Rome, Italy
| | - M Pistello
- Virology Unit, Pisa University Hospital, and Virology Section and Retrovirus Centre, Department of Translational Research, University of Pisa, Pisa, Italy.
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Coppola N, Minichini C, Starace M, Sagnelli C, Sagnelli E. Clinical impact of the hepatitis C virus mutations in the era of directly acting antivirals. J Med Virol 2016; 88:1659-71. [DOI: 10.1002/jmv.24527] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Nicola Coppola
- Department of Mental Health and Public Medicine; Section of Infectious Diseases; Second University of Naples; Naples Italy
| | - Carmine Minichini
- Department of Mental Health and Public Medicine; Section of Infectious Diseases; Second University of Naples; Naples Italy
| | - Mario Starace
- Department of Mental Health and Public Medicine; Section of Infectious Diseases; Second University of Naples; Naples Italy
| | - Caterina Sagnelli
- Department of Clinical and Experimental Medicine and Surgery; Second University of Naples; Naples Italy
| | - Evangelista Sagnelli
- Department of Mental Health and Public Medicine; Section of Infectious Diseases; Second University of Naples; Naples Italy
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