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Sorbo MC, Carioti L, Bellocchi MC, Antonucci F, Sforza D, Lenci I, Ciancio Manuelli M, Armenia D, De Leonardis F, Milana M, Manzia TM, Angelico M, Tisone G, Cento V, Perno CF, Ceccherini-Silberstein F. HCV resistance compartmentalization within tumoral and non-tumoral liver in transplanted patients with hepatocellular carcinoma. Liver Int 2019; 39:1986-1998. [PMID: 31172639 DOI: 10.1111/liv.14168] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS We investigated the HCV-RNA amount, variability and prevalence of resistance-associated substitutions (RASs), in plasma, hepatic tumoral and non-tumoral tissue samples in patients undergoing liver-transplant/hepatic-resection (LT/HR), because of hepatocellular carcinoma and/or cirrhosis. METHODS Eighteen HCV-infected patients undergoing LT/HR, 94.0% naïve to direct-acting antivirals (DAAs), were analysed. HCV-RNA was quantified in all compartments. NS3/NS5A/NS5B in plasma and/or in tumoral/non-tumoral tissues were analysed using Sanger and Ultra-deep pyrosequencing (UDPS, 9/18 patients). RASs prevalence, genetic-variability and phylogenetic analysis were evaluated. RESULTS At the time of LT/HR, HCV-RNA was quantifiable in all compartments of DAA-naïve patients and was generally lower in tumoral than in non-tumoral tissues (median [IQR] = 4.0 [1.2-4.3] vs 4.3[3.1-4.9] LogIU/µg RNA; P = 0.193). The one patient treated with sofosbuvir + ribavirin represented an exception with HCV-RNA quantifiable exclusively in the liver, but with higher level in tumoral than in non-tumoral tissues (51 vs 7 IU/µg RNA). RASs compartmentalization was found by Sanger in 4/18 infected-patients, and by UDPS in other two patients. HCV-compartmentalization resulted to be associated with HBcAb-positivity (P = 0.013). UDPS showed approximately higher genetic-variability in NS3/NS5A sequences in all compartments. Phylogenetic-analysis showed defined and intermixed HCV-clusters among/within all compartments, and were strongly evident in the only non-cirrhotic patient, with plasma and non-tumoral sequences generally more closely related. CONCLUSIONS Hepatic compartments showed differences in HCV-RNA amount, RASs and genetic variability, with a higher segregation within the tumoral compartment. HBV coinfection influenced the HCV compartmentalization. These results highlight HCV-strain diversifications within the liver, which could explain some of the failures occurring even today in the era of DAAs.
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Affiliation(s)
- Maria C Sorbo
- Chair of Virology, Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Luca Carioti
- Chair of Virology, Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Maria C Bellocchi
- Chair of Virology, Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - FrancescoPaolo Antonucci
- Chair of Virology, Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Daniele Sforza
- Hepatobiliary and Transplant Unit, Department of Surgery, Policlinico Tor Vergata/Tor Vergata University, Rome, Italy
| | - Ilaria Lenci
- Hepatology Unit, Department of Systems Medicine, Policlinico Tor Vergata/Tor Vergata University, Rome, Italy
| | - Matteo Ciancio Manuelli
- Hepatobiliary and Transplant Unit, Department of Surgery, Policlinico Tor Vergata/Tor Vergata University, Rome, Italy
| | - Daniele Armenia
- Chair of Virology, Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Francesco De Leonardis
- Hepatology Unit, Department of Systems Medicine, Policlinico Tor Vergata/Tor Vergata University, Rome, Italy
| | - Martina Milana
- Hepatology Unit, Department of Systems Medicine, Policlinico Tor Vergata/Tor Vergata University, Rome, Italy
| | - Tommaso M Manzia
- Hepatobiliary and Transplant Unit, Department of Surgery, Policlinico Tor Vergata/Tor Vergata University, Rome, Italy
| | - Mario Angelico
- Hepatology Unit, Department of Systems Medicine, Policlinico Tor Vergata/Tor Vergata University, Rome, Italy
| | - Giuseppe Tisone
- Hepatobiliary and Transplant Unit, Department of Surgery, Policlinico Tor Vergata/Tor Vergata University, Rome, Italy
| | - Valeria Cento
- Chair of Virology, Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Carlo F Perno
- Chair of Virology, Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
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Alves da Silva R, de Souza Todão J, Kamitani FL, Silva AEB, de Carvalho-Filho RJ, Ferraz MLCG, de Carvalho IMVG. Molecular characterization of hepatitis C virus in end-stage renal disease patients under hemodialysis. J Med Virol 2017; 90:537-544. [PMID: 29064576 DOI: 10.1002/jmv.24976] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 10/12/2017] [Indexed: 12/09/2022]
Abstract
New direct-acting antiviral (DAA) agents are in development or already approved for the treatment of chronic hepatitis C virus (HCV) infection. The effectiveness of these drugs is related to the previous existence of resistant variants. Certain clinical conditions can allow changes in immunological characteristics of the host and even modify genetic features of viral populations. The aim of this study was to perform HCV molecular characterization from samples of end-stage renal disease patients on hemodialysis (ESRD-HD). Nested PCR and Sanger sequencing were used to obtain genetic information from the NS5B partial region of a cohort composed by 86 treatment-naïve patients. Genomic sequences from the Los Alamos databank were employed for comparative analysis. Bioinformatics methodologies such as phylogenetic reconstructions, informational entropy, and mutation analysis were used to analyze datasets separated by geographical location, HCV genotype, and renal function status. ESRD-HD patients presented HCV genotypes 1a (n = 18), 1b (n = 16), 2a (n = 2), 2b (n = 2), and 3a (n = 4). Control subjects were infected with genotypes 1a (n = 11), 1b (n = 21), 2b (n = 4), and 3a (n = 8). Dataset phylogenetic reconstruction separated HCV subtype 1a into two distinct clades. The entropy analysis from the ESRD-HD group revealed two amino acid positions related to an epitope for cytotoxic T lymphocytes and T helper cells. Genotype 1a was found to be more diverse than subtype 1b. Also, genotype 1a ERSD-HD patients had a higher mean of amino acids changes in comparison to control group patients. The identification of specific mutations on epitopes and high genetic diversity within the NS5B HCV partial protein in hemodialysis patients can relate to host immunological features and geographical distribution patterns. This genetic diversity can affect directly the new DAA's resistance mechanisms.
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Affiliation(s)
- Rafael Alves da Silva
- Laboratório de Hepatologia Molecular Aplicada (LHeMA), Departamento de Gastroenterologia, Unidade de Hepatologia, Universidade Federal de São Paulo, UNIFESP, São Paulo, Brazil.,Instituto Butantan, Laboratório de Parasitologia, São Paulo, Brazil
| | - Jardelina de Souza Todão
- Laboratório de Hepatologia Molecular Aplicada (LHeMA), Departamento de Gastroenterologia, Unidade de Hepatologia, Universidade Federal de São Paulo, UNIFESP, São Paulo, Brazil
| | | | - Antonio Eduardo Benedito Silva
- Laboratório de Hepatologia Molecular Aplicada (LHeMA), Departamento de Gastroenterologia, Unidade de Hepatologia, Universidade Federal de São Paulo, UNIFESP, São Paulo, Brazil.,Departamento de Gastroenterologia, Unidade de Hepatologia, Universidade Federal de São Paulo, UNIFESP, São Paulo, Brazil
| | - Roberto José de Carvalho-Filho
- Laboratório de Hepatologia Molecular Aplicada (LHeMA), Departamento de Gastroenterologia, Unidade de Hepatologia, Universidade Federal de São Paulo, UNIFESP, São Paulo, Brazil.,Departamento de Gastroenterologia, Unidade de Hepatologia, Universidade Federal de São Paulo, UNIFESP, São Paulo, Brazil
| | - Maria Lucia Cardoso Gomes Ferraz
- Laboratório de Hepatologia Molecular Aplicada (LHeMA), Departamento de Gastroenterologia, Unidade de Hepatologia, Universidade Federal de São Paulo, UNIFESP, São Paulo, Brazil.,Departamento de Gastroenterologia, Unidade de Hepatologia, Universidade Federal de São Paulo, UNIFESP, São Paulo, Brazil
| | - Isabel Maria Vicente Guedes de Carvalho
- Laboratório de Hepatologia Molecular Aplicada (LHeMA), Departamento de Gastroenterologia, Unidade de Hepatologia, Universidade Federal de São Paulo, UNIFESP, São Paulo, Brazil.,Instituto Butantan, Laboratório de Parasitologia, São Paulo, Brazil
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Perales C, Quer J, Gregori J, Esteban JI, Domingo E. Resistance of Hepatitis C Virus to Inhibitors: Complexity and Clinical Implications. Viruses 2015; 7:5746-66. [PMID: 26561827 PMCID: PMC4664975 DOI: 10.3390/v7112902] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 10/23/2015] [Accepted: 10/26/2015] [Indexed: 12/20/2022] Open
Abstract
Selection of inhibitor-resistant viral mutants is universal for viruses that display quasi-species dynamics, and hepatitis C virus (HCV) is no exception. Here we review recent results on drug resistance in HCV, with emphasis on resistance to the newly-developed, directly-acting antiviral agents, as they are increasingly employed in the clinic. We put the experimental observations in the context of quasi-species dynamics, in particular what the genetic and phenotypic barriers to resistance mean in terms of exploration of sequence space while HCV replicates in the liver of infected patients or in cell culture. Strategies to diminish the probability of viral breakthrough during treatment are briefly outlined.
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Affiliation(s)
- Celia Perales
- Liver Unit, Internal Medicine, Laboratory of Malalties Hepàtiques, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain.
- Centro de Biologia Molecular "Severo Ochoa" (CSIC-UAM), Cantoblanco, 28049 Madrid, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 08035 Barcelona, Spain.
| | - Josep Quer
- Liver Unit, Internal Medicine, Laboratory of Malalties Hepàtiques, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 08035 Barcelona, Spain.
- Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.
| | - Josep Gregori
- Liver Unit, Internal Medicine, Laboratory of Malalties Hepàtiques, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 08035 Barcelona, Spain.
- Roche Diagnostics SL, 08174 Sant Cugat del Vallès, Spain.
| | - Juan Ignacio Esteban
- Liver Unit, Internal Medicine, Laboratory of Malalties Hepàtiques, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autònoma de Barcelona, 08035 Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 08035 Barcelona, Spain.
- Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.
| | - Esteban Domingo
- Centro de Biologia Molecular "Severo Ochoa" (CSIC-UAM), Cantoblanco, 28049 Madrid, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 08035 Barcelona, Spain.
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Kinugasa H, Ikeda F, Takaguchi K, Mori C, Matsubara T, Shiraha H, Takaki A, Iwasaki Y, Toyooka S, Yamamoto K. Low frequency of drug-resistant virus did not affect the therapeutic efficacy in daclatasvir plus asunaprevir therapy in patients with chronic HCV genotype-1 infection. Antivir Ther 2015; 21:37-44. [PMID: 26115551 DOI: 10.3851/imp2976] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2015] [Indexed: 02/07/2023]
Abstract
BACKGROUND The efficacy of a direct-acting antiviral agent (DAA) is compromised by the development of drug resistance. The associations between resistance-associated virus (RAV) and therapeutic outcomes have not been well-understood. METHODS A total of 30 patients with HCV genotype-1b were enrolled and treated for 24 weeks with asunaprevir (ASV) and daclatasvir (DCV). Viral sequences in non-structural (NS) regions 3 and 5A in serum and liver tissue before treatment were examined with direct sequencing, next-generation sequencing (NGS) and the PCR-invader method to evaluate the importance of drug-resistance in the prediction of the outcomes of ASV plus DCV therapy. RESULTS Of 30 patients (22 treatment-naive patients, 2 interferon-intolerant patients and 6 non-responders), 25 patients (83.3%) achieved sustained virological response (SVR) 24 weeks after the treatment. Viral breakthrough occurred in three treatment-naive patients and one non-responder. One treatment-naive patient experienced viral relapse. Among 25 patients without RAV, 24 obtained SVR, whereas 5 patients had RAV with a 1.3 to 88% frequency, resulting in various therapeutic outcomes. As for HCV compartments, similar RAVs were detected in serum and liver tissue for a patient obtaining SVR despite HCV NS5A Y93H and another developed viral breakthrough although no RAV was detected. Direct sequencing could not detect RAVs in low frequency (1.3 to 12%) for three of four patients. CONCLUSIONS Low frequency of RAVs might not affect the outcomes of ASV plus DCV therapy. Deep sequencing and PCR-invader methods can detect clinically significant RAVs for ASV plus DCV therapy.
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Affiliation(s)
- Hideaki Kinugasa
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama, Japan
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Ji H, Kozak RA, Biondi MJ, Pilon R, Vallee D, Liang BB, La D, Kim J, Van Domselaar G, Leonard L, Sandstrom P, Brooks J. Next generation sequencing of the hepatitis C virus NS5B gene reveals potential novel S282 drug resistance mutations. Virology 2015; 477:1-9. [PMID: 25600207 DOI: 10.1016/j.virol.2014.12.037] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 11/11/2014] [Accepted: 12/23/2014] [Indexed: 01/06/2023]
Abstract
Identifying HCV drug resistance mutations (DRMs) is increasingly important as new direct acting antiviral therapies (DAA) become available. Tagged pooled pyrosequencing (TPP) was originally developed as cost-effective approach for detecting low abundance HIV DRMs. Using 127 HCV-positive samples from a Canadian injection drug user cohort, we demonstrated the suitability and efficiency of TPP for evaluating DRMs in HCV NS5B gene. At a mutation identification threshold of 1%, no nucleoside inhibitor DRMs were detected among these DAA naïve subjects. Clinical NS5B resistance to non-nucleoside inhibitors and interferon/ribavirin was predicted to be low within this cohort. S282T mutation, the primary mutation selected by sofosbuvir in vitro, was not identified while S282G/C/R variants were detected in 9 subjects. Further characterization on these new S282 variants using in silico molecular modeling implied their potential association with resistance. Combining TPP with in silico analysis detects NS5B polymorphisms that may explain differences in treatment outcomes.
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Affiliation(s)
- Hezhao Ji
- National HIV & Retrovirology Laboratories, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, Canada
| | - Robert A Kozak
- Department of Pathobiology, University of Guelph, Guelph, Canada
| | - Mia J Biondi
- Arthur Labatt Family School of Nursing, Western University, London, Canada
| | - Richard Pilon
- National HIV & Retrovirology Laboratories, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, Canada
| | - Dominic Vallee
- National HIV & Retrovirology Laboratories, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, Canada
| | - Ben Binhua Liang
- Bioinformatics Core, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, Canada
| | - David La
- Bioinformatics Core, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, Canada
| | - John Kim
- National HIV & Retrovirology Laboratories, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, Canada
| | - Gary Van Domselaar
- Bioinformatics Core, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, Canada
| | - Lynne Leonard
- Department of Epidemiology and Community Medicine, University of Ottawa, Ottawa, Canada
| | - Paul Sandstrom
- National HIV & Retrovirology Laboratories, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, Canada
| | - James Brooks
- National HIV & Retrovirology Laboratories, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, Canada.
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