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Christensen KT, Pierard F, Beuselinck K, Bonsall D, Bowden R, Lagrou K, Nevens F, Schrooten Y, Simmonds P, Vandamme AM, Van Wijngaerden E, Dierckx T, Cuypers L, Van Laethem K. Full-genome next-generation sequencing of hepatitis C virus to assess the accuracy of genotyping by the commercial assay LiPA and the prevalence of resistance-associated substitutions in a Belgian cohort. J Clin Virol 2022; 155:105252. [DOI: 10.1016/j.jcv.2022.105252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/26/2022] [Accepted: 08/02/2022] [Indexed: 02/07/2023]
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2
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Quer J, Colomer-Castell S, Campos C, Andrés C, Piñana M, Cortese MF, González-Sánchez A, Garcia-Cehic D, Ibáñez M, Pumarola T, Rodríguez-Frías F, Antón A, Tabernero D. Next-Generation Sequencing for Confronting Virus Pandemics. Viruses 2022; 14:600. [PMID: 35337007 PMCID: PMC8950049 DOI: 10.3390/v14030600] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/01/2022] [Accepted: 03/10/2022] [Indexed: 02/06/2023] Open
Abstract
Virus pandemics have happened, are happening and will happen again. In recent decades, the rate of zoonotic viral spillover into humans has accelerated, mirroring the expansion of our global footprint and travel network, including the expansion of viral vectors and the destruction of natural spaces, bringing humans closer to wild animals. Once viral cross-species transmission to humans occurs, transmission cannot be stopped by cement walls but by developing barriers based on knowledge that can prevent or reduce the effects of any pandemic. Controlling a local transmission affecting few individuals is more efficient that confronting a community outbreak in which infections cannot be traced. Genetic detection, identification, and characterization of infectious agents using next-generation sequencing (NGS) has been proven to be a powerful tool allowing for the development of fast PCR-based molecular assays, the rapid development of vaccines based on mRNA and DNA, the identification of outbreaks, transmission dynamics and spill-over events, the detection of new variants and treatment of vaccine resistance mutations, the development of direct-acting antiviral drugs, the discovery of relevant minority variants to improve knowledge of the viral life cycle, strengths and weaknesses, the potential for becoming dominant to take appropriate preventive measures, and the discovery of new routes of viral transmission.
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Affiliation(s)
- Josep Quer
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (C.C.); (D.G.-C.); (M.I.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), UAB Campus, Plaça Cívica, 08193 Bellaterra, Spain
| | - Sergi Colomer-Castell
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (C.C.); (D.G.-C.); (M.I.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
| | - Carolina Campos
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (C.C.); (D.G.-C.); (M.I.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
| | - Cristina Andrés
- Microbiology Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (C.A.); (M.P.); (A.G.-S.); (T.P.)
| | - Maria Piñana
- Microbiology Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (C.A.); (M.P.); (A.G.-S.); (T.P.)
| | - Maria Francesca Cortese
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
- Clinical Biochemistry Research Group, Biochemistry Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Alejandra González-Sánchez
- Microbiology Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (C.A.); (M.P.); (A.G.-S.); (T.P.)
| | - Damir Garcia-Cehic
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (C.C.); (D.G.-C.); (M.I.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
| | - Marta Ibáñez
- Liver Diseases-Viral Hepatitis, Liver Unit, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (S.C.-C.); (C.C.); (D.G.-C.); (M.I.)
| | - Tomàs Pumarola
- Microbiology Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (C.A.); (M.P.); (A.G.-S.); (T.P.)
- Microbiology Department, Universitat Autònoma de Barcelona (UAB), UAB Campus, Plaça Cívica, 08193 Bellaterra, Spain
| | - Francisco Rodríguez-Frías
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
- Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona (UAB), UAB Campus, Plaça Cívica, 08193 Bellaterra, Spain
- Clinical Biochemistry Research Group, Biochemistry Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
| | - Andrés Antón
- Microbiology Department, Vall d’Hebron Institut of Research (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain; (C.A.); (M.P.); (A.G.-S.); (T.P.)
- Microbiology Department, Universitat Autònoma de Barcelona (UAB), UAB Campus, Plaça Cívica, 08193 Bellaterra, Spain
| | - David Tabernero
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Av. Monforte de Lemos 3-5, 28029 Madrid, Spain; (M.F.C.); (F.R.-F.); (D.T.)
- Microbiology Departments, Hospital Universitari Vall d’Hebron, Vall d’Hebron Barcelona Hospital Campus, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
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3
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Yang X, Ding T, Huang H, Xu Y, Yu J, Chen Z. Development and validation of a simple and rapid method for hepatitis C virus genotyping based on one-step RT-qPCR. Exp Ther Med 2020; 20:2284-2290. [PMID: 32765706 DOI: 10.3892/etm.2020.8912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 01/22/2020] [Indexed: 11/06/2022] Open
Abstract
Hepatitis C virus (HCV) infections caused by different subtypes require different treatments; therefore, rapid and cost-effective genotyping methods for the diagnosis of HCV are greatly needed. In the present study, a new method to diagnose HCV subtypes that depends on a one-step quantitative reverse transcription PCR (RT-qPCR) and TaqMan fluorescence probe technique is described. Five pairs of primers and five probes were designed, which were able to detect five genotypes in three reaction tubes. One reaction was used to detect the 1b subtype, one was used to detect the 2a and 6a subtypes, and the other was used to detect the 3a and 3b subtypes. Rigorous performance validation was implemented for five aspects: Precision, sensitivity, accuracy, specificity and anti-interference. The HCV subtype that infected 289 patients was evaluated in the present study via RT-qPCR and verified by sequencing. The results revealed that the 1b subtype accounted for 45% of infections, the 2a subtype accounted for 9% of infections, the 3a subtype accounted for 13% of infections, the 3b subtype accounted for 18% of infections, and the 6a subtype accounted for 15% of infections. The analytical sensitivity for the detection of each of the five HCV subtypes was 1,000 IU/ml. The new method performed well in the performance validation mentioned above, indicating its effectiveness as a HCV genotyping method. RT-qPCR has mitigated some of the former challenges of existing HCV genotyping methods, including the time commitment, expense, and inaccuracy of such methods. The performance validation of this new method showed that RT-qPCR is reliable enough to be widely applied in China for HCV genotyping.
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Affiliation(s)
- Xinyun Yang
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China.,The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Ting Ding
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China.,The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Haifeng Huang
- Triplex International Biosciences (China) Co., Ltd., Xiamen, Fujian 361000, P.R. China
| | - Yang Xu
- Department of First Generation Sequencing, Hangzhou DiAn Medical Laboratory, Hangzhou, Zhejiang 310030, P.R. China
| | - Jian Yu
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
| | - Zhanguo Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, P.R. China
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4
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Chen Q, Perales C, Soria ME, García-Cehic D, Gregori J, Rodríguez-Frías F, Buti M, Crespo J, Calleja JL, Tabernero D, Vila M, Lázaro F, Rando-Segura A, Nieto-Aponte L, Llorens-Revull M, Cortese MF, Fernandez-Alonso I, Castellote J, Niubó J, Imaz A, Xiol X, Castells L, Riveiro-Barciela M, Llaneras J, Navarro J, Vargas-Blasco V, Augustin S, Conde I, Rubín Á, Prieto M, Torras X, Margall N, Forns X, Mariño Z, Lens S, Bonacci M, Pérez-Del-Pulgar S, Londoño MC, García-Buey ML, Sanz-Cameno P, Morillas R, Martró E, Saludes V, Masnou-Ridaura H, Salmerón J, Quíles R, Carrión JA, Forné M, Rosinach M, Fernández I, García-Samaniego J, Madejón A, Castillo-Grau P, López-Núñez C, Ferri MJ, Durández R, Sáez-Royuela F, Diago M, Gimeno C, Medina R, Buenestado J, Bernet A, Turnes J, Trigo-Daporta M, Hernández-Guerra M, Delgado-Blanco M, Cañizares A, Arenas JI, Gomez-Alonso MJ, Rodríguez M, Deig E, Olivé G, Río OD, Cabezas J, Quiñones I, Roget M, Montoliu S, García-Costa J, Force L, Blanch S, Miralbés M, López-de-Goicoechea MJ, García-Flores A, Saumoy M, Casanovas T, Baliellas C, Gilabert P, Martin-Cardona A, Roca R, Barenys M, Villaverde J, Salord S, Camps B, Silvan di Yacovo M, Ocaña I, Sauleda S, Bes M, Carbonell J, Vargas-Accarino E, Ruzo SP, Guerrero-Murillo M, Von Massow G, Costafreda MI, López RM, González-Moreno L, Real Y, Acero-Fernández D, Viroles S, Pamplona X, Cairó M, Ocete MD, Macías-Sánchez JF, Estébanez A, Quer JC, Mena-de-Cea Á, Otero A, Castro-Iglesias Á, Suárez F, Vázquez Á, Vieito D, López-Calvo S, Vázquez-Rodríguez P, Martínez-Cerezo FJ, Rodríguez R, Macenlle R, Cachero A, Mereish G, Mora-Moruny C, Fábregas S, Sacristán B, Albillos A, Sánchez-Ruano JJ, Baluja-Pino R, Fernández-Fernández J, González-Portela C, García-Martin C, Sánchez-Antolín G, Andrade RJ, Simón MA, Pascasio JM, Romero-Gómez M, Antonio Del-Campo J, Domingo E, Esteban R, Esteban JI, Quer J. Deep-sequencing reveals broad subtype-specific HCV resistance mutations associated with treatment failure. Antiviral Res 2020; 174:104694. [PMID: 31857134 DOI: 10.1016/j.antiviral.2019.104694] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 10/24/2019] [Accepted: 12/11/2019] [Indexed: 02/07/2023]
Abstract
A percentage of hepatitis C virus (HCV)-infected patients fail direct acting antiviral (DAA)-based treatment regimens, often because of drug resistance-associated substitutions (RAS). The aim of this study was to characterize the resistance profile of a large cohort of patients failing DAA-based treatments, and investigate the relationship between HCV subtype and failure, as an aid to optimizing management of these patients. A new, standardized HCV-RAS testing protocol based on deep sequencing was designed and applied to 220 previously subtyped samples from patients failing DAA treatment, collected in 39 Spanish hospitals. The majority had received DAA-based interferon (IFN) α-free regimens; 79% had failed sofosbuvir-containing therapy. Genomic regions encoding the nonstructural protein (NS) 3, NS5A, and NS5B (DAA target regions) were analyzed using subtype-specific primers. Viral subtype distribution was as follows: genotype (G) 1, 62.7%; G3a, 21.4%; G4d, 12.3%; G2, 1.8%; and mixed infections 1.8%. Overall, 88.6% of patients carried at least 1 RAS, and 19% carried RAS at frequencies below 20% in the mutant spectrum. There were no differences in RAS selection between treatments with and without ribavirin. Regardless of the treatment received, each HCV subtype showed specific types of RAS. Of note, no RAS were detected in the target proteins of 18.6% of patients failing treatment, and 30.4% of patients had RAS in proteins that were not targets of the inhibitors they received. HCV patients failing DAA therapy showed a high diversity of RAS. Ribavirin use did not influence the type or number of RAS at failure. The subtype-specific pattern of RAS emergence underscores the importance of accurate HCV subtyping. The frequency of "extra-target" RAS suggests the need for RAS screening in all three DAA target regions.
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Affiliation(s)
- Qian Chen
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Celia Perales
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - María Eugenia Soria
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - Damir García-Cehic
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Josep Gregori
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Roche Diagnostics SL, Sant Cugat del Valles, Barcelona, Spain
| | - Francisco Rodríguez-Frías
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Biochemistry and Microbiology Department, VHIR-HUVH, Barcelona, Spain
| | - María Buti
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Javier Crespo
- Gastroenterology and Hepatology Department, Instituto de Investigación (IDIVAL), Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | | | - David Tabernero
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Biochemistry and Microbiology Department, VHIR-HUVH, Barcelona, Spain
| | - Marta Vila
- Biochemistry and Microbiology Department, VHIR-HUVH, Barcelona, Spain
| | - Fernando Lázaro
- Microbiology Department, Hospital Universitario La Paz, Madrid, Spain
| | | | | | - Meritxell Llorens-Revull
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Irati Fernandez-Alonso
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - José Castellote
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Jordi Niubó
- Microbiology Department, Hospital Universitari de Bellvitge, Barcelona
| | - Arkaitz Imaz
- HIV and STI Unit, Infectious Diseases Department, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Xavier Xiol
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Lluís Castells
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Mar Riveiro-Barciela
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Jordi Llaneras
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Víctor Vargas-Blasco
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Salvador Augustin
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Isabel Conde
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Hospital Universitario La Fe, Valencia, Spain
| | - Ángel Rubín
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Hospital Universitario La Fe, Valencia, Spain
| | - Martín Prieto
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Hospital Universitario La Fe, Valencia, Spain
| | - Xavier Torras
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Microbiology Department, Hospital Universitari Santa Creu i Sant Pau, Barcelona, Spain
| | - Nuria Margall
- Digestive Pathology Unit, Hospital Universitari Santa Creu i Sant Pau, Barcelona, Spain
| | - Xavier Forns
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) - Hospital Clínic de Barcelona, Barcelona, Spain
| | - Zoe Mariño
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) - Hospital Clínic de Barcelona, Barcelona, Spain
| | - Sabela Lens
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) - Hospital Clínic de Barcelona, Barcelona, Spain
| | - Martin Bonacci
- Liver Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) - Hospital Clínic de Barcelona, Barcelona, Spain
| | - Sofía Pérez-Del-Pulgar
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) - Hospital Clínic de Barcelona, Barcelona, Spain
| | - Maria Carlota Londoño
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) - Hospital Clínic de Barcelona, Barcelona, Spain
| | | | | | - Rosa Morillas
- Liver Unit, Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
| | - Elisa Martró
- Microbiology Department, Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Institut de Recerca Germans Trias i Pujol (IGTP), Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
| | - Verónica Saludes
- Microbiology Department, Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Institut de Recerca Germans Trias i Pujol (IGTP), Hospital Universitari Germans Trias i Pujol, Barcelona, Spain
| | | | - Javier Salmerón
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Complejo Hospitalario de Granada, Granada, Spain
| | - Rosa Quíles
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Complejo Hospitalario de Granada, Granada, Spain
| | - José Antonio Carrión
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Parc de Salut Mar - Hospital del Mar, Barcelona, Spain
| | - Montserrat Forné
- Gastroenterology Unit, Hospital Universitari Mútua Terrassa, Spain
| | - Mercè Rosinach
- Gastroenterology Unit, Hospital Universitari Mútua Terrassa, Spain
| | | | - Javier García-Samaniego
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Instituto de Investigación Hospital Universitario La Paz (IdiPAZ) - Hospital Universitario La Paz, Madrid, Spain
| | - Antonio Madejón
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Instituto de Investigación Hospital Universitario La Paz (IdiPAZ) - Hospital Universitario La Paz, Madrid, Spain
| | - Pilar Castillo-Grau
- Liver Unit, Instituto de Investigación Hospital Universitario La Paz (IdiPAZ) - Hospital Universitario La Paz, Madrid, Spain
| | - Carme López-Núñez
- Gastroenterology Department, Hospital Universitari Doctor Josep Trueta, Girona, Spain
| | - María José Ferri
- Clinical Laboratory, Hospital Universitari Doctor Josep Trueta, Girona, Spain
| | - Rosa Durández
- Laboratori Territorial - Hospital Santa Caterina, Girona, Spain
| | - Federico Sáez-Royuela
- Gastroenterology and Hepatology Depart., Hospital Universitario de Burgos, Burgos, Spain
| | - Moisés Diago
- Liver Unit, Hospital General de Valencia, Valencia, Spain
| | | | - Rafael Medina
- Microbiology Unit, Hospital General de Valencia, Valencia, Spain
| | - Juan Buenestado
- Medicine Department-Medical School, Hospital Univ. Arnau de Vilanova, Lleida, Spain
| | - Albert Bernet
- Microbiology Department, Hospital Universitari Arnau de Vilanova, Lleida, Spain
| | - Juan Turnes
- Gastroenterology and Hepatology Department, Instituto de Investigación Sanitaria Galicia Sur (IISGS) - Complejo Hospitalario de Pontevedra, Pontevedra, Spain
| | - Matilde Trigo-Daporta
- Microbiology and Parasitology Department, Complejo Hospitalario de Pontevedra, Pontevedra, Spain
| | | | | | - Angelina Cañizares
- Microbiology Department, Institut de Investigación Biomédica de a Coruña (INIBIC) - Complejo Hospitalario Universitario A Coruña (CHUAC), La Coruña, Spain
| | | | | | - Manuel Rodríguez
- Gastroenterology Depart., Central University Hospital of Asturias (HUCA), Oviedo, Spain
| | | | - Gemma Olivé
- Sant Jaume de Calella County Hospital, Barcelona, Spain
| | - Oscar Del Río
- Sant Jaume de Calella County Hospital, Barcelona, Spain
| | - Joaquín Cabezas
- Gastroenterology and Hepatology Department, Instituto de Investigación (IDIVAL), Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | - Ildefonso Quiñones
- Gastroenterology Department, Dr Negrin University Hospital of Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Mercè Roget
- Liver Unit, Consorci Sanitari de Terrassa - Hospital de Terrassa, Terrassa, Spain
| | - Silvia Montoliu
- Gastroenterology Unit, Joan XXIII University Hospital, Tarragona, Spain
| | - Juan García-Costa
- Virology and Molecular Biology Unit, Microbiology Department, Complexo Hospitalario Universitario de Ourense (CHUO), Ourense, Spain
| | | | - Silvia Blanch
- Hospital Universitari Sant Pau i Santa Tecla, Tarragona, Spain
| | - Miguel Miralbés
- Gastroenterology Department, Hospital Universitari Santa Maria de Lleida, Lleida, Spain
| | | | | | - María Saumoy
- HIV and STI Unit, Infectious Diseases Department, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Teresa Casanovas
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Carme Baliellas
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Pau Gilabert
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | | | - Rosa Roca
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Mercè Barenys
- Liver Unit, Hospital de Viladecans, Barcelona, Spain
| | - Joana Villaverde
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Silvia Salord
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | - Blau Camps
- Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain
| | | | - Imma Ocaña
- Infectious Disease Unit, HUVH, Barcelona, Spain
| | - Silvia Sauleda
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Banc de Sang i Teixits (BST), Barcelona, Spain
| | - Marta Bes
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Banc de Sang i Teixits (BST), Barcelona, Spain
| | - Judit Carbonell
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - Elena Vargas-Accarino
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - Sofía P Ruzo
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - Mercedes Guerrero-Murillo
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - Georg Von Massow
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain
| | - María Isabel Costafreda
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Banc de Sang i Teixits (BST), Barcelona, Spain
| | - Rosa Maria López
- Biochemistry and Microbiology Department, VHIR-HUVH, Barcelona, Spain
| | | | - Yolanda Real
- Liver Unit, Hospital Universitario La Princesa, Madrid, Spain
| | | | - Silvia Viroles
- Gastroenterology Department, Hospital Universitari Doctor Josep Trueta, Girona, Spain
| | - Xavier Pamplona
- Gastroenterology Department, Hospital Universitari Doctor Josep Trueta, Girona, Spain
| | - Mireia Cairó
- Gastroenterology Unit, Hospital Universitari Mútua Terrassa, Spain
| | | | | | - Angel Estébanez
- Gastroenterology and Hepatology Department, Instituto de Investigación (IDIVAL), Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | - Joan Carles Quer
- Gastroenterology Unit, Joan XXIII University Hospital, Tarragona, Spain
| | - Álvaro Mena-de-Cea
- Liver Unit, Complejo Hospitalario Universitario A Coruña (CHUAC), La Coruña, Spain
| | - Alejandra Otero
- Liver Unit, Complejo Hospitalario Universitario A Coruña (CHUAC), La Coruña, Spain
| | | | - Francisco Suárez
- Liver Unit, Complejo Hospitalario Universitario A Coruña (CHUAC), La Coruña, Spain
| | - Ángeles Vázquez
- Liver Unit, Complejo Hospitalario Universitario A Coruña (CHUAC), La Coruña, Spain
| | - David Vieito
- Liver Unit, Complejo Hospitalario Universitario A Coruña (CHUAC), La Coruña, Spain
| | - Soledad López-Calvo
- Liver Unit, Complejo Hospitalario Universitario A Coruña (CHUAC), La Coruña, Spain
| | | | | | - Raúl Rodríguez
- Virology and Molecular Biology Unit, Microbiology Department, Complexo Hospitalario Universitario de Ourense (CHUO), Ourense, Spain
| | - Ramiro Macenlle
- Virology and Molecular Biology Unit, Microbiology Department, Complexo Hospitalario Universitario de Ourense (CHUO), Ourense, Spain
| | - Alba Cachero
- Liver Unit, Hospital d'Igualada, Barcelona, Spain
| | | | | | - Silvia Fábregas
- Fundació Salut Empordà - Hospital de Figueres, Girona, Spain
| | | | | | | | | | | | | | | | | | | | | | | | - Manolo Romero-Gómez
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Hospital Universitario Virgen de Valme, Seville, Spain
| | - José Antonio Del-Campo
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Liver Unit, Hospital Universitario Virgen de Valme, Seville, Spain
| | - Esteban Domingo
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain; Centro de Biología Molecular "Severo Ochoa" (CBMSO), Universidad Autónoma de Madrid, Madrid, Spain
| | - Rafael Esteban
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Juan Ignacio Esteban
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain.
| | - Josep Quer
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain.
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5
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Saludes V, Antuori A, Reinhardt B, Viciana I, Clavijo E, Schreiber L, Tenenbaum M, Rodriguez-Frias F, Quer J, Matas L, Martró E. Reliable resolution of ambiguous hepatitis C virus genotype 1 results with the Abbott HCV Genotype Plus RUO assay. Sci Rep 2019; 9:3678. [PMID: 30842623 PMCID: PMC6403303 DOI: 10.1038/s41598-019-40099-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 12/27/2018] [Indexed: 12/19/2022] Open
Abstract
Accurate subtyping of hepatitis C virus genotype 1 (HCV-1) remains clinically and epidemiologically relevant. The Abbott HCV Genotype Plus RUO (GT Plus) assay, targeting the core region, was evaluated as a reflex test to resolve ambiguous HCV-1 results in a challenging sample collection. 198 HCV-1 specimens were analysed with GT Plus (38 specimens with and 160 without subtype assigned by the Abbott RealTime Genotype II (GT II) assay targeting the 5'NC and NS5B regions). Sanger sequencing of the core and/or NS5B regions were performed in 127 specimens without subtype assignment by GT II, with "not detected" results by GT Plus, or with mixed genotypes/subtypes. The remaining GT Plus results were compared to LiPA 2.0 (n = 45) or just to GT II results if concordant (n = 26). GT Plus successfully assigned the subtype in 142/160 (88.8%) samples. "Not detected" results indicated other HCV-1 subtypes/genotypes or mismatches in the core region in subtype 1b. The subtyping concordance between GT Plus and either sequencing or LiPA was 98.6% (140/142). Therefore, combined use of GT II and GT Plus assays represents a reliable and simple approach which considerably reduced the number of ambiguous HCV-1 results and enabled a successful subtyping of 98.9% of all HCV-1 samples.
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Affiliation(s)
- V Saludes
- Microbiology Department, Laboratori Clínic Metropolitana Nord, Hospital Universitari Germans Trias i Pujol; Genetics and Microbiology Department, Universitat Autònoma de Barcelona, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - A Antuori
- Microbiology Department, Laboratori Clínic Metropolitana Nord, Hospital Universitari Germans Trias i Pujol; Genetics and Microbiology Department, Universitat Autònoma de Barcelona, Badalona, Spain
| | | | - I Viciana
- Microbiology Service, Hospital Virgen de la Victoria, Málaga, Spain
| | - E Clavijo
- Microbiology Service, Hospital Virgen de la Victoria, Málaga, Spain
| | | | | | - F Rodriguez-Frias
- Liver Pathology Lab, Biochemistry and Microbiology Department, University Hospital Vall d'Hebron, Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - J Quer
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Liver Unit, Liver Diseases-Viral Hepatitis, Vall d'Hebron Institute of Research (VHIR-HUVH), Barcelona, Spain
| | - L Matas
- Microbiology Department, Laboratori Clínic Metropolitana Nord, Hospital Universitari Germans Trias i Pujol; Genetics and Microbiology Department, Universitat Autònoma de Barcelona, Badalona, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - E Martró
- Microbiology Department, Laboratori Clínic Metropolitana Nord, Hospital Universitari Germans Trias i Pujol; Genetics and Microbiology Department, Universitat Autònoma de Barcelona, Badalona, Spain.
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain.
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.
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6
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Abdel Ghaffar TY, El Naghi S, Abdel Gawad M, Helmy S, Abdel Ghaffar A, Yousef M, Moafy M. Safety and efficacy of combined sofosbuvir/daclatasvir treatment of children and adolescents with chronic hepatitis C Genotype 4. J Viral Hepat 2019; 26:263-270. [PMID: 30380158 DOI: 10.1111/jvh.13032] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 10/03/2018] [Indexed: 12/16/2022]
Abstract
Direct-acting antivirals have become available for treating chronic HCV (hepatitis C virus) infection in adults and, recently, in children at least 12 years old. Our aim was to investigate the safety and efficacy of combined sofosbuvir (SOF)/daclatasvir (DCV) for HCV Genotype 4 in children aged 8 to 18 years or weighing 17 kg or more. A total of 40 chronic HCV-infected, treatment-naïve children with well compensated livers were recruited from two sites. Patients received combined therapy of SOF (400 mg/d for patients weighing greater than 45 kg; 200 mg/d for patients weighing 17 to 45 kg) and DCV (60 mg/d for patients weighing greater than 45 kg; 30 mg/d for patients weighing 17 to 45 kg) for 12 weeks. They were followed up regularly by clinical examination and laboratory tests during treatment (weekly in the first month then monthly to the end of treatment), every 3 months for 6 months post-treatment, and at 48 weeks post-treatment. In our cohort, which included 45% of children below the age of 12 years (72.5% genotype 4 and 27.5% mixed genotype 4 and 1), end of treatment response (ETR) was 97.5%. Sustained virologic response for weeks 12 and 24 post-treatment (SVR12 and SVR24) were 97.5% and 95%, respectively, on an intention to treat basis, and 100% and 100% for those who completed the study protocol. Observed side effects were mild and none required drug cessation. Combined SOF/DCV was found to be effective and safe for treating HCV Genotype 4-infected children, 8 years of age and above.
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Affiliation(s)
- Tawhida Y Abdel Ghaffar
- Yassin Abdel Ghaffar Charity Center for Liver Disease and Research, Cairo, Egypt.,Department of Pediatrics, Ain Shams University, Cairo, Egypt
| | - Suzan El Naghi
- Yassin Abdel Ghaffar Charity Center for Liver Disease and Research, Cairo, Egypt.,Department of Pediatrics, National Hepatology & Tropical Medicine Research Institute, Cairo, Egypt
| | | | - Sarah Helmy
- Yassin Abdel Ghaffar Charity Center for Liver Disease and Research, Cairo, Egypt
| | | | | | - Mohamad Moafy
- Department of Pediatrics, Ain Shams University, Cairo, Egypt
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7
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von Massow G, Garcia-Cehic D, Gregori J, Rodriguez-Frias F, Macià MD, Escarda A, Esteban JI, Quer J. Whole-genome characterization and resistance-associated substitutions in a new HCV genotype 1 subtype. Infect Drug Resist 2019; 12:947-955. [PMID: 31118701 PMCID: PMC6499441 DOI: 10.2147/idr.s195441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 03/07/2019] [Indexed: 02/05/2023] Open
Abstract
Hepatitis C virus (HCV) is a highly variable infectious agent, classified into 8 genotypes and 86 subtypes. Our laboratory has implemented an in-house developed high-resolution HCV subtyping method based on next-generation sequencing (NGS) for error-free classification of the virus using phylogenetic analysis and analysis of genetic distances in sequences from patient samples compared to reference sequences. During routine diagnostic, a sample from an Equatorial Guinea patient could not be classified into any of the existing subtypes. The whole genome was analyzed to confirm that the new isolate could be classified as a new HCV subtype. In addition, naturally occurring resistance-associated substitutions (RAS) were analyzed by NGS. Whole-genome analysis based on p-distances suggests that the sample belongs to a new HCV genotype 1 subtype. Several RAS in the NS3 (S122T, D168E and I170V) and NS5A protein (Q(1b)24K, R(1b)30Q and Y93L+Y93F) were found, which could limit the use of some inhibitors for treating this subtype. RAS studies of new subtypes are of great interest for tailoring treatment, as no data on treatment efficacy are reported. In our case, the patient has not yet been treated, and the RAS report will be used to design the most effective treatment.
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Affiliation(s)
- Georg von Massow
- Liver Unit, Liver Diseases – Viral Hepatitis, Vall d’Hebron Institut of Research (VHIR) – Hospital Universitari Vall d’Hebron (HUVH), Barcelona, Spain
| | - Damir Garcia-Cehic
- Liver Unit, Liver Diseases – Viral Hepatitis, Vall d’Hebron Institut of Research (VHIR) – Hospital Universitari Vall d’Hebron (HUVH), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Josep Gregori
- Liver Unit, Liver Diseases – Viral Hepatitis, Vall d’Hebron Institut of Research (VHIR) – Hospital Universitari Vall d’Hebron (HUVH), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Roche Diagnostics S.L., Sant Cugat del Vallès, Barcelona, Spain
| | - Francisco Rodriguez-Frias
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Biochemistry and Microbiology Department, VHIR-HUVH, Barcelona, Spain
| | - María Dolores Macià
- Unidad de Microbiología Molecular, Servicio de Microbiología, Instituto de Investigación Sanitaria de les Illes Balears (IdISBa), Hospital Universitario Son Espases, Mallorca, Spain
| | - Ana Escarda
- Digestive Department, Hospital Universitario Son Espases, Mallorca, Spain
| | - Juan Ignacio Esteban
- Liver Unit, Liver Diseases – Viral Hepatitis, Vall d’Hebron Institut of Research (VHIR) – Hospital Universitari Vall d’Hebron (HUVH), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Medicine Department, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Josep Quer
- Liver Unit, Liver Diseases – Viral Hepatitis, Vall d’Hebron Institut of Research (VHIR) – Hospital Universitari Vall d’Hebron (HUVH), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Medicine Department, Universitat Autònoma de Barcelona, Barcelona, Spain
- Correspondence: Josep QuerLiver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d’Hebron Institut Recerca (VHIR-HUVH), Barcelona08035, SpainTel +3 493 489 4034Email
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8
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Soria ME, Gregori J, Chen Q, García-Cehic D, Llorens M, de Ávila AI, Beach NM, Domingo E, Rodríguez-Frías F, Buti M, Esteban R, Esteban JI, Quer J, Perales C. Pipeline for specific subtype amplification and drug resistance detection in hepatitis C virus. BMC Infect Dis 2018; 18:446. [PMID: 30176817 PMCID: PMC6122477 DOI: 10.1186/s12879-018-3356-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 08/23/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Despite the high sustained virological response rates achieved with current directly-acting antiviral agents (DAAs) against hepatitis C virus (HCV), around 5-10% of treated patients do not respond to current antiviral therapies, and basal resistance to DAAs is increasingly detected among treatment-naïve infected individuals. Identification of amino acid substitutions (including those in minority variants) associated with treatment failure requires analytical designs that take into account the high diversification of HCV in more than 86 subtypes according to the ICTV website (June 2017). METHODS The methodology has involved five sequential steps: (i) to design 280 oligonucleotide primers (some including a maximum of three degenerate positions), and of which 120 were tested to amplify NS3, NS5A-, and NS5B-coding regions in a subtype-specific manner, (ii) to define a reference sequence for each subtype, (iii) to perform experimental controls to define a cut-off value for detection of minority amino acids, (iv) to establish bioinformatics' tools to quantify amino acid replacements, and (v) to validate the procedure with patient samples. RESULTS A robust ultra-deep sequencing procedure to analyze HCV circulating in serum samples from patients infected with virus that belongs to the ten most prevalent subtypes worldwide: 1a, 1b, 2a, 2b, 2c, 2j, 3a, 4d, 4e, 4f has been developed. Oligonucleotide primers are subtype-specific. A cut-off value of 1% mutant frequency has been established for individual mutations and haplotypes. CONCLUSION The methodological pipeline described here is adequate to characterize in-depth mutant spectra of HCV populations, and it provides a tool to understand HCV diversification and treatment failures. The pipeline can be periodically extended in the event of HCV diversification into new genotypes or subtypes, and provides a framework applicable to other RNA viral pathogens, with potential to couple detection of drug-resistant mutations with treatment planning.
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Affiliation(s)
- María Eugenia Soria
- 0000 0004 1763 0287grid.430994.3Liver Unit, Internal Medicine Hospital Universitari Vall d’Hebron, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Josep Gregori
- 0000 0004 1763 0287grid.430994.3Liver Unit, Internal Medicine Hospital Universitari Vall d’Hebron, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain
- grid.452371.6Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- Roche Diagnostics, S.L, Sant Cugat del Vallés, Barcelona, Spain
| | - Qian Chen
- 0000 0004 1763 0287grid.430994.3Liver Unit, Internal Medicine Hospital Universitari Vall d’Hebron, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Damir García-Cehic
- 0000 0004 1763 0287grid.430994.3Liver Unit, Internal Medicine Hospital Universitari Vall d’Hebron, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain
- grid.452371.6Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
| | - Meritxell Llorens
- 0000 0004 1763 0287grid.430994.3Liver Unit, Internal Medicine Hospital Universitari Vall d’Hebron, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Ana I. de Ávila
- grid.465524.4Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Nathan M. Beach
- grid.465524.4Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Esteban Domingo
- grid.452371.6Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- grid.465524.4Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
| | - Francisco Rodríguez-Frías
- grid.452371.6Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- 0000 0001 0675 8654grid.411083.fLiver Pathology Unit, Department of Biochemistry and Microbiology, Hospital Universitari Vall d’Hebron, Barcelona, Spain
- grid.7080.fUniversitat Autónoma de Barcelona, Barcelona, Spain
| | - María Buti
- 0000 0004 1763 0287grid.430994.3Liver Unit, Internal Medicine Hospital Universitari Vall d’Hebron, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain
- grid.452371.6Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- grid.7080.fUniversitat Autónoma de Barcelona, Barcelona, Spain
| | - Rafael Esteban
- 0000 0004 1763 0287grid.430994.3Liver Unit, Internal Medicine Hospital Universitari Vall d’Hebron, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain
- grid.452371.6Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- grid.7080.fUniversitat Autónoma de Barcelona, Barcelona, Spain
| | - Juan Ignacio Esteban
- 0000 0004 1763 0287grid.430994.3Liver Unit, Internal Medicine Hospital Universitari Vall d’Hebron, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain
- grid.452371.6Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- grid.7080.fUniversitat Autónoma de Barcelona, Barcelona, Spain
| | - Josep Quer
- 0000 0004 1763 0287grid.430994.3Liver Unit, Internal Medicine Hospital Universitari Vall d’Hebron, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain
- grid.452371.6Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- grid.7080.fUniversitat Autónoma de Barcelona, Barcelona, Spain
| | - Celia Perales
- 0000 0004 1763 0287grid.430994.3Liver Unit, Internal Medicine Hospital Universitari Vall d’Hebron, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain
- grid.452371.6Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, Madrid, Spain
- grid.465524.4Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Campus de Cantoblanco, Madrid, Spain
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Rodriguez C, Soulier A, Demontant V, Poiteau L, Mercier-Darty M, Bouvier-Alias M, Pawlotsky JM, Chevaliez S. A novel standardized deep sequencing-based assay for hepatitis C virus genotype determination. Sci Rep 2018; 8:4180. [PMID: 29520035 PMCID: PMC5843601 DOI: 10.1038/s41598-018-22614-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/26/2018] [Indexed: 01/06/2023] Open
Abstract
Hepatitis C virus (HCV) genotype and subtype (1a/1b) identification is needed to tailor anti-HCV therapy. Currently available methods accurately identify the genotype and differentiate subtypes 1a from 1b. However, these assays have not been designed to identify other HCV subtypes, nor to recognize mixed genotype/subtype infections, emphasizing the need for a high-resolution system based on phylogenetic analysis of reads obtained by deep sequencing of a relevant genome region. The aim of this study was to evaluate the performance of the Sentosa SQ HCV Genotyping Assay, a novel deep sequencing-based assay targeting the HCV nonstructural 5B (NS5B) region, in clinical samples from patients with an indication for anti-HCV therapy. A high concordance rate with Sanger sequencing of the NS5B region, the reference method, was found for genotype 1 to 6 determination, 1a/1b subtype identification, and genotype 4, 5 and 6 subtyping. Discrepancies were seen essentially for HCV genotype 2 subtyping. Overall, the performance of the deep sequencing-based assay in generating the genotypes/subtype information needed to tailor anti-HCV treatment was adequate in this study. Further improvements, such as a longer NS5B fragment analyzed and enriching the database of reference prototype strains used for subtype assignment would make it a method of choice for HCV genotyping and subtyping for future clinical practice and research.
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Affiliation(s)
- Christophe Rodriguez
- National Reference Center for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
- INSERM, U955, Créteil, France
| | - Alexandre Soulier
- National Reference Center for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
- INSERM, U955, Créteil, France
| | - Vanessa Demontant
- National Reference Center for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
- INSERM, U955, Créteil, France
| | - Lila Poiteau
- National Reference Center for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
- INSERM, U955, Créteil, France
| | - Mélanie Mercier-Darty
- National Reference Center for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
- INSERM, U955, Créteil, France
| | - Magali Bouvier-Alias
- National Reference Center for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
- INSERM, U955, Créteil, France
| | - Jean-Michel Pawlotsky
- National Reference Center for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France
- INSERM, U955, Créteil, France
| | - Stéphane Chevaliez
- National Reference Center for Viral Hepatitis B, C and D, Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France.
- INSERM, U955, Créteil, France.
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10
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Ordeig L, Garcia-Cehic D, Gregori J, Soria ME, Nieto-Aponte L, Perales C, Llorens M, Chen Q, Riveiro-Barciela M, Buti M, Esteban R, Esteban JI, Rodriguez-Frias F, Quer J. New hepatitis C virus genotype 1 subtype naturally harbouring resistance-associated mutations to NS5A inhibitors. J Gen Virol 2018; 99:97-102. [PMID: 29239718 DOI: 10.1099/jgv.0.000996] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Hepatitis C virus (HCV) is a highly divergent virus currently classified into seven major genotypes and 86 subtypes (ICTV, June 2017), which can have differing responses to therapy. Accurate genotyping/subtyping using high-resolution HCV subtyping enables confident subtype identification, identifies mixed infections and allows detection of new subtypes. During routine genotyping/subtyping, one sample from an Equatorial Guinea patient could not be classified into any of the subtypes. The complete genomic sequence was compared to reference sequences by phylogenetic and sliding window analysis. Resistance-associated substitutions (RASs) were assessed by deep sequencing. The unclassified HCV genome did not belong to any of the existing genotype 1 (G1) subtypes. Sliding window analysis along the complete genome ruled out recombination phenomena suggesting that it belongs to a new HCV G1 subtype. Two NS5A RASs (L31V+Y93H) were found to be naturally combined in the genome which could limit treatment possibilities in patients infected with this subtype.
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Affiliation(s)
- Laura Ordeig
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d'Hebron (HUVH), 08035, Barcelona, Spain
| | - Damir Garcia-Cehic
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d'Hebron (HUVH), 08035, Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Josep Gregori
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d'Hebron (HUVH), 08035, Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029, Madrid, Spain
- Roche Diagnostics SL, Sant Cugat del Vallès, 08174, Barcelona, Spain
| | - Maria Eugenia Soria
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d'Hebron (HUVH), 08035, Barcelona, Spain
| | - Leonardo Nieto-Aponte
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029, Madrid, Spain
- Liver Pathology Unit, Department of Biochemistry and Microbiology, HUVH, 08035, Barcelona, Spain
| | - Celia Perales
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d'Hebron (HUVH), 08035, Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Meritxell Llorens
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d'Hebron (HUVH), 08035, Barcelona, Spain
| | - Qian Chen
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d'Hebron (HUVH), 08035, Barcelona, Spain
| | - Mar Riveiro-Barciela
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d'Hebron (HUVH), 08035, Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Maria Buti
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d'Hebron (HUVH), 08035, Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029, Madrid, Spain
- Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Rafael Esteban
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d'Hebron (HUVH), 08035, Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029, Madrid, Spain
- Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Juan Ignacio Esteban
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d'Hebron (HUVH), 08035, Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029, Madrid, Spain
- Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Francisco Rodriguez-Frias
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029, Madrid, Spain
- Liver Pathology Unit, Department of Biochemistry and Microbiology, HUVH, 08035, Barcelona, Spain
- Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Josep Quer
- Liver Unit, Liver Disease Laboratory-Viral Hepatitis, Internal Medicine Department, Vall d'Hebron Institut Recerca (VHIR)-Hospital Universitari Vall d'Hebron (HUVH), 08035, Barcelona, Spain
- Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
- Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029, Madrid, Spain
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