Deep-sequencing reveals broad subtype-specific HCV resistance mutations associated with treatment failure

Qian Chen, Celia Perales, Maria Eugenia Soria, Damir Garcia-Cehic, Josep Gregori, Francisco Rodriguez-Frias, Maria Buti, Javier Crespo, Joe Luis Calleja, David Tabernero, Marta Vila, Fernando Lazaro, Ariadna Rando-Segura, Leonardo Nieto-Aponte, Meritxell Llorens-Revull, Maria Francesca Cortese, Irati Fernandez-Alonso, Jose Castellote, Jordi Niubo, Arkaitz ImazXavier Xiol, Lluis Castells, Mar Riveiro-Barciela, Jordi Llaneras, Jordi Navarro, Victor Vargas-Blasco, Salvador Augustin, Isabel Conde, Angel Rubin, Martin Prieto, Xavier Torras, Nuria Margall, Xavier Forns, Zoe Marino, Sabela Lens, Martin Bonacci, Sofia Perez-del-Pulgar, Maria Carlota Londono, Maria Luisa Garcia-Buey, Paloma Sanz-Cameno, Rosa Morillas, Elisa Martro, Veronica Saludes, Helena Masnou-Ridaura, Javier Salmeron, Rosa Quiles, Jose Antonio Carrion, Montserrat Forne, Merce Rosinach, Inmaculada Fernandez, Javier Garcia-Samaniego, Antonio Madejon, Pilar Castillo-Grau, Carme Lopez-Nunez, Maria Jose Ferri, Rosa Durandez, Federico Saez-Royuela, Moises Diago, Concepcion Gimeno, Rafael Medina, Juan Buenestado, Albert Bernet, Juan Turnes, Matilde Trigo-Daporta, Manuel Hernandez-Guerra, Manuel Delgado-Blanco, Angelina Canizares, Juan Ignacio Arenas, Maria Juana Gomez-Alonso, Manuel Rodriguez, Elisabet Deig, Gemma Olive, Oscar del Rio, Joaquin Cabezas, Ildefonso Quinones, Merce Roget, Silvia Montoliu, Juan Garcia-Costa, Lluis Force, Silvia Blanch, Miguel Miralbes, Maria Jose Lopez-de-Goicoechea, Angels Garcia-Flores, Maria Saumoy, Teresa Casanovas, Carme Baliellas, Pau Gilabert, Albert Martin-Cardona, Rosa Roca, Merce Barenys, Joana Villaverde, Silvia Salord, Blau Camps, Maria Silvan di Yacovo, Imma Ocana, Silvia Sauleda, Marta Bes, Judit Carbonell, Elena Vargas-Accarino, Sofia P. Ruzo, Mercedes Guerrero-Murillo, Georg Von Massow, Maria Isabel Costafreda, Rosa Maria Lopez, Leticia Gonzalez-Moreno, Yolanda Real, Doroteo Acero-Fernandez, Silvia Viroles, Xavier Pamplona, Mireia Cairo, Maria Dolores Ocete, Jose Francisco Macias-Sanchez, Angel Estebanez, Joan Carles Quer, Alvaro Mena-de-Cea, Alejandra Otero, Angeles Castro-Iglesias, Francisco Suarez, Angeles Vazquez, David Vieito, Soledad Lopez-Calvo, Pilar Vazquez-Rodriguez, Francisco Jose Martinez-Cerezo, Raul Rodriguez, Ramiro Macenlle, Alba Cachero, Gasshan Mereish, Carme Mora-Moruny, Silvia Fabregas, Begona Sacristan, Agustin Albillos, Juan Jose Sanchez-Ruano, Raquel Baluja-Pino, Javier Fernandez-Fernandez, Carlos Gonzalez-Portela, Carmen Garcia-Martin, Gloria Sanchez-Antolin, Raul Jesus Andrade, Miguel Angel Simon, Juan Manuel Pascasio, Manolo Romero-Gomez, Jose Antonio del-Campo, Esteban Domingo, Rafael Esteban, Juan Ignacio Esteban, Josep Quer

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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.
Original languageSpanish
JournalAntiviral Research
Volume174
Issue number104694
Publication statusPublished - Feb 2020

Keywords

  • Antiviral treatment
  • Direct-acting antivirals
  • Failure
  • HCV
  • NGS
  • RAS

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