Author information
1 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.
2 Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut of Research (VHIR), Hospital Universitari Vall d'Hebron (HUVH), Barcelona, Spain.
3 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.
4 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.
5 Gastroenterology and Hepatology Department, Instituto de Investigación (IDIVAL), Hospital Universitario Marqués de Valdecilla, Santander, Spain.
6 Liver Unit, Hospital Universitario Puerta de Hierro, Madrid, Spain.
7 Biochemistry and Microbiology Department, VHIR-HUVH, Barcelona, Spain.
8 Microbiology Department, Hospital Universitario La Paz, Madrid, Spain.
9 Liver Unit, Hospital Universitari de Bellvitge, Barcelona, Spain.
10 Microbiology Department, Hospital Universitari de Bellvitge, Barcelona.
11 HIV and STI Unit, Infectious Diseases Department, Hospital Universitari de Bellvitge, Barcelona, Spain.
12 Infectious Disease Unit, HUVH, Barcelona, Spain.
13 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.
14 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.
15 Digestive Pathology Unit, Hospital Universitari Santa Creu i Sant Pau, Barcelona, Spain.
16 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.
17 Liver Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) - Hospital Clínic de Barcelona, Barcelona, Spain.
18 Liver Unit, Hospital Universitario La Princesa, Madrid, Spain.
19 Liver Unit, Hospital Universitari Germans Trias i Pujol, Barcelona, Spain.
20 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.
21 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.
22 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.
23 Gastroenterology Unit, Hospital Universitari Mútua Terrassa, Spain.
24 Liver Unit, Hospital Universitario 12 de Octubre, Madrid, Spain.
25 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.
26 Liver Unit, Instituto de Investigación Hospital Universitario La Paz (IdiPAZ) - Hospital Universitario La Paz, Madrid, Spain.
27 Gastroenterology Department, Hospital Universitari Doctor Josep Trueta, Girona, Spain.
28 Clinical Laboratory, Hospital Universitari Doctor Josep Trueta, Girona, Spain.
29 Laboratori Territorial - Hospital Santa Caterina, Girona, Spain.
30 Gastroenterology and Hepatology Depart., Hospital Universitario de Burgos, Burgos, Spain.
31 Liver Unit, Hospital General de Valencia, Valencia, Spain.
32 Microbiology Unit, Hospital General de Valencia, Valencia, Spain.
33 Medicine Department-Medical School, Hospital Univ. Arnau de Vilanova, Lleida, Spain.
34 Microbiology Department, Hospital Universitari Arnau de Vilanova, Lleida, Spain.
35 Gastroenterology and Hepatology Department, Instituto de Investigación Sanitaria Galicia Sur (IISGS) - Complejo Hospitalario de Pontevedra, Pontevedra, Spain.
36 Microbiology and Parasitology Department, Complejo Hospitalario de Pontevedra, Pontevedra, Spain.
37 Liver Unit, Hospital Universitario de Canarias, La Laguna, Santa Cruz de Tenerife, Spain.
38 Liver Unit, Complejo Hospitalario Universitario A Coruña (CHUAC), La Coruña, Spain.
39 Microbiology Department, Institut de Investigación Biomédica de a Coruña (INIBIC) - Complejo Hospitalario Universitario A Coruña (CHUAC), La Coruña, Spain.
40 Gastroenterology, Hospital Universitario Donostia, San Sebastián, Spain.
41 Gastroenterology Depart., Central University Hospital of Asturias (HUCA), Oviedo, Spain.
42 Granollers General Hospital, Barcelona, Spain.
43 Sant Jaume de Calella County Hospital, Barcelona, Spain.
44 Gastroenterology Department, Dr Negrin University Hospital of Gran Canaria, Las Palmas de Gran Canaria, Spain.
45 Liver Unit, Consorci Sanitari de Terrassa - Hospital de Terrassa, Terrassa, Spain.
46 Gastroenterology Unit, Joan XXIII University Hospital, Tarragona, Spain.
47 Virology and Molecular Biology Unit, Microbiology Department, Complexo Hospitalario Universitario de Ourense (CHUO), Ourense, Spain.
48 Hospital de Mataró, Barcelona, Spain.
49 Hospital Universitari Sant Pau i Santa Tecla, Tarragona, Spain.
50 Gastroenterology Department, Hospital Universitari Santa Maria de Lleida, Lleida, Spain.
51 Microbiology Unit, Hospital Universitario de Galdakao, Vizcaya, Spain.
52 County Hospital of Blanes, Girona, Spain.
53 Liver Unit, Hospital de Viladecans, Barcelona, Spain.
54 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.
55 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.
56 Hospital Universitari Sant Joan de Reus, Tarragona, Spain.
57 Liver Unit, Hospital d'Igualada, Barcelona, Spain.
58 Fundació Salut Empordà - Hospital de Figueres, Girona, Spain.
59 Hospital San Pedro-CIBIR, La Rioja, Logroño, Spain.
60 Hospital Universitario Ramón y Cajal, Madrid, Spain.
61 Gastroenterology and Hepatology Department, Hospital Univ.de Toledo, Toledo, Spain.
62 Hospital Povisa, Vigo, Spain.
63 Laboratori de Referència de Catalunya, Barcelona, Spain.
64 Hospital Universitario Río Ortega, Valladolid, Spain.
65 Gastroenterology Unit, Hospital Virgen de la Victoria, Málaga, Spain.
66 Liver Unit, Hospital Universitario Miguel Servet, Zaragoza, Spain.
67 Liver Unit, Hospital Universitario Virgen del Rocío, Seville, Spain.
68 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.
69 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.
70 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. Electronic address: jignacio.esteban@ciberehd.org.
71 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. Electronic address: josep.quer@vhir.org.
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.