Detection of Natural Resistance-Associated Substitutions by Ion Semiconductor Technology in HCV1b Positive, Direct-Acting Antiviral Agents-Naïve Patients.
Naturally occurring resistance-associated substitutions (RASs) can negatively impact the response to direct-acting antivirals (DAAs) agents-based therapies for hepatitis C virus (HCV) infection. Herein, we set out to characterize the RASs in the HCV1b genome from serum samples of DAA-naïve patients in the context of the SINERGIE (South Italian Network for Rational Guidelines and International Epidemiology, 2014) project. We deep-sequenced the NS3/4A protease region of the viral population using the Ion Torrent Personal Genome Machine, and patient-specific majority rule consensus sequence summaries were constructed with a combination of freely available next generation sequencing data analysis software. We detected NS3/4A protease major and minor variants associated with resistance to boceprevir (V36L), telaprevir (V36L, I132V), simeprevir (V36L), and grazoprevir (V36L, V170I). Furthermore, we sequenced part of HCV NS5B polymerase using Sanger-sequencing and detected a natural RAS for dasabuvir (C316N). This mutation could be important for treatment strategies in cases of previous therapy failure.
Department of Health Sciences, Institute of Microbiology, School of Medicine, University of Magna Graecia, Viale Europa, Germaneto, 88100 Catanzaro, Italy. nadiamarascio@gmail.com.|Katholieke Universiteit (KU) Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, 3000 Leuven, Belgium. nadiamarascio@gmail.com.
Nadia
N
Marascio
Department of Health Sciences, Institute of Microbiology, School of Medicine, University of Magna Graecia, Viale Europa, Germaneto, 88100 Catanzaro, Italy. grazia_pavia@libero.it.
Grazia
G
Pavia
Department of Medical and Surgical Sciences, Unit of Infectious and Tropical Diseases, School of Medicine, University of Magna Graecia, Viale Europa, Germaneto, 88100 Catanzaro, Italy. alessiostrazzulla@yahoo.it.
Alessio
A
Strazzulla
Katholieke Universiteit (KU) Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, 3000 Leuven, Belgium. tim.dierckx@kuleuven.be.
Tim
T
Dierckx
Katholieke Universiteit (KU) Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, 3000 Leuven, Belgium. lize.cuypers@kuleuven.be.
Lize
L
Cuypers
Katholieke Universiteit (KU) Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, 3000 Leuven, Belgium. bram.vrancken@kuleuven.be.
Bram
B
Vrancken
Department of Health Sciences, Institute of Microbiology, School of Medicine, University of Magna Graecia, Viale Europa, Germaneto, 88100 Catanzaro, Italy. gbarreca@unicz.it.
Giorgio Settimo
GS
Barreca
Centro di Servizio Interdipartimentale (CIS)-Genomica funzionale e Patologia Molecolare, University of Magna Graecia, Viale Europa, Germaneto, 88100 Catanzaro, Italy. teresa87@tiscalinet.it.
Teresa
T
Mirante
Department of Experimental and Clinical Medicine, University of Magna Graecia, Viale Europa, Germaneto, 88100 Catanzaro, Italy. malanga@unicz.it.
Donatella
D
Malanga
Department of Experimental and Clinical Medicine, University of Magna Graecia, Viale Europa, Germaneto, 88100 Catanzaro, Italy. oliveira@unicz.it.
Duarte Mendes
DM
Oliveira
Katholieke Universiteit (KU) Leuven-University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, 3000 Leuven, Belgium. annemie.vandamme@uzleuven.be.|Center for Global Health and Tropical Medicine, Institute for Hygiene and Tropical Medicine, University Nova de Lisboa, Rua da Junqueira 100, 1349-008 Lisbon, Portugal. annemie.vandamme@uzleuven.be.
Anne-Mieke
AM
Vandamme
Department of Medical and Surgical Sciences, Unit of Infectious and Tropical Diseases, School of Medicine, University of Magna Graecia, Viale Europa, Germaneto, 88100 Catanzaro, Italy. torti@unicz.it.
Carlo
C
Torti
Department of Health Sciences, Institute of Microbiology, School of Medicine, University of Magna Graecia, Viale Europa, Germaneto, 88100 Catanzaro, Italy. mliberto@unicz.it.
Maria Carla
MC
Liberto
Department of Health Sciences, Institute of Microbiology, School of Medicine, University of Magna Graecia, Viale Europa, Germaneto, 88100 Catanzaro, Italy. alfredofoca@gmail.com.
Alfredo
A
Focà
D000998:Antiviral Agents / Q000494:pharmacology*; D024882:Drug Resistance, Viral / Q000235:genetics; D016174:Hepacivirus / Q000187:drug effects* / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009154:Mutation; D009842:Oligopeptides / Q000494:pharmacology; D011392:Proline / Q000031:analogs & derivatives / Q000494:pharmacology; D000069616:Simeprevir / Q000494:pharmacology; D017361:Viral Nonstructural Proteins / Q000235:genetics
D000998:Antiviral Agents; D009842:Oligopeptides; D017361:Viral Nonstructural Proteins; C486464:telaprevir; C512204:N-(3-amino-1-(cyclobutylmethyl)-2,3-dioxopropyl)-3-(2-((((1,1-dimethylethyl)amino)carbonyl)amino)-3,3-dimethyl-1-oxobutyl)-6,6-dimethyl-3-azabicyclo(3.1.0)hexan-2-carboxamide; D011392:Proline; D000069616:Simeprevir
deep-sequencing; direct-acting antiviral agents; hepatitis C virus 1b; resistance-associated substitutions