Detection of Natural Resistance-Associated Substitutions by Ion Semiconductor Technology in HCV1b Positive, Direct-Acting Antiviral Agents-Naïve Patients

• Main Authors: Nadia Marascio, Grazia Pavia, Alessio Strazzulla, Tim Dierckx, Lize Cuypers, Bram Vrancken, Giorgio Settimo Barreca, Teresa Mirante, Donatella Malanga, Duarte Mendes Oliveira, Anne-Mieke Vandamme, Carlo Torti, Maria Carla Liberto, Alfredo Focà, the SINERGIE-UMG Study Group
• Format: Article
• Language: English
• Published: MDPI AG 2016-08-01
• Series: International Journal of Molecular Sciences
• Subjects: hepatitis C virus 1b; resistance-associated substitutions; direct-acting antiviral agents; deep-sequencing
• Online Access: http://www.mdpi.com/1422-0067/17/9/1416
• ISSN: 1422-0067

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.