Prevalence of Single and Multiple Natural NS3, NS5A and NS5B Resistance-Associated Substitutions in Hepatitis C Virus Genotypes 1–4 in Italy
Authors: Bertoli Ada , Sorbo Maria Chiara , Aragri Marianna , Lenci Ilaria , Teti Elisabetta , Polilli Ennio , Di Maio Velia Chiara , Gianserra Laura , Biliotti Elisa , Masetti Chiara , Magni Carlo F. , Babudieri Sergio , Nicolini Laura A. , Milana Martina , Cacciatore Pierluigi , Sarmati Loredana , Pellicelli Adriano , Paolucci Stefania , Craxì Antonio , Morisco Filomena , Palitti Valeria Pace , Siciliano Massimo , Coppola Nicola , Iapadre Nerio , Puoti Massimo , Rizzardini Giuliano , Taliani Gloria , Pasquazzi Caterina , Andreoni Massimo , Parruti Giustino , Angelico Mario , Perno Carlo Federico , Cento Valeria , Ceccherini-Silberstein Francesca ,   HCV Virology Italian Resistance Network (VIRONET-C), Andreone Pietro , Baldanti Fausto , Barbarini Giorgio , Boccaccio Vincenzo , Boglione Lucio , Bolis Matteo , Bonora Stefano , Borghi Vanni , Brancaccio Giuseppina , Bruno Savino , Bruzzone Bianca , Calvaruso Vincenza , Caporaso Nicola , Ciaccio Antonio , Ciancio Alessia , Colombatto Piero , Cozzolongo Raffaele , D’Ambrosio Cecilia , D’Ettorre Gabriella , De Leonardis Francesco , De Luca Andrea , Di Biagio Antonio , Di Perri Giovanni , Francioso Simona , Gaeta Giovanni Battista , Gasbarrini Antonio , Ghisetti Valeria , Giorgini Alessia , Grieco Antonio , Gubertini Guido , Gulminetti Roberto , Lambiase Lara , Landonio Simona , Lichtner Miriam , Maida Ivana , Marenco Simona , Marinaro Letizia , Maserati Renato , Melis Michela , Menzaghi Barbara , Meregalli Elisa , Micheli Valeria , Niero Fosca , Paoloni Maurizio , Pieri Alessandro , Rendina Maria , Romagnoli Dante , Rossetti Barbara , Ruggiero Tina , Sangiovanni Vincenzo , Starace Mario , Sticchi Laura , Tarquini Pierluigi , Toniutto Pierluigi , Vullo Vincenzo , Zazzi Maurizio 
Published: June 2018

Natural resistance-associated substitutions (RASs) are reported with highly variable prevalence across different HCV genotypes (GTs). Frequency of natural RASs in a large Italian real-life cohort of patients infected with the 4 main HCV-GTs was investigated. NS3, NS5A and NS5B sequences were analysed in 1445 HCV-infected DAA-naïve patients. Sanger-sequencing was performed by home-made protocols on 464 GT1a, 585 GT1b, 92 GT2c, 199 GT3a, 16 GT4a and 99 GT4d samples. Overall, 20.7% (301/1455) of patients showed natural RASs, and the prevalence of multiclass-resistance was 7.3% (29/372 patients analysed). NS3-RASs were particularly common in GT1a and GT1b (45.2-10.8%, respectively), mainly due to 80K presence in GT1a (17%). Almost all GTs showed high prevalence of NS5A-RASs (range: 10.2–45.4%), and especially of 93H (5.1%). NS5A-RASs with fold-change >100x were detected in 6.8% GT1a (30H/R-31M-93C/H), 10.3% GT1b (31V-93H), 28.4% GT2c (28C-31M-93H), 8.5% GT3a (30K-93H), 45.5% GT4a (28M-30R-93H) and 3.8% GT4d (28V-30S-93H). Sofosbuvir RAS 282T was never detected, while the 159F and 316N RASs were found in GT1b (13.4–19.1%, respectively). Natural RASs are common in Italian patients infected with HCV-GTs 1–4. High prevalence of clinically-relevant RASs (such as Y93H) supports the appropriateness of HCV resistance-test to properly guide DAA-based therapy.