HCV NS3 sequencing as a reliable and clinically useful tool for the assessment of genotype and resistance mutations for clinical samples with different HCV-RNA levels

V. C. Di Maio, V. Cento, Daniele Di Paolo, Marianna Aragri, F. De Leonardis, Monica Tontodonati, Valeria Micheli, Maria Concetta Bellocchi, F. P. Antonucci, A. Bertoli, Ilaria Lenci, M. Milana, Laura Gianserra, M. Melis, Antonio Di Biagio, Cesare Sarrecchia, L. Sarmati, Simona Landonio, Simona Francioso, L. LambiaseLaura Nicolini, Simona Marenco, Lorenzo Nosotti, V. Giannelli, M. Siciliano, Dante Romagnoli, Adriano M. Pellicelli, J. Vecchiet, Carlo Magni, Sergio Babudieri, M. S. Mura, G. Taliani, C. Mastroianni, U. Vespasiani Gentilucci, Mario Romano, Filomena Morisco, Adriano Gasbarrini, Vincenzo Vullo, Savino Bruno, C. Baiguera, C. Pasquazzi, G. Tisone, A. Picciotto, M. Andreoni, G. Parruti, Giuliano Rizzardini, M. Angelico, Carlo Federico Perno, Francesca Ceccherini-Silberstein, R. Mariani, Maurizio Paoloni, N. Iapadre, A. Grimaldi, Barbara Menzaghi, Tiziana Quirino, Jacopo Vecchiet, B. Bruzzone, Andrea De Maria, A. Di Biagio, S. Marenco, L. A. Nicolini, A. Picciotto, Claudio Viscoli, Katia Casinelli, Marco Delle Monache, Miriam Lichtner, C. Mastroianni, Alessio Michele Aghemo, S. Bruno, M. Cerrone, Massimo Colombo, A. D'Arminio Monforte, E. Danieli, F. Donato, G. Gubertini, S. Landonio, C. F. Magni, Alessandro Mancon, V. Micheli, S. Monico, F. Niero, M. Puoti, G. Rizzardini, M. L. Russo, R. Alfieri, M. Gnocchi, A. Orro, L. Milanesi, Enrica Baldelli, M. Bertolotti, V. Borghi, C. Mussini, D. Romagnoli, Giuseppina Brancaccio, N. Caporaso, G. B. Gaeta, V. Lembo, F. Morisco, Vicenza Calvaruso, Antonio Craxi, Viro Di Marco, A. Mazzola, S. Petta, Emilio D'amico, Pierluigi Cacciatore, A. Consorte, V. Pace Palitti, G. Parruti, Alessandro Pieri, Ennio Polilli, M. Tontodonati, M. Andreoni, Mario Angelico, F. Antenucci, Francesco Paolo Antonucci, M. Aragri, Daniele Armenia, Leonardo Baiocchi, M. Bellocchi, Ada Bertoli, E. Biliotti, Marco Biolato, Luca Carioti, F. Ceccherini-Silberstein, V. Cento, G. Cerasari, C. Cerva, M. Ciotti, C. D'Ambrosio, Gabriella D'Ettorre, F. De Leonardis, A. De Sanctis, Velia Chiara Di Maio, D. Di Paolo, S. Francioso, C. Furlan, P. Gallo, A. Gasbarrini, V. Giannelli, L. Gianserra, A. Grieco, S. Grieco, L. Lambiase, B. Lattanzi, I. Lenci, V. Malagnino, M. Manuelli, Marco Merli, Lucia Miglioresi, M. Milana, L. Nosotti, D. Palazzo, C. Pasquazzi, A. Pellicelli, Carlo Federico Perno, M. Romano, Francesco Santopaolo, Maria Mercedes Santoro, L. Sarmati, C. Sarrecchia, D. Sforza, M. Siciliano, M. C. Sorbo, M. Spaziante, Valentina Svicher, G. Taliani, E. Teti, G. Tisone, U. Vespasiani-Gentilucci, V. Vullo, Alessandra Mangia, S. Babudieri, I. Maida, M. Melis, M. S. Mura, L. Falconi, D. Di Giammartino, Pierluigi Tarquini

Research output: Contribution to journalArticlepeer-review

Abstract

Objectives: This study aims to evaluate the reliability and clinical utility of NS3 sequencing in hepatitis C virus (HCV) 1-infected patients who were candidates to start a PI-containing regimen. Methods: NS3 protease sequencing was performed by in-house-developed HCV-1 subtype-specific protocols. Phylogenetic analysis was used to test sequencing reliability and concordance with previous genotype/subtype assignment by commercial genotyping assays. Results: Five hundred and sixty-seven HCV plasma samples with quantifiable HCV-RNA from 326 HCV-infected patients were collected between 2011 and 2014. Overall, the success rate of NS3 sequencing was 88.9%. The success rate between the two subtype protocols (HCV-1a/HCV-1b) was similarly high for samples with HCV-RNA > 3 log IU/mL (>92% success rate), while it was slightly lower for HCV-1a samples with HCV-RNA ≤ 3 log IU/mL compared with HCV-1b samples. Phylogenetic analysis confirmed the genotype/subtype given by commercial genotyping assays in 92.9% (303/326) of cases analysed. In the remaining 23 cases (7.1%), 1 was HCV-1g (previously defined as subtype 1a), 1 was HCV-4d (previously defined as genotype 1b) and 1 was HCV-1b (previously defined as genotype 2a/2c). In the other cases, NS3 sequencing precisely resolved the either previous undetermined/discordant subtype 1 or double genotype/subtype assignment by commercial genotyping assays. Resistance-associated variants (RAVs) to PI were detected in 31.0% of samples. This prevalence changed according to PI experience (17.1% in PI-naive patients versus 79.2% in boceprevir/telaprevir/simeprevir-failing patients). Among 96 patients with available virological outcome following boceprevir/telaprevir treatment, a trend of association between baseline NS3 RAVs and virological failure was observed (particularly for HCV-1a-infected patients: 3/21 failing patients versus 0/22 achieving sustained virological response; P = 0.11). Conclusions: HCV-NS3 sequencing provides reliable results and at the same time gives two clinically relevant pieces of information: A correct subtype/genotype assignment and the detection of variants that may interfere with the efficacy of PI.

Original languageEnglish
Article numberdkv403
Pages (from-to)739-750
Number of pages12
JournalJournal of Antimicrobial Chemotherapy
Volume71
Issue number3
DOIs
Publication statusPublished - Mar 1 2016

ASJC Scopus subject areas

  • Pharmacology
  • Pharmacology (medical)
  • Infectious Diseases

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