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. (17th December 2015)

• Record Type: Journal Article
• Authors: Di Maio, V. C.; Cento, V.; Di Paolo, D.; Aragri, M.; De Leonardis, F.; Tontodonati, M.; Micheli, V.; Bellocchi, M. C.; Antonucci, F. P.; Bertoli, A.; Lenci, I.; Milana, M.; Gianserra, L.; Melis, M.; Di Biagio, A.; Sarrecchia, C.; Sarmati, L.; Landonio, S.; Francioso, S.; Lambiase, L.; Nicolini, L. A.; Marenco, S.; Nosotti, L.; Giannelli, V.; Siciliano, M.; Romagnoli, D.; Pellicelli, A.; Vecchiet, J.; Magni, C. F.; Babudieri, S.; Mura, M. S.; Taliani, G.; Mastroianni, C.; Vespasiani-Gentilucci, U.; Romano, M.; Morisco, F.; Gasbarrini, A.; Vullo, V.; Bruno, S.; Baiguera, C.; Pasquazzi, C.; Tisone, G.; Picciotto, A.; Andreoni, M.; Parruti, G.; Rizzardini, G.; Angelico, M.; Perno, C. F.; Ceccherini-Silberstein, F.; Mariani, R.; Paoloni, M.; Iapadre, N.; Grimaldi, A.; Menzaghi, B.; Quirino, T.; Vecchiet, J.; Bruzzone, B.; De Maria, A.; Di Biagio, A.; Marenco, S.; Nicolini, L. A.; Picciotto, A.; Viscoli, C.; Casinelli, K.; Monache, M. Delle; Lichtner, M.; Mastroianni, C.; Aghemo, A.; Bruno, S.; Cerrone, M.; Colombo, M.; Monforte, A. D'Arminio; Danieli, E.; Donato, F.; Gubertini, G.; Landonio, S.; Magni, C. F.; Mancon, A.; Micheli, V.; Monico, S.; Niero, F.; Puoti, M.; Rizzardini, G.; Russo, M. L.; Alfieri, R.; Gnocchi, M.; Orro, A.; Milanesi, L.; Baldelli, E.; Bertolotti, M.; Borghi, V.; Mussini, C.; Romagnoli, D.; Brancaccio, G.; Caporaso, N.; Gaeta, G. B.; Lembo, V.; Morisco, F.; Calvaruso, V.; Craxì, A.; Di Marco, V.; Mazzola, A.; Petta, S.; D'Amico, E.; Cacciatore, P.; Consorte, A.; Palitti, V. Pace; Parruti, G.; Pieri, A.; Polilli, E.; Tontodonati, M.; Andreoni, M.; Angelico, M.; Antenucci, F.; Antonucci, F. P.; Aragri, M.; Armenia, D.; Baiocchi, L.; Bellocchi, M.; Bertoli, A.; Biliotti, E.; Biolato, M.; Carioti, L.; Ceccherini-Silberstein, F.; Cento, V.; Cerasari, G.; Cerva, C.; Ciotti, M.; D'Ambrosio, C.; D'Ettorre, G.; De Leonardis, F.; De Sanctis, A.; Di Maio, V. C.; Di Paolo, D.; Francioso, S.; Furlan, C.; Gallo, P.; Gasbarrini, A.; Giannelli, V.; Gianserra, L.; Grieco, A.; Grieco, S.; Lambiase, L.; Lattanzi, B.; Lenci, I.; Malagnino, V.; Manuelli, M.; Merli, M.; Miglioresi, L.; Milana, M.; Nosotti, L.; Palazzo, D.; Pasquazzi, C.; Pellicelli, A.; Perno, C. F.; Romano, M.; Santopaolo, F.; Santoro, M. M.; Sarmati, L.; Sarrecchia, C.; Sforza, D.; Siciliano, M.; Sorbo, M. C.; Spaziante, M.; Svicher, V.; Taliani, G.; Teti, E.; Tisone, G.; Vespasiani-Gentilucci, U.; Vullo, V.; Mangia, A.; Babudieri, S.; Maida, I.; Melis, M.; Mura, M. S.; Falconi, L.; Di Giammartino, D.; Tarquini, P.;
• Is Part Of: Journal of antimicrobial chemotherapy. Volume 71:Number 3(2016:Mar.)
• Page Start: 739
• Page End: 750
• Publication Date: 2015-12-17
• Subjects: Anti-infective agents -- Periodicals; Chemotherapy -- Periodicals; 615.58
• DOI: 10.1093/jac/dkv403
• Languages: English
• ISSNs: 0305-7453

Abstract

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.