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

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, Gloria; Mastroianni, Claudio Maria; Vespasiani Gentilucci, U.; Romano, M.; Morisco, F.; Gasbarrini, A.; Vullo, Vincenzo; Bruno, S.; Baiguera, C.; Pasquazzi, Caterina; 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.; Picciotto, A.; Viscoli, C.; Casinelli, K.; Delle Monache, M.; Lichtner, Miriam; Mastroianni, Claudio Maria; Aghemo, A.; Bruno, S.; Cerrone, M.; Colombo, M.; D'Arminio Monforte, A.; 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.; Craxí, A.; Di Marco, V.; Mazzola, A.; Petta, S.; D'Amico, E.; Cacciatore, P.; Consorte, A.; Pace Palitti, V.; 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, Elisa; 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, Caterina; Gallo, P.; Gasbarrini, A.; Giannelli, V.; Gianserra, L.; Grieco, A.; Grieco, S.; Lambiase, L.; Lattanzi, B.; Lenci, I.; Malagnino, V.; Manuelli, M.; Merli, Manuela; Miglioresi, L.; Milana, M.; Nosotti, L.; Palazzo, D.; Pasquazzi, Caterina; 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, Gloria; Teti, E.; Tisone, G.; Vullo, Vincenzo; Mangia, A.; Babudieri, S.; Maida, I.; Melis, M.; Mura, M. S.; Falconi, L.; Di Giammartino, D.; Tarquini, P.

doi:10.1093/jac/dkv403

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.

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 / 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., et al.. - In: JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY. - ISSN 0305-7453. - STAMPA. - 71:3(2016), pp. 739-750. [10.1093/jac/dkv403]