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 journalArticle

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

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Hepacivirus
Genotype
RNA
Mutation
Peptide Hydrolases

ASJC Scopus subject areas

  • Pharmacology
  • Pharmacology (medical)
  • Infectious Diseases

Cite this

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

In: Journal of Antimicrobial Chemotherapy, Vol. 71, No. 3, dkv403, 01.03.2016, p. 739-750.

Research output: Contribution to journalArticle

Di Maio, VC, Cento, V, Di Paolo, D, Aragri, M, De Leonardis, F, Tontodonati, M, Micheli, V, Bellocchi, MC, Antonucci, FP, 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, Marenco, S, Nosotti, L, Giannelli, V, Siciliano, M, Romagnoli, D, Pellicelli, AM, Vecchiet, J, Magni, C, Babudieri, S, Mura, MS, 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, CF, 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, LA, Picciotto, A, Viscoli, C, Casinelli, K, Delle Monache, M, Lichtner, M, Mastroianni, C, Aghemo, AM, Bruno, S, Cerrone, M, Colombo, M, D'Arminio Monforte, A, Danieli, E, Donato, F, Gubertini, G, Landonio, S, Magni, CF, Mancon, A, Micheli, V, Monico, S, Niero, F, Puoti, M, Rizzardini, G, Russo, ML, Alfieri, R, Gnocchi, M, Orro, A, Milanesi, L, Baldelli, E, Bertolotti, M, Borghi, V, Mussini, C, Romagnoli, D, Brancaccio, G, Caporaso, N, Gaeta, GB, Lembo, V, Morisco, F, Calvaruso, V, Craxi, 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, FP, 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, VC, 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, CF, Romano, M, Santopaolo, F, Santoro, MM, Sarmati, L, Sarrecchia, C, Sforza, D, Siciliano, M, Sorbo, MC, Spaziante, M, Svicher, V, Taliani, G, Teti, E, Tisone, G, Vespasiani-Gentilucci, U, Vullo, V, Mangia, A, Babudieri, S, Maida, I, Melis, M, Mura, MS, Falconi, L, Di Giammartino, D & Tarquini, P 2016, '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', Journal of Antimicrobial Chemotherapy, vol. 71, no. 3, dkv403, pp. 739-750. https://doi.org/10.1093/jac/dkv403
Di Maio, V. C. ; Cento, V. ; Di Paolo, Daniele ; Aragri, Marianna ; De Leonardis, F. ; Tontodonati, Monica ; Micheli, Valeria ; Bellocchi, Maria Concetta ; Antonucci, F. P. ; Bertoli, A. ; Lenci, Ilaria ; Milana, M. ; Gianserra, Laura ; Melis, M. ; Di Biagio, Antonio ; Sarrecchia, Cesare ; Sarmati, L. ; Landonio, Simona ; Francioso, Simona ; Lambiase, L. ; Nicolini, Laura ; Marenco, Simona ; Nosotti, Lorenzo ; Giannelli, V. ; Siciliano, M. ; Romagnoli, Dante ; Pellicelli, Adriano M. ; Vecchiet, J. ; Magni, Carlo ; Babudieri, Sergio ; Mura, M. S. ; Taliani, G. ; Mastroianni, C. ; Vespasiani Gentilucci, U. ; Romano, Mario ; Morisco, Filomena ; Gasbarrini, Adriano ; Vullo, Vincenzo ; Bruno, Savino ; Baiguera, C. ; Pasquazzi, C. ; Tisone, G. ; Picciotto, A. ; Andreoni, M. ; Parruti, G. ; Rizzardini, Giuliano ; Angelico, M. ; Perno, Carlo Federico ; Ceccherini-Silberstein, Francesca ; Mariani, R. ; Paoloni, Maurizio ; Iapadre, N. ; Grimaldi, A. ; Menzaghi, Barbara ; Quirino, Tiziana ; Vecchiet, Jacopo ; Bruzzone, B. ; De Maria, Andrea ; Di Biagio, A. ; Marenco, S. ; Nicolini, L. A. ; Picciotto, A. ; Viscoli, Claudio ; Casinelli, Katia ; Delle Monache, Marco ; Lichtner, Miriam ; Mastroianni, C. ; Aghemo, Alessio Michele ; Bruno, S. ; Cerrone, M. ; Colombo, Massimo ; D'Arminio Monforte, A. ; Danieli, E. ; Donato, F. ; Gubertini, G. ; Landonio, S. ; Magni, C. F. ; Mancon, Alessandro ; Micheli, V. ; Monico, S. ; Niero, F. ; Puoti, M. ; Rizzardini, G. ; Russo, M. L. ; Alfieri, R. ; Gnocchi, M. ; Orro, A. ; Milanesi, L. ; Baldelli, Enrica ; Bertolotti, M. ; Borghi, V. ; Mussini, C. ; Romagnoli, D. ; Brancaccio, Giuseppina ; Caporaso, N. ; Gaeta, G. B. ; Lembo, V. ; Morisco, F. ; Calvaruso, Vicenza ; Craxi, Antonio ; Di Marco, Viro ; Mazzola, A. ; Petta, S. ; D'amico, Emilio ; Cacciatore, Pierluigi ; Consorte, A. ; Pace Palitti, V. ; Parruti, G. ; Pieri, Alessandro ; Polilli, Ennio ; Tontodonati, M. ; Andreoni, M. ; Angelico, Mario ; Antenucci, F. ; Antonucci, Francesco Paolo ; Aragri, M. ; Armenia, Daniele ; Baiocchi, Leonardo ; Bellocchi, M. ; Bertoli, Ada ; Biliotti, E. ; Biolato, Marco ; Carioti, Luca ; Ceccherini-Silberstein, F. ; Cento, V. ; Cerasari, G. ; Cerva, C. ; Ciotti, M. ; D'Ambrosio, C. ; D'Ettorre, Gabriella ; De Leonardis, F. ; De Sanctis, A. ; Di Maio, Velia Chiara ; 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, Marco ; Miglioresi, Lucia ; Milana, M. ; Nosotti, L. ; Palazzo, D. ; Pasquazzi, C. ; Pellicelli, A. ; Perno, Carlo Federico ; Romano, M. ; Santopaolo, Francesco ; Santoro, Maria Mercedes ; Sarmati, L. ; Sarrecchia, C. ; Sforza, D. ; Siciliano, M. ; Sorbo, M. C. ; Spaziante, M. ; Svicher, Valentina ; Taliani, G. ; Teti, E. ; Tisone, G. ; Vespasiani-Gentilucci, U. ; Vullo, V. ; Mangia, Alessandra ; Babudieri, S. ; Maida, I. ; Melis, M. ; Mura, M. S. ; Falconi, L. ; Di Giammartino, D. ; Tarquini, Pierluigi. / 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. In: Journal of Antimicrobial Chemotherapy. 2016 ; Vol. 71, No. 3. pp. 739-750.
@article{fafcb2dbc7f3461981efe10f3ebc2607,
title = "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",
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.",
author = "{Di Maio}, {V. C.} and V. Cento and {Di Paolo}, Daniele and Marianna Aragri and {De Leonardis}, F. and Monica Tontodonati and Valeria Micheli and Bellocchi, {Maria Concetta} and Antonucci, {F. P.} and A. Bertoli and Ilaria Lenci and M. Milana and Laura Gianserra and M. Melis and {Di Biagio}, Antonio and Cesare Sarrecchia and L. Sarmati and Simona Landonio and Simona Francioso and L. Lambiase and Laura Nicolini and Simona Marenco and Lorenzo Nosotti and V. Giannelli and M. Siciliano and Dante Romagnoli and Pellicelli, {Adriano M.} and J. Vecchiet and Carlo Magni and Sergio Babudieri and Mura, {M. S.} and G. Taliani and C. Mastroianni and {Vespasiani Gentilucci}, U. and Mario Romano and Filomena Morisco and Adriano Gasbarrini and Vincenzo Vullo and Savino Bruno and C. Baiguera and C. Pasquazzi and G. Tisone and A. Picciotto and M. Andreoni and G. Parruti and Giuliano Rizzardini and M. Angelico and Perno, {Carlo Federico} and Francesca Ceccherini-Silberstein and R. Mariani and Maurizio Paoloni and N. Iapadre and A. Grimaldi and Barbara Menzaghi and Tiziana Quirino and Jacopo Vecchiet and B. Bruzzone and {De Maria}, Andrea and {Di Biagio}, A. and S. Marenco and Nicolini, {L. A.} and A. Picciotto and Claudio Viscoli and Katia Casinelli and {Delle Monache}, Marco and Miriam Lichtner and C. Mastroianni and Aghemo, {Alessio Michele} and S. Bruno and M. Cerrone and Massimo Colombo and {D'Arminio Monforte}, A. and E. Danieli and F. Donato and G. Gubertini and S. Landonio and Magni, {C. F.} and Alessandro Mancon and V. Micheli and S. Monico and F. Niero and M. Puoti and G. Rizzardini and Russo, {M. L.} and R. Alfieri and M. Gnocchi and A. Orro and L. Milanesi and Enrica Baldelli and M. Bertolotti and V. Borghi and C. Mussini and D. Romagnoli and Giuseppina Brancaccio and N. Caporaso and Gaeta, {G. B.} and V. Lembo and F. Morisco and Vicenza Calvaruso and Antonio Craxi and {Di Marco}, Viro and A. Mazzola and S. Petta and Emilio D'amico and Pierluigi Cacciatore and A. Consorte and {Pace Palitti}, V. and G. Parruti and Alessandro Pieri and Ennio Polilli and M. Tontodonati and M. Andreoni and Mario Angelico and F. Antenucci and Antonucci, {Francesco Paolo} and M. Aragri and Daniele Armenia and Leonardo Baiocchi and M. Bellocchi and Ada Bertoli and E. Biliotti and Marco Biolato and Luca Carioti and F. Ceccherini-Silberstein and V. Cento and G. Cerasari and C. Cerva and M. Ciotti and C. D'Ambrosio and Gabriella D'Ettorre and {De Leonardis}, F. and {De Sanctis}, A. and {Di Maio}, {Velia Chiara} and {Di Paolo}, D. and S. Francioso and C. Furlan and P. Gallo and A. Gasbarrini and V. Giannelli and L. Gianserra and A. Grieco and S. Grieco and L. Lambiase and B. Lattanzi and I. Lenci and V. Malagnino and M. Manuelli and Marco Merli and Lucia Miglioresi and M. Milana and L. Nosotti and D. Palazzo and C. Pasquazzi and A. Pellicelli and Perno, {Carlo Federico} and M. Romano and Francesco Santopaolo and Santoro, {Maria Mercedes} and L. Sarmati and C. Sarrecchia and D. Sforza and M. Siciliano and Sorbo, {M. C.} and M. Spaziante and Valentina Svicher and G. Taliani and E. Teti and G. Tisone and U. Vespasiani-Gentilucci and V. Vullo and Alessandra Mangia and S. Babudieri and I. Maida and M. Melis and Mura, {M. S.} and L. Falconi and {Di Giammartino}, D. and Pierluigi Tarquini",
year = "2016",
month = "3",
day = "1",
doi = "10.1093/jac/dkv403",
language = "English",
volume = "71",
pages = "739--750",
journal = "Journal of Antimicrobial Chemotherapy",
issn = "0305-7453",
publisher = "Oxford University Press",
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}

TY - JOUR

T1 - 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

AU - Di Maio, V. C.

AU - Cento, V.

AU - Di Paolo, Daniele

AU - Aragri, Marianna

AU - De Leonardis, F.

AU - Tontodonati, Monica

AU - Micheli, Valeria

AU - Bellocchi, Maria Concetta

AU - Antonucci, F. P.

AU - Bertoli, A.

AU - Lenci, Ilaria

AU - Milana, M.

AU - Gianserra, Laura

AU - Melis, M.

AU - Di Biagio, Antonio

AU - Sarrecchia, Cesare

AU - Sarmati, L.

AU - Landonio, Simona

AU - Francioso, Simona

AU - Lambiase, L.

AU - Nicolini, Laura

AU - Marenco, Simona

AU - Nosotti, Lorenzo

AU - Giannelli, V.

AU - Siciliano, M.

AU - Romagnoli, Dante

AU - Pellicelli, Adriano M.

AU - Vecchiet, J.

AU - Magni, Carlo

AU - Babudieri, Sergio

AU - Mura, M. S.

AU - Taliani, G.

AU - Mastroianni, C.

AU - Vespasiani Gentilucci, U.

AU - Romano, Mario

AU - Morisco, Filomena

AU - Gasbarrini, Adriano

AU - Vullo, Vincenzo

AU - Bruno, Savino

AU - Baiguera, C.

AU - Pasquazzi, C.

AU - Tisone, G.

AU - Picciotto, A.

AU - Andreoni, M.

AU - Parruti, G.

AU - Rizzardini, Giuliano

AU - Angelico, M.

AU - Perno, Carlo Federico

AU - Ceccherini-Silberstein, Francesca

AU - Mariani, R.

AU - Paoloni, Maurizio

AU - Iapadre, N.

AU - Grimaldi, A.

AU - Menzaghi, Barbara

AU - Quirino, Tiziana

AU - Vecchiet, Jacopo

AU - Bruzzone, B.

AU - De Maria, Andrea

AU - Di Biagio, A.

AU - Marenco, S.

AU - Nicolini, L. A.

AU - Picciotto, A.

AU - Viscoli, Claudio

AU - Casinelli, Katia

AU - Delle Monache, Marco

AU - Lichtner, Miriam

AU - Mastroianni, C.

AU - Aghemo, Alessio Michele

AU - Bruno, S.

AU - Cerrone, M.

AU - Colombo, Massimo

AU - D'Arminio Monforte, A.

AU - Danieli, E.

AU - Donato, F.

AU - Gubertini, G.

AU - Landonio, S.

AU - Magni, C. F.

AU - Mancon, Alessandro

AU - Micheli, V.

AU - Monico, S.

AU - Niero, F.

AU - Puoti, M.

AU - Rizzardini, G.

AU - Russo, M. L.

AU - Alfieri, R.

AU - Gnocchi, M.

AU - Orro, A.

AU - Milanesi, L.

AU - Baldelli, Enrica

AU - Bertolotti, M.

AU - Borghi, V.

AU - Mussini, C.

AU - Romagnoli, D.

AU - Brancaccio, Giuseppina

AU - Caporaso, N.

AU - Gaeta, G. B.

AU - Lembo, V.

AU - Morisco, F.

AU - Calvaruso, Vicenza

AU - Craxi, Antonio

AU - Di Marco, Viro

AU - Mazzola, A.

AU - Petta, S.

AU - D'amico, Emilio

AU - Cacciatore, Pierluigi

AU - Consorte, A.

AU - Pace Palitti, V.

AU - Parruti, G.

AU - Pieri, Alessandro

AU - Polilli, Ennio

AU - Tontodonati, M.

AU - Andreoni, M.

AU - Angelico, Mario

AU - Antenucci, F.

AU - Antonucci, Francesco Paolo

AU - Aragri, M.

AU - Armenia, Daniele

AU - Baiocchi, Leonardo

AU - Bellocchi, M.

AU - Bertoli, Ada

AU - Biliotti, E.

AU - Biolato, Marco

AU - Carioti, Luca

AU - Ceccherini-Silberstein, F.

AU - Cento, V.

AU - Cerasari, G.

AU - Cerva, C.

AU - Ciotti, M.

AU - D'Ambrosio, C.

AU - D'Ettorre, Gabriella

AU - De Leonardis, F.

AU - De Sanctis, A.

AU - Di Maio, Velia Chiara

AU - Di Paolo, D.

AU - Francioso, S.

AU - Furlan, C.

AU - Gallo, P.

AU - Gasbarrini, A.

AU - Giannelli, V.

AU - Gianserra, L.

AU - Grieco, A.

AU - Grieco, S.

AU - Lambiase, L.

AU - Lattanzi, B.

AU - Lenci, I.

AU - Malagnino, V.

AU - Manuelli, M.

AU - Merli, Marco

AU - Miglioresi, Lucia

AU - Milana, M.

AU - Nosotti, L.

AU - Palazzo, D.

AU - Pasquazzi, C.

AU - Pellicelli, A.

AU - Perno, Carlo Federico

AU - Romano, M.

AU - Santopaolo, Francesco

AU - Santoro, Maria Mercedes

AU - Sarmati, L.

AU - Sarrecchia, C.

AU - Sforza, D.

AU - Siciliano, M.

AU - Sorbo, M. C.

AU - Spaziante, M.

AU - Svicher, Valentina

AU - Taliani, G.

AU - Teti, E.

AU - Tisone, G.

AU - Vespasiani-Gentilucci, U.

AU - Vullo, V.

AU - Mangia, Alessandra

AU - Babudieri, S.

AU - Maida, I.

AU - Melis, M.

AU - Mura, M. S.

AU - Falconi, L.

AU - Di Giammartino, D.

AU - Tarquini, Pierluigi

PY - 2016/3/1

Y1 - 2016/3/1

N2 - 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.

AB - 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.

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U2 - 10.1093/jac/dkv403

DO - 10.1093/jac/dkv403

M3 - Article

VL - 71

SP - 739

EP - 750

JO - Journal of Antimicrobial Chemotherapy

JF - Journal of Antimicrobial Chemotherapy

SN - 0305-7453

IS - 3

M1 - dkv403

ER -