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1. 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

Author

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, Collaborators (129) Mariani R, HCV Italian Resistance Network Study Group., Paoloni, M, Iapadre, N, Grimaldi, A, Menzaghi, B, Quirino, T, Bruzzone, B, De Maria, A, Nicolini, La, Viscoli, C, Casinelli, K, Monache, Md, Lichtner, M, Aghemo, A, Cerrone, M, Colombo, M, Monforte, Ad, Danieli, E, Donato, F, Gubertini, G, Magni, Cf, Mancon, A, Monico, S, Niero, F, Puoti, M, Russo, Ml, Alfieri, R, Gnocchi, M, Orro, A, Milanesi, L, Baldelli, E, Bertolotti, M, Borghi, V, Mussini, C, Brancaccio, G, Caporaso, N, Gaeta, Gb, Lembo, V, Calvaruso, V, Craxì, A, Di Marco, V, Mazzola, A, Petta, S, D'Amico, E, Cacciatore, P, Consorte, A, Palitti, Vp, Pieri, A, Polilli, E, Antenucci, F, Antonucci, Fp, Armenia, D, Baiocchi, L, Bellocchi, M, Biliotti, E, Biolato, M, Carioti, L, Cerasari, G, Cerva, C, Ciotti, M, D'Ambrosio, C, D'Ettorre, G, De Sanctis, A, Di Maio VC, Furlan, C, Gallo, P, Grieco, A, Grieco, S, Lattanzi, B, Malagnino, V, Manuelli, M, Merli, M, Miglioresi, L, Palazzo, D, Perno, Cf, Santopaolo, F, Santoro, Mm, Sforza, D, Sorbo, Mc, Spaziante, M, Svicher, V, Teti, E, Mangia, A, Maida, I, Mura, Ms, Falconi, L, Di Giammartino, D, Tarquini, P., 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, HCV Italian Resistance Network Study Group., Collaborators (129) Mariani R, Paoloni, M, Iapadre, N, Grimaldi, A, Menzaghi, B, Quirino, T, Bruzzone, B, De Maria, A, Nicolini, La, Viscoli, C, Casinelli, K, Monache, Md, Lichtner, M, Aghemo, A, Cerrone, M, Colombo, M, Monforte, Ad, Danieli, E, Donato, F, Gubertini, G, Magni, Cf, Mancon, A, Monico, S, Niero, F, Puoti, M, Russo, Ml, Alfieri, R, Gnocchi, M, Orro, A, Milanesi, L, Baldelli, E, Bertolotti, M, Borghi, V, Mussini, C, Brancaccio, G, Caporaso, N, Gaeta, Gb, Lembo, V, Calvaruso, V, Craxì, A, Di Marco, V, Mazzola, A, Petta, S, D'Amico, E, Cacciatore, P, Consorte, A, Palitti, Vp, Pieri, A, Polilli, E, Antenucci, F, Antonucci, Fp, Armenia, D, Baiocchi, L, Bellocchi, M, Biliotti, E, Biolato, M, Carioti, L, Cerasari, G, Cerva, C, Ciotti, M, D'Ambrosio, C, D'Ettorre, G, De Sanctis, A, Di Maio, Vc, Furlan, C, Gallo, P, Grieco, A, Grieco, S, Lattanzi, B, Malagnino, V, Manuelli, M, Merli, M, Miglioresi, L, Palazzo, D, Perno, Cf, Santopaolo, F, Santoro, Mm, Sforza, D, Sorbo, Mc, Spaziante, M, Svicher, V, Teti, E, Mangia, A, Maida, I, Mura, M, Falconi, L, Di Giammartino, D, Tarquini, P., Di Maio, V. C, Bellocchi, M. C, Antonucci, F. P, Nicolini, L. A, Magni, C. F, Mura, M. S, Vespasiani Gentilucci, U, Morisco, Filomena, Perno, C. F, Ceccherini Silberstein, F., Caporaso, Nicola, Di Maio, V., Cento, V., Di Paolo, D., Aragri, M., De Leonardis, F., Tontodonati, M., Micheli, V., Bellocchi, M., Antonucci, F., 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, A., Vecchiet, J., Magni, C., Babudieri, S., Mura, M., 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., Ceccherini-Silberstein, F., Mariani, R., Paoloni, M., Iapadre, N., Grimaldi, A., Menzaghi, B., Quirino, T., Bruzzone, B., De Maria, A., Viscoli, C., Casinelli, K., Delle Monache, M., Lichtner, M., Aghemo, A., Cerrone, M., Colombo, M., D'Arminio Monforte, A., Danieli, E., Donato, F., Gubertini, G., Mancon, A., Monico, S., Niero, F., Puoti, M., Russo, M., Alfieri, R., Gnocchi, M., Orro, A., Milanesi, L., Baldelli, E., Bertolotti, M., Borghi, V., Mussini, C., Brancaccio, G., Caporaso, N., Gaeta, G., Lembo, V., Calvaruso, V., Craxã­, A., DI MARCO, V., Mazzola, A., Petta, S., D'Amico, E., Cacciatore, P., Consorte, A., Pace Palitti, V., Pieri, A., Polilli, E., Antenucci, F., Armenia, D., Baiocchi, L., Biliotti, E., Biolato, M., Carioti, L., Cerasari, G., Cerva, C., Ciotti, M., D'Ambrosio, C., D'Ettorre, G., De Sanctis, A., Furlan, C., Gallo, P., Grieco, A., Grieco, S., Lattanzi, B., Malagnino, V., Manuelli, M., Merli, M., Miglioresi, L., Palazzo, D., Santopaolo, F., Santoro, M., Sforza, D., Sorbo, M., Spaziante, M., Svicher, V., Teti, E., Mangia, A., Maida, I., Falconi, L., and Di Giammartino, D.

Subjects
0301 basic medicine, ns3, Genotyping Techniques, viruses, Drug Resistance, Hepacivirus, Viral Nonstructural Proteins, medicine.disease_cause, Gastroenterology, Telaprevir, chemistry.chemical_compound, genotype, genotyping techniques, hepacivirus, hepatitis C, humans, RNA viral, retrospective studies, sequence analysis, DNA, viral nonstructural proteins, drug resistance, viral, mutation, pharmacology, infectious diseases, 0302 clinical medicine, Retrospective Studie, Genotype, Pharmacology (medical), Viral, Hepatitis C, Humans, RNA, Viral, Retrospective Studies, Sequence Analysis, DNA, Drug Resistance, Viral, Mutation, Proteolytic enzymes, virus diseases, Settore MED/07 - Microbiologia e Microbiologia Clinica, hcv-rna levels, Infectious Diseases, HCV-RNA, 030211 gastroenterology & hepatology, Sequence Analysis, medicine.drug, Human, Microbiology (medical), medicine.medical_specialty, Hepatitis C virus, Concordance, Settore MED/12 - GASTROENTEROLOGIA, Pharmacology, Biology, 03 medical and health sciences, Boceprevir, Internal medicine, medicine, hcv, Genotyping, Hepaciviru, Viral Nonstructural Protein, Settore MED/09 - MEDICINA INTERNA, Virology, digestive system diseases, 030104 developmental biology, chemistry, Sequence Analysi, RNA, Genotyping Technique
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.

Published
2016
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2. 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

Author

Di Maio, V, Cento, V, Di Paolo, D, Aragri, M, De Leonardis, F, Tontodonati, M, Micheli, V, Bellocchi, M, Antonucci, F, 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, A, Vecchiet, J, Magni, C, Babudieri, S, Mura, M, 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, Ceccherini-Silberstein, F, Mariani, R, Paoloni, M, Iapadre, N, Grimaldi, A, Menzaghi, B, Quirino, T, Bruzzone, B, De Maria, A, Viscoli, C, Casinelli, K, Delle Monache, M, Lichtner, M, Aghemo, A, Cerrone, M, Colombo, M, D'Arminio Monforte, A, Danieli, E, Donato, F, Gubertini, G, Mancon, A, Monico, S, Niero, F, Puoti, M, Russo, M, Alfieri, R, Gnocchi, M, Orro, A, Milanesi, L, Baldelli, E, Bertolotti, M, Borghi, V, Mussini, C, Brancaccio, G, Caporaso, N, Gaeta, G, Lembo, V, Calvaruso, V, Craxi, A, Di Marco, V, Mazzola, A, Petta, S, D'Amico, E, Cacciatore, P, Consorte, A, Pace Palitti, V, Pieri, A, Polilli, E, Antenucci, F, Armenia, D, Baiocchi, L, Biliotti, E, Biolato, M, Carioti, L, Cerasari, G, Cerva, C, Ciotti, M, D'Ambrosio, C, D'Ettorre, G, De Sanctis, A, Furlan, C, Gallo, P, Grieco, A, Grieco, S, Lattanzi, B, Malagnino, V, Manuelli, M, Merli, M, Miglioresi, L, Palazzo, D, Santopaolo, F, Santoro, M, Sforza, D, Sorbo, M, Spaziante, M, Svicher, V, Teti, E, Mangia, A, Maida, I, Falconi, L, Di Giammartino, D, Tarquini, P, 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., Bruzzone B., De Maria A., Viscoli C., Casinelli K., Delle Monache M., Lichtner M., Aghemo A., Cerrone M., Colombo M., D'Arminio Monforte A., Danieli E., Donato F., Gubertini G., Mancon A., Monico S., Niero F., Puoti M., Russo M. L., Alfieri R., Gnocchi M., Orro A., Milanesi L., Baldelli E., Bertolotti M., Borghi V., Mussini C., Brancaccio G., Caporaso N., Gaeta G. B., Lembo V., Calvaruso V., Craxi A., Di Marco V., Mazzola A., Petta S., D'Amico E., Cacciatore P., Consorte A., Pace Palitti V., Pieri A., Polilli E., Antenucci F., Armenia D., Baiocchi L., Biliotti E., Biolato M., Carioti L., Cerasari G., Cerva C., Ciotti M., D'Ambrosio C., D'Ettorre G., De Sanctis A., Furlan C., Gallo P., Grieco A., Grieco S., Lattanzi B., Malagnino V., Manuelli M., Merli M., Miglioresi L., Palazzo D., Santopaolo F., Santoro M. M., Sforza D., Sorbo M. C., Spaziante M., Svicher V., Teti E., Mangia A., Maida I., Falconi L., Di Giammartino D., Tarquini P., Di Maio, V, Cento, V, Di Paolo, D, Aragri, M, De Leonardis, F, Tontodonati, M, Micheli, V, Bellocchi, M, Antonucci, F, 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, A, Vecchiet, J, Magni, C, Babudieri, S, Mura, M, 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, Ceccherini-Silberstein, F, Mariani, R, Paoloni, M, Iapadre, N, Grimaldi, A, Menzaghi, B, Quirino, T, Bruzzone, B, De Maria, A, Viscoli, C, Casinelli, K, Delle Monache, M, Lichtner, M, Aghemo, A, Cerrone, M, Colombo, M, D'Arminio Monforte, A, Danieli, E, Donato, F, Gubertini, G, Mancon, A, Monico, S, Niero, F, Puoti, M, Russo, M, Alfieri, R, Gnocchi, M, Orro, A, Milanesi, L, Baldelli, E, Bertolotti, M, Borghi, V, Mussini, C, Brancaccio, G, Caporaso, N, Gaeta, G, Lembo, V, Calvaruso, V, Craxi, A, Di Marco, V, Mazzola, A, Petta, S, D'Amico, E, Cacciatore, P, Consorte, A, Pace Palitti, V, Pieri, A, Polilli, E, Antenucci, F, Armenia, D, Baiocchi, L, Biliotti, E, Biolato, M, Carioti, L, Cerasari, G, Cerva, C, Ciotti, M, D'Ambrosio, C, D'Ettorre, G, De Sanctis, A, Furlan, C, Gallo, P, Grieco, A, Grieco, S, Lattanzi, B, Malagnino, V, Manuelli, M, Merli, M, Miglioresi, L, Palazzo, D, Santopaolo, F, Santoro, M, Sforza, D, Sorbo, M, Spaziante, M, Svicher, V, Teti, E, Mangia, A, Maida, I, Falconi, L, Di Giammartino, D, Tarquini, P, 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., Bruzzone B., De Maria A., Viscoli C., Casinelli K., Delle Monache M., Lichtner M., Aghemo A., Cerrone M., Colombo M., D'Arminio Monforte A., Danieli E., Donato F., Gubertini G., Mancon A., Monico S., Niero F., Puoti M., Russo M. L., Alfieri R., Gnocchi M., Orro A., Milanesi L., Baldelli E., Bertolotti M., Borghi V., Mussini C., Brancaccio G., Caporaso N., Gaeta G. B., Lembo V., Calvaruso V., Craxi A., Di Marco V., Mazzola A., Petta S., D'Amico E., Cacciatore P., Consorte A., Pace Palitti V., Pieri A., Polilli E., Antenucci F., Armenia D., Baiocchi L., Biliotti E., Biolato M., Carioti L., Cerasari G., Cerva C., Ciotti M., D'Ambrosio C., D'Ettorre G., De Sanctis A., Furlan C., Gallo P., Grieco A., Grieco S., Lattanzi B., Malagnino V., Manuelli M., Merli M., Miglioresi L., Palazzo D., Santopaolo F., Santoro M. M., Sforza D., Sorbo M. C., Spaziante M., Svicher V., Teti E., Mangia A., Maida I., Falconi L., Di Giammartino D., and Tarquini P.

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

Published
2016

3. 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

Author

Di Maio, V. C., Centomini, Vanna, Di Paolo, D., Aragri, M., De Leonardis, F., Tontodonati, M., Micheli, V., Bellocchi, M. C., Antonucci, F. P., Bertoli, Alessia, Lenci, I., Milana, M., Gianserra, L., Milan, Melissa, Di Biagio, Anna, Sarrecchia, C., Sarmati, L., Landonio, S., Francioso, S., Lambiase, L., Nicolini, L. A., Marenco, S., Nosotti, L., Giannelli, V., Siciliano, Massimo, 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, Antonio, 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., Bruzzone, B., De Maria, A., Viscoli, C., Casinelli, K., Delle Monache, M., Lichtner, M., Aghemo, A., Cerrone, M., Colombo, M., D'Arminio Monforte, A., Danieli, E., Donato, Federica, Gubertini, G., Mancon, A., Monico, S., Niero, F., Puoti, M., Russo, M. L., Alfieri, R., Gnocchi, M., Orro, A., Milanesi, L., Baldelli, E., Bertolotti, M., Borghi, V., Mussini, C., Brancaccio, G., Caporaso, N., Gaeta, G. B., Lembo, V., Calvaruso, V., Craxí, A., Di Marco, V., Mazzola, A., Petta, S., D'Amico, E., Cacciatore, Pasquale, Consorte, A., Pace Palitti, V., Pieri, A., Polilli, E., Antenucci, F., Armenia, D., Baiocchi, L., Bellocchi, M., Biliotti, E., Biolato, Marco, Carioti, L., Cerasari, G., Cerva, C., Ciotti, M., D'Ambrosio, C., D'Ettorre, G., De Sanctis, A., Furlan, C., Gallo, P., Grieco, Antonio, Grieco, S., Lattanzi, B., Malagnino, V., Manuelli, M., Merli, M., Miglioresi, L., Palazzo, D., Santopaolo, F., Santoro, M. M., Sforza, D., Siciliano, M., Sorbo, M. C., Spaziante, M., Svicher, V., Teti, E., Mangia, A., Maida, I., Falconi, L., Di Giammartino, D., Tarquini, P., Cento, V., Bertoli, A., Melis, M., Di Biagio, A., Gasbarrini, A. (ORCID:0000-0002-7278-4823), Donato, F., Cacciatore, P., Biolato, M., Grieco, A. (ORCID:0000-0002-0544-8993), Di Maio, V. C., Centomini, Vanna, Di Paolo, D., Aragri, M., De Leonardis, F., Tontodonati, M., Micheli, V., Bellocchi, M. C., Antonucci, F. P., Bertoli, Alessia, Lenci, I., Milana, M., Gianserra, L., Milan, Melissa, Di Biagio, Anna, Sarrecchia, C., Sarmati, L., Landonio, S., Francioso, S., Lambiase, L., Nicolini, L. A., Marenco, S., Nosotti, L., Giannelli, V., Siciliano, Massimo, 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, Antonio, 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., Bruzzone, B., De Maria, A., Viscoli, C., Casinelli, K., Delle Monache, M., Lichtner, M., Aghemo, A., Cerrone, M., Colombo, M., D'Arminio Monforte, A., Danieli, E., Donato, Federica, Gubertini, G., Mancon, A., Monico, S., Niero, F., Puoti, M., Russo, M. L., Alfieri, R., Gnocchi, M., Orro, A., Milanesi, L., Baldelli, E., Bertolotti, M., Borghi, V., Mussini, C., Brancaccio, G., Caporaso, N., Gaeta, G. B., Lembo, V., Calvaruso, V., Craxí, A., Di Marco, V., Mazzola, A., Petta, S., D'Amico, E., Cacciatore, Pasquale, Consorte, A., Pace Palitti, V., Pieri, A., Polilli, E., Antenucci, F., Armenia, D., Baiocchi, L., Bellocchi, M., Biliotti, E., Biolato, Marco, Carioti, L., Cerasari, G., Cerva, C., Ciotti, M., D'Ambrosio, C., D'Ettorre, G., De Sanctis, A., Furlan, C., Gallo, P., Grieco, Antonio, Grieco, S., Lattanzi, B., Malagnino, V., Manuelli, M., Merli, M., Miglioresi, L., Palazzo, D., Santopaolo, F., Santoro, M. M., Sforza, D., Siciliano, M., Sorbo, M. C., Spaziante, M., Svicher, V., Teti, E., Mangia, A., Maida, I., Falconi, L., Di Giammartino, D., Tarquini, P., Cento, V., Bertoli, A., Melis, M., Di Biagio, A., Gasbarrini, A. (ORCID:0000-0002-7278-4823), Donato, F., Cacciatore, P., Biolato, M., and Grieco, A. (ORCID:0000-0002-0544-8993)

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

Published
2016

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