Performance of genotypic tropism testing in clinical practice using the enhanced sensitivity version of Trofile as reference assay: Results from the OSCAR Study Group

Valentina Svicher, Roberta D'Arrigo, Claudia Alteri, Massimo Andreoni, Gioacchino Angarano, Andrea Antinori, Guido Antonelli, Patrizia Bagnarelli, Fausto Baldanti, Ada Bertoli, Marco Borderi, Enzo Boeri, Isabella Bonn, Bianca Bruzzone, Anna Paola Callegaro, Roberta Cammarota, Filippo Canducci, Francesca Ceccherini-Silberstein, Massimo Clementi, Antonella D Arminio MonforteAndrea De Luca, Antonio Di Biagio, Simona Di Gianbenedetto, Giovanni Di Peni, Massimo Di Pietro, Lavinia Fabeni, Giovanni Fadda, Massimo Galli, William Gennari, Valeria Ghisetti, Andrea Giacometti, Andrea Gori, Francesco Leoncini, Franco Maggiolo, Renato Maserati, Francesco Mazzotta, Valeria Micheli, Genny Meini, Laura Monno, Cristina Mussini, Silvia Nozza, Stefania Paolucci, Saverio Parisi, Monica Pecorari, Daniele Pizzi, Tiziana Quirino, Maria Carla Re, Giuliano Rizzardini, Rosaria Santangelo, Alessandro Soria, Francesca Stazi, Gaetana Sterrantino, Ombretta Turriziani, Claudio Viscoli, Vincenzo Vullo, Adriano Lazzarin, Cario Federico Perno

Research output: Contribution to journalArticle

Abstract

Objective: The goal of the OSCAR programme is to evaluate the performances of genotypic HIV-1 tropism testing in clinical practice using the enhanced sensitivity version of Trafile (ESTA) as reference-assay. Methods: HIV-1 coreceptor-usage was assessed using plasma samples from 406 HIV-1 infected patients by ESTA and by gp120 V3 population-sequencing followed by Geno2pheno (set at a False Positive Rate [FPR] of 10% and 5%). Results: ESTA was successful in 365 (89.9%) samples indicating R5 in 254 (69.6%), and DM/X4 in 111 (30.4% of samples (104 [28.5%] DM and 7 [1.9%] X4). Genotypic-testing successfully assessed viral tropism for all 406 samples, including the 41 with undetermined result by ESTA. Genotypic-tropism testing at a FPR of 5% and 10% was 81.1% and 78.4% concordant with ESTA, respectively. Despite a sensitivity of 48.7% and 55.9% at a FPR of 5% and 10%, respectively, a high concordance (specificity: 95.3% for FPR of 5% and 88.2% for FPR of 10%) between genotypic-tropism testing and ESTA was reached in the detection of R5-tropic viruses. Conclusion: Our results are in line with other European studies, and support the routine use of genotypic tropism testing in clinical-settings for monitoring of HIV-1 infected patients candidate to or failing CCR5-antagonists.

Original languageEnglish
Pages (from-to)195-206
Number of pages12
JournalNew Microbiologica
Volume33
Issue number3
Publication statusPublished - Jul 2010

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Tropism
HIV-1
Viral Tropism
Viruses
Population

Keywords

  • Genotypic tropism testing
  • HIV
  • Trafile
  • Tropism
  • V3 loop

ASJC Scopus subject areas

  • Microbiology (medical)
  • Medicine(all)

Cite this

Performance of genotypic tropism testing in clinical practice using the enhanced sensitivity version of Trofile as reference assay : Results from the OSCAR Study Group. / Svicher, Valentina; D'Arrigo, Roberta; Alteri, Claudia; Andreoni, Massimo; Angarano, Gioacchino; Antinori, Andrea; Antonelli, Guido; Bagnarelli, Patrizia; Baldanti, Fausto; Bertoli, Ada; Borderi, Marco; Boeri, Enzo; Bonn, Isabella; Bruzzone, Bianca; Callegaro, Anna Paola; Cammarota, Roberta; Canducci, Filippo; Ceccherini-Silberstein, Francesca; Clementi, Massimo; Monforte, Antonella D Arminio; De Luca, Andrea; Di Biagio, Antonio; Di Gianbenedetto, Simona; Di Peni, Giovanni; Di Pietro, Massimo; Fabeni, Lavinia; Fadda, Giovanni; Galli, Massimo; Gennari, William; Ghisetti, Valeria; Giacometti, Andrea; Gori, Andrea; Leoncini, Francesco; Maggiolo, Franco; Maserati, Renato; Mazzotta, Francesco; Micheli, Valeria; Meini, Genny; Monno, Laura; Mussini, Cristina; Nozza, Silvia; Paolucci, Stefania; Parisi, Saverio; Pecorari, Monica; Pizzi, Daniele; Quirino, Tiziana; Re, Maria Carla; Rizzardini, Giuliano; Santangelo, Rosaria; Soria, Alessandro; Stazi, Francesca; Sterrantino, Gaetana; Turriziani, Ombretta; Viscoli, Claudio; Vullo, Vincenzo; Lazzarin, Adriano; Perno, Cario Federico.

In: New Microbiologica, Vol. 33, No. 3, 07.2010, p. 195-206.

Research output: Contribution to journalArticle

Svicher, V, D'Arrigo, R, Alteri, C, Andreoni, M, Angarano, G, Antinori, A, Antonelli, G, Bagnarelli, P, Baldanti, F, Bertoli, A, Borderi, M, Boeri, E, Bonn, I, Bruzzone, B, Callegaro, AP, Cammarota, R, Canducci, F, Ceccherini-Silberstein, F, Clementi, M, Monforte, ADA, De Luca, A, Di Biagio, A, Di Gianbenedetto, S, Di Peni, G, Di Pietro, M, Fabeni, L, Fadda, G, Galli, M, Gennari, W, Ghisetti, V, Giacometti, A, Gori, A, Leoncini, F, Maggiolo, F, Maserati, R, Mazzotta, F, Micheli, V, Meini, G, Monno, L, Mussini, C, Nozza, S, Paolucci, S, Parisi, S, Pecorari, M, Pizzi, D, Quirino, T, Re, MC, Rizzardini, G, Santangelo, R, Soria, A, Stazi, F, Sterrantino, G, Turriziani, O, Viscoli, C, Vullo, V, Lazzarin, A & Perno, CF 2010, 'Performance of genotypic tropism testing in clinical practice using the enhanced sensitivity version of Trofile as reference assay: Results from the OSCAR Study Group', New Microbiologica, vol. 33, no. 3, pp. 195-206.
Svicher, Valentina ; D'Arrigo, Roberta ; Alteri, Claudia ; Andreoni, Massimo ; Angarano, Gioacchino ; Antinori, Andrea ; Antonelli, Guido ; Bagnarelli, Patrizia ; Baldanti, Fausto ; Bertoli, Ada ; Borderi, Marco ; Boeri, Enzo ; Bonn, Isabella ; Bruzzone, Bianca ; Callegaro, Anna Paola ; Cammarota, Roberta ; Canducci, Filippo ; Ceccherini-Silberstein, Francesca ; Clementi, Massimo ; Monforte, Antonella D Arminio ; De Luca, Andrea ; Di Biagio, Antonio ; Di Gianbenedetto, Simona ; Di Peni, Giovanni ; Di Pietro, Massimo ; Fabeni, Lavinia ; Fadda, Giovanni ; Galli, Massimo ; Gennari, William ; Ghisetti, Valeria ; Giacometti, Andrea ; Gori, Andrea ; Leoncini, Francesco ; Maggiolo, Franco ; Maserati, Renato ; Mazzotta, Francesco ; Micheli, Valeria ; Meini, Genny ; Monno, Laura ; Mussini, Cristina ; Nozza, Silvia ; Paolucci, Stefania ; Parisi, Saverio ; Pecorari, Monica ; Pizzi, Daniele ; Quirino, Tiziana ; Re, Maria Carla ; Rizzardini, Giuliano ; Santangelo, Rosaria ; Soria, Alessandro ; Stazi, Francesca ; Sterrantino, Gaetana ; Turriziani, Ombretta ; Viscoli, Claudio ; Vullo, Vincenzo ; Lazzarin, Adriano ; Perno, Cario Federico. / Performance of genotypic tropism testing in clinical practice using the enhanced sensitivity version of Trofile as reference assay : Results from the OSCAR Study Group. In: New Microbiologica. 2010 ; Vol. 33, No. 3. pp. 195-206.
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abstract = "Objective: The goal of the OSCAR programme is to evaluate the performances of genotypic HIV-1 tropism testing in clinical practice using the enhanced sensitivity version of Trafile (ESTA) as reference-assay. Methods: HIV-1 coreceptor-usage was assessed using plasma samples from 406 HIV-1 infected patients by ESTA and by gp120 V3 population-sequencing followed by Geno2pheno (set at a False Positive Rate [FPR] of 10{\%} and 5{\%}). Results: ESTA was successful in 365 (89.9{\%}) samples indicating R5 in 254 (69.6{\%}), and DM/X4 in 111 (30.4{\%} of samples (104 [28.5{\%}] DM and 7 [1.9{\%}] X4). Genotypic-testing successfully assessed viral tropism for all 406 samples, including the 41 with undetermined result by ESTA. Genotypic-tropism testing at a FPR of 5{\%} and 10{\%} was 81.1{\%} and 78.4{\%} concordant with ESTA, respectively. Despite a sensitivity of 48.7{\%} and 55.9{\%} at a FPR of 5{\%} and 10{\%}, respectively, a high concordance (specificity: 95.3{\%} for FPR of 5{\%} and 88.2{\%} for FPR of 10{\%}) between genotypic-tropism testing and ESTA was reached in the detection of R5-tropic viruses. Conclusion: Our results are in line with other European studies, and support the routine use of genotypic tropism testing in clinical-settings for monitoring of HIV-1 infected patients candidate to or failing CCR5-antagonists.",
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T1 - Performance of genotypic tropism testing in clinical practice using the enhanced sensitivity version of Trofile as reference assay

T2 - Results from the OSCAR Study Group

AU - Svicher, Valentina

AU - D'Arrigo, Roberta

AU - Alteri, Claudia

AU - Andreoni, Massimo

AU - Angarano, Gioacchino

AU - Antinori, Andrea

AU - Antonelli, Guido

AU - Bagnarelli, Patrizia

AU - Baldanti, Fausto

AU - Bertoli, Ada

AU - Borderi, Marco

AU - Boeri, Enzo

AU - Bonn, Isabella

AU - Bruzzone, Bianca

AU - Callegaro, Anna Paola

AU - Cammarota, Roberta

AU - Canducci, Filippo

AU - Ceccherini-Silberstein, Francesca

AU - Clementi, Massimo

AU - Monforte, Antonella D Arminio

AU - De Luca, Andrea

AU - Di Biagio, Antonio

AU - Di Gianbenedetto, Simona

AU - Di Peni, Giovanni

AU - Di Pietro, Massimo

AU - Fabeni, Lavinia

AU - Fadda, Giovanni

AU - Galli, Massimo

AU - Gennari, William

AU - Ghisetti, Valeria

AU - Giacometti, Andrea

AU - Gori, Andrea

AU - Leoncini, Francesco

AU - Maggiolo, Franco

AU - Maserati, Renato

AU - Mazzotta, Francesco

AU - Micheli, Valeria

AU - Meini, Genny

AU - Monno, Laura

AU - Mussini, Cristina

AU - Nozza, Silvia

AU - Paolucci, Stefania

AU - Parisi, Saverio

AU - Pecorari, Monica

AU - Pizzi, Daniele

AU - Quirino, Tiziana

AU - Re, Maria Carla

AU - Rizzardini, Giuliano

AU - Santangelo, Rosaria

AU - Soria, Alessandro

AU - Stazi, Francesca

AU - Sterrantino, Gaetana

AU - Turriziani, Ombretta

AU - Viscoli, Claudio

AU - Vullo, Vincenzo

AU - Lazzarin, Adriano

AU - Perno, Cario Federico

PY - 2010/7

Y1 - 2010/7

N2 - Objective: The goal of the OSCAR programme is to evaluate the performances of genotypic HIV-1 tropism testing in clinical practice using the enhanced sensitivity version of Trafile (ESTA) as reference-assay. Methods: HIV-1 coreceptor-usage was assessed using plasma samples from 406 HIV-1 infected patients by ESTA and by gp120 V3 population-sequencing followed by Geno2pheno (set at a False Positive Rate [FPR] of 10% and 5%). Results: ESTA was successful in 365 (89.9%) samples indicating R5 in 254 (69.6%), and DM/X4 in 111 (30.4% of samples (104 [28.5%] DM and 7 [1.9%] X4). Genotypic-testing successfully assessed viral tropism for all 406 samples, including the 41 with undetermined result by ESTA. Genotypic-tropism testing at a FPR of 5% and 10% was 81.1% and 78.4% concordant with ESTA, respectively. Despite a sensitivity of 48.7% and 55.9% at a FPR of 5% and 10%, respectively, a high concordance (specificity: 95.3% for FPR of 5% and 88.2% for FPR of 10%) between genotypic-tropism testing and ESTA was reached in the detection of R5-tropic viruses. Conclusion: Our results are in line with other European studies, and support the routine use of genotypic tropism testing in clinical-settings for monitoring of HIV-1 infected patients candidate to or failing CCR5-antagonists.

AB - Objective: The goal of the OSCAR programme is to evaluate the performances of genotypic HIV-1 tropism testing in clinical practice using the enhanced sensitivity version of Trafile (ESTA) as reference-assay. Methods: HIV-1 coreceptor-usage was assessed using plasma samples from 406 HIV-1 infected patients by ESTA and by gp120 V3 population-sequencing followed by Geno2pheno (set at a False Positive Rate [FPR] of 10% and 5%). Results: ESTA was successful in 365 (89.9%) samples indicating R5 in 254 (69.6%), and DM/X4 in 111 (30.4% of samples (104 [28.5%] DM and 7 [1.9%] X4). Genotypic-testing successfully assessed viral tropism for all 406 samples, including the 41 with undetermined result by ESTA. Genotypic-tropism testing at a FPR of 5% and 10% was 81.1% and 78.4% concordant with ESTA, respectively. Despite a sensitivity of 48.7% and 55.9% at a FPR of 5% and 10%, respectively, a high concordance (specificity: 95.3% for FPR of 5% and 88.2% for FPR of 10%) between genotypic-tropism testing and ESTA was reached in the detection of R5-tropic viruses. Conclusion: Our results are in line with other European studies, and support the routine use of genotypic tropism testing in clinical-settings for monitoring of HIV-1 infected patients candidate to or failing CCR5-antagonists.

KW - Genotypic tropism testing

KW - HIV

KW - Trafile

KW - Tropism

KW - V3 loop

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