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EnglishPURPOSE: We have developed a sequencing assay for determining the usage of the genotypic HIV-1 co-receptor using peripheral blood mononuclear cell (PBMC) DNA in virologically suppressed HIV-1 infected patients. Our specific aims were to (1) evaluate the efficiency of V3 sequences in B versus non-B subtypes, (2) compare the efficiency of V3 sequences and tropism prediction using whole blood and PBMCs for DNA extraction, (3) compare the efficiency of V3 sequences and tropism prediction using a single versus a triplicate round of amplification. RESULTS: The overall rate of successful V3 sequences ranged from 100 % in samples with >3,000 copies HIV-1 DNA/10(6) PBMCs to 60 % in samples with <100 copies total HIV-1 DNA /10(6) PBMCs. Analysis of 143 paired PBMCs and whole-blood samples showed successful V3 sequences rates of 77.6 % for PBMCs and 83.9 % for whole blood. These rates are in agreement with the tropism prediction obtained using the geno2pheno co-receptor algorithm, namely, 92.1 % with a false-positive rate (FPR) of 10 or 20 % and of 96.5 % with an FPR of 5.75 %. The agreement between tropism prediction values using single versus triplicate amplification was 98.2 % (56/57) of patients using an FPR of 20 % and 92.9 % (53/57) using an FPR of 10 or 5.75 %. For 63.0 % (36/57) of patients, the FPR obtained via the single amplification procedure was superimposable to all three FPRs obtained by triplicate amplification. CONCLUSIONS: Our results show the feasibility and consistency of genotypic testing on HIV-1 DNA tropism, supporting its possible use for selecting patients with suppressed plasma HIV-1 RNA as candidates for CCR5-antagonist treatment. The high agreement between tropism prediction by single and triple amplification does not support the use of triplicate amplification in clinical practice.
| Titolo: | Genotypic testing on HIV-1 DNA as a tool to assess HIV-1 co-receptor usage in clinical practice: Results from the DIVA study group |
| Autore/i: | Svicher, V.; Alteri, C.; Montano, M.; Nori, A.; D'Arrigo, R.; Andreoni, M.; Angarano, G.; Antinori, A.; Antonelli, G.; Allice, T.; Bagnarelli, P.; Baldanti, F.; Bertoli, A.; Borderi, M.; Boeri, E.; BON, ISABELLA; Bruzzone, B.; Barresi, R.; Calderisi, S.; Callegaro, A. P.; Capobianchi, M. R.; Gargiulo, F.; Castelli, F.; Cauda, R.; Ceccherini Silberstein, F.; Clementi, M.; Chirianni, A.; Colafigli, M.; D'Arminio Monforte, A.; De Luca, A.; Di Biagio, A.; Di Nicuolo, G.; Di Perri, G.; Di Santo, F.; Fadda, G.; Galli, M.; Gennari, W.; Ghisetti, V.; Costantini, A.; Gori, A.; Gulminetti, R.; Leoncini, F.; Maffongelli, G.; Maggiolo, F.; Maserati, R.; Mazzotta, F.; Meini, G.; Micheli, V.; Monno, L.; Mussini, C.; Nozza, S.; Paolucci, S.; Palù, G.; Parisi, S.; Parruti, G.; Pignataro, A. R.; Quirino, T.; RE, MARIA CARLA; Rizzardini, G.; Sanguinetti, M.; Santangelo, R.; Scaggiante, R.; Sterrantino, G.; Turriziani, O.; Vatteroni, M. L.; Viscoli, C.; Vullo, V.; Zazzi, M.; Lazzarin, A.; Perno, C. F. |
| Autore/i Unibo: | |
| Anno: | 2014 |
| Rivista: | |
| Digital Object Identifier (DOI): | http://dx.doi.org/10.1007/s15010-013-0510-3 |
| Abstract: | PURPOSE: We have developed a sequencing assay for determining the usage of the genotypic HIV-1 co-receptor using peripheral blood mononuclear cell (PBMC) DNA in virologically suppressed HIV-1 infected patients. Our specific aims were to (1) evaluate the efficiency of V3 sequences in B versus non-B subtypes, (2) compare the efficiency of V3 sequences and tropism prediction using whole blood and PBMCs for DNA extraction, (3) compare the efficiency of V3 sequences and tropism prediction using a single versus a triplicate round of amplification. RESULTS: The overall rate of successful V3 sequences ranged from 100 % in samples with >3,000 copies HIV-1 DNA/10(6) PBMCs to 60 % in samples with <100 copies total HIV-1 DNA /10(6) PBMCs. Analysis of 143 paired PBMCs and whole-blood samples showed successful V3 sequences rates of 77.6 % for PBMCs and 83.9 % for whole blood. These rates are in agreement with the tropism prediction obtained using the geno2pheno co-receptor algorithm, namely, 92.1 % with a false-positive rate (FPR) of 10 or 20 % and of 96.5 % with an FPR of 5.75 %. The agreement between tropism prediction values using single versus triplicate amplification was 98.2 % (56/57) of patients using an FPR of 20 % and 92.9 % (53/57) using an FPR of 10 or 5.75 %. For 63.0 % (36/57) of patients, the FPR obtained via the single amplification procedure was superimposable to all three FPRs obtained by triplicate amplification. CONCLUSIONS: Our results show the feasibility and consistency of genotypic testing on HIV-1 DNA tropism, supporting its possible use for selecting patients with suppressed plasma HIV-1 RNA as candidates for CCR5-antagonist treatment. The high agreement between tropism prediction by single and triple amplification does not support the use of triplicate amplification in clinical practice. |
| Data stato definitivo: | 2015-12-17T10:56:13Z |
| Appare nelle tipologie: | 1.01 Articolo in rivista |
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