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1. Antiretroviral genotypic resistance in plasma RNA and whole blood DNA in HIV-1 infected patients failing HAART

Author

Saracino, A, Gianotti, N, Marangi, M, Cibelli, Dc, Galli, A, Punzi, G, Monno, L, Lazzarin, A, Angarano, G, Dini, M, Del Gobbo, R, Montroni, M, Butini, L, Scalise, G, Ancarani, F, Di Cesare, S, Giacometti, A, Biglino, A, Degioanni, M, Paoloni, M, Mariani, R, Calella, G, Pastore, G, Ladisa, N, Mennea, G, Gritti, Fm, Fasullo, G, Chiodo, F, Borderi, M, Carosi, Giampiero, Castelli, Francesco, Torti, Carlo, Uccelli, C, Rizzardini, G, Visoná, R, Salvo, A, Averna, A, Russo, R, Celesia, Bm, Cosentino, S, Rinaldi, E, Pusterla, L, Carnevale, G, Mondello, P, Petrini, C, Ghinelli, F, Sighinolfi, L, Mazzotta, F, Lo Caputo, S, Pierotti, P, Leoncini, F, Sterrantino, Gk, Corsi, P, Pompei, Ag, Di Toro MT, Purificato, F, Indiveri, F, Setti, M, Murdaca, G, Iannessi, A, Cellini, A, Mariani, A, Scasso, A, De Gennaro, M, Chiodera, A, Castelli, P, Maltempo, K, Mongolo, G, Caggese, L, Schlacht, I, Cargnel, A, Atzori, C, Micheli, V, Moroni, M, Bini, T, Marcatto, I, Chiesa, E, Vigevani, G, Argenteri, B, Capetti, A, Esposito, R, Guaraldi, G, Seghetto, B, Chirianni, A, Gargiulo, M, Abrescia, N, D'Abbraccio, M, Busto, T, Marchitelli, C, Santirocchi, M, Abbadessa, V, Mancuso, S, Meneghetti, F, Pranzetti, M, Ferrari, C, Pizzaferri, P, Stagni, G, Di Candilo, F, Petrelli, E, Balducci, M, Menichetti, F, Polidori, M, Tascini, C, Di Carlo, A, Palamara, G, Antinori, A, Liuzzi, G, Aiuti, F, Mezzaroma, I, Pinter, E, Barbone, B, Vullo, V, Massetti, P, Dell'Isola, S, Mura, Ms, Mannazzu, M, Delias, R, Di Giammartino, D, Tarquini, P, Marranconi, F, Ferretto, R, Caramello, P, Orofino, Gc, Cimino, T, Bramato, C, Di Perri, G, Sinicco, A, Zeme, D, Bonora, S, Trentini, L, Soranzo, Ml, Macor, A, Salassa, B, Branz, F, Delle Foglie, P, Vaglia, A, Rossi, Mc, Ciccone, L, Panzolli, L, Grossi, P, Giola, M, Raise, E, Narne, E, Poggio, A, Demin, F, Mondino, V, Serpelloni, G, Malena, M, Bosco, O., Saracino, A, Gianotti, N, Marangi, M, Cibelli, D, Galli, A, Punzi, G, Monno, L, Lazzarin, A, Angarano, G, and Mancuso, S

Subjects
Anti-HIV Agents, DNA Mutational Analysis, Molecular Sequence Data, Proviral DNA, HIV Infections, HAART failure, medicine.disease_cause, DNA Mutational Analysi, chemistry.chemical_compound, HIV Protease, Proviruses, Antiretroviral Therapy, Highly Active, Virology, Drug Resistance, Viral, medicine, Humans, Multicenter Studies as Topic, HIV Infection, Treatment Failure, Genotyping, Randomized Controlled Trials as Topic, COLD-PCR, Mutation, Plasma RNA, biology, Proviruse, Sequence Analysis, RNA, Anti-HIV Agent, RNA, Sequence Analysis, DNA, biology.organism_classification, HIV Reverse Transcriptase, Reverse transcriptase, Antiretroviral genotypic resistance, Infectious Diseases, chemistry, DNA, Viral, Lentivirus, Immunology, HIV-1, RNA, Viral, DNA, antiretroviral genotypic resistance, haart failure, hiv-1, plasma rna, proviral dna, Human
Abstract

The extent to which HIV-1 proviral DNA mutations cause clinically relevant antiretroviral resistance is still controversial. Paired plasma HIV-1 RNA and whole blood DNA were compared in patients failing HAART to investigate if the additional knowledge of archived mutations could improve the selection of potentially active drugs. Seventy-three HIV-1-infected patients with first/second HAART failure were studied before starting a new regimen based on RNA genotyping. Follow-up data after a 12-week therapy were available. DNA genotyping was retrospectively performed on stored whole blood samples and mutational profiles were compared to those from RNA. The mean number of IAS pol mutations was significantly higher in RNA (4.45 ± 2.76) than in DNA (2.88 ± 2.47) (P < 0.001). DNA genotyping provided a 6% increase in detection of resistance-associated mutations. Among 64/73 patients showing discordant DNA/RNA profiles, 54 (84%) also differed for predicted active drugs. 16/73 (22%) patients had ≥1 mutation revealed by DNA genotyping alone, probably affecting therapy success in 2/16. However, neither RNA/DNA discordance nor detection of isolated DNA mutations were statistically associated with outcome. In conclusion, plasma RNA remains the elective choice for HIV genotyping in patients with therapy failure, even if the detection of proviral resistance-associated mutations, not simultaneously found in RNA, is a frequent event. Therefore, in some cases DNA plus RNA genotyping might assist in choosing more accurately subsequent antiretroviral regimens. © 2008 Wiley-Liss, Inc.

Published
2008

2. HIV-1 coreceptor usage in paired plasma RNA and proviral DNA from patients with acute and chronic infection never treated with antiretroviral therapy

Author

I, Bon, O, Turriziani, G, Musumeci, A, Clò, C, Montagna, S, Morini, L, Calza, D, Gibellini, G, Antonelli, M C, Re, Bon, I, Turriziani, O., Musumeci, G., Clò, A., Montagna, C., Morini, S., Calza, L., Gibellini, D., Antonelli, G., and Re, M.C.

Subjects
Adult, Male, Genotyping Techniques, Genotype, antiretroviral therapy, HIV Infections, Infectious Disease, Tropism, HIV new infection, Plasma, Receptors, HIV, Proviruses, Virology, Humans, HIV Infection, proviral DNA, HIV, Proviruse, Medicine (all), PBMC, Genetic Variation, Naïve, Middle Aged, Viral Tropism, Phenotype, DNA, Viral, HIV-1, Leukocytes, Mononuclear, RNA, Viral, Female, Genotyping Technique, Human
Abstract

Although an independent evolution of viral quasispecies in different body sites might determine a differential compartmentalization of viral variants, the aim of this paper was to establish whether sequences from peripheral blood mononuclear cells (PBMCs) and plasma provide different or complementary information on HIV tropism in patients with acute or chronic infection. Tropism was predicted using genotypic testing combined with geno2pheno (coreceptor) analysis at a 10% false positive rate in paired RNA and DNA samples from 75 antiretroviral-naïve patients (divided on the basis of avidity index into patients with a recent or long-lasting infection). A high prevalence of R5 HIV strains (97%) was observed in both compartments (plasma and PBMCs) in patients infected recently. By contrast, patients with a long-lasting infection showed a quite different situation in the two compartments, revealing more (46%) X4/DM in PBMCs than patients infected recently (3%) (P = 0.008). As- a knowledge of viral strains in different biological compartments might be crucial to establish a therapeutic protocol, it could be extremely useful to detect not only viral strains in plasma, but also viruses hidden or archived in different cell compartments to better understand disease evolution and treatment efficacy in patients infected with HIV.

Published
2015

3. Performance of genotypic tropism testing on proviral DNA in clinical practice: results from the DIVA study group

Author

Svicher, V, Alteri, C, Montano, M, D'Arrigo, R, Andreoni, M, Angarano, G, Antinori, A, Antonelli, G, Allice, T, Bagnarelli, P, Baldanti, F, Bertoli, A, Borderi, M, Boeri, E, Bon, I, Bruzzone, B, Callegaro, A, Capobianchi, M, Carosi, G, 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 Pietro, M, Di Santo, F, Fabeni, L, Fadda, G, Galli, M, Gennari, W, Ghisetti, V, Giacometti, A, Gori, C, Gori, A, Gulminetti, R, Leoncini, F, Maffongelli, G, Maggiolo, F, Manca, G, Gargiulo, F, Martinelli, C, Maserati, R, Mazzotta, F, Meini, G, Micheli, V, Monno, L, Mussini, C, Narciso, P, Nozza, S, Paolucci, S, Pal, G, Parisi, S, Parruti, G, Pignataro, A, Pollicita, M, Quirino, T, Re, M, Rizzardini, G, Santangelo, R, Scaggiante, R, Sterrantino, G, Turriziani, O, Vatteroni, M, Vecchi, L, Viscoli, C, Vullo, V, Zazzi, M, Lazzarini, A, Perno, C, GORI, ANDREA, Perno, C., Svicher, V, Alteri, C, Montano, M, D'Arrigo, R, Andreoni, M, Angarano, G, Antinori, A, Antonelli, G, Allice, T, Bagnarelli, P, Baldanti, F, Bertoli, A, Borderi, M, Boeri, E, Bon, I, Bruzzone, B, Callegaro, A, Capobianchi, M, Carosi, G, 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 Pietro, M, Di Santo, F, Fabeni, L, Fadda, G, Galli, M, Gennari, W, Ghisetti, V, Giacometti, A, Gori, C, Gori, A, Gulminetti, R, Leoncini, F, Maffongelli, G, Maggiolo, F, Manca, G, Gargiulo, F, Martinelli, C, Maserati, R, Mazzotta, F, Meini, G, Micheli, V, Monno, L, Mussini, C, Narciso, P, Nozza, S, Paolucci, S, Pal, G, Parisi, S, Parruti, G, Pignataro, A, Pollicita, M, Quirino, T, Re, M, Rizzardini, G, Santangelo, R, Scaggiante, R, Sterrantino, G, Turriziani, O, Vatteroni, M, Vecchi, L, Viscoli, C, Vullo, V, Zazzi, M, Lazzarini, A, Perno, C, GORI, ANDREA, and Perno, C.

Abstract

The DIVA study is aimed at setting up a standardized genotypic tropism-testing on proviral-DNA for the routine clinical diagnostic-laboratory. Methods: Twelve local centres and 5 reference centres (previously cross-validated) were identified. For inter-center validation-procedure, 60 peripheral-blood mononuclear cells (PBMCs) aliquots from 45 HAART-treated patients were randomly chosen for population V3 sequencing on proviral-DNA at local HIV centre and at reference-laboratory. Viral tropism was predicted by Geno2Pheno algorithm (False Positive Rate [FPR] = 20%) as proposed by the European-Guidelines. Quantification of total HIV-1 DNA was based on a method described by Viard (2004). Results: Quantification of HIV-1 DNA was available for 35/45 (77.8%) samples, and gave a median value of 598 (IQR:252- 1,203) copies/10 6 PBMCs. A total of 56/60 (93.3%) samples were successfully amplified by both the reference and the local virological centers. The overall concordance of tropism prediction between local and reference centers was 54/56 (96.4%). Results of tropism prediction by local centers were: 33/54 (61.1%) R5 and 21/54 (38.9%) X4/DM. Conclusion: There was high concordance in the genotypic tropism prediction based on proviral DNA among different virological centers throughout Italy. Our results are in line with other European studies, and support the use of genotypic tropism testing on proviral DNA in patients with suppressed plasma HIV-1 RNA candidate to CCR5-antagonist treatment.

Published
2012

4. Performance of genotypic tropism testing on proviral DNA in clinical practice: Results from the DIVA study group

Author

Svicher, Valentina, Alteri, Claudia, Montano, Marco, D Arrigo, Roberta, Andreoni, Massimo, Angarano, Gioacchino, Antinori, Andrea, Antonelli, Guido, Allice, Tiziano, Bagnarelli, Patrizia, Baldanti, Fausto, Bertoli, Ada, Borderi, Marco, Boeri, Enzo, Bon, Isabella, Bruzzone, Bianca, Callegaro, Anna Paola, Capobianchi, Maria Rosaria, Carosi, Giampiero, Cauda, Roberto, Ceccherini-Silberstein, Francesca, Clementi, Massimo, Chirianni, Antonio, Manuela Colafigli, Monforte, Antonella D. Arminio, Luca, Andrea, Di Biagio, Antonio, Di Nicuolo, Giuseppe, Di Perri, Giovanni, Di Pietro, Massimo, Di Santo, Fabiola, Fabeni, Lavinia, Fadda, Giovanni, Galli, Massimo, Gennari, William, Ghisetti, Valeria, Giacometti, Andrea, Gori, Caterina, Gori, Andrea, Gulminetti, Roberto, Leoncini, Francesco, Maffongelli, Gaetano, Maggiolo, Franco, Manca, Giuseppe, Gargiulo, Franco, Martinelli, Canio, Maserati, Renato, Mazzotta, Francesco, Meini, Genny, Micheli, Valeria, Monno, Laura, Mussini, Cristina, Narciso, Pasquale, Nozza, Silvia, Paolucci, Stefania, Palu, Giorgio, Parisi, Saverio, Parruti, Giustino, Pignataro, Angela Rosa, Pollicita, Michela, Quirino, Tiziana, Re, Maria Carla, Rizzardini, Giuliano, Santangelo, Rosaria, Scaggiante, Renzo, Sterrantino, Gaetana, Turriziani, Ombretta, Vatteroni, Maria Linda, Vecchi, Laura, Viscoli, Claudio, Vullo, Vincenzo, Zazzi, Maurizio, Lazzarin, Adriano, Perno, Carlo Federico, Diva, Grp, Svicher V, Alteri C, Montano M, D'Arrigo R, Andreoni M, Angarano G, Antinori A, Antonelli G, Allice T, Bagnarelli P, Baldanti F, Bertoli A, Borderi M, Boeri E, Bon I, Bruzzone B, Callegaro AP, Capobianchi MR, Carosi G, 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 Pietro M, Di Santo F, Fabeni L, Fadda G, Galli M, Gennari W, Ghisetti V, Giacometti A, Gori C, Gori A, Gulminetti R, Leoncini F, Maffongelli G, Maggiolo F, Manca G, Gargiulo F, Martinelli C, Maserati R, Mazzotta F, Meini G, Micheli V, Monno L, Mussini C, Narciso P, Nozza S, Paolucci S, Pal G, Parisi S, Parruti G, Pignataro AR, Pollicita M, Quirino T, Re MC, Rizzardini G, Santangelo R, Scaggiante R, Sterrantino G, Turriziani O, Vatteroni ML, Vecchi L, Viscoli C, Vullo V, Zazzi M, Lazzarini A, Perno CF., Svicher, V, Alteri, C, Montano, M, D'Arrigo, R, Andreoni, M, Angarano, G, Antinori, A, Antonelli, G, Allice, T, Bagnarelli, P, Baldanti, F, Bertoli, A, Borderi, M, Boeri, E, Bon, I, Bruzzone, B, Callegaro, Ap, Capobianchi, Mr, Carosi, G, Cauda, R, Ceccherini Silberstein, F, Clementi, Massimo, Chirianni, A, Colafigli, M, Monforte, Ad, De Luca, A, Di Biagio, A, Di Nicuolo, G, Di Perri, G, Di Pietro, M, Di Santo, F, Fabeni, L, Fadda, G, Galli, M, Gennari, W, Ghisetti, V, Giacometti, A, Gori, C, Gori, A, Gulminetti, R, Leoncini, F, Maffongelli, G, Maggiolo, F, Manca, G, Gargiulo, F, Martinelli, C, Maserati, R, Mazzotta, F, Meini, G, Micheli, V, Monno, L, Mussini, C, Narciso, P, Nozza, S, Paolucci, S, Palu, G, Parisi, S, Parruti, G, Pignataro, Ar, Pollicita, M, Quirino, T, Re, Mc, Rizzardini, G, Santangelo, R, Scaggiante, R, Sterrantino, G, Turriziani, O, Vatteroni, Ml, Vecchi, L, Viscoli, C, Vullo, V, Zazzi, M, Lazzarin, Adriano, Perno, Cf, Callegaro, A, Capobianchi, M, Clementi, M, D'Arminio Monforte, A, Pal, G, Pignataro, A, Re, M, Vatteroni, M, Lazzarini, A, and Perno, C

Subjects
Male, Genotype, Genotyping Techniques, IMPACT, Mononuclear, HIV-1 TROPISM, Proviral DNA, Reproducibility of Result, HIV Infections, CORECEPTOR SWITCH, HIV Envelope Protein gp120, FREQUENCY, Tropism, CXCR4-USING HIV, HIV, AIDS, DNA provirale, ANTIRETROVIRAL THERAPY, Proviruses, INFECTION, Leukocytes, Humans, HIV Infection, CD4 CELL COUNT, PLASMA RNA, MARAVIROC, Proviruse, hiv, tropism, proviral dna, virus diseases, Reproducibility of Results, Viral Load, Settore MED/07 - Microbiologia e Microbiologia Clinica, Viral Tropism, HIV-1, Leukocytes, Mononuclear, Female, Genotyping Technique, Human
Abstract

"Objective: The DIVA study is aimed at setting up a standardized genotypic tropism-testing on proviral-DNA for the routine clinical diagnostic-laboratory Methods: Twelve local centres and 5 reference centres (previously cross-validated) were identified. For inter-center validation-procedure, 60 peripheral-blood mononuclear cells (PBMCs) aliquots from 45 HAART-treated patients were randomly chosen for population V3 sequencing on proviral-DNA at local HIV centre and at reference-laboratory Viral tropism was predicted by Geno2Pheno algorithm (False Positive Rate [FPR] = 20%) as proposed by the European-Guidelines. Quantification of total HIV-1 DNA was based on a method described by Viard (2004). Results: Quantification of HIV-1 DNA was available for 35\/45 (77.8%) samples, and gave a median value of 598 (IQR:252-1,203) copies\/10(6) PBMCs. A total of 56\/60 (93.3%) samples were successfully amplified by both the reference and the local virological centers. The overall concordance of tropism prediction between local and reference centers was 54\/56 (96.4%). Results of tropism prediction by local centers were: 33\/54 (61.1%) R5 and 21\/54 (38.9%) X4\/DM. Conclusion: There was high concordance in the genotypic tropism prediction based on proviral DNA among different virological centers throughout Italy. Our results are in line with other European studies, and support the use of genotypic tropism testing on proviral DNA in patients with suppressed plasma HIV-1 RNA candidate to CCR5-antagonist treatment."

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