162 results on '"Rozera G"'
Search Results
2. Quasispecies tropism and compartmentalization in gut and peripheral blood during early and chronic phases of HIV-1 infection: possible correlation with immune activation markers
- Author
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Rozera, G., Abbate, I., Vlassi, C., Giombini, E., Lionetti, R., Selleri, M., Zaccaro, P., Bartolini, B., Corpolongo, A., D’Offizi, G., Baiocchini, A., Del Nonno, F., Ippolito, G., and Capobianchi, M.R.
- Published
- 2014
- Full Text
- View/download PDF
3. Detection of haemagglutinin D222 polymorphisms in influenza A(H1N1)pdm09-infected patients by ultra-deep pyrosequencing
- Author
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Selleri, M., Piralla, A., Rozera, G., Giombini, E., Bartolini, B., Abbate, I., Campanini, G., Rovida, F., Dossena, L., Capobianchi, M.R., and Baldanti, F.
- Published
- 2013
- Full Text
- View/download PDF
4. Next-generation sequencing technology in clinical virology
- Author
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Capobianchi, M.R., Giombini, E., and Rozera, G.
- Published
- 2013
- Full Text
- View/download PDF
5. External quality assessment of HIV-1 DNA quantification assays used in the clinical setting in Italy
- Author
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Vicenti, I., Dragoni, F., Giannini, A., Casabianca, A., Lombardi, F., Di Sante, L., Turriziani, O., Racca, S., Paolucci, S., Lai, A., Bon, I., Abbate, I., Rozera, G., Belmonti, S., Scutari, R., Alteri, C., Saladini, F., Zazzi, M., Orlandi, C., Magnani, M., Di Giambenedetto, S., Longo, R., Menzo, S., Di Carlo, D., Mazzuti, L., Ardemagni, A., Clementi, M., Baldanti, F., Giardina, F., Bergna, A., Balotta, C., Bertoldi, A., Capobianchi, M. R., Ceccherini-Silberstein, F., Antonello, M., Perno, C. F., Andreoni, M., Lombardi F. (ORCID:0000-0001-5757-8346), Paolucci S., Lai A., Magnani M., Di Giambenedetto S. (ORCID:0000-0001-6990-5076), Longo R., Ardemagni A., Clementi M., Vicenti, I., Dragoni, F., Giannini, A., Casabianca, A., Lombardi, F., Di Sante, L., Turriziani, O., Racca, S., Paolucci, S., Lai, A., Bon, I., Abbate, I., Rozera, G., Belmonti, S., Scutari, R., Alteri, C., Saladini, F., Zazzi, M., Orlandi, C., Magnani, M., Di Giambenedetto, S., Longo, R., Menzo, S., Di Carlo, D., Mazzuti, L., Ardemagni, A., Clementi, M., Baldanti, F., Giardina, F., Bergna, A., Balotta, C., Bertoldi, A., Capobianchi, M. R., Ceccherini-Silberstein, F., Antonello, M., Perno, C. F., Andreoni, M., Lombardi F. (ORCID:0000-0001-5757-8346), Paolucci S., Lai A., Magnani M., Di Giambenedetto S. (ORCID:0000-0001-6990-5076), Longo R., Ardemagni A., and Clementi M.
- Abstract
Total cell-associated HIV-1 DNA is a surrogate marker of the HIV-1 reservoir, however, certified systems for its quantification are not available. The Italian HIV DNA Network was launched to validate HIV-1 DNA quantification methods in use at University and Hospital labs. A quality control panel including HIV-1 DNA standards, reconstructed blood samples (RBSs) and DNA from different HIV-1 subtypes was blindly tested by 12 participating labs by quantitative real-time PCR (n = 6), droplet digital PCR (n = 3) or both (n = 3). The median 95% hit rate was 4.6 (3.7–5.5) copies per test and linearity in the tested range was excellent (R2 = 1.000 [1.000–1.000]). The median values obtained across labs were 3,370 (2,287–4,245), 445 (299–498), 59 (40–81) and 7 (6–11) HIV-1 DNA copies, for the 3,584, 448, 56 and 7-copy standards, respectively. With RBSs, measured values were within twofold with respect to the median in two thirds of cases. HIV-1 subtypes were missed (CRF01_AE by 3 labs) or underestimated by > 1 log (subtypes A, C, D, F by one lab; CRF01_AE by one lab; CRF02_AG by one lab). The overall performance was excellent with HIV-1 DNA standards, however detection of different HIV-1 subtypes must be improved.
- Published
- 2022
6. Analysis of co‐receptor usage of circulating viral and proviral HIV genome quasispecies by ultra‐deep pyrosequencing in patients who are candidates for CCR5 antagonist treatment
- Author
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Abbate, I., Rozera, G., Tommasi, C., Bruselles, A., Bartolini, B., Chillemi, G., Nicastri, E., Narciso, P., Ippolito, G., and Capobianchi, M.R.
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- 2011
- Full Text
- View/download PDF
7. Bcl-2 inhibits the caspase-dependent apoptosis induced by SARS-CoV without affecting virus replication kinetics
- Author
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Bordi, L., Castilletti, C., Falasca, L., Ciccosanti, F., Calcaterra, S., Rozera, G., Di Caro, A., Zaniratti, S., Rinaldi, A., Ippolito, G., Piacentini, M., and Capobianchi, M. R.
- Published
- 2006
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- View/download PDF
8. Virological Characterization of Patients Treated Early is Able to Control HIV-1 Replication After Multiple Cycles of Structured Therapy Interruption
- Author
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Rozera, G., Abbate, I., DʼOffizi, G., Corpolongo, A., Narciso, P., Vlassi, C., Martini, F., Calcaterra, S., and Capobianchi, M. R.
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- 2007
- Full Text
- View/download PDF
9. Establishment of non-productive infection and activation of inf-alpha and -gamma gene expression in normal lymphomonocytes by sars-cov: P937
- Author
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Castilletti, C., Bordi, L., Lalle, E., Rozera, G., Poccia, F., Agrati, C., Abbate, I., and Capobianchi, M. R.
- Published
- 2005
10. Longitudinal analysis of HIV-1 coreceptor tropism by single and triplicate HIV-1 RNA and DNA sequencing in patients undergoing successful first-line antiretroviral therapy
- Author
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Meini, G., Rossetti, B., Bianco, C., Ceccherini-Silberstein, F., Di Giambenedetto, S., Sighinolfi, L., Monno, L., Castagna, A., Rozera, G., D'Arminio Monforte, A., Zazzi, M., De Luca, A., Moroni, M., Angarano, G., Antinori, A., Armignacco, O., d'Arminio Monforte, A., Castelli, F., Cauda, R., Di Perri, G., Galli, M., Iardino, R., Ippolito, G., Lazzarin, A., Perno, C. F., von Schloesser, F., Viale, P., Cozzi-Lepri, A., Girardi, E., Lo Caputo, S., Mussini, C., Puoti, M., Andreoni, M., Ammassari, A., Balotta, C., Bonfanti, P., Bonora, S., Borderi, M., Capobianchi, M. R., Cingolani, A., Cinque, P., Di Biagio, A., Gianotti, N., Gori, A., Guaraldi, G., Lapadula, G., Lichtner, M., Madeddu, G., Maggiolo, F., Marchetti, G., Marcotullio, S., Quiros Roldan, E., Rusconi, S., Cicconi, P., Fanti, I., Formenti, T., Galli, L., Lorenzini, P., Giacometti, A., Costantini, A., Santoro, C., Suardi, C., Vanino, E., Verucchi, G., Minardi, C., Quirino, T., Abeli, C., Manconi, P. E., Piano, P., Vecchiet, J., Falasca, K., Segala, D., Mazzotta, F., Cassola, G., Viscoli, G., Alessandrini, A., Piscopo, R., Mazzarello, G., Mastroianni, C., Belvisi, V., Caramma, I., Castelli, A. P., Rizzardini, G., Ridolfo, A. L., Piolini, R., Salpietro, S., Carenzi, L., Moioli, M. C., Puzzolante, C., Abrescia, N., Chirianni, A., Guida, M. G., Gargiulo, M., Baldelli, F., Francisci, D., Parruti, G., Ursini, T., Magnani, G., Ursitti, M. A., Vullo, V., d'Avino, A., Gallo, L., Nicastri, E., Acinapura, R., Capozzi, M., Libertone, R., Tebano, G., Cattelan, A., Mura, M. S., Caramello, P., Orofino, G. C., Sciandra, M., Pellizzer, G., Manfrin, V., Meini, Genny, Rossetti, Barbara, Bianco, Claudia, ICONA Fdn, Grp, Castagna, Antonella, Meini, G, Rossetti, B, Bianco, C, Ceccherini Silberstein, F, Di Giambenedetto, S, Sighinolfi, L, Monno, L, Castagna, A, Rozera, G, D'arminio Monforte, A, Zazzi, M, De Luca, A, Moroni, M, Armignacco, O, Iardino, R, Ippolito, G, Perno, C, Von Schloesser, F, Cozzi Lepri, A, Girardi, E, Balotta, C, Borderi, M, Capobianchi, M, Cinque, P, Di Biagio, A, Gianotti, N, Guaraldi, G, Lichtner, M, Marcotullio, S, Rusconi, S, Formenti, T, Galli, L, Lorenzini, P, Giacometti, A, Costantini, A, Angarano, G, Santoro, C, Maggiolo, F, Suardi, C, Viale, P, Vanino, E, Verucchi, G, Castelli, F, Quiros Roldan, E, Minardi, C, Quirino, T, Abeli, C, Manconi, P, Piano, P, Vecchiet, J, Falasca, K, Segala, D, Mazzotta, F, Lo Caputo, S, Cassola, G, Viscoli, G, Alessandrini, A, Piscopo, R, Mazzarello, G, Mastroianni, C, Belvisi, V, Bonfanti, P, Caramma, I, Castelli, A, Galli, M, Lazzarin, A, Rizzardini, G, Puoti, M, Ridolfo, A, Piolini, R, Salpietro, S, Carenzi, L, Moioli, M, Cicconi, P, Marchetti, G, Mussini, C, Puzzolante, C, Gori, A, Lapadula, G, Abrescia, N, Chirianni, A, Guida, M, Gargiulo, M, Baldelli, F, Francisci, D, Parruti, G, Ursini, T, Magnani, G, Ursitti, M, Cauda, R, Andreoni, M, Antinori, A, Vullo, V, Cingolani, A, D'Avino, A, Ammassari, A, Gallo, L, Nicastri, E, Acinapura, R, Capozzi, M, Libertone, R, Tebano, G, Cattelan, A, Mura, M, Madeddu, G, Caramello, P, Di Perri, G, Orofino, G, Bonora, S, Sciandra, M, Pellizzer, G, and Manfrin, V
- Subjects
Male ,viruses ,Salvage therapy ,HIV Infections ,Cohort Studies ,chemistry.chemical_compound ,0302 clinical medicine ,Genotype interpretation ,gp120 ,HIV type 1 ,V3 ,Adult ,Anti-Retroviral Agents ,Antiretroviral Therapy, Highly Active ,DNA, Viral ,Female ,Genotype ,HIV-1 ,Humans ,RNA, Viral ,Sequence Analysis, DNA ,Viral Tropism ,Pharmacology ,Pharmacology (medical) ,Infectious Diseases ,Medicine (all) ,HIV Infection ,Viral ,030212 general & internal medicine ,Original Research ,0303 health sciences ,tropism ,virus diseases ,Settore MED/07 - Microbiologia e Microbiologia Clinica ,3. Good health ,genotype interpretation ,Sequence Analysis ,Human ,Microbiology (medical) ,antiretroviral therapy ,Antiretroviral Therapy ,Viremia ,Infectious Disease ,CCR5 receptor antagonist ,Biology ,HIV infection ,Settore MED/17 - MALATTIE INFETTIVE ,NO ,03 medical and health sciences ,medicine ,Highly Active ,Tropism ,Maraviroc ,030306 microbiology ,RNA ,DNA ,medicine.disease ,Virology ,chemistry ,Immunology ,Tissue tropism ,Anti-Retroviral Agent ,Cohort Studie - Abstract
Objectives: Maraviroc has been shown to be effective in patients harbouring CCR5-tropic HIV-1. While this CCR5 antagonist has initially been used in salvage therapy, its excellent safety profile makes it ideal for antiretroviral treatment simplification strategies in patients with suppressed plasma viraemia. The aim of this study was to compare HIV-1 tropism as detected in baseline plasma RNA and peripheral blood mononuclear cell (PBMC) DNA prior to first-line therapy and to analyse tropism evolution while on successful treatment. Methods: HIV-1 tropism was determined using triplicate genotypic testing combined with geno2pheno[coreceptor] analysis at a 10% false positive rate in 42 patients. Paired pre-treatment plasma RNA and PBMC DNA and two subsequent PBMC DNA samples (the first obtained after reaching undetectable plasma HIV-1 RNA and the second after at least 2 years of suppression of plasma viraemia) were evaluated. Results: Coreceptor tropism was completely concordant in paired pre-treatment RNA and DNA, with 26.2% of HIV-1 sequences predicted to be non-CCR5-tropic. During follow-up, coreceptor tropism switches were detected in 4 (9.5%) patients without any preferential direction. Although false positive rate discrepancies within triplicates were common, the rate of discordance of coreceptor tropism assignment among triplicate results in this mostly CCR5-tropic dataset was only 2.1%, questioning the added value of triplicate testing compared with single testing. Conclusions: HIV-1 coreceptor tropism changes during virologically successful first-line treatment are infrequent. HIV-1 DNA analysis may thus support the choice of a CCR5 antagonist in treatment switch strategies; however, maraviroc treatment outcome data are required to confirm this option. © The Author 2013. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved
- Published
- 2013
- Full Text
- View/download PDF
11. In-depth analysis of compartmentalization of HIV-1 matrix protein p17 in PBMC and plasma
- Author
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Selleri, M., Dolcetti, R., Caccuri, F., Giombini, E., Rozera, G., Abbate, I., Mammone, A., Zanussi, S., Martorelli, D., SIMONA FIORENTINI, Caruso, A., and Capobianchi, M. R.
- Subjects
Ultra-deep pyrosequencing ,Gene Expression Regulation, Viral ,HIV Antigens ,p17 ,HIV Infections ,gag Gene Products, Human Immunodeficiency Virus ,Viral quasispecies ,HIV-1 matrix protein ,Compartmentalization ,HIV-1 ,Leukocytes, Mononuclear ,Humans ,Non-Hodgkin lymphoma ,Phylogeny - Abstract
HIV-1 p17 plays an important role in the virus life-cycle and disease pathogenesis. Recent studies indicated a high heterogeneity of p17. A high number of insertions in the p17 carboxy-terminal region have been more frequently detected in patients with non-Hodgkin lymphoma (NHL), suggesting a role of altered p17 in lymphomagenesis. Based on p17 heterogeneity, possible PBMC/plasma compartmentalization of p17 variants was explored by ultra-deep pyrosequencing in five NHL patients. The high variability of p17 with insertions at the carboxy-terminal region was confirmed in plasma and observed for the first time in proviral genomes. Quasispecies compartmentalization was evident in 4/5 patients. Further studies are needed to define the possible role of p17 quasispecies compartmentalization in lymphomagenesis.
- Published
- 2017
12. Quantitative HIV-1 proviral DNA detection: a multicentre analysis
- Author
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De Rossi A, Zanchetta M, Vitone F, Antonelli G, Bagnarelli P, Luigi Buonaguro, Capobianchi MR, Clementi M, Abbate I, Canducci F, Monachetti A, Riva E, Rozera G, Scagnolari C, Tagliamonte M, Mc, Re, Sivim, Group, De Rossi, A, Zanchetta, M, Vitone, F, Antonelli, G, Bagnarelli, P, Buonaguro, L, Capobianchi, Mr, Clementi, Massimo, Abbate, I, Canducci, F, Monachetti, A, Riva, E, Rozera, G, Scagnolari, C, Tagliamonte, M, Re, Mc, De Rossi A, Zanchetta M, Vitone F, Antonelli G, Bagnarelli P, Buonaguro L, Capobianchi MR, Clementi M, Abbate I, Canducci F, Monachetti A, Riva E, Rozera G, Scagnolari C, Tagliamonte M, and Re MC
- Subjects
DNA detection ,HIV ,HIV Infections ,Viral Load ,Polymerase Chain Reaction ,Sensitivity and Specificity ,gag Gene Products, Human Immunodeficiency Virus ,dna detection ,hiv ,standardization ,Standardization ,Cell Line ,Italy ,Proviruses ,HIV, DNA detection, Standardization ,DNA, Viral ,HIV-1 ,Humans ,Telomerase - Abstract
Despite the widespread use of molecular biology techniques, standardized methods for the measurement of HIV-1 proviral DNA are currently lacking and several discordant results are still present in different studies. To assess the clinical meaning of the proviral DNA load, a study group comprising seven different laboratories was set up to standardize a HIV-1 proviral DNA quantification method able to assess the DNA proviral load of the most relevant circulating HIV-1 subtypes. Reference samples (24 cellular samples infected with HIV-1 clade B, and 40 samples of peripheral blood mononuclear cells containing different concentrations of plasmids expressing different HIV-1 clades) were distributed and tested blindly. All laboratories employed hTERT gene as housekeeping gene and primers within the gag gene to quantify different HIV-1 clades. Inter-laboratory results did not differ statistically but showed only minor variations concerning HIV-1 DNA amounts and different HIV clades, with a good agreement among the laboratories participating in the study. Since test standardization represents a key step for future application in clinical practice, further studies of the patients' samples are in progress to establish the real meaning and utility of the proviral DNA load for clinical management of HIV-1 infected patients.
- Published
- 2010
13. The Genotypic False Positive Rate Determined by Population V3-Sequencing can Predict the Burden of X4 Quasispecies Detected by Pyrosequencing
- Author
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Cento, V, Svicher, V, Rozera, G, Abbate, I, Santoro, M, Armenia, D, Fabeni, L, Palamara, G, Latini, A, Rizzardini, G, Micheli, V, Buonomini, A, Antinori, A, Andreoni, M, Perno, Cf, Capobianchi, M, and CECCHERINI SILBERSTEIN, F
- Subjects
Settore MED/07 - Microbiologia e Microbiologia Clinica - Published
- 2011
14. Bone marrow CD34+ progenitor cells may harbour HIV-DNA even in successfully treated patients
- Author
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Bordoni, V., primary, Bibas, M., additional, Abbate, I., additional, Viola, D., additional, Rozera, G., additional, Agrati, C., additional, Rinaldi, A., additional, Amendola, A., additional, Ammassari, A., additional, Capobianchi, M.R., additional, and Martini, F., additional
- Published
- 2015
- Full Text
- View/download PDF
15. HBV genetic compartimentalization, variability and molecular correlates of histologic and immunohistochemical aspects in liver tissue: implications for the clinical management of patients with chronic hepatitis B
- Author
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Minosse, C., primary, Baiocchini, A., additional, Selleri, M., additional, Giombini, E., additional, Coen, S., additional, Zaccaro, P., additional, Rozera, G., additional, Vincenti, D., additional, Del Nonno, F., additional, Comandini, U. Visco, additional, Lionetti, R., additional, Montalbano, M., additional, D’Offizi, G., additional, Vivarelli, M., additional, Capobianchi, M.R., additional, and Menzo, S., additional
- Published
- 2015
- Full Text
- View/download PDF
16. Longitudinal analysis of HIV-1 coreceptor tropism by single and triplicate HIV-1 RNA and DNA sequencing in patients undergoing successful first-line antiretroviral therapy
- Author
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Meini, G, Rossetti, B, Bianco, C, Ceccherini Silberstein, F, Di Giambenedetto, S, Sighinolfi, L, Monno, L, Castagna, A, Rozera, G, D'arminio Monforte, A, Zazzi, M, De Luca, A, Moroni, M, Armignacco, O, Iardino, R, Ippolito, G, Perno, C, Von Schloesser, F, Cozzi Lepri, A, Girardi, E, Balotta, C, Borderi, M, Capobianchi, M, Cinque, P, Di Biagio, A, Gianotti, N, Guaraldi, G, Lichtner, M, Marcotullio, S, Rusconi, S, Formenti, T, Galli, L, Lorenzini, P, Giacometti, A, Costantini, A, Angarano, G, Santoro, C, Maggiolo, F, Suardi, C, Viale, P, Vanino, E, Verucchi, G, Castelli, F, Quiros Roldan, E, Minardi, C, Quirino, T, Abeli, C, Manconi, P, Piano, P, Vecchiet, J, Falasca, K, Segala, D, Mazzotta, F, Lo Caputo, S, Cassola, G, Viscoli, G, Alessandrini, A, Piscopo, R, Mazzarello, G, Mastroianni, C, Belvisi, V, Bonfanti, P, Caramma, I, Castelli, A, Galli, M, Lazzarin, A, Rizzardini, G, Puoti, M, Ridolfo, A, Piolini, R, Salpietro, S, Carenzi, L, Moioli, M, Cicconi, P, Marchetti, G, Mussini, C, Puzzolante, C, Gori, A, Lapadula, G, Abrescia, N, Chirianni, A, Guida, M, Gargiulo, M, Baldelli, F, Francisci, D, Parruti, G, Ursini, T, Magnani, G, Ursitti, M, Cauda, R, Andreoni, M, Antinori, A, Vullo, V, Cingolani, A, D'Avino, A, Ammassari, A, Gallo, L, Nicastri, E, Acinapura, R, Capozzi, M, Libertone, R, Tebano, G, Cattelan, A, Mura, M, Madeddu, G, Caramello, P, Di Perri, G, Orofino, G, Bonora, S, Sciandra, M, Pellizzer, G, Manfrin, V, Manfrin, V., GORI, ANDREA, Meini, G, Rossetti, B, Bianco, C, Ceccherini Silberstein, F, Di Giambenedetto, S, Sighinolfi, L, Monno, L, Castagna, A, Rozera, G, D'arminio Monforte, A, Zazzi, M, De Luca, A, Moroni, M, Armignacco, O, Iardino, R, Ippolito, G, Perno, C, Von Schloesser, F, Cozzi Lepri, A, Girardi, E, Balotta, C, Borderi, M, Capobianchi, M, Cinque, P, Di Biagio, A, Gianotti, N, Guaraldi, G, Lichtner, M, Marcotullio, S, Rusconi, S, Formenti, T, Galli, L, Lorenzini, P, Giacometti, A, Costantini, A, Angarano, G, Santoro, C, Maggiolo, F, Suardi, C, Viale, P, Vanino, E, Verucchi, G, Castelli, F, Quiros Roldan, E, Minardi, C, Quirino, T, Abeli, C, Manconi, P, Piano, P, Vecchiet, J, Falasca, K, Segala, D, Mazzotta, F, Lo Caputo, S, Cassola, G, Viscoli, G, Alessandrini, A, Piscopo, R, Mazzarello, G, Mastroianni, C, Belvisi, V, Bonfanti, P, Caramma, I, Castelli, A, Galli, M, Lazzarin, A, Rizzardini, G, Puoti, M, Ridolfo, A, Piolini, R, Salpietro, S, Carenzi, L, Moioli, M, Cicconi, P, Marchetti, G, Mussini, C, Puzzolante, C, Gori, A, Lapadula, G, Abrescia, N, Chirianni, A, Guida, M, Gargiulo, M, Baldelli, F, Francisci, D, Parruti, G, Ursini, T, Magnani, G, Ursitti, M, Cauda, R, Andreoni, M, Antinori, A, Vullo, V, Cingolani, A, D'Avino, A, Ammassari, A, Gallo, L, Nicastri, E, Acinapura, R, Capozzi, M, Libertone, R, Tebano, G, Cattelan, A, Mura, M, Madeddu, G, Caramello, P, Di Perri, G, Orofino, G, Bonora, S, Sciandra, M, Pellizzer, G, Manfrin, V, Manfrin, V., and GORI, ANDREA
- Abstract
Objectives: Maraviroc has been shown to be effective in patients harbouring CCR5-tropic HIV-1. While this CCR5 antagonist has initially been used in salvage therapy, its excellent safety profile makes it ideal for antiretroviral treatment simplification strategies in patients with suppressed plasma viraemia. The aim of this study was to compare HIV-1 tropism as detected in baseline plasma RNA and peripheral blood mononuclear cell (PBMC) DNA prior to first-line therapy and to analyse tropism evolution while on successful treatment. Methods: HIV-1 tropism was determined using triplicate genotypic testing combined with geno2pheno[coreceptor] analysis at a 10% false positive rate in 42 patients. Paired pre-treatment plasma RNA and PBMC DNA and two subsequent PBMC DNA samples (the first obtained after reaching undetectable plasma HIV-1 RNA and the second after at least 2 years of suppression of plasma viraemia) were evaluated. Results: Coreceptor tropism was completely concordant in paired pre-treatment RNA and DNA, with 26.2% of HIV-1 sequences predicted to be non-CCR5-tropic. During follow-up, coreceptor tropism switches were detected in 4 (9.5%) patients without any preferential direction. Although false positive rate discrepancies within triplicates were common, the rate of discordance of coreceptor tropism assignment among triplicate results in this mostly CCR5-tropic dataset was only 2.1%, questioning the added value of triplicate testing compared with single testing. Conclusions: HIV-1 coreceptor tropism changes during virologically successful first-line treatment are infrequent. HIV-1 DNA analysis may thus support the choice of a CCR5 antagonist in treatment switch strategies; however, maraviroc treatment outcome data are required to confirm this option. © The Author 2013. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved
- Published
- 2014
17. Evolution of HIV-1 tropism at quasispecies level after 5 years of combination antiretroviral therapy in patients always suppressed or experiencing episodes of virological failure
- Author
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Rozera, G, Abbate, I, Giombini, E, Castagna, A, De Luca, A, Ceccherini Silberstein, F, Cozzi Lepri, A, Cassola, G, Torti, C, d'Arminio Monforte, A, Ippolito, G, Capobianchi, M, Gori, A, GORI, ANDREA, Rozera, G, Abbate, I, Giombini, E, Castagna, A, De Luca, A, Ceccherini Silberstein, F, Cozzi Lepri, A, Cassola, G, Torti, C, d'Arminio Monforte, A, Ippolito, G, Capobianchi, M, Gori, A, and GORI, ANDREA
- Abstract
OBJECTIVES: Tropism evolution of HIV-1 quasispecies was analysed by ultra-deep pyrosequencing (UDPS) in patients on first-line combination antiretroviral therapy (cART) always suppressed or experiencing virological failure episodes.METHODS: Among ICONA patients, two groups of 20 patients on cART for ≥5 years, matched for baseline viraemia and therapy duration, were analysed [Group I, patients always suppressed; and Group II, patients experiencing episode(s) of virological failure]. Viral tropism was assessed by V3 UDPS on plasma RNA before therapy (T0) and on peripheral blood mononuclear cell proviral DNA before-after therapy (T0-T1), using geno2pheno false positive rate (FPR) (threshold for X4: 5.75). For each sample, quasispecies tropism was assigned according to X4 variant frequency: R5, <0.3% X4; minority X4, 0.3%-19.9% X4; and X4, ≥20% X4. An R5-X4 switch was defined as a change from R5/minority X4 in plasma/proviral genomes at T0 to X4 in provirus at T1.RESULTS: At baseline, mean FPR and %X4 of viral RNA were positively correlated with those of proviral DNA. After therapy, proviral DNA load significantly decreased in Group I; mean FPR of proviral quasispecies significantly decreased and %X4 increased in Group II. An R5-X4 switch was observed in five patients (two in Group I and three in Group II), all harbouring minority X4 variants at T0.CONCLUSIONS: UDPS analysis reveals that the tropism switch is not an 'on-off' phenomenon, but may result from a profound re-shaping of viral quasispecies, even under suppressive cART. However, episodes of virological failure seem to prevent reduction of proviral DNA and to accelerate viral evolution, as suggested by decreased FPR and increased %X4 at T1 in Group II patients
- Published
- 2014
18. Protective role of bcl-2 in the induction of cytopathic effect and of apoptotic cell death in SARS-CoV-infected VERO cells, in the absence of inhibition of viral replication
- Author
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Castilletti, C, Ciccosanti, F, Calcaterra, S, Bordi, L, Falasca, L, Rozera, G, Di Caro, A, Zaniratti, S, Ippolito, G, Piacentini, M, and Capobianchi, MR
- Subjects
ddc: 610 - Published
- 2004
19. Comparison of real-time PCR methods for measurement of HIV-1 proviral DNA
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Rozera, G., Abbate, I., Bruselles, A., Bartolini, B., D’Offizi, G., Nicastri, E., Tommasi, C., and Capobianchi, M.R.
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- 2010
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20. Longitudinal analysis of HIV-1 coreceptor tropism by single and triplicate HIV-1 RNA and DNA sequencing in patients undergoing successful first-line antiretroviral therapy
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Meini, G, Rossetti, B, Bianco, C, Ceccherini Silberstein, F, Di Giambenedetto, Simona, Sighinolfi, L, Monno, L, Castagna, A, Rozera, G, D'Arminio Monforte, A, Zazzi, M, De Luca, Andrea, Di Giambenedetto, Simona (ORCID:0000-0001-6990-5076), De Luca, Andrea (ORCID:0000-0002-8311-6935), Meini, G, Rossetti, B, Bianco, C, Ceccherini Silberstein, F, Di Giambenedetto, Simona, Sighinolfi, L, Monno, L, Castagna, A, Rozera, G, D'Arminio Monforte, A, Zazzi, M, De Luca, Andrea, Di Giambenedetto, Simona (ORCID:0000-0001-6990-5076), and De Luca, Andrea (ORCID:0000-0002-8311-6935)
- Abstract
Maraviroc has been shown to be effective in patients harbouring CCR5-tropic HIV-1. While this CCR5 antagonist has initially been used in salvage therapy, its excellent safety profile makes it ideal for antiretroviral treatment simplification strategies in patients with suppressed plasma viraemia. The aim of this study was to compare HIV-1 tropism as detected in baseline plasma RNA and peripheral blood mononuclear cell (PBMC) DNA prior to first-line therapy and to analyse tropism evolution while on successful treatment.
- Published
- 2013
21. 'Sentinel' mutations in standard population sequencing can predict the presence of HIV-1 reverse transcriptase major mutations detectable only by ultra-deep pyrosequencing
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Alteri, C., primary, Santoro, M. M., additional, Abbate, I., additional, Rozera, G., additional, Bruselles, A., additional, Bartolini, B., additional, Gori, C., additional, Forbici, F., additional, Orchi, N., additional, Tozzi, V., additional, Palamara, G., additional, Antinori, A., additional, Narciso, P., additional, Girardi, E., additional, Svicher, V., additional, Ceccherini-Silberstein, F., additional, Capobianchi, M. R., additional, and Perno, C. F., additional
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- 2011
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22. 211 Virological Charactrization of HIV-1 Acute Infection by Ultra-Sensitive Next Generation Sequencing
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Abbate, I, primary, Rozera, G, additional, Vlassi, C, additional, Bartolini, B, additional, Bruselles, A, additional, Giombini, E, additional, D'Offizi, G, additional, Narciso, P, additional, and Capobianchi, M R, additional
- Published
- 2011
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23. 890 ACTIVATION OF INNATE IMMUNITY CELLS MAY PREDICT EARLY HCV TREATMENT OUTCOME IN HIV/HCV CO-INFECTED PATIENTS
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Sacchi, A., primary, Lalle, E., additional, Vlassi, C., additional, Vitali, A., additional, D'Offizi, G., additional, Martini, F., additional, Abbate, I., additional, Rozera, G., additional, and Capobianchi, M.R., additional
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- 2009
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24. 586 METHODS FOR VIRAL POPULATION RECONSTRUCTION VIA ULTRA-DEEP PYROSEQUENCING: HEPATITIS B VIRUS CASE STUDY
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Prosperi, M., primary, Bruselles, A., additional, Vincenti, D., additional, Solmone, M.C., additional, Abbate, I., additional, Rozera, G., additional, Ippolito, G., additional, and Capobianchi, M.R., additional
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- 2009
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25. SARS-COV INDUCE L’ESPRESSIONE DI IFN-α E-γ IN PBMC DA DONATORI SANI ANCHE IN ASSENZA DI REPLICAZIONE VIRALE
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Castilletti, C., primary, Bordi, L., additional, Lalle, E., additional, Rozera, G., additional, Poccia, F., additional, Agrati, C., additional, AbbateI, A., additional, and Capobianchi, M.R., additional
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- 2005
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26. Bcl-2 inhibits the caspase-dependent apoptosis induced by SARS-CoV without affecting virus replication kinetics
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Bordi, L., primary, Castilletti, C., additional, Falasca, L., additional, Ciccosanti, F., additional, Calcaterra, S., additional, Rozera, G., additional, Di Caro, A., additional, Zaniratti, S., additional, Rinaldi, A., additional, Ippolito, G., additional, Piacentini, M., additional, and Capobianchi, M. R., additional
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- 2005
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27. Deep Sequencing of Plasma and Proviral HIV-1 to Establish Coreceptor Usage: What Is the Clinical Impact of the Quasispecies Distribution?
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Abbate I, Rozera G, Giombini E, D'Offizi G, Nicastri E, Narciso P, Ippolito G, and Capobianchi MR
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- 2011
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28. DYNAMIC VARIATIONS OF LYMPHOCYTE- AND MONOCYTE-ASSOCIATED HIV-1 QUASISPECIES AFTER DISCONTINUATION OF HIGHLY ACTIVE ANTI-RETROVIRAL THERAPY AS ASSESSED BY MASSIVELY PARALLEL PYROSEQUENCING
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Abbate, I., Rozera, G., Alessandro Bruselles, Vlassi, C., D Offizi, G., Narciso, P., Chillemi, G., Prosperi, M., Ippolito, G., and Capobianchi, M. R.
29. Assembly and characterization of pandemic influenza A H1N1 genome in nasopharyngeal swabs using high-throughput pyrosequencing
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Bartolini, B., Giovanni Chillemi, Abbate, I., Bruselles, A., Rozera, G., Castrignanò, T., Paoletti, D., Picardi, E., Desideri, A., Pesole, G., and Capobianchi, M. R.
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virus diseases ,High-throughput pyrosequencing ,Influenza ,Nasopharyngeal swabs - Abstract
De novo high-throughput pyrosequencing was used to detect and characterize 2009 pandemic influenza A (H1N1) virus directly in nasopharyngeal swabs in the context of the microbial community. Data were generated with a prior sequenceindependent amplification by 454 pyrosequencing on GS-FLX platform (Roche). Influenza A assembled reads allowed near full-length genome reconstruction with the simultaneous analysis of site-specific heterogeneity. The molecular approach applied proved to be a powerful tool to characterize the new pandemic H1N1 influenza virus in clinical samples. This approach could be of great value in identifying possibly new reassortants that may occur in the near future.
30. THE GENOTYPIC FALSE POSITIVE RATE DETERMINED BY POPULATION V3-SEQUENCING CAN PREDICT THE BURDEN OF X4 QUASISPECIES DETECTED BY PYROSEQUENCING
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Cento, V., Svicher, V., Rozera, G., Abbate, I., Santoro, M. M., Armenia, D., Fabeni, L., Palamara, G., Latini, A., Rizzardini, G., Valeria Micheli, Buonomini, A. R., Andreoni, M., Perno, C. F., Capobianchi, M. R., and Ceccherini-Silberstein, F.
31. Slow or fast viral load decay as a predictor of residual viremia level in HIV-infected patients undergoing successful first-line cART
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Amendola, A., Bibbolino, G., Navarra, A., Pisciotta, M., Marsella, P., Pinnetti, C., Abbate, I., Rozera, G., Mondi, A., Antinori, A., Capobianchi, M. R., Girardi, E., and Adriana Ammassari
32. Experimental Research on Toxicity of Furfural
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Castellino, N., primary, Elmino, O., additional, and Rozera, G., additional
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- 1963
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33. SARS-CoV-2 Serum Neutralization Assay: A Traditional Tool for a Brand-New Virus
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Matusali G., Colavita F., Lapa D., Meschi S., Bordi L., Piselli P., Gagliardini R., Corpolongo A., Nicastri E., Antinori A., Ippolito G., Capobianchi M. R., Castilletti C., Abbate I., Agrati C., Aleo L., Alonzi T., Amendola A., Apollonio C., Arduini N., Bartolini B., Berno G., Biancone S., Bibbo A., Brega C., Canali M., Cannas A., Carletti F., Carrara S., Casetti R., Castillettiy C., Chiappini R., Ciafrone L., Cimini E., Coen S., Condello R., Coppola A., D'arezzo S., Di Caro A., Di Filippo S., De Giuli C., Fabeni L., Felici L., Ferraioli V., Forbici F., Garbuglia A. R., Giombini E., Gruber C. E. M., Khouri D., Lalle E., Leone B., Mazzarelli A., Messina F., Minosse C., Montaldo C., Neri S., Nisii C., Petrivelli E., Petroni F., Petruccioli E., Pisciotta M., Pizzi D., Prota G., Rozera G., Rueca M., Sabatini R., Sarti S., Sberna G., Sciamanna R., Selleri M., Selvaggi C., Stellitano C., Toffoletti A., Truffa S., Turchi F., Valli M. B., Venditti C., Vincenti D., Vulcano A., Zambelli E., Bevilacqua N., Bordoni V., D'abramo A., Lepore L., Mariano A., Palazzolo C., Lorenzini P., Notari S., Sacchi A., Scorzolini L., Bettini A., Francalancia M., Specchiarello E., Federica M., Gaetano D., Luigi F., Barbara G., Roberto I., Giovanni M., Mirco M., Rachele S., Matusali, G., Colavita, F., Lapa, D., Meschi, S., Bordi, L., Piselli, P., Gagliardini, R., Corpolongo, A., Nicastri, E., Antinori, A., Ippolito, G., Capobianchi, M. R., Castilletti, C., Abbate, I., Agrati, C., Aleo, L., Alonzi, T., Amendola, A., Apollonio, C., Arduini, N., Bartolini, B., Berno, G., Biancone, S., Bibbo, A., Brega, C., Canali, M., Cannas, A., Carletti, F., Carrara, S., Casetti, R., Castillettiy, C., Chiappini, R., Ciafrone, L., Cimini, E., Coen, S., Condello, R., Coppola, A., D'Arezzo, S., Di Caro, A., Di Filippo, S., De Giuli, C., Fabeni, L., Felici, L., Ferraioli, V., Forbici, F., Garbuglia, A. R., Giombini, E., Gruber, C. E. M., Khouri, D., Lalle, E., Leone, B., Mazzarelli, A., Messina, F., Minosse, C., Montaldo, C., Neri, S., Nisii, C., Petrivelli, E., Petroni, F., Petruccioli, E., Pisciotta, M., Pizzi, D., Prota, G., Rozera, G., Rueca, M., Sabatini, R., Sarti, S., Sberna, G., Sciamanna, R., Selleri, M., Selvaggi, C., Stellitano, C., Toffoletti, A., Truffa, S., Turchi, F., Valli, M. B., Venditti, C., Vincenti, D., Vulcano, A., Zambelli, E., Bevilacqua, N., Bordoni, V., D'Abramo, A., Lepore, L., Mariano, A., Palazzolo, C., Lorenzini, P., Notari, S., Sacchi, A., Scorzolini, L., Bettini, A., Francalancia, M., Specchiarello, E., Federica, M., Gaetano, D., Luigi, F., Barbara, G., Roberto, I., Giovanni, M., Mirco, M., and Rachele, S.
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0301 basic medicine ,Male ,lcsh:QR1-502 ,serology ,Antibodies, Viral ,lcsh:Microbiology ,Serology ,protective immunity ,0302 clinical medicine ,Medicine ,030212 general & internal medicine ,Neutralizing antibody ,biology ,Middle Aged ,3. Good health ,Algorithm ,Titer ,Infectious Diseases ,Female ,Neutralization Test ,Algorithms ,Human ,Adult ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Protective immunity ,Article ,Virus ,COVID-19 Serological Testing ,03 medical and health sciences ,Neutralization Tests ,Immunity ,Virology ,Neutralizing antibodie ,Humans ,neutralizing antibodies ,Kinetic ,Receiver operating characteristic ,business.industry ,SARS-CoV-2 ,COVID-19 ,Gold standard (test) ,Antibodies, Neutralizing ,Kinetics ,030104 developmental biology ,ROC Curve ,Immunoglobulin G ,Immunology ,biology.protein ,business - Abstract
SARS-CoV-2 serum neutralization assay represents the gold standard for assessing antibody-mediated protection in naturally infected and vaccinated individuals. In the present study, 662 serum samples collected from February 2020 to January 2021 from acute and convalescent COVID-19 patients were tested to determine neutralizing antibody (NAb) titers using a microneutralization test (MNT) for live SARS-CoV-2. Moreover, anti-SARS-CoV-2 IgG, IgA, and IgM directed against different viral antigens were measured by high-throughput automated platforms. We observed higher levels of NAbs in elderly (>, 60 years old) individuals and in patients presenting acute respiratory distress syndrome. SARS-CoV-2 NAbs develop as soon as five days from symptom onset and, despite a decline after the second month, persist for over 11 months, showing variable dynamics. Through correlation and receiver operating characteristic (ROC) curve analysis, we set up a testing algorithm, suitable for the laboratory workload, by establishing an optimal cutoff value of anti-SARS-CoV-2 IgG for convalescent plasma donors to exclude from MNT samples foreseen to have low/negative NAb titers and ineligible for plasma donation. Overall, MNT, although cumbersome and not suitable for routine testing of large sample sizes, remains the reference tool for the assessment of antibody-mediated immunity after SARS-CoV-2 infection. Smart testing algorithms may optimize the laboratory workflow to monitor antibody-mediated protection in COVID-19 patients, plasma donors, and vaccinated individuals.
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34. Co-receptor usage prediction at quasispecies level using ultra-deep pyrosequencing on both circulating and proviral hiv in patients candidates to CCR5 antagonist treatment
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Nicastri Emanuele, Bartolini Barbara, Bruselles Alessandro, Tommasi Chiara, Rozera Gabriella, Abbate Isabella, Narciso Pasquale, and Capobianchi Maria R
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Immunologic diseases. Allergy ,RC581-607 - Published
- 2010
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35. Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing
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Vincenti Donatella, Rozera Gabriella, Abbate Isabella, Bruselles Alessandro, Prosperi Luciano, Prosperi Mattia CF, Solmone Maria, Capobianchi Maria, and Ulivi Giovanni
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Computer applications to medicine. Medical informatics ,R858-859.7 ,Biology (General) ,QH301-705.5 - Abstract
Abstract Background Next-generation sequencing (NGS) offers a unique opportunity for high-throughput genomics and has potential to replace Sanger sequencing in many fields, including de-novo sequencing, re-sequencing, meta-genomics, and characterisation of infectious pathogens, such as viral quasispecies. Although methodologies and software for whole genome assembly and genome variation analysis have been developed and refined for NGS data, reconstructing a viral quasispecies using NGS data remains a challenge. This application would be useful for analysing intra-host evolutionary pathways in relation to immune responses and antiretroviral therapy exposures. Here we introduce a set of formulae for the combinatorial analysis of a quasispecies, given a NGS re-sequencing experiment and an algorithm for quasispecies reconstruction. We require that sequenced fragments are aligned against a reference genome, and that the reference genome is partitioned into a set of sliding windows (amplicons). The reconstruction algorithm is based on combinations of multinomial distributions and is designed to minimise the reconstruction of false variants, called in-silico recombinants. Results The reconstruction algorithm was applied to error-free simulated data and reconstructed a high percentage of true variants, even at a low genetic diversity, where the chance to obtain in-silico recombinants is high. Results on empirical NGS data from patients infected with hepatitis B virus, confirmed its ability to characterise different viral variants from distinct patients. Conclusions The combinatorial analysis provided a description of the difficulty to reconstruct a quasispecies, given a determined amplicon partition and a measure of population diversity. The reconstruction algorithm showed good performance both considering simulated data and real data, even in presence of sequencing errors.
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- 2011
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36. Massively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte sub-populations
- Author
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Chillemi Giovanni, Narciso Pasquale, D'Offizi Gianpiero, Vlassi Crhysoula, Bruselles Alessandro, Abbate Isabella, Rozera Gabriella, Prosperi Mattia, Ippolito Giuseppe, and Capobianchi Maria R
- Subjects
Immunologic diseases. Allergy ,RC581-607 - Abstract
Abstract Background Virus-associated cell membrane proteins acquired by HIV-1 during budding may give information on the cellular source of circulating virions. In the present study, by applying immunosorting of the virus and of the cells with antibodies targeting monocyte (CD36) and lymphocyte (CD26) markers, it was possible to directly compare HIV-1 quasispecies archived in circulating monocytes and T lymphocytes with that present in plasma virions originated from the same cell types. Five chronically HIV-1 infected patients who underwent therapy interruption after prolonged HAART were enrolled in the study. The analysis was performed by the powerful technology of ultra-deep pyrosequencing after PCR amplification of part of the env gene, coding for the viral glycoprotein (gp) 120, encompassing the tropism-related V3 loop region. V3 amino acid sequences were used to establish heterogeneity parameters, to build phylogenetic trees and to predict co-receptor usage. Results The heterogeneity of proviral and viral genomes derived from monocytes was higher than that of T-lymphocyte origin. Both monocytes and T lymphocytes might contribute to virus rebounding in the circulation after therapy interruptions, but other virus sources might also be involved. In addition, both proviral and circulating viral sequences from monocytes and T lymphocytes were predictive of a predominant R5 coreceptor usage. However, minor variants, segregating from the most frequent quasispecies variants, were present. In particular, in proviral genomes harboured by monocytes, minority variant clusters with a predicted X4 phenotype were found. Conclusion This study provided the first direct comparison between the HIV-1 quasispecies archived as provirus in circulating monocytes and T lymphocytes with that of plasma virions replicating in the same cell types. Ultra-deep pyrosequencing generated data with some order of magnitude higher than any previously obtained with conventional approaches. Next generation sequencing allowed the analysis of previously inaccessible aspects of HIV-1 quasispecies, such as co-receptor usage of minority variants present in archived proviral sequences and in actually replicating virions, which may have clinical and therapeutic relevance.
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- 2009
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37. Evolution of HIV-1 tropism at quasispecies level after 5 years of combination antiretroviral therapy in patients always suppressed or experiencing episodes of virological failure
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Rozera, Gabriella, Abbate, Isabella, Giombini, Emanuela, Castagna, Antonella, De Luca, Andrea, Ceccherini-Silberstein, Francesca, Cozzi Lepri, Alessandro, Cassola, Giovanni, Torti, Carlo, d'Arminio Monforte, Antonella, Ippolito, Giuseppe, Capobianchi, Maria R., Quiros, Roldan, Moroni M, M. E., Andreoni, M, Angarano, G, Antinori, A, d'Arminio Monforte, A, Castelli, F, Cauda, R, Di Perri, G, Galli, M, Iardino, R, Ippolito, G, Lazzarin, A, Perno, C, von Schloesser, F, Viale, P, Castagna, A, Ceccherini-Silberstein, F, Cozzi-Lepri, A, Girardi, E, Lo Caputo, S, Mussini, C, Puoti, M, Ammassari, A, Balotta, C, Bonfanti, P, Bonora, S, Borderi, M, Capobianchi, M, Cingolani, A, Cinque, P, De Luca, A, Di Biagio, A, Gianotti, N, Gori, A, Guaraldi, G, Lapadula, G, Lichtner, M, Madeddu, G, Maggiolo, F, Marchetti, G, Marcotullio, S, Monno, L, Quiros Roldan, E, Rusconi, S, Cicconi, P, Fanti, I, Formenti, T, Galli, L, Lorenzini, P, Carletti, F, Carrara, S, Castrogiovanni, A, Di Caro, A, Petrone, F, Prota, G, Quartu, S, Giacometti, A, Costantini, A, Mazzoccato, S, Santoro, C, Suardi, C, Vanino, E, Verucchi, G, Minardi, C, Quirino, T, Abeli, C, Manconi, P, Piano, P, Vecchiet, J, Falasca, K, Sighinolfi, L, Segala, D, Mazzotta, F, Cassola, G, Viscoli, C, Alessandrini, A, Piscopo, R, Mazzarello, G, Mastroianni, C, Belvisi, V, Caramma, I, Chiodera, A, Castelli, A, Rizzardini, G, Ridolfo, A, Piolini, R, Salpietro, S, Carenzi, L, Moioli, M, Tincati, C, Puzzolante, C, Abrescia, N, Chirianni, A, Guida, M, Gargiulo, M, Baldelli, F, Francisci, D, Parruti, G, Ursini, T, Magnani, G, Ursitti, M, Vullo, V, D'Avino, A, Gallo, L, Nicastri, E, Acinapura, R, Capozzi, M, Libertone, R, Tebano, G, Cattelan, A, Sasset, L, Mura, M, Rossetti, B, Caramello, P, Orofino, G, Sciandra, M, Bassetti, M, Londero, A, Pellizzer, G, Manfrin, V., Rozera, G, Abbate, I, Giombini, E, Castagna, A, De Luca, A, Ceccherini Silberstein, F, Cozzi Lepri, A, Cassola, G, Torti, C, d'Arminio Monforte, A, Ippolito, G, Capobianchi, M, Gori, A, Rozera G, Abbate I, Giombini E, Castagna A, De Luca A, Ceccherini-Silberstein F, Cozzi Lepri A, Cassola G, Torti C, d'Arminio Monforte A, Ippolito G, Capobianchi MR, ICONA Foundation Group […, Moroni M, Andreoni M, Angarano G, Antinori A, Castelli F, Cauda R, Di Perri G, Galli M, Iardino R, Lazzarin A, Perno C, von Schloesser F, Girardi E, Lo Caputo S, Mussini C, Puoti M, Ammassari A, Balotta C, Bonfanti P, Bonora S, Borderi M, Cingolani A, Cinque P, Gianotti N, Gori A, Guaraldi G, Lapadula G, Lichtner M, Madeddu G, Maggiolo F, Marchetti G, Marcotullio S, Monno L, Quiros Roldan E, Rusconi S, Cicconi P, Fanti I, Formenti T, Galli L, Lorenzini P, Carletti F, Carrara S, Castrogiovanni A, Di Caro A, Petrone F, Prota G, Quartu S, Giacometti A, Costantini A, Mazzoccato S, Santoro C, Suardi C, Viale P, Vanino E, Verucchi G, Minardi C, Quirino T, Abeli C, Manconi P, Piano P, Vecchiet J, Falasca K, Sighinolfi L, Segala D, Mazzotta F, Viscoli C, Alessandrini A, Piscopo R, Mazzarello G, Mastroianni C, Belvisi V, Caramma I, Chiodera A, Castelli A, Rizzardini G, Ridolfo A, Piolini R, Salpietro S, Carenzi L, Moioli M, Tincati C, Puzzolante C, Abrescia N, Chirianni A, Guida M, Gargiulo M, Baldelli F, Francisci D, Parruti G, Ursini T, Magnani G, Ursitti M, Vullo V, d'Avino A, Gallo L, Nicastri E, Acinapura R, Capozzi M, Libertone R, Tebano G, Cattelan A, Sasset L, Mura M, Rossetti B, Caramello P, Orofino G, Sciandra M, Bassetti M, Londero A, Pellizzer G, Manfrin V, …], Rozera, Gabriella, Abbate, Isabella, Giombini, Emanuela, ICONA Fdn, Grp, and Castagna, Antonella
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Male ,Time Factors ,HIV Infections ,Cohort Studies ,Co-receptor usage ,CART ,HIV Infection ,Pharmacology (medical) ,Prospective Studies ,Ultra-deep pyrosequencing ,education.field_of_study ,Medicine (all) ,Provirus ,Middle Aged ,Viral Load ,Settore MED/07 - Microbiologia e Microbiologia Clinica ,Infectious Diseases ,Anti-Retroviral Agents ,Viral evolution ,Combination ,Drug Therapy, Combination ,Female ,Viral load ,Human ,Microbiology (medical) ,Adult ,Time Factor ,HIV quasispecies ,Tropism switch ,HIV-1 ,Humans ,Tropism ,Evolution, Molecular ,Pharmacology ,cART ,co-receptor usage ,tropism switch ,ultra-deep pyrosequencing ,Evolution ,Population ,Viremia ,Viral quasispecies ,Biology ,Settore MED/17 - MALATTIE INFETTIVE ,NO ,Drug Therapy ,medicine ,education ,Molecular ,medicine.disease ,HIV quasispecie ,Virology ,CART, Co-receptor usage, HIV quasispecies, Tropism switch, Ultra-deep pyrosequencing ,Prospective Studie ,Immunology ,Tissue tropism ,Anti-Retroviral Agent ,Cohort Studie - Abstract
Received 27 February 2014; returned 15 April 2014; revised 29 May 2014; accepted 12 June 2014Objectives:Tropism evolution of HIV-1 quasispecies was analysed by ultra-deep pyrosequencing (UDPS) inpatients on first-line combination antiretroviral therapy (cART) always suppressed or experiencing virologicalfailure episodes.Methods:Among ICONA patients, two groups of 20 patients on cARTfor ≥5 years, matched for baseline viraemiaand therapy duration, were analysed [Group I, patients always suppressed; and Group II, patients experiencingepisode(s) of virological failure]. Viral tropism was assessed by V3 UDPS on plasma RNA before therapy (T0) andon peripheral blood mononuclearcell proviral DNA before–after therapy (T0-T1), using geno2pheno false positiverate (FPR) (threshold for X4: 5.75). For each sample, quasispecies tropism was assigned according to X4 variantfrequency: R5, ,0.3% X4; minority X4, 0.3%–19.9% X4; and X4, ≥20% X4. An R5–X4 switch was defined as achange from R5/minority X4 in plasma/proviral genomes at T0 to X4 in provirus at T1.Results: At baseline, mean FPR and %X4 of viral RNA were positively correlated with those of proviral DNA. Aftertherapy, proviral DNA load significantly decreased in Group I; mean FPR of proviral quasispecies significantlydecreased and %X4 increased in Group II. An R5–X4 switch was observed in five patients (two in Group I andthree in Group II), all harbouring minority X4 variants at T0.Conclusions:UDPS analysis revealsthat the tropism switch isnot an ‘on–off’ phenomenon, but may result fromaprofound re-shaping of viral quasispecies, even under suppressive cART. However, episodes of virological failureseem to prevent reduction of proviral DNA and to accelerate viral evolution, as suggested by decreased FPR andincreased %X4 at T1 in Group II patients.Keywords: cART, HIV quasispecies, co-receptor usage, ultra-deep pyrosequencing, tropism switch
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- 2014
38. Multi-omics approach to COVID-19: a domain-based literature review
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Chiara Montaldo, Francesco Messina, Isabella Abbate, Manuela Antonioli, Veronica Bordoni, Alessandra Aiello, Fabiola Ciccosanti, Francesca Colavita, Chiara Farroni, Saeid Najafi Fard, Emanuela Giombini, Delia Goletti, Giulia Matusali, Gabriella Rozera, Martina Rueca, Alessandra Sacchi, Mauro Piacentini, Chiara Agrati, Gian Maria Fimia, Maria Rosaria Capobianchi, Francesco Nicola Lauria, Giuseppe Ippolito, Montaldo, C., Messina, F., Abbate, I., Antonioli, M., Bordoni, V., Aiello, A., Ciccosanti, F., Colavita, F., Farroni, C., Najafi Fard, S., Giombini, E., Goletti, D., Matusali, G., Rozera, G., Rueca, M., Sacchi, A., Piacentini, M., Agrati, C., Fimia, G. M., Capobianchi, M. R., Lauria, F. N., and Ippolito, G.
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COVID-19 ,Conceptual domain ,Host signatures ,Omics ,Pathways ,Phenotypes ,SARS-CoV-2 ,Settore BIO/06 ,Pandemic ,General Medicine ,Review ,General Biochemistry, Genetics and Molecular Biology ,Immunity, Innate ,Phenotype ,Host signature ,Omic ,Medicine ,Humans ,Pandemics ,Pathway ,Human - Abstract
Background Omics data, driven by rapid advances in laboratory techniques, have been generated very quickly during the COVID-19 pandemic. Our aim is to use omics data to highlight the involvement of specific pathways, as well as that of cell types and organs, in the pathophysiology of COVID-19, and to highlight their links with clinical phenotypes of SARS-CoV-2 infection. Methods The analysis was based on the domain model, where for domain it is intended a conceptual repository, useful to summarize multiple biological pathways involved at different levels. The relevant domains considered in the analysis were: virus, pathways and phenotypes. An interdisciplinary expert working group was defined for each domain, to carry out an independent literature scoping review. Results The analysis revealed that dysregulated pathways of innate immune responses, (i.e., complement activation, inflammatory responses, neutrophil activation and degranulation, platelet degranulation) can affect COVID-19 progression and outcomes. These results are consistent with several clinical studies. Conclusions Multi-omics approach may help to further investigate unknown aspects of the disease. However, the disease mechanisms are too complex to be explained by a single molecular signature and it is necessary to consider an integrated approach to identify hallmarks of severity.
- Published
- 2021
39. Early ART in primary HIV infection may also preserve lymphopoiesis capability in circulating haematopoietic progenitor cells: a case report
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Veronica Bordoni, Alessandra Sacchi, Chiara Agrati, Isabella Abbate, Nicoletta Orchi, Federico Martini, Gabriella Rozera, Adriana Ammassari, Rita Casetti, Nicola Tumino, Eleonora Cimini, Domenico Viola, Carmela Pinnetti, Bordoni, V., Casetti, R., Viola, D., Abbate, I., Rozera, G., Sacchi, A., Cimini, E., Tumino, N., Agrati, C., Orchi, N., Pinnetti, C., Ammassari, A., and Martini, F.
- Subjects
Pharmacology ,Microbiology (medical) ,T cell ,T cells ,Biology ,Emtricitabine ,Haematopoiesis ,Antiretroviral treatment ,Infectious Diseases ,medicine.anatomical_structure ,HPC ,Immunology ,medicine ,Pharmacology (medical) ,Lymphopoiesis ,Bone marrow ,Progenitor cell ,Viral load ,CD8 ,medicine.drug - Abstract
Sir, ART effectively suppresses viral replication and controls infection for an undefined period of time; however, viral eradication is not achievable because of long-lived cellular HIV reservoirs. We previously showed that, in chronically infected subjects with undetectable plasma HIV-RNA, bone marrow CD34+ haematopoietic progenitor cells (HPCs) are apparently free of HIV replication, but are blunted in differentiation capability, and may harbour HIV-DNA even after a long period on successful ART. Moreover, in patients treated with successful ART for a very long time, a persistent impairment in the lymphopoietic capability of circulating CD34+ HPCs was found, and lymphopoiesis exhaustion resulted correlated to systemic immune activation, only partially reversed by prolonged ART. To date, the mechanisms of HIV-related lymphopoiesis dysfunction remain largely unexplained, and in particular, little information is available on the possibility of limiting the occurrence of irreversible damage by early ART introduction. We herein describe immune activation levels, T cell profile/response and circulating HPC kinetics in a patient with primary HIV infection receiving early treatment with ART. The patient was further followed for 12 months, and blood samples were analysed before (baseline) and after 2, 24 and 48 weeks of ART. A young adult male was recently diagnosed with HIV acute infection (Fiebig IV stage according to Fiebig et al.). Baseline plasma HIV-1 RNA was 1868262 copies/mL, and CD4+ T lymphocyte count was 389 cells/mm. Ritonavir-boosted darunavir, tenofovir+ emtricitabine and raltegravir were started on day 3 after diagnosis. After 12 weeks of ART, viral load dropped ,40 copies/mL and ART was simplified to rilpivirine+emtricitabine+tenofovir. Plasma HIV-RNA remained undetectable at all timepoints thereafter. The viro-immunological parameters are shown in Figure 1(a). CD4+ cell count steadily increased over time: 534, 1218 and 1072 cells/mL at weeks 2, 24 and 48, respectively. Proviral HIV-DNA, determined as described in Rozera et al., was 82479 copies/10 PBMC at baseline and 21534, 1752 and 6809 copies/10 PBMC at weeks 2, 24 and 48, respectively. CD8+ T cell activation, measured as CD38 expression by flow cytometry, paralleled plasma HIV-RNA viral load, reaching at week 24 the level found in healthy donors. On the other hand, the level of early CD8+ T cells, evaluated by CD127 expression, steadily increased from baseline to week 48 (Figure 1b). Peripheral blood CD4+ and CD8+ T cell differentiation was evaluated by CD45RA and CCR7 expression. As shown in Figure 1(c), the variation in CD4+ subsets included a decrease in effector memory (EM; CD45RA2/CCR72) and an increase in Research letters
- Published
- 2015
40. The basal activation state of DC subsets correlates with anti-HCV treatment outcome in HCV/HIV co-infected patients
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Alessandra Sacchi, Maria Rosaria Capobianchi, Gabriella Rozera, Chiara Agrati, Gianpiero D'Offizi, Isabella Abbate, Federico Martini, Chrysoula Vlassi, Sacchi, A., Agrati, C., D'Offizi, G., Vlassi, C., Rozera, G., Abbate, I., Capobianchi, M. R., and Martini, F.
- Subjects
Myeloid ,Hepacivirus ,Hepatitis C virus ,Immunology ,chemical and pharmacologic phenomena ,HIV Infections ,Interferon alpha-2 ,medicine.disease_cause ,Antiviral Agents ,Polyethylene Glycols ,chemistry.chemical_compound ,Ribavirin ,medicine ,Immunology and Allergy ,Humans ,Interferon alfa ,IFN-α ,Retrospective Studies ,biology ,virus diseases ,HIV ,Interferon-alpha ,hemic and immune systems ,Dendritic Cells ,Hepatitis C, Chronic ,Viral Load ,biology.organism_classification ,digestive system diseases ,Recombinant Proteins ,medicine.anatomical_structure ,Treatment Outcome ,chemistry ,Lentivirus ,HCV ,Drug Therapy, Combination ,Viral disease ,Viral load ,Dendritic cell ,medicine.drug - Abstract
In this work we evaluated plasmacytoid (pDC) and myeloid dendritic (mDC) cells activation before and during anti-HCV treatment in HCV+/HIV+ individuals.HCV+/HIV+ patients received Peg-IFN-α2b subcutaneously for 28. days, followed by oral weight-based ribavirin. DCs activation was evaluated by flow cytometry.Baseline pDC CD80 and CD86 expression was correlated with HIV, but not with HCV viral load. A transient decrease of HIV RNA was found not associated with DC activation. When patients were grouped according to early/sustained virological response (EVR/SVR) to anti-HCV treatment, baseline pDC CD80 and CD86 expression was higher in non-EVR and non-SVR compared to EVR and SVR. Moreover, in responder patients CD80 and CD86 were upregulated by IFN-α. Our data suggest a correlation between DCs activation and response to therapy. These findings could be helpful to better understand the mediators of IFN-α action in HCV+/HIV+ patients and to explore possible exploitation of this knowledge to improve therapeutic response. © 2010 Elsevier Inc.
- Published
- 2010
41. Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing
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Isabella Abbate, Maria Carmela Solmone, Luciano Prosperi, Giovanni Ulivi, Maria Rosaria Capobianchi, Gabriella Rozera, Mattia Prosperi, Donatella Vincenti, Alessandro Bruselles, Prosperi, M, Prosperi, L, Bruselles, A, Abbate, I, Rozera, G, Vincenti, D, Solmone, M, Capobianchi, M, and Ulivi, Giovanni
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Hepatitis B virus ,Sequence assembly ,Genomics ,Viral quasispecies ,Genome, Viral ,Biology ,lcsh:Computer applications to medicine. Medical informatics ,Genome ,Biochemistry ,DNA sequencing ,03 medical and health sciences ,symbols.namesake ,0302 clinical medicine ,Structural Biology ,Humans ,Computer Simulation ,lcsh:QH301-705.5 ,Molecular Biology ,Phylogeny ,030304 developmental biology ,Sanger sequencing ,0303 health sciences ,Applied Mathematics ,Methodology Article ,Genetic Variation ,Sequence Analysis, DNA ,Amplicon ,3. Good health ,Computer Science Applications ,lcsh:Biology (General) ,030220 oncology & carcinogenesis ,symbols ,lcsh:R858-859.7 ,Algorithm ,Algorithms ,Software ,Reference genome - Abstract
Background Next-generation sequencing (NGS) offers a unique opportunity for high-throughput genomics and has potential to replace Sanger sequencing in many fields, including de-novo sequencing, re-sequencing, meta-genomics, and characterisation of infectious pathogens, such as viral quasispecies. Although methodologies and software for whole genome assembly and genome variation analysis have been developed and refined for NGS data, reconstructing a viral quasispecies using NGS data remains a challenge. This application would be useful for analysing intra-host evolutionary pathways in relation to immune responses and antiretroviral therapy exposures. Here we introduce a set of formulae for the combinatorial analysis of a quasispecies, given a NGS re-sequencing experiment and an algorithm for quasispecies reconstruction. We require that sequenced fragments are aligned against a reference genome, and that the reference genome is partitioned into a set of sliding windows (amplicons). The reconstruction algorithm is based on combinations of multinomial distributions and is designed to minimise the reconstruction of false variants, called in-silico recombinants. Results The reconstruction algorithm was applied to error-free simulated data and reconstructed a high percentage of true variants, even at a low genetic diversity, where the chance to obtain in-silico recombinants is high. Results on empirical NGS data from patients infected with hepatitis B virus, confirmed its ability to characterise different viral variants from distinct patients. Conclusions The combinatorial analysis provided a description of the difficulty to reconstruct a quasispecies, given a determined amplicon partition and a measure of population diversity. The reconstruction algorithm showed good performance both considering simulated data and real data, even in presence of sequencing errors.
- Published
- 2011
42. Cerebrospinal Fluid and Peripheral Blood Lymphomonocyte Single-Cell Transcriptomics in a Subject with Multiple Sclerosis Acutely Infected with HIV.
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Pinnetti C, Rozera G, Messina F, Spezia PG, Lazzari E, Fabeni L, Chillemi G, Pietrucci D, Haggiag S, Mastrorosa I, Vergori A, Girardi E, Antinori A, Maggi F, and Abbate I
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- Humans, Leukocytes, Mononuclear metabolism, Leukocytes, Mononuclear virology, HIV-1 genetics, Adult, Gene Expression Profiling methods, Male, Single-Cell Analysis methods, Multiple Sclerosis cerebrospinal fluid, Multiple Sclerosis genetics, Multiple Sclerosis virology, Multiple Sclerosis blood, HIV Infections cerebrospinal fluid, HIV Infections genetics, HIV Infections virology, Transcriptome
- Abstract
Signatures of neurodegeneration in clinical samples from a subject with multiple sclerosis (MS) acutely infected with HIV were investigated with single-cell transcriptomics using 10X Chromium technology. Sequencing was carried out on NovaSeq-TM, and the analysis was performed with Cell Ranger software (v 7.1.0) associated with a specifically established bioinformatic pipeline. A total of 1446 single-cell transcriptomes in cerebrospinal fluid (CSF) and 4647 in peripheral blood mononuclear cells (PBMCs) were obtained. In the CSF, many T-cell lymphocytes with an enriched amount of plasma cells and plasmacytoid dendritic (pDC) cells, as compared to the PBMCs, were detected. An unsupervised cluster analysis, putting together our patient transcriptomes with those of a publicly available MS scRNA-seq dataset, showed up-regulated microglial neurodegenerative gene expression in four clusters, two of which included our subject's transcriptomes. A few HIV-1 transcripts were found only in the CD4 central memory T-cells of the CSF compartment, mapping to the gag-pol , vpu , and env regions. Our data, which describe the signs of neurodegenerative gene expression in a very peculiar clinical situation, did not distinguish the cause between multiple sclerosis and HIV infection, but they can give a glimpse of the high degree of resolution that may be obtained by the single-cell transcriptomic approach.
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- 2024
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43. Role of Direct Sexual Contact in Human Transmission of Monkeypox Virus, Italy.
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Sberna G, Rozera G, Minosse C, Bordi L, Mazzotta V, D'Abramo A, Girardi E, Antinori A, Maggi F, and Lalle E
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- Humans, Italy epidemiology, Male, Female, Viral Load, Adult, Middle Aged, Virus Replication, Sexual Behavior, RNA, Viral, Semen virology, DNA, Viral, Mpox (monkeypox) transmission, Mpox (monkeypox) epidemiology, Mpox (monkeypox) virology, Monkeypox virus genetics
- Abstract
The 2022 global mpox outbreak was driven by human-to-human transmission, but modes of transmission by sexual relationship versus sexual contact remain unclear. We evaluated sexual transmission of mpox by using monkeypox virus (MPXV) G2R-mRNA as a marker of ongoing viral replication through in vitro experiments. We analyzed clinical samples of 15 MPXV-positive patients in Italy from different biological regions by using the setup method. The presence of MPXV DNA, MPXV G2R-mRNA, or both in all analyzed lesion swab samples, independent of viral load, confirmed a higher infectivity risk from skin lesions. Positivity for MPXV G2R-mRNA in nasopharyngeal swabs was associated with high MPXV load, whereas positive results for MPXV G2R-mRNA were obtained only in the 2 semen samples with the lowest MPXV loads. Our results suggest that close or skin-to-skin contact during sexual intercourse is the main route of sexual transmission and that semen is a minor driver of infection, regardless of MPXV load.
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- 2024
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44. Rapid Determination of SARS-CoV-2 Integrity and Infectivity by Using Propidium Monoazide Coupled with Digital Droplet PCR.
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Sberna G, Mija C, Lalle E, Rozera G, Matusali G, Carletti F, Girardi E, and Maggi F
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- Humans, RNA, Viral genetics, RNA, Viral isolation & purification, COVID-19 Nucleic Acid Testing methods, Polymerase Chain Reaction methods, SARS-CoV-2 genetics, SARS-CoV-2 isolation & purification, Azides chemistry, Propidium analogs & derivatives, Propidium chemistry, COVID-19 virology, Viral Load methods, Nasopharynx virology
- Abstract
SARS-CoV-2 is a highly infectious virus responsible for the COVID-19 pandemic. Therefore, it is important to assess the risk of SARS-CoV-2 infection, especially in persistently positive patients. Rapid discrimination between infectious and non-infectious viruses aids in determining whether prevention, control, and treatment measures are necessary. For this purpose, a method was developed and utilized involving a pre-treatment with 50 µM of propidium monoazide (PMAxx, a DNA intercalant) combined with a digital droplet PCR (ddPCR). The ddPCR method was performed on 40 nasopharyngeal swabs (NPSs) both before and after treatment with PMAxx, revealing a reduction in the viral load at a mean of 0.9 Log copies/mL (SD ± 0.6 Log copies/mL). Furthermore, six samples were stratified based on the Ct values of SARS-CoV-2 RNA (Ct < 20, 20 < Ct < 30, Ct > 30) and analyzed to compare the results obtained via a ddPCR with viral isolation and a negative-chain PCR. Of the five samples found positive via a ddPCR after the PMAxx treatment, two of the samples showed the highest post-treatment SARS-CoV-2 loads. The virus was isolated in vitro from both samples and the negative strand chains were detected. In three NPS samples, SARS CoV-2 was present post-treatment at a low level; it was not isolated in vitro, and, when detected, the strand was negative. Our results indicate that the established method is useful for determining whether the SARS-CoV-2 within positive NPS samples is intact and capable of causing infection.
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- 2024
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45. HIV-1 RNA monitoring with a dual-target diagnostic assay: A case report.
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Sberna G, Gagliardini R, Rozera G, Forbici F, Cicalini S, Antinori A, Maggi F, and Amendola A
- Abstract
In a restricted subset of people living with HIV-1 (PLWH) on antiretroviral therapy (ART) with persistent suppressed viral load (i.e., pol -based HIV-RNA repeatedly undetected), a dual-target ( pol and LTR ) diagnostic assay for HIV-RNA monitoring can measure quantifiable levels of viral loads (VL) above 30 copies/mL exclusively through the amplification of the LTR region, while the pol target results undetected. We report a patient who shows high levels of HIV-RNA detected exclusively through amplification of the LTR region while undetected by the pol region, during a long monitoring period, from 2018 to date. In this follow-up, the ART was modified without reaching LTR -based undetected HIV-RNA values. Immunological and virological parameters remained optimal with a progressive and steady gain of the CD4/CD8 ratio. The clinical history of this patient, shows that LTR -based viremia above 50 copies/mL can be found occasionally or persistently in the plasma of PLWH under suppressive ART, even at high levels. Based on previous studies, VL detected and quantified exclusively through the amplification of the LTR region corresponds to partial or incomplete HIV-RNA transcripts, which cannot trigger new infections. Interestingly, changes in ART do not eliminate repeated findings of these unusual viral elements., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors.)
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- 2024
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46. Human and Viral microRNA Expression in Acute and Chronic HIV Infections.
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Lazzari E, Rozera G, Gagliardini R, Esvan R, Mondi A, Mazzotta V, Camici M, Girardi E, Antinori A, Maggi F, and Abbate I
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- Humans, Gene Expression Profiling, Male, Adult, Female, Acute Disease, Chronic Disease, Middle Aged, HIV-1 genetics, Immunity, Innate, Gene Expression Regulation, MicroRNAs genetics, HIV Infections virology, HIV Infections genetics, RNA, Viral genetics, High-Throughput Nucleotide Sequencing
- Abstract
Human and viral microRNAs (miRNAs) are involved in the regulation of gene transcription, and the establishment of their profiles in acute (AHI) and chronic (CHI) HIV infections may shed light on the pathogenetic events related to different phases of HIV disease. Next-generation sequencing (NGS) of miRNA libraries was performed, and the reads were used to analyze miRNA differential expression in the plasma with AHI and CHI. Functional analysis was then undertaken to investigate the biological processes characterizing the two phases of HIV infection. Except for hsa-miR-122-5p, which was found in 3.39% AHI vs. 0.18% CHI, the most represented human miRNAs were similarly represented in AHI and CHI. However, when considering the overall detected miRNAs in AHI and CHI, 15 displayed differential expression (FDR p < 0.05). Functional analysis identified 163 target mRNAs involved in promoting angiogenesis activation in AHI versus CHI through the action of hsa-miR10b-5p, hsa-miR1290, hsa-miR1-3p, and hsa-miR296-5p. The viral miRNAs detected, all belonging to herpesviruses, accounted for only 0.014% of total reads. The present data suggest that AHI patients exhibit strong innate immune activation through the upregulation of hsa-miR-122-5p and early activation of angiogenesis. More specific investigations are needed to study the role of viral miRNAs in HIV pathogenesis.
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- 2024
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47. Development and validation of a nanoplate-based digital PCR assay for absolute MPXV quantification.
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Specchiarello E, Carletti F, Matusali G, Abbate I, Rozera G, Minosse C, Petrivelli E, Ferraioli V, Sciamanna R, and Maggi F
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- Humans, Laboratories, Real-Time Polymerase Chain Reaction, Biological Assay, DNA, Viral genetics, Mpox (monkeypox) diagnosis, Monkeypox virus isolation & purification
- Abstract
Quantification of mpox virus (MPXV) across different human body anatomical sites can provide insights about the most likely transmission routes, so methods able to release absolute and exact quantitative values of MPXV DNA are crucial. Here, we optimized a new QIAcuity digital PCR (dPCR) protocol for the detection and quantification of MPXV DNA in clinical samples and assessed the performance of the assay by comparing the results obtained in 144 biological samples with those resulting from the use of an in-house real-time PCR (qPCR). Overall, the concordance between the two assays was 95%, with samples identified concordantly as MPXV DNA positive and having a mean number of copies per μl of 1708 (95% CI: 107-2830 copies/μl). The remaining samples gave discordant results, with 5 out of 7 detected with the QIAcuity dPCR assay but not with the in-house qPCR. MPXV DNA levels measured by QIAcuity dPCR were strongly correlated with the Ct values detected by in-house qPCR and with those detected by another dPCR assay previously developed in our laboratories. The QIAcuity dPCR assay may be a robust and easy-to-perform method for MPXV DNA quantification in several biological samples., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved.)
- Published
- 2023
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48. Virological characterization of HIV-1 RNA elements detected exclusively through the LTR region by the dual-target Aptima HIV-1 Quant Dx assay in a subset of positive patients.
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Sberna G, Nardacci R, Berno G, Rozera G, Giombini E, Fabeni L, Specchiarello E, Maggi F, and Amendola A
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- Humans, Leukocytes, Mononuclear, RNA, Viral genetics, Sensitivity and Specificity, Viral Load methods, HIV Infections diagnosis, HIV-1 genetics, HIV Seropositivity
- Abstract
Background: In a restricted subset of HIV patients with suppressed viral load (i.e., pol-undetected HIV-RNA), the Aptima HIV-1 Quant Dx Assay (Aptima), a dual-target (pol and LTR) and dual-probe test for viral load (VL) monitoring, can detect HIV-RNA exclusively through amplification of the LTR region., Objectives: To analyze the virological characteristics of the HIV-RNA elements detected only through LTR amplification (LTR-e)., Study Design: LTR-e isolated from plasma and peripheral blood mononuclear cells (PBMC) were evaluated for their ability to trigger productive infections. Viral pellets morphology and ultrastructural characteristics of PBMC from LTR-e patients were examined by electron microscopy. Plasma LTR-e underwent Sanger sequencing. Exosomes were examined with Aptima for LTR-e content., Results: In-vitro, LTR-e could not infect PBMC, induce cytopathic effects, or cause syncytia, even at high VL (e.g., >10,000 copies/mL). Under the electron microscope, plasma pellets and PBMC from patients with LTR-e showed atypical vesicles. Sanger sequencing of LTR-e yielded no results. Moreover, in plasma samples, LTR-e were associated with cell debris, never with exosomes., Conclusions: Differently from other dual-target but single-probe assays, Aptima unveils VL based only on LTR amplification in some HIV patients. Here, we show that LTR-e represent partial/incomplete/non-canonical transcripts unable to trigger productive infection or transmit HIV-1 infection. The recognition of VL based only on LTR-e in infected individuals is crucial as it allows to avoid inappropriate decisions in the clinical management of HIV patients, such as retesting of VL and switching of ART. Physicians and HIV-RNA dual-target assay manufacturers should consider the important implications of not recognizing this singular type of VL., Competing Interests: Declaration of Competing Interest The authors declare no competing interests., (Copyright © 2023. Published by Elsevier B.V.)
- Published
- 2023
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49. Kinetics of TTV Loads in Peripheral Blood Mononuclear Cells of Early Treated Acute HIV Infections.
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Abbate I, Rozera G, Cimini E, Carletti F, Tartaglia E, Rubino M, Pittalis S, Esvan R, Gagliardini R, Mondi A, Mazzotta V, Camici M, Girardi E, Vaia F, Puro V, Antinori A, and Maggi F
- Subjects
- Humans, Leukocytes, Mononuclear, DNA, HIV Infections, Torque teno virus genetics, HIV-1 genetics
- Abstract
Torquetenovirus (TTV) is the most abundant component of the human blood virome and its replication is controlled by a functioning immune system. In this study, TTV replication was evaluated in 21 people with acute HIV infection (AHI) and immune reconstitution following antiretroviral therapy (ART). PBMC-associated TTV and HIV-1 DNA, as well as plasma HIV-1 RNA, were measured by real-time PCR. CD4 and CD8 differentiation, activation, exhaustion, and senescence phenotypes were analyzed by flow cytometry. Thirteen healthy donors (HD) and twenty-eight chronically infected HIV individuals (CHI), late presenters at diagnosis, were included as control groups. TTV replication in AHI seems to be controlled by the immune system being higher than in HD and lower than in CHI. During ART, a transient increase in TTV DNA levels was associated with a significant perturbation of activation and senescence markers on CD8 T cells. TTV loads were positively correlated with the expansion of CD8 effector memory and CD57+ cells. Our results shed light on the kinetics of TTV replication in the context of HIV acute infection and confirm that the virus replication is strongly regulated by the modulation of the immune system.
- Published
- 2023
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50. Kinetics of viral DNA in body fluids and antibody response in patients with acute Monkeypox virus infection.
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Colavita F, Mazzotta V, Rozera G, Abbate I, Carletti F, Pinnetti C, Matusali G, Meschi S, Mondi A, Lapa D, Vita S, Minosse C, Aguglia C, Gagliardini R, Specchiarello E, Bettini A, Nicastri E, Girardi E, Vaia F, Antinori A, and Maggi F
- Abstract
We report the follow-up laboratory investigation of three MPXV cases infected in May-June 2022 from diagnosis to disease resolution, monitoring viral shedding in different body fluids and antibody kinetics. Out of 138 non-lesion samples, viral DNA was found in 92.3% saliva, 85.7% semen, 86.2% oropharyngeal swabs, 51.7% plasma, 46.1% stool, and 9.5% urine samples. Viral load quantified by digital PCR widely varied, but tend to be higher in oropharyngeal swabs, saliva, and stool. Replication competent virus was recovered from four out of seventeen samples, including 1 saliva, 1 oropharyngeal swabs, 1 semen, and 1 stool. The analysis of the antibody kinetics revealed that IgM, IgA, and IgG antibodies were detected within two weeks post-symptoms onset for all three patients, with IgG detected early on at day 4-8 and IgM and IgA showing lower titers along the time frame of the study. Antibody levels increased during the second week of illness with IgG reaching high titers., Competing Interests: The authors declare that no conflicting financial interests or other competing relationships exist for the present study., (© 2023 The Authors.)
- Published
- 2023
- Full Text
- View/download PDF
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