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Complex systems are inherently multilevel and multiscale systems. The infectious disease system is considered a complex system resulting from the interaction between three sub-systems (host, pathogen, and environment) organized into a hierarchical structure, ranging from the cellular to the macro-ecosystem level, with multiscales. Therefore, to describe infectious disease phenomena that change through time and space and at different scales, we built a model framework where infectious disease must be considered the set of biological responses of human hosts to pathogens, with biological pathways shared with other pathologies in an ecological interaction context. In this paper, we aimed to design a framework for building a disease model for COVID-19 based on current literature evidence. The model was set up by identifying the molecular pathophysiology related to the COVID-19 phenotypes, collecting the mechanistic knowledge scattered across scientific literature and bioinformatic databases, and integrating it using a logical/conceptual model systems biology. The model framework building process began from the results of a domain-based literature review regarding a multiomics approach to COVID-19. This evidence allowed us to define a framework of COVID-19 conceptual model and to report all concepts in a multilevel and multiscale structure. The same interdisciplinary working groups that carried out the scoping review were involved. The conclusive result is a conceptual method to design multiscale models of infectious diseases. The methodology, applied in this paper, is a set of partially ordered research and development activities that result in a COVID-19 multiscale model.
Francesco Messina; Chiara Montaldo; Isabella Abbate; Manuela Antonioli; Veronica Bordoni; Giulia Matusali; Alessandra Sacchi; Emanuela Giombini; Gian Fimia; Mauro Piacentini; Maria Capobianchi; Francesco Lauria; Giuseppe Ippolito; on behalf of COVID-19 Scoping Review Working Group. Rationale and Criteria for a COVID-19 Model Framework. Viruses 2021, 13, 1309 .
AMA StyleFrancesco Messina, Chiara Montaldo, Isabella Abbate, Manuela Antonioli, Veronica Bordoni, Giulia Matusali, Alessandra Sacchi, Emanuela Giombini, Gian Fimia, Mauro Piacentini, Maria Capobianchi, Francesco Lauria, Giuseppe Ippolito, on behalf of COVID-19 Scoping Review Working Group. Rationale and Criteria for a COVID-19 Model Framework. Viruses. 2021; 13 (7):1309.
Chicago/Turabian StyleFrancesco Messina; Chiara Montaldo; Isabella Abbate; Manuela Antonioli; Veronica Bordoni; Giulia Matusali; Alessandra Sacchi; Emanuela Giombini; Gian Fimia; Mauro Piacentini; Maria Capobianchi; Francesco Lauria; Giuseppe Ippolito; on behalf of COVID-19 Scoping Review Working Group. 2021. "Rationale and Criteria for a COVID-19 Model Framework." Viruses 13, no. 7: 1309.
Molecular investigation of primary HIV infections (PHI) is crucial to describe current dynamics of HIV transmission. Aim of the study was to investigate HIV transmission clusters (TC) in PHI referred during the years 2013–2020 to the National Institute for Infectious Diseases in Rome (INMI), that is the Lazio regional AIDS reference centre, and factors possibly associated with inclusion in TC. These were identified by phylogenetic analysis, based on population sequencing of pol; a more in depth analysis was performed on TC of B subtype, using ultra-deep sequencing (UDS) of env. Of 270 patients diagnosed with PHI during the study period, 229 were enrolled (median follow-up 168 (IQR 96–232) weeks). Median age: 39 (IQR 32–48) years; 94.8% males, 86.5% Italians, 83.4% MSM, 56.8% carrying HIV-1 subtype B. Of them, 92.6% started early treatment within a median of 4 (IQR 2–7) days after diagnosis; median time to sustained suppression was 20 (IQR 8–32) weeks. Twenty TC (median size 3, range 2–9 individuals), including 68 patients, were identified. A diagnosis prior to 2015 was the unique factor associated with inclusion in a TC. Added value of UDS was the identification of shared quasispecies components in transmission pairs within TC.
Lavinia Fabeni; Gabriella Rozera; Giulia Berno; Emanuela Giombini; Caterina Gori; Nicoletta Orchi; Gabriella De Carli; Silvia Pittalis; Vincenzo Puro; Carmela Pinnetti; Annalisa Mondi; Marta Camici; Maria Plazzi; Andrea Antinori; Maria Capobianchi; Isabella Abbate. Molecular Transmission Dynamics of Primary HIV Infections in Lazio Region, Years 2013–2020. Viruses 2021, 13, 176 .
AMA StyleLavinia Fabeni, Gabriella Rozera, Giulia Berno, Emanuela Giombini, Caterina Gori, Nicoletta Orchi, Gabriella De Carli, Silvia Pittalis, Vincenzo Puro, Carmela Pinnetti, Annalisa Mondi, Marta Camici, Maria Plazzi, Andrea Antinori, Maria Capobianchi, Isabella Abbate. Molecular Transmission Dynamics of Primary HIV Infections in Lazio Region, Years 2013–2020. Viruses. 2021; 13 (2):176.
Chicago/Turabian StyleLavinia Fabeni; Gabriella Rozera; Giulia Berno; Emanuela Giombini; Caterina Gori; Nicoletta Orchi; Gabriella De Carli; Silvia Pittalis; Vincenzo Puro; Carmela Pinnetti; Annalisa Mondi; Marta Camici; Maria Plazzi; Andrea Antinori; Maria Capobianchi; Isabella Abbate. 2021. "Molecular Transmission Dynamics of Primary HIV Infections in Lazio Region, Years 2013–2020." Viruses 13, no. 2: 176.
Aim was to determine the dynamics of peripheral blood mononuclear cells (PBMC)- associated total HIV-1 DNA in successfully ART-treated HIV/HCV co-infected patients receiving DAA treatment and to explore possible virological hypotheses underlying the phenomenon. Longitudinal, single-centre study measuring total HIV-1 DNA before the start of DAA, at the end of treatment (EOT), and 3 months after treatment. Univariable and multivariable analyses were used to assess factors associated with HIV-1 DNA increase ≥0.5 Log copies/million PBMC. Episomal 2-LTR forms, residual HIV-1 viremia and proviral DNA quasispecies evolution were also investigated. 119 successfully ART-treated HIV/HCV co-infected patients were included. Median baseline HIV-1 DNA was 3.84 Log copies/million PBMC (95%CI 3.49–4.05), and no significant variation with respect to baseline was found at EOT and after 3 months of DAA termination. In 17% of cases an increase ≥0.5 Log copies/million PBMC was observed at EOT compared to baseline. HIV-1 DNA increase was independently associated with lower baseline HIV-1 DNA, longer HIV suppression, raltegravir-based ART and previous exposure to interferon/ribavirin for HCV treatment. In none of the patients with HIV-1 DNA increase, 2-LTR forms were detected at baseline, while in 2 cases 2-LTR forms were found at EOT, without association with residual HIV-1 RNA viremia. No evidence of viral evolution was observed. In successfully ART-treated HIV/HCV co-infected patients receiving DAA, PBMC-associated total HIV-1 DNA was quite stable over time, but some patients showed a considerable increase at EOT when compared to baseline. A significantly higher risk of HIV DNA increase was found, in presence of lower cellular HIV reservoir at baseline. Activation of replicative-competent virus generating new rounds of viral replication seems unlikely, while mobilization of cell-associated HIV from tissue reservoirs could be hypothesized.
Gabriella Rozera; Gabriele Fabbri; Patrizia Lorenzini; Ilaria Mastrorosa; Laura Timelli; Mauro Zaccarelli; Alessandra Amendola; Alessandra Vergori; Maria Maddalena Plazzi; Stefania Cicalini; Andrea Antinori; Maria Rosaria Capobianchi; Isabella Abbate; Adriana Ammassari. Peripheral blood HIV-1 DNA dynamics in antiretroviral-treated HIV/HCV co-infected patients receiving directly-acting antivirals. PLOS ONE 2017, 12, e0187095 .
AMA StyleGabriella Rozera, Gabriele Fabbri, Patrizia Lorenzini, Ilaria Mastrorosa, Laura Timelli, Mauro Zaccarelli, Alessandra Amendola, Alessandra Vergori, Maria Maddalena Plazzi, Stefania Cicalini, Andrea Antinori, Maria Rosaria Capobianchi, Isabella Abbate, Adriana Ammassari. Peripheral blood HIV-1 DNA dynamics in antiretroviral-treated HIV/HCV co-infected patients receiving directly-acting antivirals. PLOS ONE. 2017; 12 (10):e0187095.
Chicago/Turabian StyleGabriella Rozera; Gabriele Fabbri; Patrizia Lorenzini; Ilaria Mastrorosa; Laura Timelli; Mauro Zaccarelli; Alessandra Amendola; Alessandra Vergori; Maria Maddalena Plazzi; Stefania Cicalini; Andrea Antinori; Maria Rosaria Capobianchi; Isabella Abbate; Adriana Ammassari. 2017. "Peripheral blood HIV-1 DNA dynamics in antiretroviral-treated HIV/HCV co-infected patients receiving directly-acting antivirals." PLOS ONE 12, no. 10: e0187095.
Changes in iron metabolism frequently accompany HIV-1 infection. However, while many clinical and in vitro studies report iron overload exacerbates the development of infection, many others have found no correlation. Therefore, the multi-faceted role of iron in HIV-1 infection remains enigmatic. RT-qPCR targeting the LTR region, gag, Tat and Rev were performed to measure the levels of viral RNAs in response to iron overload. Spike-in SILAC proteomics comparing i) iron-treated, ii) HIV-1-infected and iii) HIV-1-infected/iron treated T lymphocytes was performed to define modifications in the host cell proteome. Data from quantitative proteomics were integrated with the HIV-1 Human Interaction Database for assessing any viral cofactors modulated by iron overload in infected T lymphocytes. Here, we demonstrate that the iron overload down-regulates HIV-1 gene expression by decreasing the levels of viral RNAs. In addition, we found that iron overload modulates the expression of many viral cofactors. Among them, the downregulation of the REV cofactor eIF5A may correlate with the iron-induced inhibition of HIV-1 gene expression. Therefore, we demonstrated that eiF5A downregulation by shRNA resulted in a significant decrease of Nef levels, thus hampering HIV-1 replication. Our study indicates that HIV-1 cofactors influenced by iron metabolism represent potential targets for antiretroviral therapy and suggests eIF5A as a selective target for drug development.
Carmine Mancone; Alessio Grimaldi; Giulia Refolo; Isabella Abbate; Gabriella Rozera; Dario Benelli; Gian Maria Fimia; Vincenzo Barnaba; Marco Tripodi; Mauro Piacentini; Fabiola Ciccosanti. Iron overload down-regulates the expression of the HIV-1 Rev cofactor eIF5A in infected T lymphocytes. Proteome Science 2017, 15, 1 -10.
AMA StyleCarmine Mancone, Alessio Grimaldi, Giulia Refolo, Isabella Abbate, Gabriella Rozera, Dario Benelli, Gian Maria Fimia, Vincenzo Barnaba, Marco Tripodi, Mauro Piacentini, Fabiola Ciccosanti. Iron overload down-regulates the expression of the HIV-1 Rev cofactor eIF5A in infected T lymphocytes. Proteome Science. 2017; 15 (1):1-10.
Chicago/Turabian StyleCarmine Mancone; Alessio Grimaldi; Giulia Refolo; Isabella Abbate; Gabriella Rozera; Dario Benelli; Gian Maria Fimia; Vincenzo Barnaba; Marco Tripodi; Mauro Piacentini; Fabiola Ciccosanti. 2017. "Iron overload down-regulates the expression of the HIV-1 Rev cofactor eIF5A in infected T lymphocytes." Proteome Science 15, no. 1: 1-10.
The performances of the new Geenius rapid confirmatory test (Bio-Rad) were evaluated with emphasis towards identifying acute infection (AHI) and discriminating HIV-1/2 in a clinical setting Serum samples from individuals attending the L. Spallanzani Institute in Rome, Italy, for HIV diagnosis (one year retrospective collection), repeatedly reactive at 4th generation HIV-1/2 screening assays, confirmed with HIV-1 and HIV-2 Western blot (New LAV I and II Bio-Rad), were retested with Geenius. Of 6,200 samples, 406 resulted repeatedly reactive at screening, including samples from clinically confirmed AHI. New LAV I identified 378 HIV-1-positive samples. Of these, Geenius found 377 HIV-1-positive and one unclassified HIV-positive. New LAV I classified as indeterminate 18 samples, including 14 from AHI. Among these 14, Geenius results were: 12 positive, 1 indeterminate and 1 negative. Of the remaining, 2 resulted Geenius negative (false-positive screening results) and 2 HIV-2. Ten samples were New LAV I-negative (5 AHI). Geenius results were: 1 (AHI) positive and 9 negative. Geenius detected 110 additional positive samples with no p31 reactivity with respect to New LAV I, with an almost similar prevalence of low avidity samples. Geenius confirmed 3 out of 4 HIV-2 infections identified by New LAV II (one coinfected with HIV-1), while rated as HIV-1 the remaining sample, classified as coinfection by New LAV I and II. Geenius allows fast, sensitive and accurate confirmation of HIV serodiagnosis, including AHI and HIV-2 infections. The high sensitivity, in particular towards AHI, could avoid additional sampling and molecular tests.
I. Abbate; C. Pergola; M. Pisciotta; R. Sciamanna; C. Sias; N. Orchi; R. Libertone; Giuseppe Ippolito; M.R. Capobianchi. Evaluation in a clinical setting of the performances of a new rapid confirmatory assay for HIV1/2 serodiagnosis. Journal of Clinical Virology 2014, 61, 166 -169.
AMA StyleI. Abbate, C. Pergola, M. Pisciotta, R. Sciamanna, C. Sias, N. Orchi, R. Libertone, Giuseppe Ippolito, M.R. Capobianchi. Evaluation in a clinical setting of the performances of a new rapid confirmatory assay for HIV1/2 serodiagnosis. Journal of Clinical Virology. 2014; 61 (1):166-169.
Chicago/Turabian StyleI. Abbate; C. Pergola; M. Pisciotta; R. Sciamanna; C. Sias; N. Orchi; R. Libertone; Giuseppe Ippolito; M.R. Capobianchi. 2014. "Evaluation in a clinical setting of the performances of a new rapid confirmatory assay for HIV1/2 serodiagnosis." Journal of Clinical Virology 61, no. 1: 166-169.
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. 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. 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. 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.
Gabriella Rozera; Isabella Abbate; Emanuela Giombini; Antonella Castagna; Andrea De Luca; Francesca Ceccherini-Silberstein; Alessandro Cozzi Lepri; Giovanni Cassola; Carlo Torti; Antonella D'arminio Monforte; Giuseppe Ippolito; Maria R. Capobianchi; M. Moroni; M. Andreoni; G. Angarano; A. Antinori; F. Castelli; R. Cauda; G. Di Perri; M. Galli; R. Iardino; A. Lazzarin; C. F. Perno; F. von Schloesser; P. Viale; E. Girardi; S. Lo Caputo; C. Mussini; M. Puoti; A. Ammassari; C. Balotta; P. Bonfanti; S. Bonora; M. Borderi; A. Cingolani; P. Cinque; A. Di Biagio; N. Gianotti; A. Gori; G. Guaraldi; G. Lapadula; M. Lichtner; G. Madeddu; F. Maggiolo; G. Marchetti; S. Marcotullio; L. Monno; E. Quiros Roldan; S. Rusconi; P. Cicconi; I. Fanti; T. Formenti; L. Galli; P. Lorenzini; F. Carletti; S. Carrara; A. Castrogiovanni; A. Di Caro; F. Petrone; G. Prota; S. Quartu; A. Giacometti; A. Costantini; S. Mazzoccato; C. Santoro; C. Suardi; E. Vanino; G. Verucchi; C. Minardi; T. Quirino; C. Abeli; P. E. Manconi; P. Piano; J. Vecchiet; K. Falasca; L. Sighinolfi; D. Segala; F. Mazzotta; C. Viscoli; A. Alessandrini; R. Piscopo; G. Mazzarello; C. Mastroianni; V. Belvisi; I. Caramma; A. Chiodera; A. P. Castelli; G. Rizzardini; A. L. Ridolfo; R. Piolini; S. Salpietro; L. Carenzi; M. C. Moioli; C. Tincati; C. Puzzolante; N. Abrescia; A. Chirianni; M. G. Guida; M. Gargiulo; F. Baldelli; D. Francisci; G. Parruti; T. Ursini; G. Magnani; M. A. Ursitti; V. Vullo; A. D'Avino; L. Gallo; E. Nicastri; R. Acinapura; M. Capozzi; R. Libertone; G. Tebano; A. Cattelan; L. Sasset; M. S. Mura; B. Rossetti; P. Caramello; G. C. Orofino; M. Sciandra; M. Bassetti; A. Londero; G. Pellizzer; V. Manfrin; on behalf of the ICONA Foundation Group. 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. Journal of Antimicrobial Chemotherapy 2014, 69, 3085 -3094.
AMA StyleGabriella Rozera, Isabella Abbate, Emanuela Giombini, Antonella Castagna, Andrea De Luca, Francesca Ceccherini-Silberstein, Alessandro Cozzi Lepri, Giovanni Cassola, Carlo Torti, Antonella D'arminio Monforte, Giuseppe Ippolito, Maria R. Capobianchi, M. Moroni, M. Andreoni, G. Angarano, A. Antinori, F. Castelli, R. Cauda, G. Di Perri, M. Galli, R. Iardino, A. Lazzarin, C. F. Perno, F. von Schloesser, P. Viale, E. Girardi, S. Lo Caputo, C. Mussini, M. Puoti, A. Ammassari, C. Balotta, P. Bonfanti, S. Bonora, M. Borderi, A. Cingolani, P. Cinque, A. Di Biagio, N. Gianotti, A. Gori, G. Guaraldi, G. Lapadula, M. Lichtner, G. Madeddu, F. Maggiolo, G. Marchetti, S. Marcotullio, L. Monno, E. Quiros Roldan, S. Rusconi, P. Cicconi, I. Fanti, T. Formenti, L. Galli, P. Lorenzini, F. Carletti, S. Carrara, A. Castrogiovanni, A. Di Caro, F. Petrone, G. Prota, S. Quartu, A. Giacometti, A. Costantini, S. Mazzoccato, C. Santoro, C. Suardi, E. Vanino, G. Verucchi, C. Minardi, T. Quirino, C. Abeli, P. E. Manconi, P. Piano, J. Vecchiet, K. Falasca, L. Sighinolfi, D. Segala, F. Mazzotta, C. Viscoli, A. Alessandrini, R. Piscopo, G. Mazzarello, C. Mastroianni, V. Belvisi, I. Caramma, A. Chiodera, A. P. Castelli, G. Rizzardini, A. L. Ridolfo, R. Piolini, S. Salpietro, L. Carenzi, M. C. Moioli, C. Tincati, C. Puzzolante, N. Abrescia, A. Chirianni, M. G. Guida, M. Gargiulo, F. Baldelli, D. Francisci, G. Parruti, T. Ursini, G. Magnani, M. A. Ursitti, V. Vullo, A. D'Avino, L. Gallo, E. Nicastri, R. Acinapura, M. Capozzi, R. Libertone, G. Tebano, A. Cattelan, L. Sasset, M. S. Mura, B. Rossetti, P. Caramello, G. C. Orofino, M. Sciandra, M. Bassetti, A. Londero, G. Pellizzer, V. Manfrin, on behalf of the ICONA Foundation Group. 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. Journal of Antimicrobial Chemotherapy. 2014; 69 (11):3085-3094.
Chicago/Turabian StyleGabriella Rozera; Isabella Abbate; Emanuela Giombini; Antonella Castagna; Andrea De Luca; Francesca Ceccherini-Silberstein; Alessandro Cozzi Lepri; Giovanni Cassola; Carlo Torti; Antonella D'arminio Monforte; Giuseppe Ippolito; Maria R. Capobianchi; M. Moroni; M. Andreoni; G. Angarano; A. Antinori; F. Castelli; R. Cauda; G. Di Perri; M. Galli; R. Iardino; A. Lazzarin; C. F. Perno; F. von Schloesser; P. Viale; E. Girardi; S. Lo Caputo; C. Mussini; M. Puoti; A. Ammassari; C. Balotta; P. Bonfanti; S. Bonora; M. Borderi; A. Cingolani; P. Cinque; A. Di Biagio; N. Gianotti; A. Gori; G. Guaraldi; G. Lapadula; M. Lichtner; G. Madeddu; F. Maggiolo; G. Marchetti; S. Marcotullio; L. Monno; E. Quiros Roldan; S. Rusconi; P. Cicconi; I. Fanti; T. Formenti; L. Galli; P. Lorenzini; F. Carletti; S. Carrara; A. Castrogiovanni; A. Di Caro; F. Petrone; G. Prota; S. Quartu; A. Giacometti; A. Costantini; S. Mazzoccato; C. Santoro; C. Suardi; E. Vanino; G. Verucchi; C. Minardi; T. Quirino; C. Abeli; P. E. Manconi; P. Piano; J. Vecchiet; K. Falasca; L. Sighinolfi; D. Segala; F. Mazzotta; C. Viscoli; A. Alessandrini; R. Piscopo; G. Mazzarello; C. Mastroianni; V. Belvisi; I. Caramma; A. Chiodera; A. P. Castelli; G. Rizzardini; A. L. Ridolfo; R. Piolini; S. Salpietro; L. Carenzi; M. C. Moioli; C. Tincati; C. Puzzolante; N. Abrescia; A. Chirianni; M. G. Guida; M. Gargiulo; F. Baldelli; D. Francisci; G. Parruti; T. Ursini; G. Magnani; M. A. Ursitti; V. Vullo; A. D'Avino; L. Gallo; E. Nicastri; R. Acinapura; M. Capozzi; R. Libertone; G. Tebano; A. Cattelan; L. Sasset; M. S. Mura; B. Rossetti; P. Caramello; G. C. Orofino; M. Sciandra; M. Bassetti; A. Londero; G. Pellizzer; V. Manfrin; on behalf of the ICONA Foundation Group. 2014. "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." Journal of Antimicrobial Chemotherapy 69, no. 11: 3085-3094.
HIV quasispecies was analysed in plasma and proviral genomes hosted by duodenal mucosa and peripheral blood cells (PBMC) from patients with early or chronic infection, with respect to viral heterogeneity, tropism compartmentalization and extent of immune activation. Seventeen HIV-1-infected combined antiretroviral therapy naive patients were enrolled (11 early infection and six chronic infection). V3 and nef genomic regions were analysed by ultra-deep pyrosequencing. Sequences were used to infer co-receptor usage and to construct phylogenetic trees. As markers of immune activation, plasma sCD14 and soluble tumour necrosis factor receptor II (sTNFRII) levels were measured. Median diversity of HIV RNA was lower in patients with early infection versus chronic infection patients. Overall, direct correlation was observed between V3 diversity and X4 frequency; V3 diversity of HIV RNA was inversely correlated with CD4 T-cell count; median sCD14 and sTNFRII values were similar in early and chronic patients, but X4 frequency of HIV RNA was directly correlated with plasma sCD14. The proportion of patients harbouring X4 variants and median intra-patient X4 frequency of proviral genomes tended to be higher in chronic infection than early infection patients. More pronounced compartmentalization of proviral quasispecies in gut compared with PBMC samples was observed in patients with early infection compared with chronic patients. The loss of gut/PBMC compartmentalization in more advanced stages of HIV infection was confirmed by longitudinal observation. More studies are needed to understand the pathogenetic significance of early HIV quasispecies compartmentalization and progressive intermixing of viral variants in subsequent phases of the infection, as well as the role of immune activation in tropism switch.
Gabriella Rozera; I. Abbate; C. Vlassi; E. Giombini; R. Lionetti; M. Selleri; P. Zaccaro; B. Bartolini; A. Corpolongo; G. D'offizi; A. Baiocchini; F. Del Nonno; Giuseppe Ippolito; Maria Rosaria Capobianchi. Quasispecies tropism and compartmentalization in gut and peripheral blood during early and chronic phases of HIV-1 infection: possible correlation with immune activation markers. Clinical Microbiology and Infection 2014, 20, O157 -O166.
AMA StyleGabriella Rozera, I. Abbate, C. Vlassi, E. Giombini, R. Lionetti, M. Selleri, P. Zaccaro, B. Bartolini, A. Corpolongo, G. D'offizi, A. Baiocchini, F. Del Nonno, Giuseppe Ippolito, Maria Rosaria Capobianchi. Quasispecies tropism and compartmentalization in gut and peripheral blood during early and chronic phases of HIV-1 infection: possible correlation with immune activation markers. Clinical Microbiology and Infection. 2014; 20 (3):O157-O166.
Chicago/Turabian StyleGabriella Rozera; I. Abbate; C. Vlassi; E. Giombini; R. Lionetti; M. Selleri; P. Zaccaro; B. Bartolini; A. Corpolongo; G. D'offizi; A. Baiocchini; F. Del Nonno; Giuseppe Ippolito; Maria Rosaria Capobianchi. 2014. "Quasispecies tropism and compartmentalization in gut and peripheral blood during early and chronic phases of HIV-1 infection: possible correlation with immune activation markers." Clinical Microbiology and Infection 20, no. 3: O157-O166.
HIV infection affects dendritic cells (DCs) number, maturation, and function although the cause remains largely unknown. Purified CD34+ hematopoietic progenitor cells (HPCs) obtained from bone marrow of chronic HIV-infected patients were investigated for the differentiative capability toward mature DCs. HIV, although not in active replication, was found able to impair CD34+ HPC differentiation into mature DCs. These results suggest that DCs impairment found in HIV-infected patients may be related to a failure by bone marrow CD34+ HPCs to produce an adequate number of DCs.
Veronica Bordoni; Michele Bibas; Domenico Viola; Alessandra Sacchi; Chiara Agrati; Germana Castelli; Adriana Ammassari; Alessandra Amendola; Isabella Abbate; Federico Martini. Chronic HIV-Infected Patients Show an Impaired Dendritic Cells Differentiation of Bone Marrow CD34+ Cells. JAIDS Journal of Acquired Immune Deficiency Syndromes 2013, 64, 342 -344.
AMA StyleVeronica Bordoni, Michele Bibas, Domenico Viola, Alessandra Sacchi, Chiara Agrati, Germana Castelli, Adriana Ammassari, Alessandra Amendola, Isabella Abbate, Federico Martini. Chronic HIV-Infected Patients Show an Impaired Dendritic Cells Differentiation of Bone Marrow CD34+ Cells. JAIDS Journal of Acquired Immune Deficiency Syndromes. 2013; 64 (4):342-344.
Chicago/Turabian StyleVeronica Bordoni; Michele Bibas; Domenico Viola; Alessandra Sacchi; Chiara Agrati; Germana Castelli; Adriana Ammassari; Alessandra Amendola; Isabella Abbate; Federico Martini. 2013. "Chronic HIV-Infected Patients Show an Impaired Dendritic Cells Differentiation of Bone Marrow CD34+ Cells." JAIDS Journal of Acquired Immune Deficiency Syndromes 64, no. 4: 342-344.
Viruses represent the most abundant biological components on earth.They can be found in every environment, from deep layers of oceans to animal bodies.Although several viruses have been isolated and sequenced, in each environment there are millions of different types of viruses that have not been identified yet.The advent of nextgeneration sequencing technologies with their high throughput capabilities make possible to study in a single experiment all the community of microorganisms present in a particular sample “microbioma”.They made more feasible the application of the metagenomic approach, by which it is also possible to discover and identify new pathogens, that may pose a threat to public health.This paper summarizes the most recent applications of nextgeneration sequencing to discover new viral pathogens during the occurrence of infection disease outbreaks.
Emanuela Giombini; Barbara Bartolini; Gabriella Rozera; Marina Selleri; Paola Zaccaro; Maria Rosaria Capobianchi; Isabella Abbate. Metagenomic approach for discovering new pathogens in infection disease outbreaks. Microbiologia Medica 2011, 26, 1 .
AMA StyleEmanuela Giombini, Barbara Bartolini, Gabriella Rozera, Marina Selleri, Paola Zaccaro, Maria Rosaria Capobianchi, Isabella Abbate. Metagenomic approach for discovering new pathogens in infection disease outbreaks. Microbiologia Medica. 2011; 26 (3):1.
Chicago/Turabian StyleEmanuela Giombini; Barbara Bartolini; Gabriella Rozera; Marina Selleri; Paola Zaccaro; Maria Rosaria Capobianchi; Isabella Abbate. 2011. "Metagenomic approach for discovering new pathogens in infection disease outbreaks." Microbiologia Medica 26, no. 3: 1.
Objectives: HIV-1 V3 quasispecies was analyzed by ultra-deep pyrosequencing, in early HIV-infected patients, to assess possible correlations between quasispecies diversity, frequency of variants predicted to use CXCR4 and need for early antiretroviral treatment. Methods: Twenty patients were retrospectively enrolled: 10 patients (group A) required HAART within 6 months from seroconversion and 10 (group B) remained free of therapy during this period. V3 quasispecies was assessed on plasma viral RNA and in peripheral blood mononuclear cell-associated proviral DNA. Prediction of coreceptor usage was performed by position-specific score matrix analysis. Results: Variants predicted to use CXCR4 were detected (frequency ≥0.3%) in the plasma of 50% of early infected patients (60% from group A and 40% from group B). Intrapatient frequency of these variants was highly variable (0.3–56.3%). A positive correlation was observed between the proportion of X4 variants and intrapatient quasispecies diversity. Quasispecies diversity and absolute numbers of X4 variants were significantly higher in patients from group A. The analysis of proviral DNA quasispecies, performed in a subgroup of five patients, showed that X4 variants were not detected in patients with RNA frequency below 0.3%, and detected at 3.6% in the patient with 56.3% of X4 plasma variants. Conclusion: Our findings show that X4 variants may be frequently found, at variable intrapatient frequency, in early infected patients, and that quasispecies diversity and absolute numbers of X4 variants are significantly higher in patients undergoing early antiretroviral treatment. Further studies are mandatory to explore the clinical relevance of X4 variants present during early infection with respect to clinical progression and possible therapeutic implications.
Isabella Abbate; Chrysoula Vlassi; Gabriella Rozera; Alessandro Bruselles; Barbara Bartolini; Emanuela Giombini; Angela Corpolongo; Gianpiero D'Offizi; Pasquale Narciso; Alessandro Desideri; Giuseppe Ippolito; Maria R Capobianchi. Detection of quasispecies variants predicted to use CXCR4 by ultra-deep pyrosequencing during early HIV infection. AIDS 2011, 25, 611 -617.
AMA StyleIsabella Abbate, Chrysoula Vlassi, Gabriella Rozera, Alessandro Bruselles, Barbara Bartolini, Emanuela Giombini, Angela Corpolongo, Gianpiero D'Offizi, Pasquale Narciso, Alessandro Desideri, Giuseppe Ippolito, Maria R Capobianchi. Detection of quasispecies variants predicted to use CXCR4 by ultra-deep pyrosequencing during early HIV infection. AIDS. 2011; 25 (5):611-617.
Chicago/Turabian StyleIsabella Abbate; Chrysoula Vlassi; Gabriella Rozera; Alessandro Bruselles; Barbara Bartolini; Emanuela Giombini; Angela Corpolongo; Gianpiero D'Offizi; Pasquale Narciso; Alessandro Desideri; Giuseppe Ippolito; Maria R Capobianchi. 2011. "Detection of quasispecies variants predicted to use CXCR4 by ultra-deep pyrosequencing during early HIV infection." AIDS 25, no. 5: 611-617.