1
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Moroncini G, Svegliati S, Grieco A, Cuccioloni M, Mozzicafreddo M, Paolini C, Agarbati S, Spadoni T, Amoresano A, Pinto G, Chen Q, Benfaremo D, Tonnini C, Senzacqua M, Alizzi S, Nieto K, Finke D, Viola N, Amico D, Galgani M, Gasparini S, Zuccatosta L, Menzo S, Müller M, Kleinschmidt J, Funaro A, Giordano A, La Cava A, Dorfmüller P, Amoroso A, Pucci P, Pezone A, Avvedimento EV, Gabrielli A. Adeno-Associated Virus Type 5 Infection via PDGFRα Is Associated With Interstitial Lung Disease in Systemic Sclerosis and Generates Composite Peptides and Epitopes Recognized by the Agonistic Immunoglobulins Present in Patients With Systemic Sclerosis. Arthritis Rheumatol 2024; 76:620-630. [PMID: 37975161 DOI: 10.1002/art.42746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 09/14/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023]
Abstract
OBJECTIVE The etiopathogenesis of systemic sclerosis (SSc) is unknown. Platelet-derived growth factor receptors (PDGFRs) are overexpressed in patients with SSc. Because PDGFRα is targeted by the adeno-associated virus type 5 (AAV5), we investigated whether AAV5 forms a complex with PDGFRα exposing epitopes that may induce the immune responses to the virus-PDGFRα complex. METHODS The binding of monomeric human PDGFRα to the AAV5 capsid was analyzed by in silico molecular docking, surface plasmon resonance (SPR), and genome editing of the PDGFRα locus. AAV5 was detected in SSc lungs by in situ hybridization, immunohistochemistry, confocal microscopy, and molecular analysis of bronchoalveolar lavage (BAL) fluid. Immune responses to AAV5 and PDGFRα were evaluated by SPR using SSc monoclonal anti-PDGFRα antibodies and immunoaffinity-purified anti-PDGFRα antibodies from sera of patients with SSc. RESULTS AAV5 was detected in the BAL fluid of 41 of 66 patients with SSc with interstitial lung disease (62.1%) and in 17 of 66 controls (25.75%) (P < 0.001). In SSc lungs, AAV5 localized in type II pneumocytes and in interstitial cells. A molecular complex formed of spatially contiguous epitopes of the AAV5 capsid and of PDGFRα was identified and characterized. In silico molecular docking analysis and binding to the agonistic anti-PDGFRα antibodies identified spatially contiguous epitopes derived from PDGFRα and AAV5 that interacted with SSc agonistic antibodies to PDGFRα. These peptides were also able to bind total IgG isolated from patients with SSc, not from healthy controls. CONCLUSION These data link AVV5 with the immune reactivity to endogenous antigens in SSc and provide a novel element in the pathogenesis of SSc.
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Affiliation(s)
- Gianluca Moroncini
- Università Politecnica delle Marche and Azienda Ospedaliero Universitaria delle Marche, Ancona, Italy
| | | | | | | | | | | | | | | | | | | | - Qingxin Chen
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Devis Benfaremo
- Università Politecnica delle Marche and Azienda Ospedaliero Universitaria delle Marche, Ancona, Italy
| | | | | | - Silvia Alizzi
- Università di Torino and Azienda Ospedaliera Universitaria Città della Salute e della Scienza, di Torino, Torino, Italy
| | - Karen Nieto
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Doreen Finke
- Università Politecnica delle Marche, Ancona, Italy
| | - Nadia Viola
- Azienda Ospedaliero Universitaria delle Marche, Ancona, Italy
| | | | | | - Stefano Gasparini
- Università Politecnica delle Marche and Azienda Ospedaliero Universitaria delle Marche, Ancona, Italy
| | - Lina Zuccatosta
- Azienda Ospedaliero Universitaria delle Marche, Ancona, Italy
| | - Stefano Menzo
- Università Politecnica delle Marche and Azienda Ospedaliero Universitaria delle Marche, Ancona, Italy
| | - Martin Müller
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | | | | | - Antonio La Cava
- Federico II University, Napoli, Italy
- University of California, Los Angeles, CA
| | | | - Antonio Amoroso
- Università di Torino and Azienda Ospedaliera Universitaria Città della Salute e della Scienza, di Torino, Torino, Italy
| | | | | | | | - Armando Gabrielli
- Università Politecnica delle Marche, Ancona, Italy, Azienda Ospedaliero Universitaria delle Marche, Ancona, Italy, and Heinrich Heine University, Düsseldorf, Germany
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2
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Diotallevi A, Buffi G, Barocci S, Ceccarelli M, Bencardino D, Andreoni F, Orlandi C, Ferri M, Vandini D, Menzo S, Carlotti E, Casabianca A, Magnani M, Galluzzi L. Rapid monitoring of SARS-CoV-2 variants of concern through high-resolution melt analysis. Sci Rep 2023; 13:21598. [PMID: 38062105 PMCID: PMC10703772 DOI: 10.1038/s41598-023-48929-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
The current global pandemic of COVID-19 is characterized by waves of infection due to the emergence of new SARS-CoV-2 variants carrying mutations on the Spike (S) protein gene. Since autumn 2020 many Variants of Concern (VOC) have been reported: Alpha/B.1.1.7, Beta/B.1.351, Gamma/P.1, Delta/B.1.617.2, Omicron/B.1.1.529, and sublineages. Surveillance of genomic variants is currently based on whole-genome sequencing (WGS) of viral genomes on a random fraction of samples positive to molecular tests. WGS involves high costs, extended analysis time, specialized staff, and expensive instruments compared to a PCR-based test. To rapidly identify the VOCs in positive samples, six assays based on real-time PCR and high-resolution melting (HRM) were designed on the S gene and applied to 120 oro/nasopharyngeal swab samples collected from October 2020 to June 2022 (106 positive and 14 negative samples). Overall, the assays showed 100% specificity and sensitivity compared with commercial PCR tests for COVID-19. Moreover, 104 samples out of 106 (98.1%) were correctly identified as follows: 8 Wuhan (wild type), 12 Alpha, 23 Delta, 46 Omicron BA.1/BA.1.1, 15 Omicron BA.2/BA.4/BA.5. With our lab equipment, about 10 samples can be processed every 3 h at the cost of less than € 10 ($ 10.60) per sample, including RNA extraction. The implementation of this approach could help local epidemiological surveillance and clinical decision-making.
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Affiliation(s)
- Aurora Diotallevi
- Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy.
| | - Gloria Buffi
- Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy
| | - Simone Barocci
- Department of Clinical Pathology, Azienda Sanitaria Territoriale (AST) Pesaro e Urbino, Marche, 61029, Urbino, PU, Italy
| | - Marcello Ceccarelli
- Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy
- Department of Clinical Pathology, Azienda Sanitaria Territoriale (AST) Pesaro e Urbino, Marche, 61029, Urbino, PU, Italy
| | - Daniela Bencardino
- Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy
| | - Francesca Andreoni
- Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy
- Department of Clinical Pathology, Azienda Sanitaria Territoriale (AST) Pesaro e Urbino, Marche, 61029, Urbino, PU, Italy
| | - Chiara Orlandi
- Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy
| | - Marilisa Ferri
- Department of Clinical Pathology, Azienda Sanitaria Territoriale (AST) Pesaro e Urbino, Marche, 61029, Urbino, PU, Italy
| | - Daniela Vandini
- Department of Clinical Pathology, Azienda Sanitaria Territoriale (AST) Pesaro e Urbino, Marche, 61029, Urbino, PU, Italy
| | - Stefano Menzo
- Virology Laboratory, Azienda Ospedaliero Universitaria delle Marche, 60126, Ancona, AN, Italy
| | - Eugenio Carlotti
- Department of Prevention, Azienda Sanitaria Territoriale (AST) Pesaro e Urbino Marche, 61029, Urbino, PU, Italy
| | - Anna Casabianca
- Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy
| | - Mauro Magnani
- Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy
| | - Luca Galluzzi
- Section of Biotechnology, Department of Biomolecular Sciences, University of Urbino Carlo Bo, 60132, Fano, PU, Italy
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3
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Pierangeli A, Piralla A, Uceda Renteria S, Giacomel G, Lunghi G, Pagani E, Giacobazzi E, Vian E, Biscaro V, Piccirilli G, Lazzarotto T, Menzo S, Ferreri ML, Novazzi F, Petrarca L, Licari A, Ferrari G, Oliveto G, Antonelli G, Binda S, Galli C, Pellegrinelli L, Pariani E, Baldanti F. Multicenter epidemiological investigation and genetic characterization of respiratory syncytial virus and metapneumovirus infections in the pre-pandemic 2018-2019 season in northern and central Italy. Clin Exp Med 2023; 23:2725-2737. [PMID: 36522554 PMCID: PMC9754777 DOI: 10.1007/s10238-022-00973-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022]
Abstract
Respiratory syncytial virus (RSV) and human metapneumovirus (HMPV) cause a high burden of disease, particularly in children and the elderly. With the aim to add knowledge on RSV and HMPV infections in Italy, a prospective, multicenter study was conducted by eight centers of the Working Group on Respiratory Virus Infections (GLIViRe), from December 2018-April 2019. Weekly distribution and patients' demographic and clinical data were compared in 1300 RSV and 222 HMPV-positive cases. Phylogenetic analysis of the G-glycoprotein coding region was performed to characterize circulating strains. RSV positivity ranged from 6.4% in outpatients of all ages to 31.7% in hospitalized children; HMPV positivity was 4-1.2% with no age-association. RSV season peaked in February and ended in mid-April: HMPV circulation was higher when RSV decreased in early spring. RSV was more frequent in infants, whereas HMPV infected comparatively more elderly adults; despite, their clinical course was similar. RSV-B cases were two-thirds of the total and had similar clinical severity compared to RSV-A. Phylogenetic analysis showed the circulation of RSV-A ON1 variants and the predominance of RSV-B genotype BA10. HMPV genotype A2c was the prevalent one and presented insertions of different lengths in G. This first multicenter Italian report on seasonality, age-specific distribution, and clinical presentation of RSV and HMPV demonstrated their substantial disease burden in young patients but also in the elderly. These data may provide the basis for a national respiratory virus surveillance network.
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Affiliation(s)
- Alessandra Pierangeli
- Virology Laboratory, Department of Molecular Medicine, Sapienza University of Rome, V.Le Porta Tiburtina, 28; 00185, Rome, Italy
| | - Antonio Piralla
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Sara Uceda Renteria
- Virology Unit, Clinical Laboratory, Foundation IRCCS Ca’ Granda Ospedale Maggiore, Milan, Italy
| | - Giovanni Giacomel
- Virology Unit, Clinical Laboratory, Foundation IRCCS Ca’ Granda Ospedale Maggiore, Milan, Italy
| | - Giovanna Lunghi
- Virology Unit, Clinical Laboratory, Foundation IRCCS Ca’ Granda Ospedale Maggiore, Milan, Italy
| | - Elisabetta Pagani
- Laboratorio Aziendale Di Microbiologia E Virologia, Hospital of Bolzano (SABES-ASDAA), Bolzano, Italy
| | - Elisabetta Giacobazzi
- Laboratorio Aziendale Di Microbiologia E Virologia, Hospital of Bolzano (SABES-ASDAA), Bolzano, Italy
| | - Elisa Vian
- Microbiology Unit, Hospital of Treviso (AULSS2), Treviso, Italy
| | - Valeria Biscaro
- Microbiology Unit, Hospital of Treviso (AULSS2), Treviso, Italy
| | - Giulia Piccirilli
- Microbiology Unit, IRCCS Azienda Ospedaliero-Universitaria, Bologna, Italy
| | - Tiziana Lazzarotto
- Section of Microbiology, Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Stefano Menzo
- Department of Biomedical Sciences and Public Health, Università Politecnica Delle Marche, Ancona, Italy
| | - Monica Lucia Ferreri
- Virology Laboratory, Azienda Ospedaliera Ospedali Riuniti Di Ancona, Ancona, Italy
| | - Federica Novazzi
- Ospedale Di Circolo E Fondazione Macchi, ASST Sette Laghi, Varese, Italy
| | - Laura Petrarca
- Department of Maternal Infantile and Urological Sciences, Sapienza University of Rome, Rome, Italy
| | - Amelia Licari
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Guglielmo Ferrari
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Giuseppe Oliveto
- Virology Laboratory, Department of Molecular Medicine, Sapienza University of Rome, V.Le Porta Tiburtina, 28; 00185, Rome, Italy
| | - Guido Antonelli
- Virology Laboratory, Department of Molecular Medicine, Sapienza University of Rome, V.Le Porta Tiburtina, 28; 00185, Rome, Italy
| | - Sandro Binda
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Cristina Galli
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Laura Pellegrinelli
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Elena Pariani
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Fausto Baldanti
- Microbiology and Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
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4
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Montori M, Martini F, DE Blasio F, Buono T, Quatraccioni C, Guardati P, Calzolari M, Rossi C, Bendia E, Menzo S, Valenza C, Pellicano R, Maroni L, Benedetti A. Serological response after anti-SARS-CoV-2 BNT162b2 vaccine in IBD patients on biological therapy: a monocentric case-control study. Minerva Gastroenterol (Torino) 2023; 69:268-276. [PMID: 36255283 DOI: 10.23736/s2724-5985.22.03134-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
BACKGROUND Inflammatory bowel disease (IBD) patients on biological therapy are receiving vaccines against severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2). However, it is unclear if IBD therapy could influence the response to this vaccine. In a case-control study, we assessed the antibody profiling after anti-SARS-CoV-2 BNT162b2 vaccine in IBD patients on biological therapy. METHODS We analyzed seroprevalence and antibody titer, after 14 weeks from the first BNT162b2 vaccine dose, in IBD patients on biological therapy and health care workers (HCWs). In IBD patients, medical history and disease data were recorded. RESULTS Eighty-two subjects were enrolled in this study. Among them, 40 were IBD patients on biological therapy and 42 were HCWs. All subjects developed an IgG anti-Spike antibody titer above the cut-off. IBD patients on biological therapy developed a lower antibody titer than HCWs (P<0.00001). No differences were reported in patients who received at least one dose of the vaccine within a period of 7 days from the last biological drug administration, compared to all other IBD patients. A difference was found between patients who were on concomitant immunosuppressive therapy and patients on sole biological therapy (P=0.0287). Patients with presence of any sign of disease activity (clinical, endoscopic or laboratory) showed a higher development of antibody titer compared to those in complete disease remission (P=0.0468). CONCLUSIONS Our data indicate that in IBD patients, treatment with biological therapies do not affect the seroprevalence but leads to a lower antibody titer development after anti-SARS-CoV-2 BNT162b2 vaccine.
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Affiliation(s)
- Michele Montori
- Clinic of Gastroenterology, Hepatology and Emergency Digestive Endoscopy, Ospedali Riuniti di Ancona, Ancona, Italy -
| | - Francesco Martini
- Clinic of Gastroenterology, Hepatology and Emergency Digestive Endoscopy, Ospedali Riuniti di Ancona, Ancona, Italy
| | - Federico DE Blasio
- Clinic of Gastroenterology, Hepatology and Emergency Digestive Endoscopy, Ospedali Riuniti di Ancona, Ancona, Italy
| | - Tiziana Buono
- Clinic of Gastroenterology, Hepatology and Emergency Digestive Endoscopy, Ospedali Riuniti di Ancona, Ancona, Italy
| | - Claudia Quatraccioni
- Clinic of Gastroenterology, Hepatology and Emergency Digestive Endoscopy, Ospedali Riuniti di Ancona, Ancona, Italy
| | - Paola Guardati
- Clinic of Gastroenterology, Hepatology and Emergency Digestive Endoscopy, Ospedali Riuniti di Ancona, Ancona, Italy
| | - Manuela Calzolari
- Clinic of Gastroenterology, Hepatology and Emergency Digestive Endoscopy, Ospedali Riuniti di Ancona, Ancona, Italy
| | - Chiara Rossi
- Clinic of Gastroenterology, Hepatology and Emergency Digestive Endoscopy, Ospedali Riuniti di Ancona, Ancona, Italy
| | - Emanuele Bendia
- Department of Digestive System Diseases, Digestive Endoscopy and Chronic Inflammatory Bowel Diseases, Ospedali Riuniti di Ancona, Ancona, Italy
| | - Stefano Menzo
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Carmine Valenza
- Division of New Drugs and Early Drug Development for Innovative Therapies, European Institute of Oncology IRCCS, Milan, Italy
| | | | - Luca Maroni
- Clinic of Gastroenterology, Hepatology and Emergency Digestive Endoscopy, Ospedali Riuniti di Ancona, Ancona, Italy
| | - Antonio Benedetti
- Clinic of Gastroenterology, Hepatology and Emergency Digestive Endoscopy, Ospedali Riuniti di Ancona, Ancona, Italy
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5
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Romagnoli A, D'Agostino M, Pavoni E, Ardiccioni C, Motta S, Crippa P, Biagetti G, Notarstefano V, Rexha J, Perta N, Barocci S, Costabile BK, Colasurdo G, Caucci S, Mencarelli D, Turchetti C, Farina M, Pierantoni L, La Teana A, Al Hadi R, Cicconardi F, Chinappi M, Trucchi E, Mancia F, Menzo S, Morozzo Della Rocca B, D'Annessa I, Di Marino D. SARS-CoV-2 multi-variant rapid detector based on graphene transistor functionalized with an engineered dimeric ACE2 receptor. Nano Today 2023; 48:101729. [PMID: 36536857 PMCID: PMC9750890 DOI: 10.1016/j.nantod.2022.101729] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/14/2022] [Accepted: 12/11/2022] [Indexed: 05/14/2023]
Abstract
Reliable point-of-care (POC) rapid tests are crucial to detect infection and contain the spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The emergence of several variants of concern (VOC) can reduce binding affinity to diagnostic antibodies, limiting the efficacy of the currently adopted tests, while showing unaltered or increased affinity for the host receptor, angiotensin converting enzyme 2 (ACE2). We present a graphene field-effect transistor (gFET) biosensor design, which exploits the Spike-ACE2 interaction, the crucial step for SARS-CoV-2 infection. Extensive computational analyses show that a chimeric ACE2-Fragment crystallizable (ACE2-Fc) construct mimics the native receptor dimeric conformation. ACE2-Fc functionalized gFET allows in vitro detection of the trimeric Spike protein, outperforming functionalization with a diagnostic antibody or with the soluble ACE2 portion, resulting in a sensitivity of 20 pg/mL. Our miniaturized POC biosensor successfully detects B.1.610 (pre-VOC), Alpha, Beta, Gamma, Delta, Omicron (i.e., BA.1, BA.2, BA.4, BA.5, BA.2.75 and BQ.1) variants in isolated viruses and patient's clinical nasopharyngeal swabs. The biosensor reached a Limit Of Detection (LOD) of 65 cps/mL in swab specimens of Omicron BA.5. Our approach paves the way for a new and reusable class of highly sensitive, rapid and variant-robust SARS-CoV-2 detection systems.
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Affiliation(s)
- Alice Romagnoli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
- New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Mattia D'Agostino
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Eleonora Pavoni
- Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Chiara Ardiccioni
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
- New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Stefano Motta
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Paolo Crippa
- Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Giorgio Biagetti
- Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Valentina Notarstefano
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Jesmina Rexha
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
| | - Nunzio Perta
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
| | - Simone Barocci
- Department of Clinical Pathology, ASUR Marche AV1, Urbino, PU, Italy
| | - Brianna K Costabile
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | | | - Sara Caucci
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Torrette, 60126 Ancona, Italy
| | - Davide Mencarelli
- Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Claudio Turchetti
- Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Marco Farina
- Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Luca Pierantoni
- Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Anna La Teana
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
- New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Richard Al Hadi
- Alcatera Inc., 1401 Westwood Blvd Suite 280, Los Angeles, CA 90024, USA
| | - Francesco Cicconardi
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Ave, Bristol BS8 1TQ, UK
| | - Mauro Chinappi
- Department of Industrial Engineering, University of Rome Tor Vergata, Via del Politecnico 1, 00133 Rome, Italy
| | - Emiliano Trucchi
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Stefano Menzo
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Torrette, 60126 Ancona, Italy
| | - Blasco Morozzo Della Rocca
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Ilda D'Annessa
- Institute of Chemical Science and Technologies, SCITEC-CNR, Via Mario Bianco 9, 20131 Milan, Italy
| | - Daniele Di Marino
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
- New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
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6
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Lai A, Bergna A, Della Ventura C, Menzo S, Bruzzone B, Sagradi F, Ceccherini-Silberstein F, Weisz A, Clementi N, Brindicci G, Vicenti I, Sasset L, Caucci S, Corvaro B, Ippoliti S, Acciarri C, De Pace V, Lanfranchi L, Bellocchi MC, Giurato G, Ferrarese R, Lagioia A, Francisci D, Colombo ML, Lazzarin S, Ogliastro M, Cappelletti MR, Iannetta M, Rizzo F, Torti C, Fumi M, d’Avenia M, Brusa S, Greco F, Menchise A, Letizia V, Vaccaro E, Santoro CR, Fraccalvieri C, Testa S, Carioti L, Rocco T, Saracino A, Cattelan A, Clementi M, Sarmati L, Riva A, Galli M, Antinori S, Zehender G. Epidemiological and Clinical Features of SARS-CoV-2 Variants Circulating between April-December 2021 in Italy. Viruses 2022; 14:v14112508. [PMID: 36423117 PMCID: PMC9699621 DOI: 10.3390/v14112508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/03/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
SARS-CoV-2 is constantly evolving, leading to new variants. We analysed data from 4400 SARS-CoV-2-positive samples in order to pursue epidemiological variant surveillance and to evaluate their impact on public health in Italy in the period of April-December 2021. The main circulating strain (76.2%) was the Delta variant, followed by the Alpha (13.3%), the Omicron (5.3%), and the Gamma variants (2.9%). The B.1.1 lineages, Eta, Beta, Iota, Mu, and Kappa variants, represented around 1% of cases. There were 48.2% of subjects who had not been vaccinated, and they had a lower median age compared to the vaccinated subjects (47 vs. 61 years). An increasing number of infections in the vaccinated subjects were observed over time, with the highest proportion in November (85.2%). The variants correlated with clinical status; the largest proportion of symptomatic patients (59.6%) was observed with the Delta variant, while subjects harbouring the Gamma variant showed the highest proportion of asymptomatic infection (21.6%), albeit also deaths (5.4%). The Omicron variant was only found in the vaccinated subjects, of which 47% had been hospitalised. The diffusivity and pathogenicity associated with the different SARS-CoV-2 variants are likely to have relevant public health implications, both at the national and international levels. Our study provides data on the rapid changes in the epidemiological landscape of the SARS-CoV-2 variants in Italy.
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Affiliation(s)
- Alessia Lai
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
- Correspondence: ; Tel.: +39-0250319775
| | - Annalisa Bergna
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
| | - Carla Della Ventura
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
| | - Stefano Menzo
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60131 Ancona, Italy
| | | | - Fabio Sagradi
- Unit of Infectious Diseases, Azienda Socio Sanitaria Territoriale Cremona, 26100 Cremona, Italy
| | | | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84084 Salerno, Italy
| | - Nicola Clementi
- Laboratory of Microbiology and Virology, Università “Vita-Salute” San Raffaele, 20158 Milan, Italy
| | | | - Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Lolita Sasset
- Infectious Diseases Unit, Azienda Ospedale Università di Padova, 35128 Padova, Italy
| | - Sara Caucci
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Benedetta Corvaro
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Silvia Ippoliti
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Carla Acciarri
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, 60131 Ancona, Italy
| | | | - Leonardo Lanfranchi
- Unit of Infectious Diseases, Azienda Socio Sanitaria Territoriale Cremona, 26100 Cremona, Italy
| | - Maria C. Bellocchi
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84084 Salerno, Italy
| | - Roberto Ferrarese
- Laboratory of Microbiology and Virology, Università “Vita-Salute” San Raffaele, 20158 Milan, Italy
| | | | - Daniela Francisci
- Department of Medicine and Surgery, Clinic of Infectious Diseases, Santa Maria della Misericordia Hospital, University of Perugia, 06123 Perugia, Italy
| | - Martina L. Colombo
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
| | - Samuel Lazzarin
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
| | - Matilde Ogliastro
- Department of Health Sciences (DISSAL), University of Genoa, 16126 Genoa, Italy
| | - Maria R. Cappelletti
- Unit of Infectious Diseases, Azienda Socio Sanitaria Territoriale Cremona, 26100 Cremona, Italy
| | - Marco Iannetta
- Infectious Disease Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84084 Salerno, Italy
| | - Carlo Torti
- Infectious and Tropical Disease Unit, Department of Medical and Surgical Sciences, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
| | - Maurizio Fumi
- UOC Patologia Clinica, AO San Pio Benevento, 82100 Benevento, Italy
| | - Morena d’Avenia
- UOSVD di Citopatologia e Screening, Department of Laboratory Medicines, 70131 Bari, Italy
| | - Stefano Brusa
- Department of Translational Medical Sciences, Università Federico II, 80138 Naples, Italy
| | - Francesca Greco
- UOC Microbiologia e Virologia, PO Cosenza, 87100 Cosenza, Italy
| | - Angela Menchise
- Microbiology and Virology Laboratory, A.O.R. San Carlo Potenza, 85100 Potenza, Italy
| | - Vittoria Letizia
- UOSD Genetics and Molecular Biology, AORN Sant’Anna e San Sebastiano di Caserta, 81100 Caserta, Italy
| | - Emilia Vaccaro
- Molecular Biology Units, AOU ‘S. Giovanni di Dio e Ruggi d’Aragona’ Università di Salerno, 84131 Salerno, Italy
| | | | | | - Sophie Testa
- Unit of Infectious Diseases, Azienda Socio Sanitaria Territoriale Cremona, 26100 Cremona, Italy
| | - Luca Carioti
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Teresa Rocco
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84084 Salerno, Italy
| | | | - Annamaria Cattelan
- Infectious Diseases Unit, Azienda Ospedale Università di Padova, 35128 Padova, Italy
| | - Massimo Clementi
- Laboratory of Microbiology and Virology, Università “Vita-Salute” San Raffaele, 20158 Milan, Italy
| | - Loredana Sarmati
- Infectious Disease Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Agostino Riva
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
| | - Massimo Galli
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
| | - Spinello Antinori
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
| | - Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences, Università degli Studi di Milano, 20174 Milan, Italy
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7
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Lai A, Bergna A, Toppo S, Morganti M, Menzo S, Ghisetti V, Bruzzone B, Codeluppi M, Fiore V, Rullo EV, Antonelli G, Sarmati L, Brindicci G, Callegaro A, Sagnelli C, Francisci D, Vicenti I, Miola A, Tonon G, Cirillo D, Menozzi I, Caucci S, Cerutti F, Orsi A, Schiavo R, Babudieri S, Nunnari G, Mastroianni CM, Andreoni M, Monno L, Guarneri D, Coppola N, Crisanti A, Galli M, Zehender G. Phylogeography and genomic epidemiology of SARS-CoV-2 in Italy and Europe with newly characterized Italian genomes between February-June 2020. Sci Rep 2022; 12:5736. [PMID: 35388091 PMCID: PMC8986836 DOI: 10.1038/s41598-022-09738-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 03/25/2022] [Indexed: 12/29/2022] Open
Abstract
The aims of this study were to characterize new SARS-CoV-2 genomes sampled all over Italy and to reconstruct the origin and the evolutionary dynamics in Italy and Europe between February and June 2020. The cluster analysis showed only small clusters including < 80 Italian isolates, while most of the Italian strains were intermixed in the whole tree. Pure Italian clusters were observed mainly after the lockdown and distancing measures were adopted. Lineage B and B.1 spread between late January and early February 2020, from China to Veneto and Lombardy, respectively. Lineage B.1.1 (20B) most probably evolved within Italy and spread from central to south Italian regions, and to European countries. The lineage B.1.1.1 (20D) developed most probably in other European countries entering Italy only in the second half of March and remained localized in Piedmont until June 2020. In conclusion, within the limitations of phylogeographical reconstruction, the estimated ancestral scenario suggests an important role of China and Italy in the widespread diffusion of the D614G variant in Europe in the early phase of the pandemic and more dispersed exchanges involving several European countries from the second half of March 2020.
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Affiliation(s)
- Alessia Lai
- Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy.,Pediatric Clinical Research Center Fondazione Romeo ed Enrica Invernizzi, University of Milan, Milan, Italy
| | - Annalisa Bergna
- Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy
| | - Stefano Toppo
- Department of Molecular Medicine, University of Padova, Padua, Italy.,CRIBI Biotech Center, University of Padova, Padua, Italy
| | - Marina Morganti
- Risk Analyses and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Parma, Italy
| | - Stefano Menzo
- Department of Biomedical Sciences and Public Health, Virology Unit, Polytechnic University of Marche, Ancona, Italy
| | - Valeria Ghisetti
- Laboratory of Microbiology and Virology, Amedeo di Savoia, ASL Città di Torino, Torino, Italy
| | | | - Mauro Codeluppi
- UOC of Infectious Diseases, Department of Oncology and Hematology, Guglielmo da Saliceto Hospital, AUSL Piacenza, Piacenza, Italy
| | - Vito Fiore
- Infectious and Tropical Disease Clinic, Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Emmanuele Venanzi Rullo
- Unit of Infectious Diseases, Department of Experimental and Clinical Medicine, University of Messina, Messina, Italy
| | - Guido Antonelli
- Department of Molecular Medicine, University Hospital Policlinico Umberto I, Sapienza University of Rome, Rome, Italy
| | | | | | - Annapaola Callegaro
- Microbiology and Virology Laboratory, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Caterina Sagnelli
- Department of Mental Health and Public Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Daniela Francisci
- Department of Medicine and Surgery, Clinic of Infectious Diseases, "Santa Maria della Misericordia" Hospital, University of Perugia, Perugia, Italy
| | - Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Arianna Miola
- Intesa San Paolo Innovation Center-AI LAB, Turin, Italy
| | - Giovanni Tonon
- Center for Omics Sciences, IRCCS Ospedale San Raffaele, Milan, Italy.,Division of Experimental Oncology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Daniela Cirillo
- Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Ilaria Menozzi
- Risk Analyses and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Parma, Italy
| | - Sara Caucci
- Department of Biomedical Sciences and Public Health, Virology Unit, Polytechnic University of Marche, Ancona, Italy
| | - Francesco Cerutti
- Laboratory of Microbiology and Virology, Amedeo di Savoia, ASL Città di Torino, Torino, Italy
| | - Andrea Orsi
- Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy
| | - Roberta Schiavo
- UOC of Microbiology, Department of Clinical Pathology, Guglielmo da Saliceto Hospital, AUSL Piacenza, Piacenza, Italy
| | - Sergio Babudieri
- Infectious and Tropical Disease Clinic, Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Giuseppe Nunnari
- Unit of Infectious Diseases, Department of Experimental and Clinical Medicine, University of Messina, Messina, Italy
| | - Claudio M Mastroianni
- Department of Public Health and Infectious Diseases, University Hospital Policlinico Umberto I, Sapienza University of Rome, Rome, Italy
| | | | - Laura Monno
- Infectious Diseases Unit, University of Bari, Bari, Italy
| | - Davide Guarneri
- Microbiology and Virology Laboratory, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Nicola Coppola
- Department of Mental Health and Public Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Andrea Crisanti
- Microbiology and Virology Diagnostic Unit, Padua University Hospital, Padua, Italy.,Department of Life Science, Imperial College London, South Kensington Campus Imperial College Road, London, SW7 AZ, UK
| | - Massimo Galli
- Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy
| | - Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy. .,Pediatric Clinical Research Center Fondazione Romeo ed Enrica Invernizzi, University of Milan, Milan, Italy. .,CRC-Coordinated Research Center "EpiSoMI", University of Milan, Milan, Italy.
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8
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Colleluori G, Graciotti L, Pesaresi M, Di Vincenzo A, Perugini J, Di Mercurio E, Caucci S, Bagnarelli P, Zingaretti CM, Nisoli E, Menzo S, Tagliabracci A, Ladoux A, Dani C, Giordano A, Cinti S. Visceral fat inflammation and fat embolism are associated with lung’s lipidic hyaline membranes in subjects with COVID-19. Int J Obes (Lond) 2022; 46:1009-1017. [PMID: 35082385 PMCID: PMC8790008 DOI: 10.1038/s41366-022-01071-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/05/2022] [Accepted: 01/12/2022] [Indexed: 12/15/2022]
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9
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Caucci S, Corvaro B, Tiano SML, Valenza A, Longo R, Marinelli K, Ferreri ML, Spiridigliozzi P, Salvoni G, Bagnarelli P, Menzo S. Weak Cross-Lineage Neutralization by Anti SARS-CoV-2 Spike Antibodies after Natural Infection or Vaccination Is Rescued by Repeated Immunological Stimulation. Vaccines (Basel) 2021; 9:1124. [PMID: 34696232 PMCID: PMC8537215 DOI: 10.3390/vaccines9101124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/23/2021] [Accepted: 09/28/2021] [Indexed: 12/03/2022] Open
Abstract
After over one year of evolution, through billions of infections in humans, SARS-CoV-2 has evolved into a score of slightly divergent lineages. A few different amino acids in the spike proteins of these lineages can hamper both natural immunity against reinfection, and vaccine efficacy. In this study, the in vitro neutralizing potency of sera from convalescent COVID-19 patients and vaccinated subjects was analyzed against six different SARS-CoV-2 lineages, including the latest B.1.617.2 (or Delta variant), in order to assess the cross-neutralization by anti-spike antibodies. After both single dose vaccination, or natural infection, the neutralizing activity was low and fully effective only against the original lineage, while a double dose or a single dose of vaccine, even one year after natural infection, boosted the cross-neutralizing activity against different lineages. Neither binding, nor the neutralizing activity of sera after vaccination, could predict vaccine failure, underlining the need for additional immunological markers. This study points at the importance of the anamnestic response and repeated vaccine stimulations to elicit a reasonable cross-lineage neutralizing antibody response.
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Affiliation(s)
- Sara Caucci
- Department of Biomedical Sciences and Public Health, Università Politecnica delle Marche, 60126 Ancona, Italy; (S.C.); (B.C.); (S.M.L.T.); (P.B.)
| | - Benedetta Corvaro
- Department of Biomedical Sciences and Public Health, Università Politecnica delle Marche, 60126 Ancona, Italy; (S.C.); (B.C.); (S.M.L.T.); (P.B.)
| | - Sofia Maria Luigia Tiano
- Department of Biomedical Sciences and Public Health, Università Politecnica delle Marche, 60126 Ancona, Italy; (S.C.); (B.C.); (S.M.L.T.); (P.B.)
| | - Anna Valenza
- Virology Laboratory, Azienda Ospedaliera Ospedali Riuniti di Ancona, 60126 Ancona, Italy; (A.V.); (K.M.); (M.L.F.); (P.S.); (G.S.)
| | - Roberta Longo
- Department of Biomedical Sciences and Public Health, Università Politecnica delle Marche, 60126 Ancona, Italy; (S.C.); (B.C.); (S.M.L.T.); (P.B.)
| | - Katia Marinelli
- Virology Laboratory, Azienda Ospedaliera Ospedali Riuniti di Ancona, 60126 Ancona, Italy; (A.V.); (K.M.); (M.L.F.); (P.S.); (G.S.)
| | - Monica Lucia Ferreri
- Virology Laboratory, Azienda Ospedaliera Ospedali Riuniti di Ancona, 60126 Ancona, Italy; (A.V.); (K.M.); (M.L.F.); (P.S.); (G.S.)
| | - Patrik Spiridigliozzi
- Virology Laboratory, Azienda Ospedaliera Ospedali Riuniti di Ancona, 60126 Ancona, Italy; (A.V.); (K.M.); (M.L.F.); (P.S.); (G.S.)
| | - Giovanna Salvoni
- Virology Laboratory, Azienda Ospedaliera Ospedali Riuniti di Ancona, 60126 Ancona, Italy; (A.V.); (K.M.); (M.L.F.); (P.S.); (G.S.)
| | - Patrizia Bagnarelli
- Department of Biomedical Sciences and Public Health, Università Politecnica delle Marche, 60126 Ancona, Italy; (S.C.); (B.C.); (S.M.L.T.); (P.B.)
- Virology Laboratory, Azienda Ospedaliera Ospedali Riuniti di Ancona, 60126 Ancona, Italy; (A.V.); (K.M.); (M.L.F.); (P.S.); (G.S.)
| | - Stefano Menzo
- Department of Biomedical Sciences and Public Health, Università Politecnica delle Marche, 60126 Ancona, Italy; (S.C.); (B.C.); (S.M.L.T.); (P.B.)
- Virology Laboratory, Azienda Ospedaliera Ospedali Riuniti di Ancona, 60126 Ancona, Italy; (A.V.); (K.M.); (M.L.F.); (P.S.); (G.S.)
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10
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Magi G, Tontarelli F, Caucci S, Sante LD, Brenciani A, Morroni G, Giovanetti E, Menzo S, Mingoia M. High prevalence of carbapenem-resistant Klebsiella pneumoniae ST307 recovered from fecal samples in an Italian hospital. Future Microbiol 2021; 16:703-711. [PMID: 34223790 DOI: 10.2217/fmb-2020-0246] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Aim: This study reports the characterization of carbapenem-resistant colonizing strains of K. pneumoniae. Methods: 650 stool samples were screened for carbapenem-resistant K. pneumoniae (CR-Kp). All strains were characterized for antibiotic susceptibility, typing features, main carbapenemases and extended-spectrum ß-lactamases. The carbapenemase transferability was assessed by interspecific conjugation. Results: Eighteen CR-Kp were multidrug resistant, five were KPC producing. A predominance of ST307 isolates, constituting the predominant cluster by PFGE analysis, was identified (50% were KPC-2 producers). Conjugation data showed the co-transfer of blaKPC-2, blaTEM-1, blaOXA-1, blaCTX-M-15 in a single large pKPN3-like plasmid. Conclusion: Our data pointed out the diversity of colonizing K. pneumoniae strains compared with clinical ones. The predominance of ST307 strains suggested an increased spreading, even in our area, of this high-risk clone.
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Affiliation(s)
- Gloria Magi
- Unit of Microbiology, Department of Biomedical Sciences & Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Federica Tontarelli
- Unit of Microbiology, Department of Biomedical Sciences & Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Sara Caucci
- Unit of Microbiology, Department of Biomedical Sciences & Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Laura Di Sante
- Unit of Microbiology, Department of Biomedical Sciences & Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Andrea Brenciani
- Unit of Microbiology, Department of Biomedical Sciences & Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Gianluca Morroni
- Unit of Microbiology, Department of Biomedical Sciences & Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Eleonora Giovanetti
- Unit of Microbiology, Department of Life & Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Stefano Menzo
- Unit of Microbiology, Department of Biomedical Sciences & Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Marina Mingoia
- Unit of Microbiology, Department of Biomedical Sciences & Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
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11
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Pomponio G, Ferrarini A, Bonifazi M, Moretti M, Salvi A, Giacometti A, Tavio M, Titolo G, Morbidoni L, Frausini G, Onesta M, Amico D, Rocchi MLB, Menzo S, Zuccatosta L, Mei F, Menditto V, Svegliati S, Donati A, D'Errico MM, Pavani M, Gabrielli A. Tocilizumab in COVID-19 interstitial pneumonia. J Intern Med 2021; 289:738-746. [PMID: 33511686 PMCID: PMC8013903 DOI: 10.1111/joim.13231] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/25/2020] [Accepted: 12/14/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND Published reports on tocilizumab in COVID-19 pneumonitis show conflicting results due to weak designs or heterogeneity in critical methodological issues. METHODS This open-label trial, structured according to Simon's optimal design, aims to identify factors predicting which patients could benefit from anti-IL6 strategies and to enhance the design of unequivocal and reliable future randomized trials. A total of 46 patients with COVID-19 pneumonia needing of oxygen therapy to maintain SO2 > 93% and with recent worsening of lung function received a single infusion of tocilizumab. Clinical and biological markers were measured to test their predictive values. Primary end point was early and sustained clinical response. RESULTS Twenty-one patients fulfilled pre-defined response criteria. Lower levels of IL-6 at 24 h after tocilizumab infusion (P = 0.049) and higher baseline values of PaO2/FiO2 (P = 0.008) predicted a favourable response. CONCLUSIONS Objective clinical response rate overcame the pre-defined threshold of 30%. Efficacy of tocilizumab to improve respiratory function in patients selected according to our inclusion criteria warrants investigations in randomized trials.
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Affiliation(s)
- G Pomponio
- From the, Clinica Medica, Ospedali Riuniti di Ancona, Ancona, Italy
| | - A Ferrarini
- From the, Clinica Medica, Ospedali Riuniti di Ancona, Ancona, Italy
| | - M Bonifazi
- Pneumologia, Ospedali Riuniti di Ancona, Ancona, Italy
| | - M Moretti
- SOD Medicina di Laboratorio Ospedali Riuniti di Ancona, Ancona, Italy
| | - A Salvi
- Medicina Interna e Sub Intensiva, Ospedali Riuniti di Ancona, Ancona, Italy
| | - A Giacometti
- Clinica di Malattie Infettive, Ospedali Riuniti di Ancona, Ancona, Italy
| | - M Tavio
- Malattie Infettive, Ospedali Riuniti di Ancona, Ancona, Italy
| | - G Titolo
- Medicina di Urgenza, Ospedali Riuniti Marche Nord, Pesaro/Fano, Italy
| | - L Morbidoni
- Medicina Interna, Ospedale di Senigallia, Senigallia, Italy
| | - G Frausini
- Medicina Interna, Ospedali Riuniti Marche Nord, Pesaro/Fano, Italy
| | - M Onesta
- Medicina Interna, Ospedale di Fabriano, Fabriano, Italy
| | - D Amico
- Pneumologia, Ospedali Riuniti Marche Nord, Pesaro/Fano, Italy
| | - M L B Rocchi
- Statistica Medica, Dipartimento di Scienze Biomolecolari, Università di Urbino, Urbino, Italy
| | - S Menzo
- Virologia, Ospedali Riuniti di Ancona, Ancona, Italy
| | - L Zuccatosta
- Pneumologia, Ospedali Riuniti di Ancona, Ancona, Italy
| | - F Mei
- Pneumologia, Ospedali Riuniti di Ancona, Ancona, Italy
| | - V Menditto
- Medicina Interna e Sub Intensiva, Ospedali Riuniti di Ancona, Ancona, Italy
| | - S Svegliati
- Clinica Medica, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy
| | - A Donati
- Clinica di Rianimazione, Ospedali Riuniti di Ancona, Ancona, Italy
| | - M M D'Errico
- Dip. Scienze biomediche e sanità pubblica, Università Politecnica delle Marche, Ancona, Italy
| | - M Pavani
- Laboratorio di Patologia Sperimentale, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy
| | - A Gabrielli
- From the, Clinica Medica, Ospedali Riuniti di Ancona, Ancona, Italy.,Clinica Medica, DISCLIMO, Università Politecnica delle Marche, Ancona, Italy
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12
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Fioriti S, Simoni S, Caucci S, Morroni G, Ponzio E, Coccitto SN, Brescini L, Cirioni O, Menzo S, Biavasco F, Giovanetti E, Brenciani A, Vignaroli C. Trend of clinical vancomycin-resistant enterococci isolated in a regional Italian hospital from 2001 to 2018. Braz J Microbiol 2020; 51:1607-1613. [PMID: 32783169 PMCID: PMC7688800 DOI: 10.1007/s42770-020-00360-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/04/2020] [Indexed: 11/25/2022] Open
Abstract
A retrospective study of the epidemiology of vancomycin-resistant enterococci (VRE) in a regional hospital of central Italy in 2001-2018 demonstrated an increased VRE prevalence since 2016. A total of 113 VRE isolates, 89 E. faecium (VREfm) and 24 E. faecalis (VREfs), were collected in the study period. All strains showed high-level resistance to vancomycin; 107 also showed teicoplanin resistance. Altogether, 84 VREfm and 20 VREfs carried vanA, whereas 5 VREfm and 1 VREfs carried vanB. MLST analysis documented that 89 VREfm isolates mainly belonged to ST78, ST80, and ST117. Most strains were isolated from 2001 to 2007, ST78 being the predominant clone. VREfm re-emerged in 2016 with a prevalence of the ST80 lineage. Most VREfs were isolated from 2001 to 2006; although they belonged to 7 different STs, there was a prevalence of ST88 and ST6. Notably, ST88 was sporadically recovered throughout the study period. The increasing rate of VREfm isolation from 2016 to 2018 may be related to the influx of new successful clones and to the renewed and widespread use of vancomycin. Improved infection control measures in hospital wards should be adopted to limit the spread of new epidemic VRE strains.
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Affiliation(s)
- Simona Fioriti
- Unit of Microbiology of Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Via Tronto 10/A, 60126, Ancona, Italy
| | - Serena Simoni
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Sara Caucci
- Unit of Microbiology of Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Via Tronto 10/A, 60126, Ancona, Italy
| | - Gianluca Morroni
- Unit of Microbiology of Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Via Tronto 10/A, 60126, Ancona, Italy
| | - Elisa Ponzio
- Section of Hygiene of Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
| | - Sonia Nina Coccitto
- Unit of Microbiology of Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Via Tronto 10/A, 60126, Ancona, Italy
| | - Lucia Brescini
- Infectious Diseases Clinic of Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
| | - Oscar Cirioni
- Infectious Diseases Clinic of Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
| | - Stefano Menzo
- Unit of Microbiology of Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Via Tronto 10/A, 60126, Ancona, Italy
| | - Francesca Biavasco
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Eleonora Giovanetti
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Andrea Brenciani
- Unit of Microbiology of Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Via Tronto 10/A, 60126, Ancona, Italy.
| | - Carla Vignaroli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
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13
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Alessandrini F, Caucci S, Onofri V, Melchionda F, Tagliabracci A, Bagnarelli P, Di Sante L, Turchi C, Menzo S. Evaluation of the Ion AmpliSeq SARS-CoV-2 Research Panel by Massive Parallel Sequencing. Genes (Basel) 2020; 11:E929. [PMID: 32806776 PMCID: PMC7463572 DOI: 10.3390/genes11080929] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/30/2020] [Accepted: 08/10/2020] [Indexed: 12/17/2022] Open
Abstract
Deep knowledge of the genetic features of SARS-CoV-2 is essential to track the ongoing pandemic through different geographical areas and to design and develop early diagnostic procedures, therapeutic strategies, public health interventions, and vaccines. We describe protocols and first results of the Ion AmpliSeq™ SARS-CoV-2 Research Panel by a massively parallel sequencing (MPS) assay. The panel allows for targeted sequencing by overlapping amplicons, thereby providing specific, accurate, and high throughput analysis. A modified reverse transcription reaction, which consists of the use of a SARS-CoV-2 specific primers pool from the Ion AmpliSeq SARS-CoV-2 Research Panel, was assessed in order to promote viral RNA specific reverse transcription. The aim of this study was to evaluate the effectiveness of the Ion AmpliSeq™ SARS-CoV-2 Research Panel in sequencing the entire viral genome in different samples. SARS-CoV-2 sequence data were obtained from ten viral isolates and one nasopharyngeal swab from different patients. The ten isolate samples amplified with 12 PCR cycles displayed high mean depth values compared to those of the two isolates amplified with 20 PCR cycles. High mean depth values were also obtained for the nasopharyngeal swab processed by use of a target-specific reverse transcription. The relative depth of coverage (rDoC) analysis showed that when 12 PCR cycles were used, all target regions were amplified with high sequencing coverage, while in libraries amplified at 20 cycles, a poor uniformity of amplification, with absent or low coverage of many target regions, was observed. Our results show that the Ion AmpliSeq SARS-CoV-2 Research Panel can achieve rapid and high throughput SARS-CoV-2 whole genome sequencing from 10 ng of DNA-free viral RNA from isolates and from 1 ng of DNA-free viral RNA from a nasopharyngeal swab using 12 PCR cycles for library amplification. The modified RT-PCR protocol yielded superior results on the nasopharyngeal swab compared to the reverse transcription reaction set up according to the manufacturer's instructions.
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Affiliation(s)
- Federica Alessandrini
- Legal Medicine Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Torrette, 60126 Ancona, Italy; (F.A.); (F.M.); (A.T.)
| | - Sara Caucci
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Torrette, 60126 Ancona, Italy; (S.C.); (P.B.); (L.D.S.); (S.M.)
| | - Valerio Onofri
- Legal Medicine Unit, AOU Ospedali Riuniti, Torrette, 60126 Ancona, Italy;
| | - Filomena Melchionda
- Legal Medicine Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Torrette, 60126 Ancona, Italy; (F.A.); (F.M.); (A.T.)
| | - Adriano Tagliabracci
- Legal Medicine Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Torrette, 60126 Ancona, Italy; (F.A.); (F.M.); (A.T.)
| | - Patrizia Bagnarelli
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Torrette, 60126 Ancona, Italy; (S.C.); (P.B.); (L.D.S.); (S.M.)
| | - Laura Di Sante
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Torrette, 60126 Ancona, Italy; (S.C.); (P.B.); (L.D.S.); (S.M.)
| | - Chiara Turchi
- Legal Medicine Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Torrette, 60126 Ancona, Italy; (F.A.); (F.M.); (A.T.)
| | - Stefano Menzo
- Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Torrette, 60126 Ancona, Italy; (S.C.); (P.B.); (L.D.S.); (S.M.)
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14
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Lai A, Bergna A, Caucci S, Clementi N, Vicenti I, Dragoni F, Cattelan AM, Menzo S, Pan A, Callegaro A, Tagliabracci A, Caruso A, Caccuri F, Ronchiadin S, Balotta C, Zazzi M, Vaccher E, Clementi M, Galli M, Zehender G. Molecular Tracing of SARS-CoV-2 in Italy in the First Three Months of the Epidemic. Viruses 2020; 12:v12080798. [PMID: 32722343 PMCID: PMC7472216 DOI: 10.3390/v12080798] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 07/17/2020] [Accepted: 07/21/2020] [Indexed: 01/15/2023] Open
Abstract
The aim of this study is the characterization and genomic tracing by phylogenetic analyses of 59 new SARS-CoV-2 Italian isolates obtained from patients attending clinical centres in North and Central Italy until the end of April 2020. All but one of the newly-characterized genomes belonged to the lineage B.1, the most frequently identified in European countries, including Italy. Only a single sequence was found to belong to lineage B. A mean of 6 nucleotide substitutions per viral genome was observed, without significant differences between synonymous and non-synonymous mutations, indicating genetic drift as a major source for virus evolution. tMRCA estimation confirmed the probable origin of the epidemic between the end of January and the beginning of February with a rapid increase in the number of infections between the end of February and mid-March. Since early February, an effective reproduction number (Re) greater than 1 was estimated, which then increased reaching the peak of 2.3 in early March, confirming the circulation of the virus before the first COVID-19 cases were documented. Continuous use of state-of-the-art methods for molecular surveillance is warranted to trace virus circulation and evolution and inform effective prevention and containment of future SARS-CoV-2 outbreaks.
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Affiliation(s)
- Alessia Lai
- Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, 20157 Milan, Italy; (A.B.); (C.B.); (M.G.); (G.Z.)
- Correspondence: ; Tel.: +39-0250319775
| | - Annalisa Bergna
- Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, 20157 Milan, Italy; (A.B.); (C.B.); (M.G.); (G.Z.)
| | - Sara Caucci
- Department of Biomedical Sciences and Public Health, Virology Unit, Polytechnic University of Marche, 60131 Ancona, Italy; (S.C.); (S.M.)
| | - Nicola Clementi
- Microbiology and Virology Unit, “Vita-Salute” San Raffaele University, 20132 Milan, Italy; (N.C.); (M.C.)
| | - Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (I.V.); (F.D.); (M.Z.)
| | - Filippo Dragoni
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (I.V.); (F.D.); (M.Z.)
| | - Anna Maria Cattelan
- Infectious Diseases Unit, Department of Internal Medicine, Azienda Ospedaliera-Universitaria di Padova, 35128 Padua, Italy;
| | - Stefano Menzo
- Department of Biomedical Sciences and Public Health, Virology Unit, Polytechnic University of Marche, 60131 Ancona, Italy; (S.C.); (S.M.)
| | - Angelo Pan
- Infectious Diseases, ASST Cremona, 26100 Cremona, Italy;
| | - Annapaola Callegaro
- Microbiology and Virology Laboratory, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy;
| | - Adriano Tagliabracci
- Section of Legal Medicine, Universita Politecnica delle Marche, 60126 Ancona, Italy;
| | - Arnaldo Caruso
- Microbiology Unit, Department of Molecular and Translational Medicine, University of Brescia and ASST Spedali Civili Hospital, 25123 Brescia, Italy; (A.C.); (F.C.)
| | - Francesca Caccuri
- Microbiology Unit, Department of Molecular and Translational Medicine, University of Brescia and ASST Spedali Civili Hospital, 25123 Brescia, Italy; (A.C.); (F.C.)
| | | | - Claudia Balotta
- Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, 20157 Milan, Italy; (A.B.); (C.B.); (M.G.); (G.Z.)
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (I.V.); (F.D.); (M.Z.)
| | - Emanuela Vaccher
- Medical Oncology and Immune-related Tumors, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy;
| | - Massimo Clementi
- Microbiology and Virology Unit, “Vita-Salute” San Raffaele University, 20132 Milan, Italy; (N.C.); (M.C.)
| | - Massimo Galli
- Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, 20157 Milan, Italy; (A.B.); (C.B.); (M.G.); (G.Z.)
| | - Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, 20157 Milan, Italy; (A.B.); (C.B.); (M.G.); (G.Z.)
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15
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Mei F, Bonifazi M, Menzo S, Di Marco Berardino A, Sediari M, Paolini L, Re A, Gonnelli F, Duranti C, Grilli M, Vennarucci GS, Latini MA, Zuccatosta L, Gasparini S. First Detection of SARS-CoV-2 by Real-Time Reverse Transcriptase-Polymerase Chain Reaction Assay in Pleural Fluid. Chest 2020; 158:e143-e146. [PMID: 32534909 PMCID: PMC7287448 DOI: 10.1016/j.chest.2020.05.583] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/19/2020] [Accepted: 05/29/2020] [Indexed: 12/25/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a pandemic infection due to the spread of a novel coronavirus (severe acute respiratory syndrome coronavirus 2), resulting in a wide range of clinical features, from asymptomatic carriers to ARDS. The gold standard for diagnosis is nucleic acid detection by real-time reverse transcriptase-polymerase chain reaction in nasopharyngeal swabs. However, due to limitations in this technique’s sensitivity, thoracic imaging plays a crucial, complementary role in diagnostic evaluation and also allows for detection of atypical findings and potential alternative targets for sampling (eg, pleural effusion). Although less common, pleural involvement has been described in a minority of patients. This report describes the first case of reverse transcriptase-polymerase chain reaction detection of severe acute respiratory syndrome coronavirus 2 in pleural fluid obtained by means of ultrasound-guided thoracentesis, and its main characteristics are detailed. Pleural effusion is not a common finding in COVID-19 infection, but a prompt recognition of this potential localization may be useful to optimize diagnostic evaluation as well as the management of these patients.
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Affiliation(s)
- Federico Mei
- Pulmonology Unit, Department of Internal Medicine, Azienda Ospedaliero-Universitaria Ospedali Riuniti, Ancona, Italy.
| | - Martina Bonifazi
- Pulmonology Unit, Department of Internal Medicine, Azienda Ospedaliero-Universitaria Ospedali Riuniti, Ancona, Italy; Department of Biomedical Sciences and Public Health, Università Politecnica delle Marche, Ancona, Italy
| | - Stefano Menzo
- Department of Biomedical Sciences and Public Health, Università Politecnica delle Marche, Ancona, Italy
| | - Alessandro Di Marco Berardino
- Pulmonology Unit, Department of Internal Medicine, Azienda Ospedaliero-Universitaria Ospedali Riuniti, Ancona, Italy
| | - Michele Sediari
- Pulmonology Unit, Department of Internal Medicine, Azienda Ospedaliero-Universitaria Ospedali Riuniti, Ancona, Italy
| | - Luca Paolini
- Pulmonology Unit, Department of Internal Medicine, Azienda Ospedaliero-Universitaria Ospedali Riuniti, Ancona, Italy
| | - Antonina Re
- Pulmonology Unit, Department of Internal Medicine, Azienda Ospedaliero-Universitaria Ospedali Riuniti, Ancona, Italy
| | - Francesca Gonnelli
- Pulmonology Unit, Department of Internal Medicine, Azienda Ospedaliero-Universitaria Ospedali Riuniti, Ancona, Italy
| | - Claudia Duranti
- Pulmonology Unit, Department of Internal Medicine, Azienda Ospedaliero-Universitaria Ospedali Riuniti, Ancona, Italy
| | - Martina Grilli
- Pulmonology Unit, Department of Internal Medicine, Azienda Ospedaliero-Universitaria Ospedali Riuniti, Ancona, Italy
| | - Giacomo Spurio Vennarucci
- Pulmonology Unit, Department of Internal Medicine, Azienda Ospedaliero-Universitaria Ospedali Riuniti, Ancona, Italy
| | - Maria Agnese Latini
- Pulmonology Unit, Department of Internal Medicine, Azienda Ospedaliero-Universitaria Ospedali Riuniti, Ancona, Italy
| | - Lina Zuccatosta
- Pulmonology Unit, Department of Internal Medicine, Azienda Ospedaliero-Universitaria Ospedali Riuniti, Ancona, Italy
| | - Stefano Gasparini
- Pulmonology Unit, Department of Internal Medicine, Azienda Ospedaliero-Universitaria Ospedali Riuniti, Ancona, Italy; Department of Biomedical Sciences and Public Health, Università Politecnica delle Marche, Ancona, Italy
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16
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Di Sante L, Costantini A, Caucci S, Corsi A, Brescini L, Menzo S, Bagnarelli P. Quantification of the HIV-1 total reservoir in the peripheral blood of naïve and treated patients by a standardised method derived from a commercial HIV-1 RNA quantification assay. Clin Chem Lab Med 2020; 59:609-617. [PMID: 33326413 DOI: 10.1515/cclm-2020-0142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 04/05/2020] [Indexed: 11/15/2022]
Abstract
OBJECTIVES HIV-1 DNA can persist in host cells, establishing a latent reservoir. This study was aimed to develop an extraction and amplification protocol for HIV-1 DNA quantification by modifying a quantitative commercial assay. METHODS HIV-1 DNA was extracted on an Abbott m2000sp instrument, using an open-mode protocol. Two calibrators, spiked with a plasmid containing HIV-1 genome (103 and 105 cps/mL), were extracted and amplified to generate a master calibration curve. Precision, accuracy, linear dynamic range, limit of quantification (LOQ) and limit of detection (LOD) were determined. A cohort of patients, naïve or chronically infected, was analysed. RESULTS Calibration curve was obtained from 42 replicates of standards (stds); precision was calculated (coefficients of variability [CVs] below 10%); accuracy was higher than 90%. Linearity covered the entire range tested (10-104 copies per reaction), and LOD (95%) was 12 copies per reaction. HIV-1 DNA was significantly higher (p < 0.0001) in drug-naïve (62) than in chronically treated patients (50), and proviral loads correlated with lymphocytes (p = 0.0002) and CD4+ (p < 0.0001) counts only in naïve patients. Both groups displayed a significant inverse correlation between CD4+ nadir and proviral loads. A significant correlation (p < 0.0001) between viraemia and HIV-1 reservoir was disclosed. No significant difference was obtained from the comparison between proviral loads on whole blood and peripheral blood mononuclear cells (PBMCs) from the same patient. CONCLUSIONS The novelty of our approach relies on the selection of appropriate reference standard extracted and amplified as clinical specimens avoiding any underestimation of the reservoir. Results confirm HIV-1 DNA as a marker of disease progression, supporting the relationship between the width of latent reservoir and the immunological status of the patient.
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Affiliation(s)
- Laura Di Sante
- Department of Molecular and Clinical Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Andrea Costantini
- Department of Molecular and Clinical Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Sara Caucci
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
| | - Alice Corsi
- Department of Molecular and Clinical Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Lucia Brescini
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
| | - Stefano Menzo
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
| | - Patrizia Bagnarelli
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
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17
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Simoni S, Caucci S, Brenciani A, Morroni G, Giovanetti E, Menzo S, Facinelli B, Mingoia M. Increase and diversity of carbapenemase-producing Escherichia coli isolates, Italy. Future Microbiol 2019; 14:1035-1042. [DOI: 10.2217/fmb-2019-0069] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: This study reports on a surveillance in an Italian hospital focused on carbapenemase-producing Escherichia coli (CP-Ec). Materials & methods: Eighteen isolates (nine from clinical specimens and nine from rectal swab) were characterized for antibiotic susceptibilities, typing features, main carbapenemase, extended-spectrum ß-lactamases (ESBLs) and other bla genes, and their transferability by conjugation and transformation. Results: An increase in CP-Ec isolates was observed during 3-year surveillance period. Compared with the clinical isolates, all belonging to one sequence type (ST), ST131, those from rectal swab were very heterogeneous and belonged to eight STs. Transfer data confirmed the role of conjugative plasmids in the spreading of carbapenemase genes. Conclusion: The prevalence of CP-Ec in Italy has risen, with a substantial increase over the last year.
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Affiliation(s)
- Serena Simoni
- Unit of Microbiology, Department of Biomedical Sciences & Public Health Polytechnic University of Marche Medical School, Ancona, Italy
| | - Sara Caucci
- Unit of Microbiology, Department of Biomedical Sciences & Public Health Polytechnic University of Marche Medical School, Ancona, Italy
| | - Andrea Brenciani
- Unit of Microbiology, Department of Biomedical Sciences & Public Health Polytechnic University of Marche Medical School, Ancona, Italy
| | - Gianluca Morroni
- Unit of Microbiology, Department of Biomedical Sciences & Public Health Polytechnic University of Marche Medical School, Ancona, Italy
| | - Eleonora Giovanetti
- Unit of Microbiology, Department of Life & Environmental Sciences Polytechnic University of Marche, Ancona, Italy
| | - Stefano Menzo
- Unit of Microbiology, Department of Biomedical Sciences & Public Health Polytechnic University of Marche Medical School, Ancona, Italy
| | - Bruna Facinelli
- Unit of Microbiology, Department of Biomedical Sciences & Public Health Polytechnic University of Marche Medical School, Ancona, Italy
| | - Marina Mingoia
- Unit of Microbiology, Department of Biomedical Sciences & Public Health Polytechnic University of Marche Medical School, Ancona, Italy
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18
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Lai A, Simonetti FR, Brindicci G, Bergna A, Di Giambenedetto S, Sterrantino G, Mussini C, Menzo S, Bagnarelli P, Zazzi M, Angarano G, Galli M, Monno L, Balotta C. Local Epidemics Gone Viral: Evolution and Diffusion of the Italian HIV-1 Recombinant Form CRF60_BC. Front Microbiol 2019; 10:769. [PMID: 31031735 PMCID: PMC6474184 DOI: 10.3389/fmicb.2019.00769] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/26/2019] [Indexed: 12/15/2022] Open
Abstract
The molecular epidemiology of HIV-1 in Italy is becoming increasingly complex, mainly due to the spread of non-B subtypes and the emergence of new recombinant forms. We previously characterized the outbreak of the first Italian circulating recombinant form (CRF60_BC), occurring among young MSM living in Apulia between the years 2009 and 2011. Here we show a 5-year follow-up surveillance to trace the evolution of CRF60_BC and to investigate its further spread in Italy. We collected additional sequences and clinical data from patients harboring CRF60_BC, enrolled at the Infectious Diseases Clinic of the University of Bari. In addition to the 24 previously identified sequences, we retrieved 27 CRF60_BC sequences from patients residing in Apulia, whose epidemiological and clinical features did not differ from those of the initial outbreak, i.e., the Italian origin, young age at HIV diagnosis (median: 24 years; range: 18–37), MSM risk factor (23/25, 92%) and recent infection (from 2008 to 2017). Sequence analysis revealed a growing overall nucleotide diversity, with few nucleotide changes that were fixed over time. Twenty-seven additional sequences were detected across Italy, spanning multiple distant regions. Using a BLAST search, we also identified a CRF60_BC sequence isolated in United Kingdom in 2013. Three patients harbored a unique second generation recombinant form in which CRF60_BC was one of the parental strains. Our data show that CRF60_BC gained epidemic importance, spreading among young MSM in multiple Italian regions and increasing its population size in few years, as the number of sequences identified so far has triplicated since our first report. The observed further divergence of CRF60_BC is likely due to evolutionary bottlenecks and host adaptation during transmission chains. Of note, we detected three second-generation recombinants, further supporting a widespread circulation of CRF60_BC and the increasing complexity of the HIV-1 epidemic in Italy.
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Affiliation(s)
- Alessia Lai
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | | | - Gaetano Brindicci
- Clinic of Infectious Diseases, University of Bari Aldo Moro, Bari, Italy
| | - Annalisa Bergna
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | | | - Gaetana Sterrantino
- Division of Tropical and Infectious Diseases, Careggi Hospital, Florence, Italy
| | - Cristina Mussini
- Clinic of Infectious Diseases, University of Modena and Reggio Emilia, Modena, Italy
| | - Stefano Menzo
- Unit of Virology, Azienda Ospedaliero-Universitaria 'Ospedali Riuniti', Torrette, Italy
| | - Patrizia Bagnarelli
- Unit of Virology, Azienda Ospedaliero-Universitaria 'Ospedali Riuniti', Torrette, Italy
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - Massimo Galli
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
| | - Laura Monno
- Clinic of Infectious Diseases, University of Bari Aldo Moro, Bari, Italy
| | - Claudia Balotta
- Department of Biomedical and Clinical Sciences L. Sacco, University of Milan, Milan, Italy
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19
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Tarantino G, Bagnarelli P, Marzioni M, Marinelli K, Surace G, Traini S, Baroni GS, Menzo S, Benedetti A. Hepatitis E in a region of Italy: An emerging autochthonous infection? Dig Liver Dis 2016; 48:1340-1345. [PMID: 27476463 DOI: 10.1016/j.dld.2016.06.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 06/21/2016] [Accepted: 06/22/2016] [Indexed: 12/11/2022]
Abstract
BACKGROUND Recent data showed an increasing number of "autochthonous" cases of hepatitis E in Italy. AIMS Analysing cases of acute hepatitis E to define frequency, clinical features, prognosis and risk factors. METHODS We considered all the patients admitted to our Regional Hospital between August 2011 and September 2014, with a diagnosis of acute hepatitis; serological screening for hepatitis B, C and A viruses was performed; in the event of negative results, sera were tested for cytomegalovirus, Epstein-Barr and hepatitis E viruses. RESULTS Among 200 patients, 66 were affected by viral infection. IgM anti-HEV was detected in 14 patients with a predominance of males (79%) with a mean age of 55. Genotype 3 of HEV was found in 8 patients. Only one patient died of acute on chronic liver failure; all others evolved favourably towards clinical remission within two months from clinical onset. Thirteen patients had had local exposure to infection and 9 reported the consumption of raw or undercooked locally produced pork. CONCLUSION The incidence of HEV in our cohort of patients with acute viral hepatitis is high (about 20% per year). In over 85% an autochthonous exposure to infection could be recognised, with a clear link with food habits.
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Affiliation(s)
- Giuseppe Tarantino
- Department of Gastroenterology and Transplants, Clinic of Gastroenterology, Hospital of Ancona, Università Politecnica delle Marche, Italy.
| | - Patrizia Bagnarelli
- Department of Biomedical Sciences and Public Health, Virology, Hospital of Ancona, Università Politecnica delle Marche, Italy
| | - Marco Marzioni
- Department of Gastroenterology and Transplants, Clinic of Gastroenterology, Hospital of Ancona, Università Politecnica delle Marche, Italy
| | - Katia Marinelli
- Department of Biomedical Sciences and Public Health, Virology, Hospital of Ancona, Università Politecnica delle Marche, Italy
| | - Giulia Surace
- Department of Gastroenterology and Transplants, Clinic of Gastroenterology, Hospital of Ancona, Università Politecnica delle Marche, Italy
| | - Sara Traini
- Department of Gastroenterology and Transplants, Clinic of Gastroenterology, Hospital of Ancona, Università Politecnica delle Marche, Italy
| | - Gianluca Svegliati Baroni
- Department of Gastroenterology and Transplants, Clinic of Gastroenterology, Hospital of Ancona, Università Politecnica delle Marche, Italy
| | - Stefano Menzo
- Department of Biomedical Sciences and Public Health, Virology, Hospital of Ancona, Università Politecnica delle Marche, Italy
| | - Antonio Benedetti
- Department of Gastroenterology and Transplants, Clinic of Gastroenterology, Hospital of Ancona, Università Politecnica delle Marche, Italy
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20
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Morroni G, Brenciani A, Vincenzi C, Barocci S, Tili E, Manso E, Mingoia M, Menzo S, Varaldo PE, Giovanetti E. A clone of linezolid-resistant Staphylococcus epidermidis bearing the G2576T mutation is endemic in an Italian hospital. J Hosp Infect 2016; 94:203-6. [PMID: 27546457 DOI: 10.1016/j.jhin.2016.07.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 07/19/2016] [Indexed: 10/21/2022]
Affiliation(s)
- G Morroni
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - A Brenciani
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy.
| | - C Vincenzi
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy; Clinical Microbiology Laboratory, Torrette Regional Hospital, Ancona, Italy
| | - S Barocci
- Clinical Laboratory, Hospital Principe di Piemonte, Senigallia, Italy
| | - E Tili
- Clinical Laboratory, Hospital Carlo Urbani, Jesi, Italy
| | - E Manso
- Clinical Microbiology Laboratory, Torrette Regional Hospital, Ancona, Italy
| | - M Mingoia
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - S Menzo
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - P E Varaldo
- Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - E Giovanetti
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
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21
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Minosse C, Coen S, Visco Comandini U, Lionetti R, Montalbano M, Cerilli S, Vincenti D, Baiocchini A, Capobianchi MR, Menzo S. Simple and Reliable Method to Quantify the Hepatitis B Viral Load and Replicative Capacity in Liver Tissue and Blood Leukocytes. Hepat Mon 2016; 16:e28751. [PMID: 27882060 PMCID: PMC5111393 DOI: 10.5812/hepatmon.28751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 07/17/2015] [Accepted: 08/12/2015] [Indexed: 12/11/2022]
Abstract
BACKGROUND A functional cure of chronic hepatitis B (CHB) is feasible, but a clear view of the intrahepatic viral dynamics in each patient is needed. Intrahepatic covalently closed circular DNA (cccDNA) is the stable form of the viral genome in infected cells, and represents the ideal marker of parenchymal colonization. Its relationships with easily accessible peripheral parameters need to be elucidated in order to avoid invasive procedures in patients. OBJECTIVES The goal of this study was to design, set up, and validate a reliable and straightforward method for the quantification of the cccDNA and total DNA of the hepatitis B virus (HBV) in a variety of clinical samples. PATIENTS AND METHODS Clinical samples from a cohort of CHB patients, including liver biopsies in some, were collected for the analysis of intracellular HBV molecular markers using novel molecular assays. RESULTS A plasmid construct, including sequences from the HBV genome and from the human gene hTERT, was generated as an isomolar multi-standard for HBV quantitation and normalization to the cellular contents. The specificity of the real-time assay for the cccDNA was assessed using Dane particles isolated on a density gradient. A comparison of liver tissue from 6 untreated and 6 treated patients showed that the treatment deeply reduced the replicative capacity (total DNA/cccDNA), but had limited impact on the parenchymal colonization. The peripheral blood mononuclear cells (PBMCs) and granulocytes from the treated and untreated patients were also analyzed. CONCLUSIONS A straightforward method for the quantification of intracellular HBV molecular parameters in clinical samples was developed and validated. The widespread use of such versatile assays could better define the prognosis of CHB, and allow a more rational approach to time-limited tailored treatment strategies.
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Affiliation(s)
- Claudia Minosse
- Laboratory of Virology, National Institute for Infectious Diseases “L. Spallanzani”, Rome, Italy
| | - Sabrina Coen
- Laboratory of Virology, National Institute for Infectious Diseases “L. Spallanzani”, Rome, Italy
| | | | - Raffaella Lionetti
- Liver Unit, National Institute for Infectious Diseases “L. Spallanzani”, Rome, Italy
| | - Marzia Montalbano
- Liver Unit, National Institute for Infectious Diseases “L. Spallanzani”, Rome, Italy
| | - Stefano Cerilli
- Liver Unit, National Institute for Infectious Diseases “L. Spallanzani”, Rome, Italy
| | - Donatella Vincenti
- Laboratory of Virology, National Institute for Infectious Diseases “L. Spallanzani”, Rome, Italy
| | - Andrea Baiocchini
- Laboratory of Pathology, National Institute for Infectious Diseases “L. Spallanzani”, Rome, Italy
| | - Maria R. Capobianchi
- Laboratory of Virology, National Institute for Infectious Diseases “L. Spallanzani”, Rome, Italy
| | - Stefano Menzo
- Laboratory of Virology, Marche Polytechnic University, Ancona, Italy
- Corresponding Author: Stefano Menzo, Laboratory of Virology, Marche Polytechnic University, Ancona, Italy. Tel: +39-715964044, E-mail:
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22
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Colavita F, Venditti C, Vulcano A, Castilletti C, Zaccaro P, Mazzarelli A, Quartu S, Coen S, Cannas A, Chiappini R, Minosse C, Meschi S, Biava M, Menzo S, Beatrice Valli M, Grassi G, Lapa D, Vairo F, Portella G, Miccio R, Sponziello E, Rolla L, Delli Guanti M, Jocic M, Berti M, Ghezzo F, Radicchi L, Cataldi G, Monti G, Scaccabarozzi G, Strada G, Capobianchi MR, Ippolito G, Di Caro A. INMI/Emergency NGO Italian Laboratory Established In Sierra Leone during Ebola Virus Disease Outbreak in West Africa. ACTA ACUST UNITED AC 2016. [DOI: 10.15761/cmid.1000s1001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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23
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Tavio M, Vivarelli M, Menzo S, Gori A, Grossi PA, Marigliano A. Prophylaxis of HCV reinfection and direct-acting antiviral agents during liver transplantation. Liver Transpl 2015; 21:1327-9. [PMID: 26123079 DOI: 10.1002/lt.24204] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 06/10/2015] [Indexed: 01/13/2023]
Affiliation(s)
- Marcello Tavio
- Unit of Emerging and Immunosuppressed Infectious Diseases, Department of Gastroenterology and Transplantation, Azienda Ospedaliero-Universitaria "Ospedali Riuniti", Torrette Ancona, Italy
| | - Marco Vivarelli
- Unit of Hepatobiliary Surgery and Transplantation, Department of Gastroenterology and Transplantation, Azienda Ospedaliero-Universitaria "Ospedali Riuniti", Torrette Ancona, Italy
| | - Stefano Menzo
- Unit of Virology, Azienda Ospedaliero-Universitaria "Ospedali Riuniti", Torrette Ancona, Italy
| | - Andrea Gori
- Unit of Infectious Diseases, Azienda Ospedaliera San Gerardo, Monza, Italy
| | - Paolo Antonio Grossi
- Unit of Tropical and Infectious Diseases, Azienda Ospedaliera Universitaria Ospedale di Circolo, Fondazione Macchi, Varese, Italy
| | - Anna Marigliano
- Unit of Emerging and Immunosuppressed Infectious Diseases, Department of Gastroenterology and Transplantation, Azienda Ospedaliero-Universitaria "Ospedali Riuniti", Torrette Ancona, Italy
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24
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Lanini S, Ćosić G, Menzo S, Puro V, Đurić P, Garbuglia AR, Milošević V, Karać T, Capobianchi MR, Ippolito G. A Large Epidemic of Hepatitis B in Serbia: An Integrated Model for Outbreak Investigations in Healthcare Settings. Infect Control Hosp Epidemiol 2015. [DOI: 10.1086/599166] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We report a comprehensive approach for outbreak investigations, including cluster analysis (Bernoulli model), an algorithm to build inferential models, and molecular techniques to confirm cases. Our approach may be an interesting tool to best exploit the large amount of unsystematically collected information available during outbreak investigations in healthcare settings.Infect Control Hosp Epidemiol2014;35(6):732–735
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25
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Coen S, Angeletti C, Piselli P, Tronchin M, Vincenti D, Capobianchi MR, Galli C, Menzo S. a statistical model based on serological parameters for predicting occult HBV infection: implications for organ/ blood donations. New Microbiol 2015; 38:39-49. [PMID: 25742146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Accepted: 11/30/2014] [Indexed: 06/04/2023]
Abstract
The transmission of hepatitis B virus by donors with occult HBV infection (OBI) is a threat for blood transfusion and organ/tissue transplantation. The risk of carrying HBV DNA is currently not predictable by simple serologic markers, while HBV DNA testing is not universally deployed. This study evaluated an integrated serologic approach for assessing this risk. Anti-HBc positive subjects (461 HIV-negative, 262 HIV-positive) were selected for the study. Serology was analyzed by a commercial CMIA technique. HBV DNA was analyzed by both commercial and home-brew real-time amplification assays. A penalized maximum likelihood logistic approach was used to analyze the data. In HBsAg-negative subjects (HIV-negative), anti-HBc signal/cut off values, the presence of anti-HBc IgM, the absence of anti-HBsAg, and the absence of anti-HCV were correlated to the probability of finding circulating HBV DNA. A model for predicting HBV DNA presence by 4 serological parameters is therefore proposed. The predictive value of the logistic model based on simple serologic markers may represent a reasonable tool for the assessment of HBV transmission risk by transfusion or organ/tissue donation in the context of limited resources and where nucleic acid testing is not performed. In addition, it may be helpful for assessing the risk of reactivation in immunosuppressed OBI patients.
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Affiliation(s)
- Sabrina Coen
- Laboratory of Virology, National Institute of Infectious Diseases "L. Spallanzani", Roma, Italy
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26
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Lanini S, Ćosić G, Menzo S, Puro V, Đurić P, Garbuglia AR, Milošević V, Karać T, Capobianchi MR, Ippolito G. A large epidemic of hepatitis B in Serbia: an integrated model for outbreak investigations in healthcare settings. Infect Control Hosp Epidemiol 2014; 35:732-5. [PMID: 24799653 DOI: 10.1086/676432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We report a comprehensive approach for outbreak investigations, including cluster analysis (Bernoulli model), an algorithm to build inferential models, and molecular techniques to confirm cases. Our approach may be an interesting tool to best exploit the large amount of unsystematically collected information available during outbreak investigations in healthcare settings.
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Affiliation(s)
- Simone Lanini
- National Institute for Infectious Diseases, Istituto Nazionale per le Malattie Infettive-Lazzaro Spallanzani, Rome, Italy
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27
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Solmone M, Giombini E, Vincenti D, Rozera G, Testa A, Moscetti A, Catalano M, Abbate I, Capobianchi MR, Menzo S. Slow response to entecavir treatment in treatment-naive HBV patients is conditioned by immune response rather than by the presence or selection of refractory variants. Antivir Ther 2013; 19:201-9. [DOI: 10.3851/imp2700] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2013] [Indexed: 10/26/2022]
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28
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Bagnarelli P, Marinelli K, Trotta D, Monachetti A, Tavio M, Del Gobbo R, Capobianchi M, Menzo S, Nicoletti L, Magurano F, Varaldo P. Human case of autochthonous West Nile virus lineage 2 infection in Italy, September 2011. Euro Surveill 2011; 16:20002. [PMID: 22085600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023] Open
Abstract
On 10 September 2011, a patient in his 50s was admitted to hospital in Ancona, Italy, after six days of high fever and no response to antibiotics. West Nile virus (WNV) infection was suspected after tests to determine the aetiology of the fever were inconclusive. On 20 September, WNV-specific IgM and IgG antibodies were detected in the patient’s serum. Genomic sequencing of the viral isolate showed that the virus belonged to WNV lineage 2.
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Affiliation(s)
- P Bagnarelli
- Universita Politecnica Marche, Virology Unit, Department of Biomedical Sciences and Public Health, Ancona, Italy.
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Bagnarelli P, Marinelli K, Trotta D, Monachetti A, Tavio M, Del Gobbo R, Capobianchi MR, Menzo S, Nicoletti L, Magurano F, Varaldo PE. Human case of autochthonous West Nile virus lineage 2 infection in Italy, September 2011. Euro Surveill 2011. [DOI: 10.2807/ese.16.43.20002-en] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Binary file ES_Abstracts_Final_ECDC.txt matches
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Affiliation(s)
- P Bagnarelli
- Università Politecnica Marche, Virology Unit, Department of Biomedical Sciences and Public Health, Ancona, Italy
| | - K Marinelli
- Università Politecnica Marche, Virology Unit, Department of Biomedical Sciences and Public Health, Ancona, Italy
| | - D Trotta
- Università Politecnica Marche, Virology Unit, Department of Biomedical Sciences and Public Health, Ancona, Italy
| | - A Monachetti
- Università Politecnica Marche, Virology Unit, Department of Biomedical Sciences and Public Health, Ancona, Italy
| | - M Tavio
- Azienda Ospedaliero-Universitaria Ospedali Riuniti di Ancona, Infectious Disease Unit, Department of Gastroenterology and Transplantation, Ancona, Italy
| | - R Del Gobbo
- Azienda Ospedaliero-Universitaria Ospedali Riuniti di Ancona, Infectious Disease Unit, Department of Gastroenterology and Transplantation, Ancona, Italy
| | - M R Capobianchi
- National Institute of Infectious Diseases L.Spallanzani, Rome, Italy
| | - S Menzo
- National Institute of Infectious Diseases L.Spallanzani, Rome, Italy
| | | | - F Magurano
- Istituto Superiore di Sanitá, Rome, Italy
| | - P E Varaldo
- Università Politecnica Marche, Virology Unit, Department of Biomedical Sciences and Public Health, Ancona, Italy
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30
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Valli MB, Selleri M, Meschi S, Zaccaro P, Vincenti D, Lalle E, Capobianchi MR, Menzo S. Hemagglutinin 222 variants in pandemic (H1N1) 2009 virus. Emerg Infect Dis 2011. [PMID: 21470481 PMCID: PMC3377393 DOI: 10.3201/eid1704.100784] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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31
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Valli MB, Selleri M, Meschi S, Zaccaro P, Vincenti D, Lalle E, Capobianchi MR, Menzo S. Hemagglutinin 222 variants in pandemic (H1N1) 2009 virus. Emerg Infect Dis 2011; 17:749-51. [PMID: 21470481 DOI: 10.3201/eid1706.100784] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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32
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Prosperi MCF, Mackie N, Di Giambenedetto S, Zazzi M, Camacho R, Fanti I, Torti C, Sönnerborg A, Kaiser R, Codoñer FM, Van Laethem K, Bansi L, van de Vijver DAMC, Geretti AM, De Luca A, Giacometti A, Butini L, del Gobbo R, Menzo S, Tacconi D, Corbelli G, Zanussi S, Monno L, Punzi G, Maggiolo F, Callegaro A, Calza L, Carla Re M, Pristerà R, Turconi P, Mandas A, Tini S, Zoncada A, Paolini E, Amadio G, Sighinolfi L, Zuccati G, Morfini M, Manetti R, Corsi P, Galli L, Di Pietro M, Bartalesi F, Colao G, Tosti A, Di Biagio A, Setti M, Bruzzone B, Penco G, Trezzi M, Orani A, Pardelli R, De Gennaro M, Chiodera A, Scalzini A, Palvarini L, Almi P, Todaro G, d'Arminio Monforte A, Cicconi P, Rusconi S, Gismondo MR, Gismondo MR, Micheli V, Biondi ML, Gianotti N, Capetti A, Meraviglia P, Boeri E, Mussini C, Pecorari M, Soria A, Vecchi L, Santirocchi M, Brustia D, Ravanini P, Bello FD, Romano N, Mancuso S, Calzetti C, Maserati R, Filice G, Baldanti F, Francisci D, Parruti G, Polilli E, Sacchini D, Martinelli C, Consolini R, Vatteroni L, Vivarelli A, Dionisio D, Nerli A, Lenzi L, Magnani G, Ortolani P, Andreoni M, Palamara G, Fimiani C, Palmisano L, De Luca A, Fadda G, Vullo V, Turriziani O, Montano M, Cenderello G, Gonnelli A, Zazzi M, Palumbo M, Ghisetti V, Bonora S, Foglie PD, Rossi C, Grossi P, Seminari E, Poletti F, Mondino V, Malena M, Lattuada E, Lengauer T, Däumer M, Hoffmann D, Kaiser R, Schülter E, Müller C, Oette M, Reuter S, Esser S, Fätkenheuer G, Rockstroh J, van de Vijver DAMC, Incardona F, Rosen-Zvi M, Lengauer T, Camacho R, Clotet B, Thalme A, Svedhem V, Bratt G, Gargiulo F, Lapadula G, Manca N, Paraninfo G, Quiros-Roldan E, Carosi G, Castelnuovo F, Vandamme AM, Van Laethem K, Van Wijngaerden E, Ainsworth J, Anderson J, Babiker A, Dunn D, Easterbrook P, Fisher M, Gazzard B, Garrett N, Gilson R, Gompels M, Hill T, Johnson M, Leen C, Orkin C, Phillips A, Pillay D, Porter K, Post F, Sabin C, Sadiq T, Schwenk A, Walsh J, Delpech V, Palfreeman A, Dunn D, Glabay A, Porter K, Bansi L, Hill T, Phillips A, Sabin C, Orkin C, Garrett N, Lynch J, Hand J, de Souza C, Fisher M, Perry N, Tilbury S, Churchill D, Gazzard B, Nelson M, Waxman M, Mandalia S, Delpech V, Anderson J, Kall M, Post F, Korat H, Taylor C, Ibrahim F, Campbell L, Easterbrook P, Babiker A, Dunn D, Glabay A, Porter K, Gilson R, James L, Brima N, Williams I, Schwenk A, Johnson M, Youle M, Lampe F, Smith C, Grabowska H, Chaloner C, Puradiredja DI, Bansi L, Hill T, Phillips A, Sabin C, Walsh J, Weber J, Ramzan F, Carder M, Leen C, Wilson A, Gompels M, Dooley D, Palfreeman A, Anderson J, Asboe D, Pozniak A, Cameron S, Cane P, Chadwick D, Churchill D, Clark D, Collins S, Delpech V, Pillay D, Lazarus L, Dunn D, Dolling D, Fearnhill E, Castro H, Porter K, Coughlin K, Dolling D, Zuckerman M, Anna Maria G, Booth C, Goldberg D, Gompels M, Hale A, Kaye S, Kellam P, Leigh-Brown A, Mackie N, Orkin C, Pillay D, Phillips A, Sabin C, Smit E, Templeton K, Tilston P, Tong W, Williams I, Zhang H, Zhang H, Clark D, Ushiro-Lumb I, Oliver T, Bibby D, Mitchell S, Smit E, Mbisa T, Wildfire A, Tandy R, Shepherd J, Chadwick D, MacLean A, Tong W, Bennett D, Hopkins M, Tilston P, Booth C, Garcia-Diaz A, Kaye S, Kirk S. Detection of drug resistance mutations at low plasma HIV-1 RNA load in a European multicentre cohort study. J Antimicrob Chemother 2011; 66:1886-96. [DOI: 10.1093/jac/dkr171] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Mattia C. F. Prosperi
- Clinic of Infectious Diseases, Catholic University of the Sacred Heart, Rome, Italy
- Informa PRO Contract Research Organization, Rome, Italy
- Department of Pathology, Emerging Pathogens Institute, College of Medicine, University of Florida, Gainesville, USA
| | - Nicola Mackie
- Department of HIV Medicine, Imperial College Healthcare NHS Trust, London, UK
| | | | - Maurizio Zazzi
- Department of Molecular Biology, University of Siena, Siena, Italy
| | - Ricardo Camacho
- Molecular Biology Laboratory, Centro Hospitalar de Lisboa Ocidenta, Lisbon, Portugal
| | - Iuri Fanti
- Clinic of Infectious Diseases, Catholic University of the Sacred Heart, Rome, Italy
| | - Carlo Torti
- Clinic of Infectious and Tropical Diseases, University of Brescia, Brescia, Italy
| | - Anders Sönnerborg
- Division of Infectious Diseases, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, Cologne, Germany
| | | | - Kristel Van Laethem
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Loveleen Bansi
- Division of Population Health, UCL Medical School, Royal Free Campus, London, UK
| | | | - Anna Maria Geretti
- Department of Virology, University College London Medical School, London, UK
| | - Andrea De Luca
- Clinic of Infectious Diseases, Catholic University of the Sacred Heart, Rome, Italy
- Infectious Diseases Unit, University Hospital of Siena, Siena, Italy
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Gianotti N, Galli L, Zazzi M, Ghisetti V, Bonora S, Micheli V, Meraviglia P, Corsi P, Bruzzone B, Menzo S, Di Giambenedetto S, De Luca A, Filice G, Penco G, Castagna A. No pol mutation is associated independently with the lack of immune recovery in patients infected with HIV and failing antiretroviral therapy. J Med Virol 2011; 83:391-8. [PMID: 21264858 DOI: 10.1002/jmv.21989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
An investigation was undertaken to determine whether specific pol mutations hinder long-term immune recovery regardless of virological response. In total, 826 patients with >50 HIV RNA copies/ml, who underwent genotypic resistance testing between 1 January 2000 and 31 December 2003 after >3 years of antiretroviral treatment, and were followed up for >3 years after genotypic resistance testing, were analyzed retrospectively. The outcome of the study was the lack of immune recovery after >3 years of follow-up, defined as a slope by linear regression <0. The viremia detectability ratio was defined as the number of HIV RNA values of >50 copies/ml divided by the number of HIV RNA measurements during follow-up. Logistic regression was used for univariable and multivariable analysis. Median (Q1, Q3) values at baseline were the following: age 40 (37, 45) years, years on antiretroviral therapy 4.45 (3.65, 5.47), HIV RNA 3.91 (3.39, 4.53) log(10) copies/ml, CD4+ T-cell 358 (211, 524)/µl. After 3.13 years of follow-up, 375 patients (45.4%) showed a lack of immune recovery. The risk of lack of immune recovery increased independently with increasing baseline CD4+ counts (OR=1.104 per 50-cell increase, 95% CI=1.069-1.142, P<0.0001), increasing viremia detectability ratio during follow-up (OR=1.145 per 0.1-unit increase, 95% CI=1.093-1.202, P<0.0001), and with earlier calendar years of resistance testing (overall effect: P=0.0007). In conclusion, no pol mutation is associated independently with the lack of immune recovery.
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Affiliation(s)
- Nicola Gianotti
- Department of Infectious Diseases, IRCCS San Raffaele, Milan, Italy.
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Morelli MC, Sambri V, Grazi GL, Gaibani P, Pierro A, Cescon M, Ercolani G, Cavrini F, Rossini G, Capobianchi MR, Di Caro A, Menzo S, Pagliaro PP, Ghinelli F, Lazzarotto T, Landini MP, Pinna AD. Absence of neuroinvasive disease in a liver transplant recipient who acquired West Nile virus (WNV) infection from the organ donor and who received WNV antibodies prophylactically. Clin Infect Dis 2010; 51:e34-7. [PMID: 20597692 DOI: 10.1086/655146] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We describe the first case of West Nile virus (WNV) infection in Europe with transmission from donor to recipient following liver transplantation. The infection was detected in the recipient 3 days after transplantation, during the asymptomatic phase. We also report an innovative prophylactic strategy based on infusion of WNV hyperimmune plasma and gamma globulins that could be effective in preventing the appearance of a neuroinvasive disease.
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Scartozzi M, Mandolesi A, Giampieri R, Pierantoni C, Loupakis F, Zaniboni A, Galizia E, Giustini L, Silva RR, Bisonni R, Berardi R, Biagetti S, Menzo S, Falcone A, Bearzi I, Cascinu S. Insulin-like growth factor 1 expression correlates with clinical outcome in K-RAS wild type colorectal cancer patients treated with cetuximab and irinotecan. Int J Cancer 2010; 127:1941-7. [PMID: 20099280 DOI: 10.1002/ijc.25193] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Seventy to 40% of K-RAS wild type colorectal tumors does not seem to benefit from treatment with antiepidermal growth factor receptor (anti-EGFR) monoclonal antibodies. Recent data suggested that in presence of IGF-1 system, altered activation colorectal cancer cells may escape anti-EGFR mediated cell death. The interaction between IGF-1 expression and K-RAS mutational analysis was tested to verify the ability of IGF-1 to identify a subgroup of patients more likely to benefit from EGFR-targeted antibodies treatment. IGF-1 expression and K-RAS mutational status was assessed in advanced colorectal cancer patients receiving irinotecan/cetuximab. One hundred twelve patients were analyzed. IGF-1 was negative in 30 patients (27%) and overexpressed in the remaining 82 cases (73%). In IGF-1 negative and IGF-1 positive tumors, we observed progressive disease in 9 (30%) and 55 (67%) patients, respectively (p = 0.001). Median progression-free survival was 7.5 mo in patients showing IGF-1 negative tumors and 3 mo for IGF-1 expressing tumors (p = 0.002). Among K-RAS wild type patients, IGF-1 negative and positive tumors showed a partial response to cetuximab-irinotecan in 13 (65%) and 11 (22%) cases, respectively (p = 0.002). Median progression-free survival in IGF-1 negative tumors was 10 mo and 3.2 mo in IGF-1 positive colorectal cancers (p = 0.02). IGF-1 proved to be a possible predictive factor for resistance to anti-EGFR monoclonal antibodies in K-RAS wild type colorectal cancer. Combined IGF-1 and K-RAS analysis may represent an effective strategy for a better selection of responding colorectal cancer patients.
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Affiliation(s)
- Mario Scartozzi
- Department of Clinica di Oncologia Medica, AO Ospedali Riuniti-Università Politecnica delle Marche, Ancona, Italy
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Valli MB, Meschi S, Selleri M, Zaccaro P, Ippolito G, Capobianchi MR, Menzo S. Evolutionary pattern of pandemic influenza (H1N1) 2009 virus in the late phases of the 2009 pandemic. PLoS Curr 2010; 2:RRN1149. [PMID: 20228856 PMCID: PMC2832123 DOI: 10.1371/currents.rrn1149] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 03/04/2010] [Indexed: 11/18/2022]
Abstract
Influenza A( H1N1)v has spread rapidly in all parts of the globe in 2009 as a true pandemic, although fortunately a clinically mild one. The relevant evolutionary steps for the new virus to adapt to human populations occurred very early during the pandemic, before the end of April. Of the several resulting clades or clusters, clade 7 appeared later and proved more successful, substituting all other early clades before the bulk of the worldwide infections occurred.
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Affiliation(s)
- Maria Beatrice Valli
- INMI "L. Spallanzani" Rome; INMI "L. Spallanzani" Rome, Italy and INMI "L. Spallanzani" Roma
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Menzo S, Vincenti D, Solmone M, Prosperi M, Bruselles A, Abbate I, Rozera G, Capobianchi M. Low‐Abundance Drug Resistance Mutations: Extending the HIV Paradigm to Hepatitis B Virus. J Infect Dis 2009; 200:1798-9; author reply 1799-1800. [DOI: 10.1086/647991] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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Zazzi M, Prosperi M, Vicenti I, Di Giambenedetto S, Callegaro A, Bruzzone B, Baldanti F, Gonnelli A, Boeri E, Paolini E, Rusconi S, Giacometti A, Maggiolo F, Menzo S, De Luca A. Rules-based HIV-1 genotypic resistance interpretation systems predict 8 week and 24 week virological antiretroviral treatment outcome and benefit from drug potency weighting. J Antimicrob Chemother 2009; 64:616-24. [PMID: 19620134 DOI: 10.1093/jac/dkp252] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To test retrospectively the ability of four freely available rules-based expert systems to predict short- and medium-term virological outcome following an antiretroviral treatment switch in pre-treated HIV-1 patients. METHODS The HIV-1 genotype interpretation systems (GISs) HIVdb, ANRS, Rega and AntiRetroScan were tested for their accuracy in predicting response to highly active antiretroviral therapy using 8 week (n = 765) and 24 week (n = 634) follow-up standardized treatment change episodes extracted from the Italian Antiretroviral Resistance Cohort Analysis (ARCA) database. A genotypic sensitivity score (GSS) was derived for each genotype-treatment pair for the different GISs and tested as a predictor of virological treatment outcome by univariable and multivariable logistic regression as well as by receiver operating characteristic curve analysis. The two systems implementing drug potency weights (AntiRetroScan and Rega) were evaluated with and without this correction factor. RESULTS All four GSSs were strong predictors of virological treatment outcome at both 8 and 24 weeks after adjusting for baseline viro-immunological parameters and previous drug exposure (odds ratios ranging from 2.04 to 2.43 per 1 unit GSS increase; P < 0.001 for all the systems). The accuracy of AntiRetroScan and Rega was significantly increased by drug potency weighting with respect to the unweighted versions (P <or= 0.001). HIVdb and ANRS also increased their performance with the same drug potency weighting adopted by AntiRetroScan and Rega, respectively (P < 0.001 for both analyses). CONCLUSIONS Currently available GISs are valuable tools for assisting antiretroviral treatment choices. Drug potency weighting can increase the accuracy of all systems.
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Affiliation(s)
- Maurizio Zazzi
- Department of Molecular Biology, University of Siena, Siena, Italy
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Di Giambenedetto S, Zazzi M, Corsi P, Gonnelli A, Di Pietro M, Giacometti A, Almi P, Trezzi M, Boeri E, Gianotti N, Menzo S, Gobbo RD, Francisci D, Nerli A, Galli L, Luca AD. Evolution and predictors of HIV type-1 drug resistance in patients failing combination antiretroviral therapy in Italy. Antivir Ther 2009. [DOI: 10.1177/135965350901400308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Background This study aimed to examine the evolution of genotypic drug resistance prevalence in treatment-failing patients in the multicentre, Italian, Antiretroviral Resistance Cohort Analysis (ARCA). Methods Patients with a drug resistance genotype test performed between 1999 and 2006 at failure of a combination antiretroviral therapy and with complete treatment history were selected. The prevalence of resistance was measured overall, per calendar year, per drug class and per treatment line at failure. Results The overall resistance prevalence was 81%. Resistance to nucleoside reverse transcriptase inhibitors (NRTIs) declined after 2002 (68% in 2006; χ2 for trend P=0.004); resistance to non-NRTIs (NNRTIs) stabilized after 2004; and resistance to protease inhibitors (PIs) declined after 2001 (43% in 2006; P=0.004). In first-line failures, NRTI resistance decreased after 2002 ( P=0.006), NNRTI resistance decreased after 2003 ( P=0.001) and PI resistance decreased after 2001 ( P<0.001). Independent predictors of resistance to any class were HIV type-1 transmission by heterosexual contacts as compared with injecting drug use, a higher number of experienced regimens, prior history of suboptimal therapy, higher viral load and CD4+ T-cell counts, more recent calendar year and viral subtype B carriage, whereas the use of PI-based versus NNRTI-based regimens at failure was associated with a reduced risk of resistance. There was an increase of type-1 thymidine analogue and of protease mutations L33F, I47A/V, I50V and I54L/M, whereas L90M decreased over calendar years. Conclusions During more recent years, emerging drug resistance has decreased, particularly in first-line failures. The prevalence continues to be high in multiregimen-failing patients.
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Affiliation(s)
| | - Maurizio Zazzi
- Department of Molecular Biology, University of Siena, Siena, Italy
| | - Paola Corsi
- Division of Infectious Diseases, Careggi University Hospital, Firenze, Italy
| | - Angela Gonnelli
- Unit of Infectious Diseases, Siena University Hospital, Siena, Italy
| | - Massimo Di Pietro
- Division of Infectious Diseases, SM Annunziata Hospital, Firenze, Italy
| | - Andrea Giacometti
- Institute of Clinical Infectious Diseases, University Hospital of Ancona, Ancona, Italy
| | - Paolo Almi
- Unit of Infectious Diseases, Hospital of Massa, Massa, Italy
| | - Michele Trezzi
- Unit of Infectious Diseases, Hospital of Grosseto, Grosseto, Italy
| | - Enzo Boeri
- Infectious Diseases Clinic, San Raffaele Hospital, Milan, Italy
| | - Nicola Gianotti
- Infectious Diseases Clinic, San Raffaele Hospital, Milan, Italy
| | - Stefano Menzo
- Institute of Microbiology, University of Ancona, Ancona, Italy
| | - Romana Del Gobbo
- Institute of Clinical Infectious Diseases, Catholic University, Rome, Italy
| | - Daniela Francisci
- Unit of Infectious Diseases, Perugia University Hospital, Perugia, Italy
| | | | - Luisa Galli
- Unit of Infectious Diseases, Meyer Hospital, Firenze, Italy
| | - Andrea De Luca
- Institute of Clinical Infectious Diseases, Catholic University, Rome, Italy
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Di Giambenedetto S, Zazzi M, Corsi P, Gonnelli A, Di Pietro M, Giacometti A, Almi P, Trezzi M, Boeri E, Gianotti N, Menzo S, Del Gobbo R, Francisci D, Nerli A, Galli L, De Luca A. Evolution and predictors of HIV type-1 drug resistance in patients failing combination antiretroviral therapy in Italy. Antivir Ther 2009; 14:359-369. [PMID: 19474470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
BACKGROUND This study aimed to examine the evolution of genotypic drug resistance prevalence in treatment-failing patients in the multicentre, Italian, Antiretroviral Resistance Cohort Analysis (ARCA). METHODS Patients with a drug resistance genotype test performed between 1999 and 2006 at failure of a combination antiretroviral therapy and with complete treatment history were selected. The prevalence of resistance was measured overall, per calendar year, per drug class and per treatment line at failure. RESULTS The overall resistance prevalence was 81%. Resistance to nucleoside reverse transcriptase inhibitors (NRTIs) declined after 2002 (68% in 2006; chi(2) for trend P=0.004); resistance to non-NRTIs (NNRTIs) stabilized after 2004; and resistance to protease inhibitors (PIs) declined after 2001 (43% in 2006; P=0.004). In first-line failures, NRTI resistance decreased after 2002 (P=0.006), NNRTI resistance decreased after 2003 (P=0.001) and PI resistance decreased after 2001 (P<0.001). Independent predictors of resistance to any class were HIV type-1 transmission by heterosexual contacts as compared with injecting drug use, a higher number of experienced regimens, prior history of suboptimal therapy, higher viral load and CD4+ T-cell counts, more recent calendar year and viral subtype B carriage, whereas the use of PI-based versus NNRTI-based regimens at failure was associated with a reduced risk of resistance. There was an increase of type-1 thymidine analogue and of protease mutations L33F, I47A/V, I50V and I54L/M, whereas L90M decreased over calendar years. CONCLUSIONS During more recent years, emerging drug resistance has decreased, particularly in first-line failures. The prevalence continues to be high in multiregimen-failing patients.
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Menzo S, Ciavattini A, Bagnarelli P, Marinelli K, Sisti S, Clementi M. Molecular epidemiology and pathogenic potential of underdiagnosed human papillomavirus types. BMC Microbiol 2008; 8:112. [PMID: 18601724 PMCID: PMC2491624 DOI: 10.1186/1471-2180-8-112] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2008] [Accepted: 07/04/2008] [Indexed: 11/22/2022] Open
Abstract
Background Human papillomavirus (HPV) tests are crucial diagnostic tools for the prevention of neoplastic lesions of the uterine cervix. However most commercial methods are designed to detect high-risk (HR) HPV types and a limited selection of low-risk ones, thus missing a fair number of intermediate/low-risk types. As a result, many HPV infections remain undiagnosed, generating distrust in virological diagnosis among gynaecologists, who continue to rely preferentially on cytological and colposcopic findings. Results In this study, we tested 6,335 consecutive clinical samples, most of them from Italian patients with cytological abnormalities. The samples, collected in 2000–2007, were analyzed using PCR amplification of a 173–206 bp (depending on HPV type) conserved region in the L1 open reading frame, restriction endonuclease analysis and, where required, sequence analysis for type determination. Analysis of a smaller male sample and long term follow-up of a few female subjects was also performed. A total of 2,161 samples tested positive for HPV DNA (32.1%); 21.3% of them were mixed infections. Overall, 59 known and 2 unknown HPV types were detected. Their relative prevalence was calculated; notably, types not clearly identifiable using the most common commercial method accounted for 36% of infections. Clinical findings associated with the underdiagnosed types ranged from H-SIL to low-grade abnormalities, although none of these infections resulted in invasive cancer. Conclusion Given the high prevalence of some underdiagnosed HPV types in the population (principally HPV53, HPV66, HPV84, and HPV87) and their frequent association with cytological abnormalities, techniques capable of detecting and typing them would prove extremely useful.
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Affiliation(s)
- Stefano Menzo
- Institute of Microbiology, Università Politecnica delle Marche, Ancona, Italy.
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Goteri G, Ranaldi R, Simonetti O, Capretti R, Menzo S, Stramazzotti D, Morichetti D, Offidani AM, Rupoli S, Leoni P. Clinicopathological features of primary cutaneous B-cell lymphomas from an academic regional hospital in central Italy: no evidence of Borrelia burgdorferi association. Leuk Lymphoma 2008; 48:2184-8. [PMID: 17926178 DOI: 10.1080/10428190701618250] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
We reviewed the clinico-pathological features of 73 primary cutaneous B-cell lymphomas (PCBCLs), diagnosed in 10 years in Marche region in central Italy, which included 16 marginal zone lymphomas (MZL), 33 follicle centre lymphomas (FCL) and 24 diffuse large B cell lymphomas (DLBCL). We also investigated the presence of Borrelia burgdorferi in tissues by polymerase chain reaction. Differences in age, sex, location site, response to therapy, disease recurrence and 5-year disease-specific survival were observed among the 3 histological groups. Specific DNA sequences of Borrelia burgdorferi were not detected in any of the 73 cases of PCBCL. We conclude that PCBCLs in Marche region behave according to the literature data and do not seem to be associated with Borrelia burgdorferi. Additional investigations should be performed on other possible etiologies, at least in our geographical area.
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Affiliation(s)
- Gaia Goteri
- Anatomia Patologica, Università Politecnica delle Marche, Ospedali Riuniti di Ancona Umberto I, G.M. Lancisi, G. Salesi, Ancona, Italy.
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Gianotti N, Tiberi S, Menzo S, Danise A, Boeri E, Galli L, Clementi M, Lazzarin A, Castagna A. HIV-1 replication capacity and genotype changes in patients undergoing treatment interruption or lamivudine monotherapy. J Med Virol 2008; 80:201-8. [PMID: 18098142 DOI: 10.1002/jmv.21085] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The objective of this study was to investigate the mechanisms underlying the virological and immunological changes occurring in failing HIV-1 infected patients undergoing treatment interruption or lamivudine monotherapy (the E-184V Study). Associations were sought between the de-selection of individual reverse transcriptase and protease resistance mutations and replication capacity recovery, HIV-RNA changes, and immunological changes. The replication capacity recovery was defined as the ratio between the replication capacity at weeks 24 or 48, and that measured at baseline. The replication capacity recovery, which was evaluable in 21 patients at week 24 and in 18 at week 48, was significantly higher in the treatment interruption than in the lamivudine group at week 24 (P = 0.002). Forty-eight week replication capacity recovery was greater when the 184V (P = 0.023), the 41L (P = 0.02), or the 215Y mutation (P = 0.037) were deselected at week 12. A greater reduction in the CD4+/CD8+ ratio at week 48 (P = 0.038) was observed as the 184V mutation was deselected and the de-selection of the 184V mutation at week 12 was the only independent predictor of the change of the CD4+/CD8+ ratio at week 48 from baseline at multivariable analysis (F-value = 6.72, P = 0.021). In conclusion, among patients undergoing treatment interruption or lamivudine monotherapy, the recovery of HIV-1 replication capacity was associated with the de-selection of reverse transcriptase mutations. The de-selection of the 184V mutation predicts independently a reduction in the CD4+/CD8+ ratio.
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Affiliation(s)
- Nicola Gianotti
- Divisione di Malattie Infettive, Istituto Scientifico San Raffaele, Milan, Italy.
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Valli MB, Crema A, Lanzilli G, Serafino A, Bertolini L, Ravagnan G, Ponzetto A, Menzo S, Clementi M, Carloni G. Molecular and cellular determinants of cell-to-cell transmission of HCV in vitro. J Med Virol 2007; 79:1491-9. [PMID: 17705190 DOI: 10.1002/jmv.20947] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
It was reported previously that HCV can be transmitted from persistently infected human bone-marrow-derived B-lymphoblastoid cells (TO.FE(HCV)) to human hepatoma cells by cell-to-cell contact. The present study confirms and characterize further such type of HCV infection in vitro. TO.FE(HCV) cells were co-cultured with 2.2.15 hepatoma cells, that are not susceptible to cell-free infection by sera containing HCV of 1b genotype. By this co-cultivation system it was demonstrated that HCV transmission to recipient cells requires de novo virus RNA replication. Several factors may favor HCV-transmission, evidence is provided that TO.FE(HCV) cells were able to select HCV-quasispecies. 5'-UTR and core sequence analysis revealed differences in the HCV-quasispecies composition in serum inoculum and in infected TO.FE B-cells at 4 months post-inoculation. It is considered that the latter may be more successful in replicating HCV in vitro and used to express surface molecules which may be involved in cell-to-cell contact. In TO.FE(HCV) cells replicate distinct, or few close related, HCV-variants correlated with those of serum inoculum. Comparative analysis of tetra-spans and integrins expression undertaken by cytofluorimetry displayed higher level of expression for TO.FE cells in comparison to other human bone-marrow-derived B-cell lines. Overall, the observed persistent in vitro HCV replication is mediated by a continuous cell-to-cell reinfection that may be favored by selection of viral variants and expression of molecules involved in cell adhesion. These observations may provide an explanation for the establishment of HCV infection, the occurrence of chronic infection and HCV-related lymphoproliferative diseases.
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Affiliation(s)
- Maria Beatrice Valli
- Institute of Neurobiology and Molecular Medicine, National Research Council (CNR), Roma, Italy
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Marinelli K, Bagnarelli P, Gaffi G, Trappolini S, Leoni P, Paggi AM, Della Vittoria A, Scalise G, Varaldo PE, Menzo S. PCR real time assays for the early detection of BKV-DNA in immunocompromised patients. New Microbiol 2007; 30:275-8. [PMID: 17802908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Testing for viral BKV-DNA in urine is a non-invasive early detection and monitoring tool in the diagnostic of BKV-related pathologies: quantitative analysis by Real-Time PCR can provide useful information in addition to cytologic analysis, although our study suggests that high BKV viruria is not necessarily associated with kidney or bladder damage.
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Affiliation(s)
- Katia Marinelli
- Istitito di Microbiologia e Scienze Biomediche, Università Politecnica delle Marche, Ancona, Italy
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Menzo S, Marinelli K, Bagnarelli P, Rolla S, Clementi M. Human papillomavirus infections: new perspectives for prevention and treatment. New Microbiol 2007; 30:189-212. [PMID: 17802897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Human papillomaviruses (HPVs) have been recognized as the main etiologic agent of cervical cancer and other anogenital neoplasms, and a leading cause of death from cancer worldwide. In the last twenty years, extensive research has contributed to document the molecular mechanisms of virus persistence and malignant transformation, confirming a direct role of viral proteins in these processes. A clear understanding of the molecular epidemiology of HPVs and the availability of powerful molecular diagnostic techniques have provided the background for prevention strategies of HPV-related carcinomas. Since these viruses are highly prevalent in the general population, strict screening programs are still necessary. Recently, major breakthroughs have emerged from immunological studies. Indeed, these studies have paved the way for medical treatment of HPV infections and provided the first highly effective preventive vaccines. For these principal reasons, the time has come for a great effort towards the eradication of these important human pathogens. The present review summarizes the main aspects of the virology, molecular epidemiology and molecular biology of HPV infection and highlights the recent perspectives of prevention and treatment of the HPV-related disease.
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Affiliation(s)
- Stefano Menzo
- Istituto di Microbiologia e Scienze Biomediche, Universita Politecnica delle Marche, Ancona, Italy.
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Castagna A, Danise A, Menzo S, Galli L, Gianotti N, Carini E, Boeri E, Galli A, Cernuschi M, Hasson H, Clementi M, Lazzarin A. Lamivudine monotherapy in HIV-1-infected patients harbouring a lamivudine-resistant virus: a randomized pilot study (E-184V study). AIDS 2006; 20:795-803. [PMID: 16549962 DOI: 10.1097/01.aids.0000218542.08845.b2] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE We compared the immunological and clinical outcomes of lamivudine monotherapy and complete therapy interruption in the treatment of HIV-1-infected patients harbouring lamivudine-resistant virus. METHODS This 48-week, open-label pilot study randomly assigned HIV-infected patients receiving lamivudine-containing HAART and harbouring the M184V mutation to monotherapy with lamivudine 300 mg once daily (lamivudine group) or the discontinuation of all antiretroviral drugs (TI group). The primary endpoint was the occurrence of immunological or clinical failure; immunological failure was defined as the first report of a CD4 T-cell count less than 350 cells/microl, and clinical failure as the occurrence of a Centers for Disease Control and Prevention grade B or C event. The data were analysed on the basis of the intention-to-treat principle. RESULTS By week 48, 20 of 29 patients in the TI group (69%; 95% CI 51-83%) and 12 of 29 in the lamivudine group (41%; 95% CI 26-59%) had discontinued the study because of immunological or clinical failure, which was significantly delayed in the lamivudine group (P = 0.018). Only patients in the TI group (6/29, 20.7%) experienced grade 3-4 clinical adverse events at least possibly related to HIV-1 (P = 0.02). The mean decline in CD4 cell percentage, viral rebound and recovery of HIV-1 replication capacity were significantly lower in the lamivudine group. The 24-week virological and immunological response after therapy resumption in patients who prematurely discontinued the study was similar in the two groups. CONCLUSION In HIV-1-infected patients harbouring a lamivudine-resistant virus, lamivudine monotherapy may lead to a better immunological and clinical outcome than complete therapy interruption.
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Affiliation(s)
- Antonella Castagna
- Clinic of Infectious Diseases, Vita-Salute San Raffaele University, Milan, Italy.
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De Luca A, Di Giambenedetto S, Romano L, Gonnelli A, Corsi P, Baldari M, Di Pietro M, Menzo S, Francisci D, Almi P, Zazzi M. Frequency and treatment-related predictors of thymidine-analogue mutation patterns in HIV-1 isolates after unsuccessful antiretroviral therapy. J Infect Dis 2006; 193:1219-22. [PMID: 16586357 DOI: 10.1086/502976] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2005] [Accepted: 11/21/2005] [Indexed: 11/04/2022] Open
Abstract
We investigated, in patients tested between 1991 and 2004, the patterns of mutually exclusive human immunodeficiency virus-1 thymidine-analogue mutations (TAMs) in 4039 reverse-transcriptase sequences with > or = 1 TAM. TAM pattern 1, which included M41L and L210W and excluded K70R and is coupled with more-extensive cross-resistance to drugs, became the most frequent pattern after 1996. In 1465 genotypes from 684 patients in whom highly active antiretroviral therapy (HAART) was unsuccessful, predictors of this pattern were the number of previous HAART regimens undergone (adjusted odds ratio [OR], 1.09 [95% confidence interval {CI}, 1.02-1.16]), use of stavudine/lamivudine (adjusted OR, 1.42 [95% CI, 1.05-1.99]), use of nevirapine (adjusted OR, 1.60 [95% CI, 1.14-2.24]), use of efavirenz (adjusted OR, 1.56 [95% CI, 1.08-2.27]), and use of ritonavir (adjusted OR, 1.35 [95% CI, 1.04-1.75]).
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Affiliation(s)
- Andrea De Luca
- Clinical Infectious Diseases, Catholic University, Rome, Italy.
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Brenciani A, Ojo KK, Monachetti A, Menzo S, Roberts MC, Varaldo PE, Giovanetti E. Distribution and molecular analysis of mef(A)-containing elements in tetracycline-susceptible and -resistant Streptococcus pyogenes clinical isolates with efflux-mediated erythromycin resistance. J Antimicrob Chemother 2004; 54:991-8. [PMID: 15563518 DOI: 10.1093/jac/dkh481] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES To analyse the distribution and molecular features of mef(A)-containing elements in a large collection of different Streptococcus pyogenes clinical isolates with efflux-mediated erythromycin resistance. To further characterize a tet(O)-mef(A) element. METHODS Gene detection was carried out by PCR using primers designed from established sequences or from sequences in this study. From a tet(O)-mef(A) element (approximately 60 kb), an 11 972 bp region including the tet(O) and mef(A) genes was sequenced. RESULTS In the tetracycline-susceptible isolates (n =28), the mef(A) gene was contained in a regular Tn1207.1 transposon (7.2 kb), which was inserted into one of two previously described elements, Tn1207.3 (approximately 52 kb) or a 58.8 kb chimeric element, both flanked by the comEC gene. In the tetracycline-resistant isolates (n =61), all of which carried the tet(O) gene, the mef(A) gene was part of a variable Tn1207.1-related transposon inserted into unique elements which contained the tet(O) gene approximately 2.3 to 5.5 kb upstream of the mef(A) gene and were not flanked by the comEC gene. In the Tn1207.1-like transposon of these tet(O)-mef(A) elements, only msr(D) (orf5) and a modified orf6, in addition to mef(A), were detected by PCR in all isolates tested; while orf1 and orf2 were always undetectable, orf3, orf7 and orf8 were found in variable percentages. In an orf3-positive element, sequencing identified four new open reading frames downstream of the tet(O) gene, followed by three short sequences with homology to sequences of the pneumococcal mega element. CONCLUSIONS The mef(A) gene is carried on different chromosomal genetic elements depending on whether the isolates are susceptible or resistant to tetracycline.
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Affiliation(s)
- Andrea Brenciani
- Institute of Microbiology and Biomedical Sciences, Marche Polytechnic University, 60131 Ancona, Italy
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Bagnarelli P, Vecchi M, Burighel N, Bellanova D, Menzo S, Clementi M, De Rossi A. Genotypic and phenotypic correlates of the HIV Type 1 env gene evolution in infected children with discordant response to antiretroviral therapy. AIDS Res Hum Retroviruses 2004; 20:1306-13. [PMID: 15650423 DOI: 10.1089/aid.2004.20.1306] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The genotypic-phenotypic correlates of human immunodeficiency virus type 1 (HIV-1) env gene evolution were investigated in samples from eight infected children under antiretroviral therapy (ART) and virological failure. Evolution of the gp120 C2-V5 env sequence was demonstrated in all subjects but one by sequence analysis of the replicating plasma virus collected at baseline and 12-15 months after ART initiation. The analysis of the host's selective pressure showed that in four subjects, the ratio of nonsynonymous to synonymous amino acid substitutions was higher in the V3 sequences than in the C2-V5 region ([K (a)/K (s)](V3)/[K (a)/K (s)](C2V5) >1.0). Interestingly, this feature was observed only in subjects (four of five) showing an increase in T cell receptor rearrangement excision circle (TREC)-bearing cells and in CD4(+) T-lymphocytes despite persistent viremia (discordant therapeutic response) (p = 0.02), thus suggesting that the V3 loop is a target of the immune reconstitution under ART. Using phenotypic analysis of recombinant viruses expressing exogenous V3 sequences, a reverse shift from CXCR4-tropic to CCR5-tropic variants was demonstrated in two of the four subjects, further indicating that the host's selective pressure sharply forces the V3 evolution of replicating variants. The data indicate that a complex HIV-1-host interplay occurs in children receiving antiretroviral treatments and suggest that the recovery of thymic function places a selective constraint on the viral V3 loop.
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Affiliation(s)
- Patrizia Bagnarelli
- Istituto di Microbiologia e Scienze Biomediche, Università Politecnica delle Marche, Ancona, Italy.
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