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Pedrazzoli P, Lasagna A, Cassaniti I, Piralla A, Squeri A, Bruno R, Sacchi P, Baldanti F, Di Maio M, Beretta GD, Cinieri S, Silvestris N. Vaccination for seasonal flu, pneumococcal infection, and SARS-CoV-2 in patients with solid tumors: recommendations of the Associazione Italiana di Oncologia Medica (AIOM). ESMO Open 2023; 8:101215. [PMID: 37104930 PMCID: PMC10067463 DOI: 10.1016/j.esmoop.2023.101215] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/13/2023] [Accepted: 03/22/2023] [Indexed: 04/05/2023] Open
Abstract
Patients with cancer have a well-known and higher risk of vaccine-preventable diseases (VPDs). VPDs may cause severe complications in this setting due to the immune system impairment, malnutrition and oncological treatments. Despite this evidence, vaccination rates are inadequate. The Italian Association of Medical Oncology (AIOM) has been involved in vaccination awareness since 2014. Based on a careful review of the available data about the immunogenicity, effectiveness and safety of flu, pneumococcal and anti-SARS-CoV-2 vaccines, we report the recommendations of the Associazione Italiana di Oncologia Medica about these vaccinations in adult patients with solid tumors. AIOM recommends comprehensive education on the issue of VPDs. We believe that a multidisciplinary care model may improve the vaccination coverage in immunocompromised patients. Continued surveillance, implementation of preventive practices and future well-designed immunological prospective studies are essential for a better management of our patients with cancer.
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Affiliation(s)
- P Pedrazzoli
- Department of Internal Medicine and Medical Therapy, University of Pavia, Pavia, Italy; Medical Oncology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - A Lasagna
- Medical Oncology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.
| | - I Cassaniti
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - A Piralla
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - A Squeri
- Medical Oncology Unit, Department of Human Pathology "G. Barresi", University of Messina, Messina, Italy; School of Specialization in Medical Oncology, University of Messina, Messina, Italy
| | - R Bruno
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy; Division of Infectious Diseases I, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - P Sacchi
- Division of Infectious Diseases I, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - F Baldanti
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy; Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - M Di Maio
- Department of Oncology, University of Turin, Division of Medical Oncology, Ordine Mauriziano Hospital, Turin, Italy
| | - G D Beretta
- Medical Oncology Unit, Santo Spirito Hospital, Pescara, Italy
| | - S Cinieri
- Medical Oncology Division and Breast Unit, Senatore Antonio Perrino Hospital, ASL Brindisi, Brindisi, Italy
| | - N Silvestris
- Medical Oncology Unit, Department of Human Pathology "G. Barresi", University of Messina, Messina, Italy
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2
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Hayes A, Nguyen D, Andersson M, Antón A, Bailly J, Beard S, Benschop KSM, Berginc N, Blomqvist S, Cunningham E, Davis D, Dembinski JL, Diedrich S, Dudman SG, Dyrdak R, Eltringham GJA, Gonzales‐Goggia S, Gunson R, Howson‐Wells HC, Jääskeläinen AJ, López‐Labrador FX, Maier M, Majumdar M, Midgley S, Mirand A, Morley U, Nordbø SA, Oikarinen S, Osman H, Papa A, Pellegrinelli L, Piralla A, Rabella N, Richter J, Smith M, Söderlund Strand A, Templeton K, Vipond B, Vuorinen T, Williams C, Wollants E, Zakikhany K, Fischer TK, Harvala H, Simmonds P. A European multicentre evaluation of detection and typing methods for human enteroviruses and parechoviruses using RNA transcripts. J Med Virol 2020; 92:1065-1074. [PMID: 31883139 PMCID: PMC7496258 DOI: 10.1002/jmv.25659] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 10/17/2019] [Accepted: 12/24/2019] [Indexed: 12/28/2022]
Abstract
Polymerase chain reaction (PCR) detection has become the gold standard for diagnosis and typing of enterovirus (EV) and human parechovirus (HPeV) infections. Its effectiveness depends critically on using the appropriate sample types and high assay sensitivity as viral loads in cerebrospinal fluid samples from meningitis and sepsis clinical presentation can be extremely low. This study evaluated the sensitivity and specificity of currently used commercial and in-house diagnostic and typing assays. Accurately quantified RNA transcript controls were distributed to 27 diagnostic and 12 reference laboratories in 17 European countries for blinded testing. Transcripts represented the four human EV species (EV-A71, echovirus 30, coxsackie A virus 21, and EV-D68), HPeV3, and specificity controls. Reported results from 48 in-house and 15 commercial assays showed 98% detection frequencies of high copy (1000 RNA copies/5 µL) transcripts. In-house assays showed significantly greater detection frequencies of the low copy (10 copies/5 µL) EV and HPeV transcripts (81% and 86%, respectively) compared with commercial assays (56%, 50%; P = 7 × 10-5 ). EV-specific PCRs showed low cross-reactivity with human rhinovirus C (3 of 42 tests) and infrequent positivity in the negative control (2 of 63 tests). Most or all high copy EV and HPeV controls were successfully typed (88%, 100%) by reference laboratories, but showed reduced effectiveness for low copy controls (41%, 67%). Stabilized RNA transcripts provide an effective, logistically simple and inexpensive reagent for evaluation of diagnostic assay performance. The study provides reassurance of the performance of the many in-house assay formats used across Europe. However, it identified often substantially reduced sensitivities of commercial assays often used as point-of-care tests.
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Affiliation(s)
- A. Hayes
- Nuffield Department of MedicineUniversity of OxfordOxfordUK
| | - D. Nguyen
- Nuffield Department of MedicineUniversity of OxfordOxfordUK
| | - M. Andersson
- Microbiology Laboratory, John Radcliffe Hospital, Headley Way, HeadingtonOxfordUK
| | - A. Antón
- Respiratory Viruses Unit, Virology Section, Microbiology DepartmentHospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Passeig Vall d'HebronBarcelonaSpain
| | - J.‐L. Bailly
- Université Clermont Auvergne, LMGE UMR CNRS, UFR MédecineClermont‐FerrandFrance
- CHU Clermont‐Ferrand, National Reference Center for EV and Parechovirus‐Associated LaboratoryClermont‐FerrandFrance
| | - S. Beard
- Enteric Virus Unit, Virus Reference DepartmentNational Infection Service, Public Health EnglandLondonUK
| | - K. S. M. Benschop
- National Institute for Public Health and the Environment (RIVM)BilthovenThe Netherlands
| | - N. Berginc
- Department for Public Health VirologyNational Laboratory of Health, Environment and FoodLjubljanaSlovenia
| | - S. Blomqvist
- National Institute for Health and Welfare, MannerheimintieHelsinkiFinland
| | - E. Cunningham
- Viapath Infection Sciences, St. Thomas' HospitalLondonUK
| | - D. Davis
- Microbiology, Virology and infection Prevention & ControlGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK
| | - J. L. Dembinski
- Department of VirologyNorwegian Institute of Public HealthOsloNorway
| | - S. Diedrich
- National Reference Center for Poliomyelitis and Enteroviruses, Robert Koch InstituteBerlinGermany
| | - S. G. Dudman
- Department of MicrobiologyOslo University Hospital Rikshospitalet, Inst. Clinical Medicine, University of OsloOsloNorway
| | - R. Dyrdak
- Department of Clinical MicrobiologyKarolinska University HospitalStockholmSweden
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstituteStockholmSweden
| | - G. J. A. Eltringham
- Molecular Diagnostics Laboratory, Microbiology, Freeman HospitalNewcastle Upon TyneUK
| | - S. Gonzales‐Goggia
- Public Health England Poliovirus Reference Laboratory, National Infection Service, Public Health EnglandLondonUK
| | - R. Gunson
- West of Scotland Specialist Virology CentreGlasgow Royal InfirmaryGlasgowUK
| | - H. C. Howson‐Wells
- Nottingham University Hospitals NHS Trust, Clinical Microbiology, Queens Medical CentreNottinghamUK
| | - A. J. Jääskeläinen
- University of Helsinki and Helsinki University Hospital, HUSLAB, Virology and ImmunologyHelsinkiFinland
| | - F. X. López‐Labrador
- Virology Laboratory, Joint Units in Genomics and Health and Infection and Health, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO‐Public Health)/Universitat de València, Av. CatalunyaValènciaSpain
- CIBEResp, Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública, Instituto de Salud Carlos IIIMadridSpain
| | - M. Maier
- Institute of VirologyLeipzig University HospitalLeipzigGermany
| | - M. Majumdar
- The National Institute for Biological Standards and ControlHertfordshireUK
| | - S. Midgley
- Department of Virus and Special Microbiological DiagnosticsVirus Surveillance and Research Section, Statens Serum InstitutCopenhagenDenmark
| | - A. Mirand
- CHU Clermont‐Ferrand, Laboratoire de Virologie—Centre National de Référence des Entérovirus et Parechovirus, Laboratoire Associé—Clermont‐FerrandFrance
| | - U. Morley
- UCD National Virus Reference LaboratoryUniversity College Dublin, BelfieldDublinIreland
| | - S. A. Nordbø
- Department of Medical MicrobiologySt. Olavs University HospitalTrondheimNorway
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health SciencesNorwegian University of Science and TechnologyTrondheimNorway
| | - S. Oikarinen
- Faculty of Medicine and Health TechnologyTampere UniversityTampereFinland
| | - H. Osman
- Public Health England Birmingham Public Health Laboratory, Heartlands HospitalBirminghamUK
| | - A. Papa
- Department of MicrobiologyMedical School, Aristotle University of ThessalonikiThessalonikiGreece
| | - L. Pellegrinelli
- Department of Biomedical Sciences for HealthUniversity of MilanMilanItaly
| | - A. Piralla
- Molecular Virology Unit, Microbiology and Virology DepartmentFondazione IRCCS Policlinico San MatteoPaviaItaly
| | - N. Rabella
- Virology Section, Santa Creu i Sant Pau University HospitalBarcelonaSpain
| | - J. Richter
- Department of Molecular VirologyCyprus Institute of Neurology and GeneticsNicosiaCyprus
| | - M. Smith
- Department of Biomedical Sciences for HealthUniversity of MilanMilanItaly
- King's College Hospital, Bessemer Wing, Denmark HillLondonUK
| | - A. Söderlund Strand
- Laboratory Medicine, Department of Clinical MicrobiologyLund University Hospital, SölvegatanLundSweden
| | - K. Templeton
- Edinburgh Specialist Virology, Royal Infirmary of EdinburghEdinburghUK
| | - B. Vipond
- Public Health England, South West Regional Laboratory, Pathology Sciences Building, Science QuarterSouthmead HospitalBristolUK
| | - T. Vuorinen
- Clinical MicrobiologyTurku University Hospital and Institute of Biomedicine University of TurkuTurkuFinland
| | | | - E. Wollants
- Clinical and Epidemiological Virology, KU Leuven, REGA Institute, Clinical and Epidemiological VirologyLeuvenBelgium
| | - K. Zakikhany
- Katherina Zakikhany‐Gilg, Public Health Agency of Sweden, Department of MicrobiologyUnit of Laboratory Surveillance of Viral Pathogens and Vaccine Preventable DiseasesStockholmSweden
| | - T. K. Fischer
- CIBEResp, Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública, Instituto de Salud Carlos IIIMadridSpain
- Department of Virus and Special Microbiological DiagnosticsVirus Surveillance and Research Section, Statens Serum InstitutCopenhagenDenmark
| | - H. Harvala
- NHS Blood and Transplant, ColindaleLondonUK
| | - P. Simmonds
- Nuffield Department of MedicineUniversity of OxfordOxfordUK
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3
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Balmelli C, Merlani G, Martinetti G, Reinholz D, Paolucci S, Baldanti F, Piralla A, Del Grande F, Bernasconi E. Outbreak of hepatitis C virus infections originating from a breach in safe injection practices before contrast-enhanced computed tomography scanning. J Hosp Infect 2020; 106:600-604. [PMID: 32497652 DOI: 10.1016/j.jhin.2020.05.041] [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: 01/08/2020] [Accepted: 05/26/2020] [Indexed: 11/29/2022]
Abstract
Four patients who underwent contrast-enhanced computed tomography (CT) scanning were infected with hepatitis C virus from a contaminated multi-dose vial of NaCl. The outbreak likely occurred due to a breach in safe injection practices, resulting in contamination of the vial. Not all patients exposed to the same vial were infected. The uneven distribution of infections could be attributed to a stochastic effect of a low infectious dose. This implies that outbreak investigations need to be extended to all patients scheduled before and after the first identified infected patient to confirm or rule out nosocomial transmission.
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Affiliation(s)
- C Balmelli
- Division of Infection Control and Hospital Epidemiology, Ente Ospedaliero Cantonale, Bellinzona, Ticino, Switzerland.
| | - G Merlani
- Division of Public Health, Canton Ticino, Bellinzona, Ticino, Switzerland
| | - G Martinetti
- Division of Infection Control and Hospital Epidemiology, Ente Ospedaliero Cantonale, Bellinzona, Ticino, Switzerland
| | - D Reinholz
- Division of Public Health, Canton Ticino, Bellinzona, Ticino, Switzerland.
| | - S Paolucci
- Fondazione IRCCS Policlinico San Matteo, Pavia, Lombardy, Italy
| | - F Baldanti
- University of Pavia, Pavia, Lombardy, Italy
| | - A Piralla
- Fondazione IRCCS Policlinico San Matteo, Pavia, Lombardy, Italy; University of Pavia, Pavia, Lombardy, Italy
| | - F Del Grande
- Clinica di Radiologia EOC, Istituto di Imaging della Svizzera Italiana, Ospedale Regionale di Lugano, Ticino, Switzerland
| | - E Bernasconi
- Division of Infectious Diseases, Ospedale Regionale di Lugano, Lugano, Ticino, Switzerland
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4
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Ciceri G, Canuti M, Bianchi S, Gori M, Piralla A, Colzani D, Libretti M, Frati ER, Baggieri M, Lai A, Rovida F, Zehender G, Baldanti F, Magurano F, Tanzi E, Amendola A. Genetic variability of the measles virus hemagglutinin gene in B3 genotype strains circulating in Northern Italy. Infect Genet Evol 2019; 75:103943. [PMID: 31255832 DOI: 10.1016/j.meegid.2019.103943] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/24/2019] [Accepted: 06/26/2019] [Indexed: 11/18/2022]
Abstract
Sequencing the whole measles virus hemagglutinin (H) gene, in conjunction with a 450-nucleotide region of the nucleoprotein gene (N-450), is helpful for the identification of new genotypes and as an auxiliary in outbreak characterization. In addition, it is essential to be able to predict the antigenic changes of the H protein to gain a better monitoring of the response to the vaccine. In this study, we obtained the full-length H gene sequences from 19 measles virus (MV) strains belonging to two B3 genotype variants circulating in Lombardy (Northern Italy) between July 2015 and February 2016 and evaluated the variability of the whole MV-H gene. Furthermore, we compared the obtained H amino acid sequences to all MV sequences available in the GenBank database (n = 1152 in total) and analyzed the amino acid substitutions in the H protein within clades where the Italian strains were included. We identified a higher variability in the H gene compared to the N-450 region and our results support previous studies, highlighting that the H gene is more informative for characterizing the MV B3 genotype than the N-450 sequence. Some of the amino acid substitutions were fixed in the viral population and, remarkably, some of the amino acid substitutions were typically present only in the Italian sequences. Accumulating further molecular information about MV-H gene will be necessary to enable in-depth analyses of the variability of this gene in the vaccinated population.
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Affiliation(s)
- G Ciceri
- Department of Biomedical Sciences for Health, University of Milan, via Carlo Pascal, 36, 20133 Milan, Italy.
| | - M Canuti
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John's, NL A1B 3X9, Canada
| | - S Bianchi
- Department of Biomedical Sciences for Health, University of Milan, via Carlo Pascal, 36, 20133 Milan, Italy.
| | - M Gori
- Department of Biomedical Sciences for Health, University of Milan, via Carlo Pascal, 36, 20133 Milan, Italy
| | - A Piralla
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, via Taramelli, 5, 27100 Pavia, Italy.
| | - D Colzani
- Department of Biomedical Sciences for Health, University of Milan, via Carlo Pascal, 36, 20133 Milan, Italy.
| | - M Libretti
- Department of Biomedical Sciences for Health, University of Milan, via Carlo Pascal, 36, 20133 Milan, Italy
| | - E R Frati
- Department of Biomedical Sciences for Health, University of Milan, via Carlo Pascal, 36, 20133 Milan, Italy
| | - M Baggieri
- Department of Infectious Parasitic and Immune-Mediated Diseases, National Reference Laboratory for Measles and Rubella, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161 Rome, Italy.
| | - A Lai
- Department of Biomedical and Clinical Sciences "Luigi Sacco", Section of Infectious Diseases, University of Milan, Via Gian Battista Grassi, 74, 20157 Milan, Italy.
| | - F Rovida
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, via Taramelli, 5, 27100 Pavia, Italy.
| | - G Zehender
- Department of Biomedical and Clinical Sciences "Luigi Sacco", Section of Infectious Diseases, University of Milan, Via Gian Battista Grassi, 74, 20157 Milan, Italy; Coordinated Research Center "EpiSoMI", University of Milan, via Carlo Pascal, 36, 20133 Milan, Italy.
| | - F Baldanti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, via Taramelli, 5, 27100 Pavia, Italy.
| | - F Magurano
- Department of Infectious Parasitic and Immune-Mediated Diseases, National Reference Laboratory for Measles and Rubella, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161 Rome, Italy.
| | - E Tanzi
- Department of Biomedical Sciences for Health, University of Milan, via Carlo Pascal, 36, 20133 Milan, Italy; Coordinated Research Center "EpiSoMI", University of Milan, via Carlo Pascal, 36, 20133 Milan, Italy.
| | - A Amendola
- Department of Biomedical Sciences for Health, University of Milan, via Carlo Pascal, 36, 20133 Milan, Italy; Coordinated Research Center "EpiSoMI", University of Milan, via Carlo Pascal, 36, 20133 Milan, Italy.
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5
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Pedrazzoli P, Piralla A, Valentino F, Cinieri S, Baldanti F. Update of the recommendations of the Italian Society of Medical Oncology on vaccination for seasonal influenza and pneumococcal infection in patients with cancer: Focus on prevention of pneumonia. Eur J Cancer Care (Engl) 2018; 27:e12817. [PMID: 29575267 DOI: 10.1111/ecc.12817] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/17/2017] [Indexed: 11/26/2022]
Affiliation(s)
- P. Pedrazzoli
- Medical Oncology; Department of Oncology and Precision Medicine; Fondazione IRCCS Policlinico San Matteo; Pavia Italy
| | - A. Piralla
- Molecular Virology Unit, Microbiology and Virology Department; Fondazione IRCCS Policlinico San Matteo; Pavia Italy
| | - F. Valentino
- Medical Oncology; Department of Oncology and Precision Medicine; Fondazione IRCCS Policlinico San Matteo; Pavia Italy
| | - S. Cinieri
- Medical Oncology Division; Antonio Perrino Hospital; Brindisi Italy
| | - F. Baldanti
- Molecular Virology Unit, Microbiology and Virology Department; Fondazione IRCCS Policlinico San Matteo; Pavia Italy
- Department of Clinical; Surgical, Diagnostic and Pediatric Sciences; University of Pavia; Pavia Italy
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6
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Narra R, Bono P, Zoccoli A, Orlandi A, Piconi S, Grasselli G, Crotti S, Girello A, Piralla A, Baldanti F, Lunghi G. Acute respiratory distress syndrome in adenovirus type 4 pneumonia: A case report. J Clin Virol 2016; 81:78-81. [PMID: 27354307 DOI: 10.1016/j.jcv.2016.06.005] [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] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 06/06/2016] [Accepted: 06/10/2016] [Indexed: 10/21/2022]
Abstract
Human adenoviruses (HAdVs) cause a wide spectrum of clinical syndromes, depending on species and types, from mild respiratory infections to deadly pneumonia: in particular, severe infections occur in immunocompromised patients. In this report, we describe the case of a 36 years-old woman admitted to our intensive care unit (ICU) with severe respiratory distress syndrome caused by adenovirus pneumonia, that required invasive respiratory support (mechanical ventilation and extracorporeal membrane oxygenation). Molecular assays detected the virus in respiratory and plasma specimen and sequencing procedure identified HAdV type 4. Patient improved after cidofovir administration. Leukopenia and subsequent bacterial infection occurred, but the patient recovered completely and was discharged from the hospital after 54days.
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Affiliation(s)
- R Narra
- Virology Unit, Fondazione IRCCS Ospedale Maggiore Ca' Granda, Milan, Italy;, Italy
| | - P Bono
- Virology Unit, Fondazione IRCCS Ospedale Maggiore Ca' Granda, Milan, Italy;, Italy
| | - A Zoccoli
- Virology Unit, Fondazione IRCCS Ospedale Maggiore Ca' Granda, Milan, Italy;, Italy
| | - A Orlandi
- Virology Unit, Fondazione IRCCS Ospedale Maggiore Ca' Granda, Milan, Italy;, Italy
| | - S Piconi
- First Infectious Disease Department, A.O. Luigi Sacco, Milan, Italy
| | - G Grasselli
- Intensive Care Unit, Fondazione IRCCS Ospedale Maggiore Ca' Granda, Italy
| | - S Crotti
- Intensive Care Unit, Fondazione IRCCS Ospedale Maggiore Ca' Granda, Italy
| | - A Girello
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - A Piralla
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - F Baldanti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; Section of Microbiology, Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - G Lunghi
- Virology Unit, Fondazione IRCCS Ospedale Maggiore Ca' Granda, Milan, Italy;, Italy.
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7
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Piralla A, Girello A, Rovida F, Premoli M, Mojoli F, Braschi A, Iotti G, Baldanti F. Viral population dynamics in the lower respiratory tract of ICU-admitted patients with influenza H1N1pdm09 infections during the 2014–2015 season in Northern Italy. J Clin Virol 2015. [DOI: 10.1016/j.jcv.2015.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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8
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Barzon L, Papa A, Lavezzo E, Franchin E, Pacenti M, Sinigaglia A, Masi G, Trevisan M, Squarzon L, Toppo S, Papadopoulou E, Nowotny N, Ulbert S, Piralla A, Rovida F, Baldanti F, Percivalle E, Palù G. Phylogenetic characterization of Central/Southern European lineage 2 West Nile virus: analysis of human outbreaks in Italy and Greece, 2013-2014. Clin Microbiol Infect 2015; 21:1122.e1-10. [PMID: 26235197 DOI: 10.1016/j.cmi.2015.07.018] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 06/29/2015] [Accepted: 07/23/2015] [Indexed: 01/10/2023]
Abstract
In recent years, West Nile virus (WNV) lineage 2 has been spreading and causing disease outbreaks in humans and animals in Europe. In order to characterize viral diversity, we performed full-length genome sequencing of WNV lineage 2 from human samples collected during outbreaks in Italy and Greece in 2013 and 2014. Phylogenetic analysis showed that these WNV lineage 2 genomes belonged to a monophyletic clade derived from a single introduction into Europe of the prototype Hungarian strain. Correlation of phylogenetic data with geospatial information showed geographical clustering of WNV genome sequences both in Italy and in Greece, indicating that the virus had evolved and diverged during its dispersal in Europe, leading to the emergence of novel genotypes, as it adapted to local ecological niches. These genotypes carried divergent conserved amino acid substitutions, which might have been relevant for viral adaptation, as suggested by selection pressure analysis and in silico and experimental modelling of sequence changes. In conclusion, the results of this study provide further information on WNV lineage 2 transmission dynamics in Europe, and emphasize the need for WNV surveillance activities to monitor viral evolution and diversity.
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Affiliation(s)
- L Barzon
- Department of Molecular Medicine, University of Padova, Padova, Italy; Microbiology and Virology Unit, Padova University Hospital, Padova, Italy.
| | - A Papa
- National Reference Centre for Arboviruses, Department of Microbiology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - E Lavezzo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - E Franchin
- Department of Molecular Medicine, University of Padova, Padova, Italy; Microbiology and Virology Unit, Padova University Hospital, Padova, Italy
| | - M Pacenti
- Microbiology and Virology Unit, Padova University Hospital, Padova, Italy
| | - A Sinigaglia
- IRCCS-IOV Istituto Oncologico Veneto, Padova, Italy
| | - G Masi
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - M Trevisan
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - L Squarzon
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - S Toppo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - E Papadopoulou
- National Reference Centre for Arboviruses, Department of Microbiology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - N Nowotny
- Institute of Virology, University of Veterinary Medicine, Vienna, Austria; Department of Microbiology and Immunology, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Oman
| | - S Ulbert
- Department of Immunology, Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - A Piralla
- Molecular Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - F Rovida
- Molecular Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - F Baldanti
- Molecular Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; Department of Clinical Sciences, Surgery, Diagnostics and Paediatrics, University of Pavia, Pavia, Italy
| | - E Percivalle
- Molecular Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - G Palù
- Department of Molecular Medicine, University of Padova, Padova, Italy; Microbiology and Virology Unit, Padova University Hospital, Padova, Italy
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Piralla A, Daleno C, Girello A, Esposito S, Baldanti F. Circulation of two Enterovirus C105 (EV-C105) lineages in Europe and Africa. J Gen Virol 2015; 96:1374-1379. [PMID: 25667329 DOI: 10.1099/vir.0.000088] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Accepted: 02/05/2015] [Indexed: 11/18/2022] Open
Abstract
The coding sequences of five human enterovirus (HEV)-C genotype 105 strains recovered in Italy, Romania and Burundi from patients with upper and lower respiratory tract infections were analysed and phylogenetically compared with other circulating HEV-C strains. The EV-C105 was closely related to EV-C109 and EV-C118 strains. The European strains were similar to other circulating EV-C105 strains, while the two African EV-C105 clustered in separate bootstrap-supported (>0.90) branches of the P2 and P3 region trees. Minor inconsistencies in the clustering pattern of EV-C105 in the capsid region (P1) and non-capsid region (P3) suggest that recombination may have occurred in EV-C105 group B viruses. In conclusion, phylogenetic analysis revealed the circulation of two distinct EV-C105 lineages in Europe and Africa. A different pattern of evolution could be hypothesized for the two EV-C105 lineages.
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Affiliation(s)
- A Piralla
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - C Daleno
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, University of Milan, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - A Girello
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - S Esposito
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, University of Milan, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - F Baldanti
- Section of Microbiology, Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Pavia, Italy.,Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
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Piralla A, Gozalo-Margüello M, Fiorina L, Rovida F, Muzzi A, Colombo A, Alessandrino P, Baldanti F. Different drug-resistant influenza A(H3N2) variants in two immunocompromised patients treated with oseltamivir during the 2011–2012 influenza season in Italy. J Clin Virol 2013; 58:132-7. [DOI: 10.1016/j.jcv.2013.06.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 05/27/2013] [Accepted: 06/04/2013] [Indexed: 10/26/2022]
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Selleri M, Piralla A, Rozera G, Giombini E, Bartolini B, Abbate I, Campanini G, Rovida F, Dossena L, Capobianchi MR, Baldanti F. Detection of haemagglutinin D222 polymorphisms in influenza A(H1N1)pdm09-infected patients by ultra-deep pyrosequencing. Clin Microbiol Infect 2012; 19:668-73. [PMID: 22862843 DOI: 10.1111/j.1469-0691.2012.03984.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
This study was aimed at establishing the genetic heterogeneity of influenza virus haemagglutinin (HA) gene quasi-species and the polymorphisms at codon 222, by application of ultra-deep pyrosequencing (UDPS) to respiratory samples from patients hospitalized for influenza A(H1N1)pdm09 infection, presenting with severe or moderate-mild disease. HA diversity was significantly higher in samples collected from patients with severe manifestations than in those from patients with moderate-mild manifestations (p 0.02). D222 polymorphism was detected in 40.7% of patients by UDPS, and in only 7.1% by Sanger sequencing. D222E, D222G, D222N and D222A were observed in 37.0%, 11.1%, 7.4% and 3.7% of patients, respectively; 10.7% of samples harboured more than two variants. The relative frequency of each single variant showed a wide range of intrapatient variation. D222G/N/A were detected, as either minor or predominant variants, only in severe cases, whereas D222E was equally represented in severe and moderate-mild infections. Other amino acid variants were observed at different positions within the analysed HA fragment. Consistent with higher heterogeneity, non-D222 variants were more frequently detected in severe cases than in moderate-mild cases. In addition, seven non-D222 mutations carried by minority variants, not previously described, were observed.
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Affiliation(s)
- M Selleri
- Laboratory of Virology, National Institute for Infectious Diseases INMI IRCCS L. Spallanzani, Rome, Italy
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Pariani E, Piralla A, Frati E, Anselmi G, Campanini G, Rovida F, Ranghiero A, Percivalle E, Amendola A, Baldanti F, Zanetti AR. Early co-circulation of different clades of influenza A/H1N1v pandemic virus in northern Italy. J Prev Med Hyg 2011; 52:17-20. [PMID: 21710819] [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: 05/31/2023]
Abstract
INTRODUCTION The spatial diffusion over time of pandemic influenza A/HINI virus (A/HIN1v) was surveyed in Northern Italy (nearly 10 million inhabitants)from April to December 2009, and the molecular characteristics of circulating viruses were analyzed to identify the appearance of drift variants. About 45% of analyzed samples were laboratory-confirmed cases of A/HINlv. Sporadic cases occurred until the middle of June 2009, then, case numbers began to increase delineating distinct epidemiological phases of viral circulation. METHODS RNA was extracted using RNeasy Mini kit (QIAGEN GmbH, Germany). Virological diagnosis of A/HINlv infection was carried out by real-time RT-PCR assay. Sequence analysis of hemagglutinin (HA) gene was performed through a RT-PCR assay specific for a 995 bp fragment (nt. 64-1,058) in the HAl domain. The nucleotide sequences were obtained by automated DNA sequencing. The HAl sequences were aligned with other sequences collected from GenBank database by ClustalX software. The multiple sequence alignment was used to perform a basic phylogenetic analysis and a phylogenetic tree from HA sequences was constructed. RESULTS The HA gene sequences ofA/HINlv analyzed segregated into three genetically distinct clades and were characterized by the appearance of amino acid variations that were progressively fixed in the field viral population under scrutiny. CONCLUSIONS These data suggest an early co-circulation of genetically distinct A/HNINv variants and emphasize the importance of a close molecular surveillance to detect rapidly the spread of new viral variants and to define their epidemiological impact.
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Affiliation(s)
- E Pariani
- Department of Public Health-Microbiology-Virology, University of Milan, Italy
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Baldanti F, Campanini G, Piralla A, Rovida F, Braschi A, Mojoli F, Iotti G, Belliato M, Conaldi PG, Arcadipane A, Pariani E, Zanetti A, Minoli L, Emmi V. Severe outcome of influenza A/H1N1/09v infection associated with 222G/N polymorphisms in the haemagglutinin: a multicentre study. Clin Microbiol Infect 2010; 17:1166-9. [PMID: 20946414 DOI: 10.1111/j.1469-0691.2010.03403.x] [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: 12/14/2022]
Abstract
In a multicentre study, influenza A/H1N1/09v 222G/N variants were more frequently detected in patients admitted to the intensive-care unit for invasive mechanical ventilation or extracorporeal membrane oxygenation (10/23; 43.5%) than in patients hospitalized in other units (2/27; 7.4%) and community patients (0/81; 0.0%) (p <0.01). A significantly higher virus load (p 0.02) in the lower vs the upper respiratory tract was observed. Predominance of 222G/N variants in the lower respiratory tract (40% of total virus population) vs the upper respiratory tract (10%) was shown by clonal analysis of haemagglutinin sequences in paired nasal swab and bronchoalveolar lavage samples. The time from illness onset to sampling was significantly longer in patients with severe infection vs community patients (p <0.001). It was concluded that the 222G/N variants showed increased virulence; mutant variants were probably selected in individual patients; and the longer duration of illness might have favoured the emergence of adaptive mutations through multiple replication cycles.
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Affiliation(s)
- F Baldanti
- Molecular Virology Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.
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Gerna G, Piralla A, Rovida F, Rognoni V, Marchi A, Locatelli F, Meloni F. Correlation of rhinovirus load in the respiratory tract and clinical symptoms in hospitalized immunocompetent and immunocompromised patients. J Med Virol 2009; 81:1498-507. [PMID: 19551831 PMCID: PMC7159321 DOI: 10.1002/jmv.21548] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
While human rhinoviruses (HRVs) are well accepted as a major cause of common cold syndromes (rhinitis), their role in the etiology of lower respiratory tract infections is still controversial, and their detection in asymptomatic patients is relatively common. The HRV pathogenic role in four groups of hospitalized patients (pediatric immunocompetent and immunocompromised patients, and adult immunocompetent and immunocompromised patients) was investigated by quantifying HRV load in nasopharyngeal aspirates or bronchoalveolar lavage samples by real-time reverse transcription PCR (RT-PCR). Real-time RT-PCR was performed in duplicate on all respiratory samples resulting positive by qualitative RT-PCR. In addition, molecular typing allowed detection of all known HRV species (A, B, and C). In immunocompetent pediatric patients HRVs were mostly associated with lower respiratory tract infections (in the absence of other viral agents) and wheezing, when viral load was > or =10(6) RNA copies/ml. In young immunocompromised patients (stem cell transplantation recipients), an inverse correlation between HRV persistence over time and time at which the infection occurred after transplantation was observed, whereas in adult immunocompromised patients (lung transplant recipients) HRVs could be detected at a medium-low level (<10(5) RNA copies/ml) in bronchoalveolar lavage samples taken routinely from asymptomatic patients. In conclusion, when detected at high viral load, HRVs may cause severe upper and lower respiratory tract infections, whereas when detected at a medium-low viral load, an event more frequent in immunocompromised subjects, they may represent only bystander viruses.
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Affiliation(s)
- G Gerna
- Servizio di Virologia, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy.
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Piralla A, Rovida F, Campanini G, Rognoni V, Marchi A, Locatelli F, Gerna G. Clinical severity and molecular typing of human rhinovirus C strains during a fall outbreak affecting hospitalized patients. J Clin Virol 2009; 45:311-7. [PMID: 19473873 DOI: 10.1016/j.jcv.2009.04.016] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2009] [Accepted: 04/24/2009] [Indexed: 11/25/2022]
Abstract
BACKGROUND The circulation rate and the clinical severity of infections caused by members of the new human rhinovirus C (HRV-C) species remain to be defined. OBJECTIVES To investigate the epidemiologic and clinical impact of HRV-C strains in a fall outbreak interesting hospitalized patients. STUDY DESIGN HRV species (A-C) were determined by phylogenetic analysis following amplification of two genome regions (5'NCR and VP4/VP2) by RT-PCR. HRV species were correlated with age, respiratory tract involvement, clinical symptoms, and HRV load in respiratory secretions. RESULTS During the first week of the period October-November 2008, single HRV infections were associated with 95% of all respiratory syndromes affecting hospitalized patients. Then, HRV infections (single+coinfections) interested about 90% of positive samples until the end of October, when they declined in frequency until reaching about 30% at the end of November. Overall, 104 HRV strains were detected and, of these, 90 could be classified by phylogenetic analysis, as follows: 45 HRV-A, 12 HRV-B, 28 HRV-C, and 5 human enterovirus D strains. HRV-C identity was confirmed by detection of cis-acting replication elements (cre) in 23/23 strains. As for severity of respiratory syndromes, unlike HRV-A and HRV-B strains, HRV-C strains were responsible for a significantly higher rate (p<0.05) of lower respiratory tract infections in the pediatric as compared to adult patient population. CONCLUSIONS HRV-C strains have been shown to circulate at a rate intermediate between HRV-A and HRV-B strains, showing a greater degree of clinical severity in the pediatric population.
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Affiliation(s)
- A Piralla
- Servizio di Virologia, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
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