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Giordano M, Iacoviello O, Santangelo L, Martino M, Torres D, Carbone V, Scavia G, Loconsole D, Chironna M, Cristofori F, Francavilla R. Gastrointestinal involvement in STEC-associated hemolytic uremic syndrome: 10 years in a pediatric center. Pediatr Nephrol 2024; 39:1885-1891. [PMID: 38189960 PMCID: PMC11026196 DOI: 10.1007/s00467-023-06258-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 12/09/2023] [Accepted: 12/11/2023] [Indexed: 01/09/2024]
Abstract
BACKGROUND The gastrointestinal (GI) tract represents one of the main targets of typical hemolytic uremic syndrome (HUS) in children. In this observational study, we tried to establish (1) the main features of GI complications during STEC-HUS and (2) the relationship between Escherichia coli serotypes and Shiga toxin (Stx) variants with hepatopancreatic involvement. METHODS A total of 79 STEC-HUS patients were admitted to our pediatric nephrology department between January 2012 and June 2021. Evidence of intestinal, hepatobiliary, and pancreatic involvements was reported for each patient, alongside demographic, clinical, and laboratory features. Frequency of gastrointestinal complications across groups of patients infected by specific E. coli serotypes and Stx gene variants was evaluated. RESULTS Six patients developed a bowel complication: two developed rectal prolapse, and four developed bowel perforation which resulted in death for three of them and in bowel stenosis in one patient. Acute pancreatitis was diagnosed in 13 patients. An isolated increase in pancreatic enzymes and/or liver transaminases was observed in 41 and 15 patients, respectively. Biliary sludge was detected in three, cholelithiasis in one. Forty-seven patients developed direct hyperbilirubinemia. Neither E. coli serotypes nor Shiga toxin variants correlated with hepatic or pancreatic involvement. CONCLUSIONS During STEC-HUS, GI complications are common, ranging from self-limited elevation of laboratory markers to bowel perforation, a severe complication with a relevant impact on morbidity and mortality. Hepatopancreatic involvement is frequent, but usually short-lasting and self-limiting.
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Affiliation(s)
- Mario Giordano
- Pediatric Nephrology and Dialysis Unit, Pediatric Hospital Giovanni XXIII - AOU Consorziale Policlinico, Bari, Italy.
| | - Onofrio Iacoviello
- Interdisciplinary Department of Medicine, Pediatric Section, University of Bari "Aldo Moro, " Pediatric Hospital Giovanni XXIII, Bari, Italy
| | - Luisa Santangelo
- Pediatric Nephrology and Dialysis Unit, Pediatric Hospital Giovanni XXIII - AOU Consorziale Policlinico, Bari, Italy
| | - Marida Martino
- Pediatric Nephrology and Dialysis Unit, Pediatric Hospital Giovanni XXIII - AOU Consorziale Policlinico, Bari, Italy
| | - Diletta Torres
- Pediatric Nephrology and Dialysis Unit, Pediatric Hospital Giovanni XXIII - AOU Consorziale Policlinico, Bari, Italy
| | - Vincenza Carbone
- Pediatric Nephrology and Dialysis Unit, Pediatric Hospital Giovanni XXIII - AOU Consorziale Policlinico, Bari, Italy
| | - Gaia Scavia
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore Di Sanità, Rome, Italy
| | - Daniela Loconsole
- Department of Biomedical Sciences and Human Oncology, Hygiene Section, University of Bari "Aldo Moro", Bari, Italy
| | - Maria Chironna
- Department of Biomedical Sciences and Human Oncology, Hygiene Section, University of Bari "Aldo Moro", Bari, Italy
| | - Fernanda Cristofori
- Interdisciplinary Department of Medicine, Pediatric Section, University of Bari "Aldo Moro, " Pediatric Hospital Giovanni XXIII, Bari, Italy
| | - Ruggiero Francavilla
- Interdisciplinary Department of Medicine, Pediatric Section, University of Bari "Aldo Moro, " Pediatric Hospital Giovanni XXIII, Bari, Italy
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Loconsole D, Centrone F, Sallustio A, Casulli D, Zagaria R, Sacco D, Colella V, Albano N, Caselli D, Cardinale F, Giordano P, Lofù I, Laforgia N, Chironna M. Echovirus 11 lineage I and other enterovirus in hospitalized children with acute respiratory infection in Southern Italy (2022- 2023). Int J Infect Dis 2024:107091. [PMID: 38729515 DOI: 10.1016/j.ijid.2024.107091] [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: 03/21/2024] [Revised: 04/24/2024] [Accepted: 05/07/2024] [Indexed: 05/12/2024] Open
Abstract
OBJECTIVES A new variant of echovirus 11 (E11) infection is a major health concern in neonates. Here, we describe the clinical and virological characteristics of enterovirus (EV) infections in children hospitalized with acute respiratory infection in Southern Italy. METHODS Between July 2022-August 2023, 173 EV infections were identified. Demographic and clinical characteristics, comorbidities, and coinfections were analyzed. Genotypes were identified by sequencing of VP1. Whole-genome sequencing of five E11 strains was performed. RESULTS Case numbers peaked in July 2022, November-December 2022, and June-July 2023. Coxsackievirus A2 was identified in 36.7%, coxsackievirus B5 in 13.8%, echovirus E11 in 9.2%, and EV-D68 in 6.4% of cases. No child had critical symptoms or a severe infection. The only neonate infected by E11 recovered fully after 5 days in hospital. Phylogenetic analysis revealed that four E11 strains were closely related to divergent lineage I E11 strains identified in France and Italy. CONCLUSIONS The new variant of E11 was identified in children in Southern Italy. Although the cases were mild, the data suggest that transmission routes and host factors are likely to be main drivers for the development of potentially severe diseases. Systematic epidemiological/molecular surveillance will help us better understand the clinical impact of EV infections and develop preventive strategies.
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Affiliation(s)
- Daniela Loconsole
- Department of Interdisciplinary Medicine, Hygiene Section, "Aldo Moro" University of Bari, 70124 Bari, Italy
| | - Francesca Centrone
- Hygiene Unit, Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, 70124 Bari, Italy
| | - Anna Sallustio
- Hygiene Unit, Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, 70124 Bari, Italy
| | - Daniele Casulli
- Hygiene Unit, Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, 70124 Bari, Italy
| | - Riccardo Zagaria
- Department of Interdisciplinary Medicine, Hygiene Section, "Aldo Moro" University of Bari, 70124 Bari, Italy
| | - Davide Sacco
- Department of Interdisciplinary Medicine, Hygiene Section, "Aldo Moro" University of Bari, 70124 Bari, Italy
| | - Vito Colella
- Department of Interdisciplinary Medicine, Hygiene Section, "Aldo Moro" University of Bari, 70124 Bari, Italy
| | - Nelhudoff Albano
- Department of Health Promotion and Animal Welfare, Apulia Region, 70100 Bari, Italy
| | - Desiree Caselli
- Infectious Diseases, Children's Hospital Giovanni XXIII, A.O.U.C. Policlinico di Bari, 70124 Bari, Italy
| | - Fabio Cardinale
- Pediatric and Emergency Department, Pediatric Pulmonology and Immunology section, Giovanni XXIII Pediatric Hospital, "Aldo Moro" University of Bari, 70124 Bari, Italy
| | - Paola Giordano
- Department of Interdisciplinary Medicine, Pediatric Section, "Aldo Moro" University of Bari, 70124 Bari, Italy
| | - Ignazio Lofù
- Pediatric Unit, Maternal and Child Health Department, "S. Giacomo" Hospital, ASL BA, 70043 Monopoli (Bari), Italy
| | - Nicola Laforgia
- Section of Neonatology and Neonatal Intensive Care Unit, Department of Interdisciplinary Medicine, "Aldo Moro" University of Bari, 70121 Bari, Italy
| | - Maria Chironna
- Department of Interdisciplinary Medicine, Hygiene Section, "Aldo Moro" University of Bari, 70124 Bari, Italy.
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Pandolfi E, Loconsole D, Chironna M, van Summeren J, Paget J, Raponi M, Russo L, Campagna I, Croci I, Concato C, Perno CF, Tozzi AE, Linardos G, Bartolucci V, Ciampini S, Muda AO, De Angelis L, Ciofi Degli Atti ML, Rizzo C. Pre-COVID-19-pandemic RSV epidemiology and clinical burden in pediatric primary care in Italy: a comparative analysis across two regions for the 2019/2020 season. BMC Infect Dis 2024; 24:388. [PMID: 38605310 PMCID: PMC11007985 DOI: 10.1186/s12879-024-09229-9] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 03/15/2024] [Indexed: 04/13/2024] Open
Abstract
BACKGROUND Respiratory syncytial virus (RSV) infection in children under 5 years have a significant clinical burden, also in primary care settings. This study investigates the epidemiology and burden of RSV in Italian children during the 2019/20 pre-pandemic winter season. METHODS A prospective cohort study was conducted in two Italian regions. Children with Acute Respiratory Infection (ARI) visiting pediatricians were eligible. Nasopharyngeal swabs were collected and analyzed via multiplex PCR for RSV detection. A follow-up questionnaire after 14 days assessed disease burden, encompassing healthcare utilization and illness duration. Statistical analyses, including regression models, explored associations between variables such as RSV subtype and regional variations. RESULTS Of 293 children with ARI, 41% (119) tested positive for RSV. Median illness duration for RSV-positive cases was 7 days; 6% required hospitalization (median stay: 7 days). Medication was prescribed to 95% (110/116) of RSV cases, with 31% (34/116) receiving antibiotics. RSV subtype B and regional factors predicted increased healthcare utilization. Children with shortness of breath experienced a 36% longer illness duration. CONCLUSIONS This study highlights a significant clinical burden and healthcare utilization associated with RSV in pre-pandemic Italian primary care settings. Identified predictors, including RSV subtype and symptomatology, indicate the need for targeted interventions and resource allocation strategies. RSV epidemiology can guide public health strategies for the implementation of preventive measures.
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Affiliation(s)
- Elisabetta Pandolfi
- Predictive and Preventive Medicine Research Unit, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Daniela Loconsole
- Department of Interdisciplinary Medicine, University of Bari, Bari, Italy
| | - Maria Chironna
- Department of Interdisciplinary Medicine, University of Bari, Bari, Italy
| | | | - John Paget
- Nivel, Netherlands Institute for Health Services Research, Utrecht, The Netherlands
| | | | - Luisa Russo
- Division of Metabolism, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Ilaria Campagna
- Predictive and Preventive Medicine Research Unit, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Ileana Croci
- Predictive and Preventive Medicine Research Unit, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Carlo Concato
- Virology Unit, Laboratory Department, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Carlo Federico Perno
- Virology Unit, Laboratory Department, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Alberto Eugenio Tozzi
- Predictive and Preventive Medicine Research Unit, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Giulia Linardos
- Virology Unit, Laboratory Department, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Veronica Bartolucci
- Predictive and Preventive Medicine Research Unit, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Sara Ciampini
- Local Health Unit, Public Health Service, Rome, Italy
| | - Andrea Onetti Muda
- Department of Laboratories, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Luigi De Angelis
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy.
| | | | - Caterina Rizzo
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
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Scarpaci M, Bracaloni S, Esposito E, De Angelis L, Baglivo F, Casini B, Panatto D, Ogliastro M, Loconsole D, Chironna M, Pariani E, Pellegrinelli L, Pandolfi E, Croci I, Rizzo C. RSV Disease Burden in Primary Care in Italy: A Multi-Region Pediatric Study, Winter Season 2022-2023. Influenza Other Respir Viruses 2024; 18:e13282. [PMID: 38622776 PMCID: PMC11018906 DOI: 10.1111/irv.13282] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 02/05/2024] [Accepted: 03/11/2024] [Indexed: 04/17/2024] Open
Abstract
INTRODUCTION Human respiratory syncytial virus (RSV) is one of the most frequent causes of respiratory infections in children under 5 years of age, but its socioeconomic impact and burden in primary care settings is still little studied. METHODS During the 2022/2023 winter season, 55 pediatricians from five Italian regions participated in our community-based study. They collected a nasal swab for RSV molecular test from 650 patients under the age of 5 with acute respiratory infections (ARIs) and performed a baseline questionnaire. The clinical and socioeconomic burden of RSV disease in primary care was evaluated by two follow-up questionnaires completed by the parents of positive children on Days 14 and 30. RESULTS RSV laboratory-confirmed cases were 37.8% of the total recruited ARI cases, with RSV subtype B accounting for the majority (65.4%) of RSV-positive swabs. RSV-positive children were younger than RSV-negative ones (median 12.5 vs. 16.5 months). The mean duration of symptoms for all children infected by RSV was 11.47 ± 6.27 days. We did not observe substantial differences in clinical severity between the two RSV subtypes, but RSV-A positive patients required more additional pediatric examinations than RSV-B cases. The socioeconomic impact of RSV infection was considerable, causing 53% of children to be absent from school, 46% of parents to lose working days, and 25% of families to incur extra costs. CONCLUSIONS Our findings describe a baseline of the RSV disease burden in primary care in Italy before the introduction of upcoming immunization strategies.
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Affiliation(s)
- Michela Scarpaci
- Department of Translational Research and New Technologies in Medicine and SurgeryUniversity of PisaPisaItaly
| | - Sara Bracaloni
- Department of Translational Research and New Technologies in Medicine and SurgeryUniversity of PisaPisaItaly
| | - Enrica Esposito
- Department of Translational Research and New Technologies in Medicine and SurgeryUniversity of PisaPisaItaly
| | - Luigi De Angelis
- Department of Translational Research and New Technologies in Medicine and SurgeryUniversity of PisaPisaItaly
| | - Francesco Baglivo
- Department of Translational Research and New Technologies in Medicine and SurgeryUniversity of PisaPisaItaly
| | - Beatrice Casini
- Department of Translational Research and New Technologies in Medicine and SurgeryUniversity of PisaPisaItaly
| | | | | | - Daniela Loconsole
- Hygiene Section, Department of Interdisciplinary MedicineUniversity of Bari “A. Moro”BariItaly
| | - Maria Chironna
- Hygiene Section, Department of Interdisciplinary MedicineUniversity of Bari “A. Moro”BariItaly
| | - Elena Pariani
- Department of Biomedical Sciences for HealthUniversity of MilanMilanItaly
| | | | - Elisabetta Pandolfi
- Predictive and Preventive Medicine Research UnitBambino Gesù Children's Hospital, IRCCSRomeItaly
| | - Ileana Croci
- Predictive and Preventive Medicine Research UnitBambino Gesù Children's Hospital, IRCCSRomeItaly
| | - Caterina Rizzo
- Department of Translational Research and New Technologies in Medicine and SurgeryUniversity of PisaPisaItaly
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Favia G, Barile G, Tempesta A, Copelli C, Novielli G, Dell'Olio F, Capodiferro S, Spirito F, Brienza N, Ribezzi M, Vestito MC, Corriero A, Carpagnano E, Moschetta A, Chironna M, Loconsole D, Centrone F, Quadri MFA, Tartaglia GM, Limongelli L. Relationship between oral lesions and severe SARS-CoV-2 infection in intensive care unit patients. Oral Dis 2024; 30:1296-1303. [PMID: 36680407 DOI: 10.1111/odi.14515] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 01/02/2023] [Accepted: 01/15/2023] [Indexed: 01/22/2023]
Abstract
OBJECTIVE Oral lesions received increased attention as likely new signs or secondary manifestations of COVID-19. Therefore, we clinically examined oral cavity of patients with COVID-19 and investigated oral lesions and patient comorbidities as possible risk factors of COVID-19 disease outcome. METHODS From January to March 2022, a prospective study was conducted by recruiting all COVID-19 patients admitted to the Intensive Care Unit and Respiratory Intensive Care Unit of Maxi-Emergencies Hospital in Bari, Italy. RESULTS From the enrolled 103 COVID-19 patients, 46.6% were females and 53.4% were males. Findings show that risk of presenting with severe COVID-19 disease was higher in patients who developed oral lesions related to COVID-19 than those with no oral lesions (RR = 7.998, p = .002). Next, patients with concomitant autoimmune diseases were at higher risk of a negative COVID-19 disease outcome than those without comorbidities (OR = 8.838, p = .026). CONCLUSIONS COVID-19-related lesions of oral mucosa should not be ignored as they can be early and easily detectable signs of severe COVID-19 disease condition, thus, serving as a prevention measure for any potential unfortunate event. Findings of this study, without implying causation, offer a direction for future investigations that aim to confirm the presence of specific oral lesions in COVID-19 patients as signs of severe disease progression.
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Affiliation(s)
- Gianfranco Favia
- Complex Operating Unit of Odontostomatological Diseases, Department of Interdisciplinary Medicine, University of Bari, Bari, Italy
| | - Giuseppe Barile
- Complex Operating Unit of Odontostomatological Diseases, Department of Interdisciplinary Medicine, University of Bari, Bari, Italy
| | - Angela Tempesta
- Complex Operating Unit of Odontostomatological Diseases, Department of Interdisciplinary Medicine, University of Bari, Bari, Italy
| | - Chiara Copelli
- Operating Unit of Maxillofacial Surgery, Department of Interdisciplinary Medicine, University of Bari, Bari, Italy
| | - Gianluigi Novielli
- Complex Operating Unit of Odontostomatological Diseases, Department of Interdisciplinary Medicine, University of Bari, Bari, Italy
| | - Fabio Dell'Olio
- Complex Operating Unit of Odontostomatological Diseases, Department of Interdisciplinary Medicine, University of Bari, Bari, Italy
| | - Saverio Capodiferro
- Complex Operating Unit of Odontostomatological Diseases, Department of Interdisciplinary Medicine, University of Bari, Bari, Italy
| | - Francesca Spirito
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Nicola Brienza
- Department of Interdisciplinary Medicine, University of Bari, Bari, Italy
| | - Mario Ribezzi
- Intensive Care Unit 1, University of Bari, Bari, Italy
| | | | | | - Elisiana Carpagnano
- Respiratory Diseases Section, Department of Basic Medical Science Neuroscience and Sense Organs, University of Bari, Bari, Italy
| | - Antonio Moschetta
- Department of Interdisciplinary Medicine, University of Bari, Bari, Italy
| | - Maria Chironna
- Department of Interdisciplinary Medicine, University of Bari, Bari, Italy
| | - Daniela Loconsole
- Department of Interdisciplinary Medicine, University of Bari, Bari, Italy
| | - Francesca Centrone
- Department of Interdisciplinary Medicine, University of Bari, Bari, Italy
| | - Mir Faeq Ali Quadri
- Department of Oral Health Sciences, School of Dentistry, University of Washington, Seattle, Washington, USA
| | - Gianluca Martino Tartaglia
- Department of Biomedical Surgical and Dental Sciences, School of Orthodontics, University of Milan, Milan, Italy
| | - Luisa Limongelli
- Complex Operating Unit of Odontostomatological Diseases, Department of Interdisciplinary Medicine, University of Bari, Bari, Italy
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Loconsole D, Sallustio A, Sacco D, Santantonio M, Casulli D, Gatti D, Accogli M, Parisi A, Zagaria R, Colella V, Centrone F, Chironna M. Genomic surveillance of carbapenem-resistant Klebsiella pneumoniae reveals a prolonged outbreak of extensively drug-resistant ST147 NDM-1 during the COVID-19 pandemic in the Apulia region (Southern Italy). J Glob Antimicrob Resist 2024; 36:260-266. [PMID: 38280719 DOI: 10.1016/j.jgar.2024.01.015] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/22/2023] [Accepted: 01/18/2024] [Indexed: 01/29/2024] Open
Abstract
OBJECTIVES The recent worldwide spread of New Delhi metallo-beta-lactamase-producing Klebsiella pneumoniae (NDM-KP) in health-care settings remains a concern. The aim of the study was to describe an outbreak of extensively drug-resistant ST147 NDM-1-KP in the Apulia region of Southern Italy that occurred between 2020 and 2022 through genomic surveillance of carbapenem-resistant Enterobacterales. METHODS A total of 459 carbapenem-resistant KP isolates collected from patients hospitalised with bloodstream infections were tested using a commercial multiplex real-time polymerase chain reaction to identify carbapenemase genes. A subset of 27 isolates was subjected to whole-genome sequencing. Core-genome multilocus sequence typing was performed by analysing a panel of 4884 genes. RESULTS Molecular testing revealed that 104 (22.6%) isolates carried the carbapenemase NDM gene. Phylogenetic analysis of the 27 isolates subjected to whole-genome sequencing revealed high genetic relatedness among strains. All isolates were resistant to all first-line antibiotics. Virulome analysis identified the ybt locus, the two well-recognised virulence factors iucABCDiutA and rmpA, and the genes encoding the type 3 pilus virulence factor. Plasmids IncFIB(pkPHS1), IncFIB(pNDM-Mar), IncFIB(pQil), IncHI1B(pNDM-MAR), IncR, and Col(pHAD28) were identified in all isolates. Moreover, further analysis identified the IncFIB-type plasmid carrying the NDM-1 genes. CONCLUSION The increasing circulation of extensively drug-resistant NDM-1 ST147 KP strains in Southern Italy in recent years is worrisome, because these clones pose a real risk, particularly in hospital settings. Genomic surveillance is a crucial tool for early identification of emerging threats such as the spread of high-risk pathogens. Rapid infection control measures and antimicrobial stewardship are key to preventing further spread of hypervirulent KP strains.
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Affiliation(s)
- Daniela Loconsole
- Department of Interdisciplinary Medicine, Hygiene Section, University of Bari, Bari, Italy
| | - Anna Sallustio
- Hygiene Unit, Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, Bari, Italy
| | - Davide Sacco
- Department of Interdisciplinary Medicine, Hygiene Section, University of Bari, Bari, Italy
| | - Marilina Santantonio
- Hygiene Unit, Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, Bari, Italy
| | - Daniele Casulli
- Hygiene Unit, Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, Bari, Italy
| | - Domenico Gatti
- Hygiene Unit, Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, Bari, Italy
| | - Marisa Accogli
- Hygiene Unit, Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, Bari, Italy
| | - Antonio Parisi
- Experimental Zooprophylactic Institute of Apulia and Basilicata, Foggia, Italy
| | - Riccardo Zagaria
- Department of Interdisciplinary Medicine, Hygiene Section, University of Bari, Bari, Italy
| | - Vito Colella
- Department of Interdisciplinary Medicine, Hygiene Section, University of Bari, Bari, Italy
| | - Francesca Centrone
- Hygiene Unit, Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, Bari, Italy
| | - Maria Chironna
- Department of Interdisciplinary Medicine, Hygiene Section, University of Bari, Bari, Italy.
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Loconsole D, Centrone F, Sallustio A, Casulli D, Colella V, Mongelli O, Venturi G, Bella A, Marino L, Martinelli D, Chironna M. Abrupt Increase in Detection of Locally Acquired West-Nile-Virus-Lineage-2-Mediated Neuroinvasive Disease in a Previously Non-Endemic Area of Southern Italy (2023). Viruses 2023; 16:53. [PMID: 38257753 PMCID: PMC10819189 DOI: 10.3390/v16010053] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/27/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
West Nile virus (WNV) is a public health concern in Europe. Rising temperatures and the migration of potential vectors promote the spread of viruses to previously unaffected areas. In 2023, the Apulia region of Southern Italy experienced an unexpected increase in West Nile neuroinvasive disease (WNND); no such cases had been reported in the previous 10 years. Overall, eight autochthonous cases of WNV infection were identified between July and October 2023, six of which were WNND. All cases were male (median age, 73 years). Two of the cases were blood donors. All WNND cases were hospitalized and all recovered within a few weeks. Surveillance data showed that, in the Apulia region, WNV Lineage 2 was detected in humans, mosquitoes, and horses. Based on the number of WNND cases reported, we can assume that a high number of infections occurred during the summer period. Changes in the climate in the region over recent years could be considered among the main drivers of the rapid increase in WNV infections. Therefore, integrated surveillance should be strengthened to avoid the potential massive spread of WNV in Southern Italy. Moreover, the implementation of whole-genome sequencing of WNV strains, as well as seroepidemiological studies in the area, will facilitate a better understanding of circulation dynamics.
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Affiliation(s)
- Daniela Loconsole
- Hygiene Section, Department of Interdisciplinary Medicine, University of Bari, 70124 Bari, Italy; (D.L.)
| | - Francesca Centrone
- Hygiene Unit, Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, 70124 Bari, Italy
| | - Anna Sallustio
- Hygiene Unit, Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, 70124 Bari, Italy
| | - Daniele Casulli
- Hygiene Unit, Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, 70124 Bari, Italy
| | - Vito Colella
- Hygiene Section, Department of Interdisciplinary Medicine, University of Bari, 70124 Bari, Italy; (D.L.)
| | - Onofrio Mongelli
- Department of Health Promotion and Animal Welfare, Apulia Region, 70124 Bari, Italy
| | - Giulietta Venturi
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Antonino Bella
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Leonardo Marino
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy
| | - Domenico Martinelli
- Hygiene Section, Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy
| | - Maria Chironna
- Hygiene Section, Department of Interdisciplinary Medicine, University of Bari, 70124 Bari, Italy; (D.L.)
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8
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Dalfino L, Stufano M, Bavaro DF, Diella L, Belati A, Stolfa S, Romanelli F, Ronga L, Di Mussi R, Murgolo F, Loconsole D, Chironna M, Mosca A, Montagna MT, Saracino A, Grasso S. Effectiveness of First-Line Therapy with Old and Novel Antibiotics in Ventilator-Associated Pneumonia Caused by Carbapenem-Resistant Acinetobacter baumannii: A Real Life, Prospective, Observational, Single-Center Study. Antibiotics (Basel) 2023; 12:1048. [PMID: 37370367 DOI: 10.3390/antibiotics12061048] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 05/24/2023] [Revised: 06/11/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Evidence-based, standard antibiotic therapy for ventilator-associated pneumonia (VAP) caused by carbapenem-resistant Acinetobacter baumannii (CRAB) is a relevant unmet clinical need in the intensive care unit (ICU). We aimed to evaluate the effectiveness of first-line therapy with old and novel CRAB active antibiotics in monomicrobial VAP caused by CRAB. A prospective, observational study was performed in a mixed non-COVID-19 ICU. The primary outcome measure was clinical failure upon first-line targeted therapy. Features independently influencing failure occurrence were also investigated via Cox proportional multivariable analysis. To account for the imbalance in antibiotic treatment allocation, a propensity score analysis with an inverse probability treatment weighting approach was adopted. Of the 90 enrolled patients, 34 (38%) experienced clinical failure. Compared to patients who experienced a clinical resolution of VAP, those who had clinical failure were of an older age (median age 71 (IQR 64-78) vs. 62 (IQR 52-69) years), and showed greater burden of comorbidities (median Charlson comorbidity index 8 (IQR 6-8) vs. 4 (IQR 2-6)), higher frequency of immunodepression (44% vs. 21%), and greater clinical severity at VAP onset (median SOFA score 10 (IQR 9-11) vs. 9 (IQR 7-11)). Lower rates of use of fast molecular diagnostics for nosocomial pneumonia (8.8% vs. 30.3%) and of timely CRAB active therapy administration (65% vs. 89%), and higher rates of colistin-based targeted therapy (71% vs. 46%) were also observed in patients who failed first-line therapy. Overall, CRAB active iv regimens were colistin-based in 50 patients and cefiderocol-based in 40 patients, both always combined with inhaled colistin. According to the backbone agent of first-line regimens, clinical failure was lower in the cefiderocol group, compared to that in the colistin group (25% vs. 48%, respectively). In multivariable Cox regression analysis, the burden of comorbid conditions independently predicted clinical failure occurrence (Charlson index aHR = 1.21, 95% CI = 1.04-1.42, p = 0.01), while timely targeted antibiotic treatment (aHR = 0.40, 95% CI = 0.19-0.84, p = 0.01) and cefiderocol-based first-line regimens (aHR = 0.38, 95% CI = 0.17-0.85, p = 0.02) strongly reduced failure risk. In patients with VAP caused by CRAB, timely active therapy improves infection outcomes and cefiderocol holds promise as a first-line therapeutic option.
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Affiliation(s)
- Lidia Dalfino
- Intensive Care Unit II, Department of Precision Medicine, Ionic Area, University of Bari "A. Moro", 70124 Bari, Italy
| | - Monica Stufano
- Intensive Care Unit II, Department of Precision Medicine, Ionic Area, University of Bari "A. Moro", 70124 Bari, Italy
| | - Davide Fiore Bavaro
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari "A. Moro", 70124 Bari, Italy
| | - Lucia Diella
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari "A. Moro", 70124 Bari, Italy
| | - Alessandra Belati
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari "A. Moro", 70124 Bari, Italy
| | - Stefania Stolfa
- Microbiology and Virology Unit, Department of Interdisciplinary Medicine, University of Bari "A. Moro", 70124 Bari, Italy
| | - Federica Romanelli
- Microbiology and Virology Unit, Department of Interdisciplinary Medicine, University of Bari "A. Moro", 70124 Bari, Italy
| | - Luigi Ronga
- Microbiology and Virology Unit, Department of Interdisciplinary Medicine, University of Bari "A. Moro", 70124 Bari, Italy
| | - Rosa Di Mussi
- Intensive Care Unit II, Department of Precision Medicine, Ionic Area, University of Bari "A. Moro", 70124 Bari, Italy
| | - Francesco Murgolo
- Intensive Care Unit II, Department of Precision Medicine, Ionic Area, University of Bari "A. Moro", 70124 Bari, Italy
| | - Daniela Loconsole
- Hygiene Section, Department of Interdisciplinary Medicine, University of Bari "A. Moro", 70124 Bari, Italy
| | - Maria Chironna
- Hygiene Section, Department of Interdisciplinary Medicine, University of Bari "A. Moro", 70124 Bari, Italy
| | - Adriana Mosca
- Microbiology and Virology Unit, Department of Interdisciplinary Medicine, University of Bari "A. Moro", 70124 Bari, Italy
| | - Maria Teresa Montagna
- Hygiene Section, Department of Interdisciplinary Medicine, University of Bari "A. Moro", 70124 Bari, Italy
| | - Annalisa Saracino
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari "A. Moro", 70124 Bari, Italy
| | - Salvatore Grasso
- Intensive Care Unit II, Department of Precision Medicine, Ionic Area, University of Bari "A. Moro", 70124 Bari, Italy
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9
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Baldassarre ME, Loconsole D, Centrone F, Caselli D, Martire B, Quartulli L, Acquafredda A, D'Amato G, Maffei G, Latorre G, Riganti A, Di Noia M, Chironna M, Laforgia N. Hospitalization for bronchiolitis in children aged ≤ 1year, Southern Italy, year 2021: need for new preventive strategies? Ital J Pediatr 2023; 49:66. [PMID: 37280662 DOI: 10.1186/s13052-023-01455-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 12/28/2022] [Accepted: 04/07/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND Bronchiolitis is a major cause of hospitalization in infants, particularly in the first six months of life, with approximately 60-80% of admissions due to respiratory syncytial virus (RSV) infection. Currently, no prophylactic options are available for healthy infants. The present study aimed at describing the demographic, clinical, and epidemiological characteristics of infants hospitalized for bronchiolitis in the Apulia region of Italy in 2021. METHODS From January to December 2021, data on children aged 0-12 months admitted for bronchiolitis in nine neonatal or pediatric units covering 61% of pediatric beds of hospitals in the Apulia region of Italy were analyzed. Demographic data, comorbidities, need for oxygen support, length of hospital stay, palivizumab administration, and outcomes were collected. For the purpose of the analysis, patients were divided into those aged 0-3 months and > 3 months. A multivariate logistic regression model was used to explore associations between the need for oxygen support and sex, age, comorbidities, history of prematurity, length of hospital stay, and palivizumab administration. RESULTS This study included 349 children aged 0-12 months admitted for bronchiolitis, with a peak of hospitalization in November (7.4 cases/1,000 children). Of these patients, 70.5% were RSV positive, 80.2% were aged 0-3 months, and 73.1% required oxygen support. Moreover, 34.9% required observation in the sub-intensive care unit, and 12.9% in the intensive care unit. Of the infants who required intensive care, 96.9% were aged 0-3 months and 78.8% were born at term. Three patients required mechanical ventilation and one, who required Extra Corporeal Membrane Oxygenation, died. Children aged 0-3 months were more likely to show dyspnea, need oxygen support, and have a longer hospital stay. CONCLUSIONS The present study showed that almost all of the children who required intensive care support were aged ≤ 3 months and most were born at term. Therefore, this age group remains the highest risk group for severe bronchiolitis. Preventive measures such as single-dose monoclonal antibody immunoprophylaxis, and maternal and childhood vaccination against RSV, may reduce the high public health burden of bronchiolitis.
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Affiliation(s)
- Maria Elisabetta Baldassarre
- Unit of Neonatology and Intensive Care, Interdisciplinary Department of Medicine, Aldo Moro University, Bari, 70124, Italy
| | - Daniela Loconsole
- Hygiene Section, Interdisciplinary Department of Medicine, Aldo Moro University, Bari, 70124, Italy
| | - Francesca Centrone
- Hygiene Section, Interdisciplinary Department of Medicine, Aldo Moro University, Bari, 70124, Italy
| | - Desiree Caselli
- Pediatric Infectious Diseases Unit, Giovanni XXIII Children Hospital, Azienda Ospedaliero Universitaria Consorziale Policlinico, Bari, 70124, Italy
| | - Baldassarre Martire
- Unit of Pediatrics and Neonatology, "Monsignor Dimiccoli" Hospital, Barletta, BT, Italy
| | | | - Angelo Acquafredda
- Unit of Pediatrics and Neonatology, "G. Tatarella" Hospital, Cerignola, Foggia, Italy
| | | | - Gianfranco Maffei
- Neonatology and Intensive Care Unit, "Ospedali Riuniti" Hospital, Foggia, Italy
| | - Giuseppe Latorre
- Neonatology and Intensive Care Unit, "Miulli" Hospital, Acquaviva delle Fonti, Bari, Italy
| | - Anita Riganti
- Neonatology Unit, "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Foggia, Italy
| | | | - Maria Chironna
- Hygiene Section, Interdisciplinary Department of Medicine, Aldo Moro University, Bari, 70124, Italy.
| | - Nicola Laforgia
- Unit of Neonatology and Intensive Care, Interdisciplinary Department of Medicine, Aldo Moro University, Bari, 70124, Italy
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10
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Fortunato F, Prato R, Iannelli G, Ascatigno L, Loconsole D, Lopalco PL, Martinelli D. Safety of heterologous ChAdOx1-S/BNT162b2 primary schedule versus homologous BNT162b2 vaccination: Insights from an Italian post-marketing study, 2021. Hum Vaccin Immunother 2023:2209919. [PMID: 37226552 DOI: 10.1080/21645515.2023.2209919] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
During COVID-19 vaccination campaign, possible ChAdOx1-S-associated risks of thrombosis with thrombocytopenia syndrome led to implement ChAdOx1-S/BNT162b2 heterologous vaccination, despite the limited information on its reactogenicity and safety. We conducted a prospective observational post-marketing surveillance study to assess the safety of this heterologous schedule. A casually selected sample of recipients (n: 85; age: 18-60 years) of ChAdOx1-S/BNT162b2 at the vaccination hub of the Foggia Hospital, Italy, was matched with an equal sample of recipients of homologous BNT162b2. Safety was evaluated 7 days, 1 month and 14 weeks after the primary vaccination series using an adapted version of the "V-safe active surveillance for COVID-19 vaccine safety" CDC standardized questionnaire. After 7 days, local reactions were highly frequent (>80%) in both groups, and systemic reactions were less common (<70%). Moderate or severe pain at the injection site (OR = 3.62; 95%CI, 1.45-9.33), moderate/severe fatigue (OR = 3.40; 95%CI, 1.22-9.49), moderate/severe headache (OR = 4.72; 95%CI, 1.37-16.23), intake of antipyretics (OR = 3.05; 95 CI%, 1.35-6.88), inability to perform daily activities and work (OR = 2.64; 95%CI, 1.24-5.62) were significantly more common with heterologous than homologous vaccination. No significant difference in self-reported health status was recorded 1 month or 14 weeks after the second dose with BNT162b2 or ChAdOx1-S/BNT162b2. Our study confirms the safety of both heterologous and homologous vaccination, with a slight increase in some short-term adverse events for the heterologous regimen. Therefore, administering a second dose of a mRNA vaccine to the recipients of a previous dose of viral vector vaccine may have represented an advantageous strategy to improve flexibility and to accelerate the vaccination campaign.
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Affiliation(s)
- Francesca Fortunato
- Hygiene Unit, Policlinico Foggia Hospital, Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
| | - Rosa Prato
- Hygiene Unit, Policlinico Foggia Hospital, Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
| | - Giuseppina Iannelli
- Hygiene Unit, Policlinico Foggia Hospital, Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
| | - Leonardo Ascatigno
- Hygiene Unit, Policlinico Foggia Hospital, Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
| | - Daniela Loconsole
- Hygiene Section, Department of Interdisciplinary Medicine, University of Bari, Bari, Italy
| | - Pier Luigi Lopalco
- Department of Biological and Environmental Sciences and Technology, University of Salento, Lecce, Italy
| | - Domenico Martinelli
- Hygiene Unit, Policlinico Foggia Hospital, Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
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11
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La Torre F, Elicio MP, Monno VA, Chironna M, Moramarco F, Campanozzi A, Civino A, Cecinati V, Vairo U, Giordano M, Milella L, Loconsole D, Cardinale F. Incidence and Prevalence of Multisystem Inflammatory Syndrome in Children (MIS-C) in Southern Italy. Children (Basel) 2023; 10:children10050766. [PMID: 37238314 DOI: 10.3390/children10050766] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 03/26/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023]
Abstract
Multisystem inflammatory syndrome in children (MIS-C) is a pediatric hyperinflammatory syndrome related to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection whose epidemiology is not very well known at present. The objective of the study was to better understand the incidence of MIS-C in the Apulia region in southern Italy. Our primary goal was to estimate the incidence of newly identified cases of MIS-C in children aged 0-18 years, during a period of six months, encompassing the second pandemic wave. We also analyzed the characteristics of our cohort in terms of clinical features, treatment, and outcomes. The cumulative incidence of MIS-C was 3.27 per 100,000 residents between 0 and 18 years of age. In our cohort, gastrointestinal, mucocutaneous, and cardiac involvement were the most common clinical features. With our step-up approach to therapy, no patients required intensive care unit (ICU) admission and no cardiac sequelae after 6 months of onset were found in echocardiograms. Conclusion: Our epidemiological study of MIS-C in southern Italy showed unexpectedly overlapping figures with other US studies.
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Affiliation(s)
- Francesco La Torre
- Department of Pediatrics, Giovanni XXIII Pediatric Hospital, University of Bari, 70126 Bari, Italy
| | - Maria Pia Elicio
- Department of Pediatrics, Giovanni XXIII Pediatric Hospital, University of Bari, 70126 Bari, Italy
| | - Viviana Anna Monno
- Department of Pediatrics, Giovanni XXIII Pediatric Hospital, University of Bari, 70126 Bari, Italy
| | - Maria Chironna
- Department of Interdisciplinary Medicine, Hygiene Section, University of Bari, 70123 Bari, Italy
| | - Fulvio Moramarco
- Department of Pediatrics, Antonio Perrino Hospital, 72100 Brindisi, Italy
| | - Angelo Campanozzi
- Department of Medical and Surgical Sciences, Pediatric Section, University of Foggia, 71122 Foggia, Italy
| | - Adele Civino
- Division of Pediatric Rheumatology and Immunology, Vito Fazzi Hospital, 73100 Lecce, Italy
| | - Valerio Cecinati
- Department of Pediatrics, SS Annunziata Hospital, 74100 Taranto, Italy
| | - Ugo Vairo
- Division of Pediatric Cardiology, Giovanni XXIII Pediatric Hospital, 70126 Bari, Italy
| | - Mario Giordano
- Division of Pediatric Nephrology and Dialysis, Giovanni XXIII Pediatric Hospital, 70126 Bari, Italy
| | - Leonardo Milella
- Division of Intensive Care, Giovanni XXIII Pediatric Hospital, 70126 Bari, Italy
| | - Daniela Loconsole
- Department of Interdisciplinary Medicine, Hygiene Section, University of Bari, 70123 Bari, Italy
| | - Fabio Cardinale
- Department of Pediatrics, Giovanni XXIII Pediatric Hospital, University of Bari, 70126 Bari, Italy
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12
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Chironna M, Dipierro G, Franzini JM, Icardi G, Loconsole D, Pariani E, Pastore S, Volpe M. Assessment of 2021/22 influenza epidemic scenarios in Italy during SARS-CoV-2 outbreak. PLoS One 2023; 18:e0282782. [PMID: 36893137 PMCID: PMC9997945 DOI: 10.1371/journal.pone.0282782] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/22/2023] [Indexed: 03/10/2023] Open
Abstract
Global mitigation strategies to tackle the threat posed by SARS-CoV-2 have produced a significant decrease of the severity of 2020/21 seasonal influenza, which might result in a reduced population natural immunity for the upcoming 2021/22 influenza season. To predict the spread of influenza virus in Italy and the impact of prevention and control measures, we present an age-structured Susceptible-Exposed-Infectious-Removed (SEIR) model including the role of social mixing patterns and the impact of age-stratified vaccination strategies and Non-Pharmaceutical Interventions (NPIs) such as school closures, partial lockdown, as well as the adoption of personal protective equipment and the practice of hand hygiene. We find that vaccination campaigns with standard coverage would produce a remarkable mitigation of the spread of the disease in moderate influenza seasons, making the adoption of NPIs unnecessary. However, in case of severe seasonal epidemics, a standard vaccination coverage would not be sufficiently effective in fighting the epidemic, thus implying that a combination with the adoption of NPIs is necessary to contain the disease. Alternatively, our results show that the enhancement of the vaccination coverage would reduce the need to adopt NPIs, thus limiting the economic and social impacts that NPIs might produce. Our results highlight the need to respond to the influenza epidemic by strengthening the vaccination coverage.
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Affiliation(s)
- Maria Chironna
- Department of interdisciplinary Medicine, University of Bari, Aldo Moro Policlinico, Bari, Italy
| | | | | | - Giancarlo Icardi
- Department of Health’s Science (DiSSal), University of Genoa, Genoa, Italy
- Hygiene Unit, San Martino Policlinico Hospital-IRCCS for Oncology and Neurosciences, Genoa, Italy
| | - Daniela Loconsole
- Department of interdisciplinary Medicine, University of Bari, Aldo Moro Policlinico, Bari, Italy
| | - Elena Pariani
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
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13
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Antonella V, De Nola R, Battaglia S, Di Mussi R, Cazzato G, Resta L, Chironna M, Loconsole D, Vinci L, Chiarello G, Marucci M, Cicinelli E. Adverse Maternal Outcomes in Pregnant Women Affected by Severe-Critical COVID-19 Illness: Correlation with Vaccination Status in the Time of Different Viral Strains' Dominancy. Vaccines (Basel) 2022; 10:vaccines10122061. [PMID: 36560471 PMCID: PMC9783263 DOI: 10.3390/vaccines10122061] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/15/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022] Open
Abstract
This is a monocentric and cross-sectional study conducted at the COVID-19 Division of the Obstetrical and Gynecological Unit and Intensive Care Units (ICUs) of Policlinico di Bari, in Bari, Italy, between September 2020 and April 2022. This study aimed to identify the prevalence of severe-critical COVID-19 illness requiring access to the Intensive Care Unit (ICU) among 287 pregnant patients, and possible correlations between the SARS-CoV-2 variants, the specific pandemic wave (dominated by wild, Alpha, Delta, and Omicron strains), and severe-critical adverse maternal outcomes. The prevalence of severe-critical COVID-19 illness was 2.8% (8/287), reaching 4.9% (8/163) excluding the 4th wave (Omicron dominant). The Delta variant determined the highest risk ratio and odds for access to the ICU due to severe-critical COVID-19-related symptoms compared to the other variants (wild, Alpha, Omicron). During the third wave (Delta), the ICU cases underwent a higher rate of hyperimmune plasma infusion (75%), antibiotic therapy (75%), and remdesivir (33%); all of the patients were intubated. During the Omicron wave, the patients were asymptomatic or with few symptoms: most of them (70%) were vaccinated with a median of two doses. The maternal outcome worsened in the case of Alpha and, especially, Delta variants for severe-critical COVID-19-related symptoms and ICU access.
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Affiliation(s)
- Vimercati Antonella
- Unit of Obstetrics and Gynecology, Department of Biomedical and Human Oncologic Science, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Rosalba De Nola
- Unit of Obstetrics and Gynecology, Department of Biomedical and Human Oncologic Science, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
- Correspondence:
| | - Stefano Battaglia
- Interdisciplinary Department of Medicine, University of Bari School of Medicine, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Rossella Di Mussi
- Department of Emergency and Organ Transplantation, Anaesthesia and Resuscitation Division, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Gerardo Cazzato
- Department of Emergency and Organ Transplant, Pathology Division, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Leonardo Resta
- Department of Emergency and Organ Transplant, Pathology Division, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Maria Chironna
- Department of Interdisciplinary Medicine (Laboratory of Molecular Epidemiology and Public Health), University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Daniela Loconsole
- Department of Interdisciplinary Medicine (Laboratory of Molecular Epidemiology and Public Health), University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Lorenzo Vinci
- Unit of Obstetrics and Gynecology, Department of Biomedical and Human Oncologic Science, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Giulia Chiarello
- Unit of Obstetrics and Gynecology, Department of Biomedical and Human Oncologic Science, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Massimo Marucci
- Department of Emergency and Organ Transplantation, Anaesthesia and Resuscitation Division, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Ettore Cicinelli
- Unit of Obstetrics and Gynecology, Department of Biomedical and Human Oncologic Science, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
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14
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Loconsole D, Centrone F, Aprile V, Sallustio A, Casulli D, Accogli M, Sacco D, Zagaria R, Chironna M. What's Next for Flu? Out-of-Season Circulation of Influenza Viruses in Southern Italy, August 2022. Viruses 2022; 14:v14122689. [PMID: 36560693 PMCID: PMC9783519 DOI: 10.3390/v14122689] [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: 10/31/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022] Open
Abstract
The COVID-19 pandemic has modified the seasonal pattern of respiratory infections. The objective of the present study is to characterize the out-of-season circulation of influenza viruses and an influenza outbreak that occurred in southern Italy in August 2022. Nasopharyngeal swabs collected from patients with influenza-like illnesses (ILI) were tested for the presence of influenza and other respiratory viruses. Epidemiological investigations on 85 patients involved in an influenza outbreak were performed. Sequencing and phylogenetic analysis of hemagglutinin genes was undertaken on samples positive for influenza A. In August 2022, in the Apulia region (Italy), influenza A infection was diagnosed in 19 patients, 18 infected with A/H3N2 and one with A/H1N1pdm09 virus. Seven influenza-positive patients were hospitalized with ILI. A further 17 symptomatic subjects, associated with an influenza outbreak, were also tested; 11 were positive for influenza A/H3N2 virus. Phylogenetic analysis of 12 of the A/H3N2 sequences showed that they all belonged to subclade 3C.2a1b.2a.2. The A/H1N1pdm09 strain belonged to subclade 6B.1A.5a.2. The out-of-season circulation of the influenza virus during the summer months could be linked to changing dynamics in the post-COVID-19 era, as well as to the impact of climate change. Year-round surveillance of respiratory viruses is needed to monitor this phenomenon and to provide effective prevention strategies.
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Affiliation(s)
- Daniela Loconsole
- Department of Interdisciplinary Medicine, Hygiene Section, University of Bari, 70124 Bari, Italy
| | - Francesca Centrone
- Department of Interdisciplinary Medicine, Hygiene Section, University of Bari, 70124 Bari, Italy
| | - Valerio Aprile
- Department of Prevention, Local Health Unit of Lecce, 73100 Lecce, Italy
| | - Anna Sallustio
- Hygiene Unit, Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, 70124 Bari, Italy
| | - Daniele Casulli
- Hygiene Unit, Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, 70124 Bari, Italy
| | - Marisa Accogli
- Department of Interdisciplinary Medicine, Hygiene Section, University of Bari, 70124 Bari, Italy
| | - Davide Sacco
- Department of Interdisciplinary Medicine, Hygiene Section, University of Bari, 70124 Bari, Italy
| | - Riccardo Zagaria
- Department of Interdisciplinary Medicine, Hygiene Section, University of Bari, 70124 Bari, Italy
| | - Maria Chironna
- Department of Interdisciplinary Medicine, Hygiene Section, University of Bari, 70124 Bari, Italy
- Correspondence: ; Tel.: +39-080-5478498; Fax: +39-080-5593887
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15
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Loconsole D, Sallustio A, Centrone F, Casulli D, Accogli M, Saracino A, Foti C, Grandolfo M, Buccoliero GB, Vitale V, De Nitto S, Conversano M, Desiante F, Del Sambro L, Simone D, Parisi A, Prato R, Martinelli D, Chironna M. Monkeypox Virus Infections in Southern Italy: Is There a Risk for Community Spread? Int J Environ Res Public Health 2022; 19:ijerph191811719. [PMID: 36141993 PMCID: PMC9517482 DOI: 10.3390/ijerph191811719] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 08/17/2022] [Revised: 09/06/2022] [Accepted: 09/15/2022] [Indexed: 06/07/2023]
Abstract
The ongoing outbreak of the Monkeypox virus (MPXV) is characterized by sustained human-to-human transmission, particularly among men who have sex with men (MSM). The aim of the study was to describe the characteristics of the MPXV infection identified in Southern Italy. Clinical samples for each suspected case identified from 1 June to 1 August 2022 were tested for MPXV, and whole-genome sequencing (WGS) was performed on two strains. Ten cases were identified: eight were young adult males, including six MSMs, and two were female. Nine subjects reported recent sexual exposure. One female subject without sexual exposure only reported attendance at a social gathering. Overall, 7 of 10 skin lesion samples had a high viral load of MPXV DNA, and 6/9 whole blood samples and 6/8 nasopharyngeal swab samples also tested positive. The analyzed sequences belonged to Clade 3, lineage B.1, and B.1.5, respectively. Despite this recent multinational outbreak of MPXV cases having revealed a high proportion of cases occurring among MSM, the identification of cases among heterosexual subjects and in a female subject without sexual risk factors should raise awareness among clinicians about the possible spread of MPXV in the general population.
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Affiliation(s)
- Daniela Loconsole
- Hygiene Section, Department of Interdisciplinary Medicine, University of Bari, 70124 Bari, Italy
| | - Anna Sallustio
- Hygiene Unit, Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, 70124 Bari, Italy
| | - Francesca Centrone
- Hygiene Section, Department of Interdisciplinary Medicine, University of Bari, 70124 Bari, Italy
| | - Daniele Casulli
- Hygiene Unit, Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, 70124 Bari, Italy
| | - Marisa Accogli
- Hygiene Section, Department of Interdisciplinary Medicine, University of Bari, 70124 Bari, Italy
| | - Annalisa Saracino
- Infectious Diseases Section, Department of Biomedical Sciences and Human Oncology, University of Bari, 70124 Bari, Italy
| | - Caterina Foti
- Section of Dermatology, Department of Biomedical Sciences and Human Oncology, University of Bari, 70124 Bari, Italy
| | - Mauro Grandolfo
- Section of Dermatology, Department of Biomedical Sciences and Human Oncology, University of Bari, 70124 Bari, Italy
| | | | - Viviana Vitale
- Department of Prevention, Local Health Authority of Bari, 70100 Bari, Italy
| | - Sara De Nitto
- Department of Prevention, Local Health Authority of Bari, 70100 Bari, Italy
| | - Michele Conversano
- Department of Prevention, Local Health Authority of Taranto, 74121 Taranto, Italy
| | - Francesco Desiante
- Department of Prevention, Local Health Authority of Taranto, 74121 Taranto, Italy
| | - Laura Del Sambro
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy
| | - Domenico Simone
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy
| | - Rosa Prato
- Hygiene Section, Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy
| | - Domenico Martinelli
- Hygiene Section, Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy
| | - Maria Chironna
- Hygiene Section, Department of Interdisciplinary Medicine, University of Bari, 70124 Bari, Italy
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16
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Stufano A, Iatta R, Sgroi G, Jahantigh HR, Cagnazzo F, Flöel A, Lucchese G, Loconsole D, Centrone F, Mendoza-Roldan JA, Chironna M, Otranto D, Lovreglio P. Seroprevalence of vector-borne pathogens in outdoor workers from southern Italy and associated occupational risk factors. Parasit Vectors 2022; 15:264. [PMID: 35879782 PMCID: PMC9310498 DOI: 10.1186/s13071-022-05385-6] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/22/2022] [Indexed: 11/26/2022] Open
Abstract
Background Vector-borne diseases (VBDs) represent an emerging global threat to public health due to the geographical expansion of arthropod vectors. The study aims to assess the seroprevalence of selected vector-borne pathogens (VBPs) in different groups of outdoor workers and the occupational risk factors for exposure to arthropod bites. Methods A cross-sectional study was conducted on 170 workers recruited in two different regions of southern Italy, including farmers, forestry workers, veterinarians, geologists/agronomists and administrative employees, and tested for IgG antibodies against Bartonella henselae, Borrelia spp. Coxiella burnetii and Rickettsia conorii, using a chemiluminescent immunoassay (CLIA). The relationship among job characteristics, tick exposure and the prevalence of seropositive subjects for each pathogen was investigated by applying categorical principal component analysis (CATPCA). Results A high seroprevalence for C. burnetii (30.0%) and R. conorii (15.3%) was reported, mainly in farmers (67.7% and 54.8%, respectively) and forestry workers (29.0% and 16.1%, respectively), while a low prevalence was observed for B. henselae and Borrelia spp. (8.8% and 4.1%, respectively). The regression equation by CATPCA was significant for C. burnetii and R. conorii (P < 0.001), showing a positive association with job, tick bite exposure, working area and contact with animals. Conclusions These findings highlight the need of activating an appropriate occupational health response for minimizing the risk of arthropod vector exposure in workplaces, considering specific preventive measures in particular in high-risk job categories. Graphical Abstract ![]()
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Affiliation(s)
- Angela Stufano
- Interdisciplinary Department of Medicine, University of Bari, Bari, Italy
| | - Roberta Iatta
- Interdisciplinary Department of Medicine, University of Bari, Bari, Italy.
| | - Giovanni Sgroi
- Department of Veterinary Medicine, University of Bari, Valenzano, Italy
| | | | - Francesco Cagnazzo
- Interdisciplinary Department of Medicine, University of Bari, Bari, Italy
| | - Agnes Flöel
- Department of Neurology, University Medicine Greifswald, Greifswald, Germany.,German Center for Neurodegenerative Diseases Rostock-Greifswald, Greifswald, Germany
| | - Guglielmo Lucchese
- Department of Neurology, University Medicine Greifswald, Greifswald, Germany
| | - Daniela Loconsole
- Interdisciplinary Department of Medicine, University of Bari, Bari, Italy
| | - Francesca Centrone
- Interdisciplinary Department of Medicine, University of Bari, Bari, Italy
| | | | - Maria Chironna
- Interdisciplinary Department of Medicine, University of Bari, Bari, Italy
| | - Domenico Otranto
- Department of Veterinary Medicine, University of Bari, Valenzano, Italy.,Faculty of Veterinary Sciences, Bu-Ali Sina University, Hamedan, Iran
| | - Piero Lovreglio
- Interdisciplinary Department of Medicine, University of Bari, Bari, Italy
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17
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Macchia E, Kovács-Vajna ZM, Loconsole D, Sarcina L, Redolfi M, Chironna M, Torricelli F, Torsi L. A handheld intelligent single-molecule binary bioelectronic system for fast and reliable immunometric point-of-care testing. Sci Adv 2022; 8:eabo0881. [PMID: 35857467 PMCID: PMC9258948 DOI: 10.1126/sciadv.abo0881] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Molecular tests are highly reliable and sensitive but lack portability and are not simple to use; conversely, easy-to-use antigenic tests still lack high performance. BioScreen combines single-molecule sensitivity and outstanding reliability with ultraportability and simplicity of use. This digital platform is capable of artificial intelligence-based binary classification at the limit of identification of a single marker/virus in 0.1 ml. The diagnostic sensitivity, specificity, and accuracy reach 99.2% as validated through 240 assays, including a pilot clinical trial. The versatile immunometric system can detect the SARS-CoV-2 virus, spike S1, and immunoglobulin G antigen proteins in saliva, blood serum, and swab. BioScreen has a small footprint comprising a disposable cartridge and a handheld electronic reader connected to a smart device. The sample handling is minimal, and the assay time to result is 21 min. Reliable and sensitive self-testing with an ultraportable and easy-to-use diagnostic system operated directly by a patient holds the potential to revolutionize point-of-care testing and early diagnosis.
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Affiliation(s)
- Eleonora Macchia
- Dipartimento di Farmacia-Scienze del Farmaco, Universit. degli Studi di Bari “Aldo Moro,” 70125 Bari, Italy
- Faculty of Science and Engineering, Åbo Akademi University, 20500 Turku, Finland
| | - Zsolt M. Kovács-Vajna
- Dipartimento di Ingegneria dell’Informazione, Università degli Studi di Brescia, 25123 Brescia, Italy
| | - Daniela Loconsole
- Dipartimento di Scienze Biomediche e Oncologia Umana, Università degli Studi di Bari “Aldo Moro,” 70125 Bari, Italy
| | - Lucia Sarcina
- Dipartimento di Chimica, Università degli Studi di Bari “Aldo Moro,” 70125 Bari, Italy
| | | | - Maria Chironna
- Dipartimento di Scienze Biomediche e Oncologia Umana, Università degli Studi di Bari “Aldo Moro,” 70125 Bari, Italy
| | - Fabrizio Torricelli
- Dipartimento di Ingegneria dell’Informazione, Università degli Studi di Brescia, 25123 Brescia, Italy
- Corrresponding author. (F.T.); (L.T.)
| | - Luisa Torsi
- Dipartimento di Chimica, Università degli Studi di Bari “Aldo Moro,” 70125 Bari, Italy
- Corrresponding author. (F.T.); (L.T.)
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18
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Corriero A, Ribezzi M, Mele F, Angrisani C, Romaniello F, Daleno A, Loconsole D, Centrone F, Chironna M, Brienza N. COVID-19 Variants in Critically Ill Patients: A Comparison of the Delta and Omicron Variant Profiles. Infect Dis Rep 2022; 14:492-500. [PMID: 35735762 PMCID: PMC9222818 DOI: 10.3390/idr14030052] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Coronavirus disease is a pandemic that has disrupted many human lives, threatening people's physical and mental health. Each pandemic wave struck in different ways, infectiveness-wise and mortality-wise. This investigation focuses on critically ill patients affected by the last two variants, Delta and Omicron, and aims to analyse if any difference exists between the two groups. METHODS intensive care unit (ICU) COVID-19 consecutive admissions between 1 October 2021 and 31 March 2022 were recorded daily, and data concerning the patients' demographics, variants, main comorbidities, ICU parameters on admission, and the outcome were analysed by a univariate procedure and by a multivariate analysis. RESULTS 65 patients were enrolled, 31 (47.69%) belonging to the Omicron versus 34 (52.31%) to the Delta group. The mortality rate was 52.94% for the Omicron group versus 41.9% for the Delta group. A univariate analysis showed that the Omicron variant was associated with total comorbidities number, Charlson Comorbidity Index (CCI), pre-existing pulmonary disease, vaccination status, and acute kidney injury (AKI). In stepwise multivariate analysis, the total number of comorbidities was positively associated with the Omicron group, while pulmonary embolism was negatively correlated with the Omicron group. CONCLUSION Omicron appears to have lost some of the hallmarks of the Delta variant, such as endothelialitis and more limited cellular tropism when it comes to the patients in the ICU. Further studies are encouraged to explore different therapeutic approaches to treat critical patients with COVID-19.
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Affiliation(s)
- Alberto Corriero
- Unit of Anesthesia and Resuscitation, University of Bari Aldo Moro, Piazza G. Cesare 11, 70124 Bari, Italy
- Correspondence: (A.C.); (N.B.)
| | - Mario Ribezzi
- Department of Interdisciplinary Medicine—Intensive Care Unit Section, University of Bari Aldo Moro, Piazza G. Cesare 11, 70124 Bari, Italy;
| | - Federica Mele
- Department of Interdisciplinary Medicine—Section of Legal Medicine, Policlinico di Bari Hospital, University of Bari, 70124 Bari, Italy; (F.M.); (C.A.)
| | - Carmelinda Angrisani
- Department of Interdisciplinary Medicine—Section of Legal Medicine, Policlinico di Bari Hospital, University of Bari, 70124 Bari, Italy; (F.M.); (C.A.)
| | - Fabio Romaniello
- Department of Biomedical Science and Human Oncology, University of Bari Aldo Moro, Piazza G. Cesare 11, 70124 Bari, Italy;
| | - Antonio Daleno
- Hospital Direction, Azienda Universitaria Ospedaliera Consorziale Policlinico Bari, Piazza G. Cesare 11, 70124 Bari, Italy;
| | - Daniela Loconsole
- Department of Interdisciplinary Medicine—Hygiene Section, University of Bari Aldo Moro, Piazza G. Cesare 11, 70124 Bari, Italy; (D.L.); (F.C.); (M.C.)
| | - Francesca Centrone
- Department of Interdisciplinary Medicine—Hygiene Section, University of Bari Aldo Moro, Piazza G. Cesare 11, 70124 Bari, Italy; (D.L.); (F.C.); (M.C.)
| | - Maria Chironna
- Department of Interdisciplinary Medicine—Hygiene Section, University of Bari Aldo Moro, Piazza G. Cesare 11, 70124 Bari, Italy; (D.L.); (F.C.); (M.C.)
| | - Nicola Brienza
- Department of Interdisciplinary Medicine—Intensive Care Unit Section, University of Bari Aldo Moro, Piazza G. Cesare 11, 70124 Bari, Italy;
- Correspondence: (A.C.); (N.B.)
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19
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Loconsole D, Pierucci P, Casulli D, Barratta F, Chironna M, Carpagnano GE. Exhaled Breath Condensate (EBC) for SARS-CoV-2 diagnosis still an open debate. J Breath Res 2022; 16. [DOI: 10.1088/1752-7163/ac4dd3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 01/21/2022] [Indexed: 11/11/2022]
Abstract
Abstract
The real-time PCR (RT-PCR) on nasopharyngeal swabs (NPS) is the gold standard for the diagnosis of SARS-CoV-2. The exhaled breath condensate (EBC) is used to perform collection of biological fluid condensed in a refrigerated device from deep airways’ exhaled air. We aimed to verify the presence of SARS-CoV-2 virus in the EBC from patients with confirmed SARS-CoV-2 infection by RT-PCR, and to determine if the EBC may represent a valid alternative to the NPS. Methods: Seventeen consecutive patients admitted to the Emergency Department of the Policlinico were enrolled in the present study with RT-PCR, clinical and radiological evidence of SARS-CoV-2. Within 24 hours from the NPS collection the EBC collection was performed on SARS-CoV-2 positive patients. Informed written consent was gathered and the Ethic Committee approved the study. Results: The mean age of patients was 60 years (24-92) and 64.7% (11/17) were male. Patient n. 9 and n.17 died. All NPS resulted positive for SARS-CoV-2 at RT-PCR. RT-PCR on EBC resulted negative for all but one patients (patient n.12). Conclusion: In this study we did not find any correlation between positive NPS and the EBC in all but one patients enrolled. Based on these data which greatly differ from previous reports on the topic, this study opens several questions related to small differences in the complex process of EBC collection and how EBC could be really standardized for the diagnosis of SARS-CoV-2 infection. Further studies will be warranted to deepen this topic.
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20
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Caselli D, Cafagno C, Loconsole D, Giannini A, Tansella F, Saracino A, Chironna M, Aricò M. Limited Additive Diagnostic Impact of Isolated Gastrointestinal Involvement for the Triage of Children with Suspected COVID-19. Children 2022; 9:children9010041. [PMID: 35053666 PMCID: PMC8773987 DOI: 10.3390/children9010041] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/12/2021] [Accepted: 12/28/2021] [Indexed: 01/08/2023]
Abstract
The strategy for the selection of patients with a suspected SARS-CoV-2 infection is relevant for the organization of a children’s hospital to provide optimal separation into COVID-19 and non-COVID-19 areas and pathways. We analyzed the proportion of children with COVID-19 presenting with gastrointestinal (GI) symptoms in 137 consecutive patients admitted between January 2020 and August 2021. GI symptoms were present as follows: diarrhea in 35 patients (26%), vomiting in 16 (12%), and both of them in five (3%); the combination of fever, respiratory symptoms, and diarrhea was observed in 16 patients (12%). Of the 676 adult patients with COVID-19 admitted to our hospital in the same time interval, 62 (9.2%) had diarrhea, 30 (4.4%) had vomiting, and 11 (1.6%) had nausea; only one patient, a 38-year-old male, presented with isolated GI symptoms at the diagnosis. Although diarrhea was observed in one quarter of cases, one-half of them had the complete triad of fever, respiratory syndrome, and diarrhea, and only five had isolated diarrhea, of which two were diagnosed with a Campylobacter infection. The occurrence of either respiratory symptoms or gastrointestinal symptoms in our patients was not related to the patient age, while younger children were more likely to have a fever. Of the 137 patients, 73 (53%) could be tested for their serum level of SARS-CoV-2 specific IgG antibodies. The observed titer ranged between 0 (n = 3) and 1729 BAU/mL (median, 425 BAU/mL). Of 137 consecutive patients with COVID-19 admitted to our referral children’s hospital, only three presented with an isolated GI manifestation. It is interesting to note that this finding turned out to be fully in keeping with what was observed on adult patients with COVID-19 in our hospital. The additive diagnostic impact of gastrointestinal involvement for the triage of children with suspected COVID-19 appears limited.
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Affiliation(s)
- Désirée Caselli
- Pediatric Infectious Diseases, Giovanni XXIII Children Hospital, Azienda Ospedaliero Universitaria Consorziale Policlinico, 70124 Bari, Italy; (D.C.); (C.C.); (A.G.); (F.T.)
| | - Claudio Cafagno
- Pediatric Infectious Diseases, Giovanni XXIII Children Hospital, Azienda Ospedaliero Universitaria Consorziale Policlinico, 70124 Bari, Italy; (D.C.); (C.C.); (A.G.); (F.T.)
| | - Daniela Loconsole
- Hygiene Section, Department of Biomedical Sciences and Human Oncology, University of Bari, 70124 Bari, Italy; (D.L.); (M.C.)
| | - Annamaria Giannini
- Pediatric Infectious Diseases, Giovanni XXIII Children Hospital, Azienda Ospedaliero Universitaria Consorziale Policlinico, 70124 Bari, Italy; (D.C.); (C.C.); (A.G.); (F.T.)
| | - Francesco Tansella
- Pediatric Infectious Diseases, Giovanni XXIII Children Hospital, Azienda Ospedaliero Universitaria Consorziale Policlinico, 70124 Bari, Italy; (D.C.); (C.C.); (A.G.); (F.T.)
| | - Annalisa Saracino
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari, Azienda Ospedaliero Universitaria Consorziale Policlinico, 70124 Bari, Italy;
| | - Maria Chironna
- Hygiene Section, Department of Biomedical Sciences and Human Oncology, University of Bari, 70124 Bari, Italy; (D.L.); (M.C.)
| | - Maurizio Aricò
- Strategic Control, Azienda Ospedaliero Universitaria Consorziale Policlinico, 70124 Bari, Italy
- Correspondence:
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21
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Panatto D, Orsi A, Pennati BM, Lai PL, Mosca S, Bruzzone B, Caligiuri P, Napoli C, Bertamino E, Orsi GB, Manini I, Loconsole D, Centrone F, Pandolfi E, Ciofi Degli Atti ML, Concato C, Linardos G, Onetti Muda A, Raponi M, Piccioni L, Rizzo C, Chironna M, Icardi G. No evidence of SARS-CoV-2 in hospitalized patients with severe acute respiratory syndrome in five Italian hospitals from 1st November 2019 to 29th February 2020. PLoS One 2021; 16:e0260947. [PMID: 34874956 PMCID: PMC8653811 DOI: 10.1371/journal.pone.0260947] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 11/19/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND On 9th January 2020, China CDC reported a novel coronavirus (later named SARS-CoV-2) as the causative agent of the coronavirus disease 2019 (COVID-19). Identifying the first appearance of virus is of epidemiological importance to tracking and mapping the spread of SARS-CoV-2 in a country. We therefore conducted a retrospective observational study to detect SARS-CoV-2 in oropharyngeal samples collected from hospitalized patients with a Severe Acute Respiratory Infection (SARI) enrolled in the DRIVE (Development of Robust and Innovative Vaccine Effectiveness) study in five Italian hospitals (CIRI-IT BIVE hospitals network) (1st November 2019 - 29th February 2020). OBJECTIVES To acquire new information on the real trend in SARS-CoV-2 infection during pandemic phase I and to determine the possible early appearance of the virus in Italy. MATERIALS AND METHODS Samples were tested for influenza [RT-PCR assay (A/H1N1, A/H3N2, B/Yam, B/Vic)] in accordance with the DRIVE study protocol. Subsequently, swabs underwent molecular testing for SARS-COV-2. [one-step real-time multiplex retro-transcription (RT) PCR]. RESULTS In the 1683 samples collected, no evidence of SARS-CoV-2 was found. Moreover, 28.3% (477/1683) of swabs were positive for influenza viruses, the majority being type A (358 vs 119 type B). A/H3N2 was predominant among influenza A viruses (55%); among influenza B viruses, B/Victoria was prevalent. The highest influenza incidence rate was reported in patients aged 0-17 years (40.3%) followed by those aged 18-64 years (24.4%) and ≥65 years (14.8%). CONCLUSIONS In Italy, some studies have shown the early circulation of SARS-CoV-2 in northern regions, those most severely affected during phase I of the pandemic. In central and southern regions, by contrast no early circulation of the virus was registered. These results are in line with ours. These findings highlight the need to continue to carry out retrospective studies, in order to understand the epidemiology of the novel coronavirus, to better identify the clinical characteristics of COVID-19 in comparison with other acute respiratory illnesses (ARI), and to evaluate the real burden of COVID-19 on the healthcare system.
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MESH Headings
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- COVID-19/diagnosis
- COVID-19/virology
- Female
- Hospitals
- Humans
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/isolation & purification
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/isolation & purification
- Influenza B virus/genetics
- Influenza B virus/isolation & purification
- Influenza, Human/epidemiology
- Influenza, Human/pathology
- Influenza, Human/virology
- Italy/epidemiology
- Male
- Middle Aged
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Retrospective Studies
- SARS-CoV-2/genetics
- SARS-CoV-2/isolation & purification
- Severe Acute Respiratory Syndrome/epidemiology
- Severe Acute Respiratory Syndrome/pathology
- Severe Acute Respiratory Syndrome/virology
- Young Adult
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Affiliation(s)
- Donatella Panatto
- Interuniversity Research Center on Influenza and Other Transmissible
Infections (CIRI-IT), Genoa, Italy
- Department of Health Sciences, University of Genoa, Genoa,
Italy
| | - Andrea Orsi
- Interuniversity Research Center on Influenza and Other Transmissible
Infections (CIRI-IT), Genoa, Italy
- Department of Health Sciences, University of Genoa, Genoa,
Italy
- Policlinico San Martino Hospital, Genoa, Italy
| | - Beatrice Marina Pennati
- Interuniversity Research Center on Influenza and Other Transmissible
Infections (CIRI-IT), Genoa, Italy
| | - Piero Luigi Lai
- Interuniversity Research Center on Influenza and Other Transmissible
Infections (CIRI-IT), Genoa, Italy
- Department of Health Sciences, University of Genoa, Genoa,
Italy
| | - Stefano Mosca
- Interuniversity Research Center on Influenza and Other Transmissible
Infections (CIRI-IT), Genoa, Italy
| | | | | | - Christian Napoli
- Department of Medical Surgical Sciences and Translational Medicine,
University La Sapienza, Rome, Italy
| | | | - Giovanni Battista Orsi
- Department of Public Health and Infectious Diseases, University La
Sapienza, Rome, Italy
| | - Ilaria Manini
- Interuniversity Research Center on Influenza and Other Transmissible
Infections (CIRI-IT), Genoa, Italy
- Department of Molecular and Developmental Medicine, University of Siena,
Siena, Italy
| | - Daniela Loconsole
- Hygiene Section, Department of Biomedical Sciences and Human Oncology,
University of Bari, Bari, Italy
| | - Francesca Centrone
- Hygiene Section, Department of Biomedical Sciences and Human Oncology,
University of Bari, Bari, Italy
| | | | | | | | | | | | | | | | | | - Maria Chironna
- Hygiene Section, Department of Biomedical Sciences and Human Oncology,
University of Bari, Bari, Italy
| | - Giancarlo Icardi
- Interuniversity Research Center on Influenza and Other Transmissible
Infections (CIRI-IT), Genoa, Italy
- Department of Health Sciences, University of Genoa, Genoa,
Italy
- Policlinico San Martino Hospital, Genoa, Italy
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22
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O'Toole Á, Hill V, Pybus OG, Watts A, Bogoch II, Khan K, Messina JP, Tegally H, Lessells RR, Giandhari J, Pillay S, Tumedi KA, Nyepetsi G, Kebabonye M, Matsheka M, Mine M, Tokajian S, Hassan H, Salloum T, Merhi G, Koweyes J, Geoghegan JL, de Ligt J, Ren X, Storey M, Freed NE, Pattabiraman C, Prasad P, Desai AS, Vasanthapuram R, Schulz TF, Steinbrück L, Stadler T, Parisi A, Bianco A, García de Viedma D, Buenestado-Serrano S, Borges V, Isidro J, Duarte S, Gomes JP, Zuckerman NS, Mandelboim M, Mor O, Seemann T, Arnott A, Draper J, Gall M, Rawlinson W, Deveson I, Schlebusch S, McMahon J, Leong L, Lim CK, Chironna M, Loconsole D, Bal A, Josset L, Holmes E, St. George K, Lasek-Nesselquist E, Sikkema RS, Oude Munnink B, Koopmans M, Brytting M, Sudha rani V, Pavani S, Smura T, Heim A, Kurkela S, Umair M, Salman M, Bartolini B, Rueca M, Drosten C, Wolff T, Silander O, Eggink D, Reusken C, Vennema H, Park A, Carrington C, Sahadeo N, Carr M, Gonzalez G, de Oliveira T, Faria N, Rambaut A, Kraemer MUG. Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch. Wellcome Open Res 2021; 6:121. [PMID: 34095513 PMCID: PMC8176267 DOI: 10.12688/wellcomeopenres.16661.2] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [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] [Accepted: 09/10/2021] [Indexed: 11/20/2022] Open
Abstract
Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.
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Affiliation(s)
- Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Alexander Watts
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
| | - Issac I. Bogoch
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
| | - Kamran Khan
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
| | | | - The COVID-19 Genomics UK (COG-UK) consortium
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Network for Genomic Surveillance in South Africa (NGS-SA)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Brazil-UK CADDE Genomic Network
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard R. Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | | | | | | | - Madisa Mine
- National Health Laboratory, Gaborone, Botswana
| | - Sima Tokajian
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Hamad Hassan
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
| | - Tamara Salloum
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Georgi Merhi
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Jad Koweyes
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Jemma L. Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Joep de Ligt
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Xiaoyun Ren
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Matthew Storey
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Nikki E. Freed
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Chitra Pattabiraman
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Pramada Prasad
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Anita S. Desai
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Ravi Vasanthapuram
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Thomas F. Schulz
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Lars Steinbrück
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
| | - Swiss Viollier Sequencing Consortium
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Antonio Parisi
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
| | - Angelica Bianco
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
| | - Darío García de Viedma
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
| | - Sergio Buenestado-Serrano
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Sílvia Duarte
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Neta S. Zuckerman
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Orna Mor
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Alicia Arnott
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - Jenny Draper
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - Mailie Gall
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - William Rawlinson
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
| | - Ira Deveson
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
| | - Sanmarié Schlebusch
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
| | - Jamie McMahon
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
| | - Lex Leong
- South Australia Pathology, Adelaide, Australia
| | | | - Maria Chironna
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
| | - Daniela Loconsole
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
| | - Antonin Bal
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | - Laurence Josset
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | | | - Kirsten St. George
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | | | - Reina S. Sikkema
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Bas Oude Munnink
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Marion Koopmans
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Mia Brytting
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
| | - V. Sudha rani
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
| | - S. Pavani
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
| | - Teemu Smura
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - Albert Heim
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Satu Kurkela
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Massab Umair
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Muhammad Salman
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Barbara Bartolini
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
| | - Martina Rueca
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
| | - Christian Drosten
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
| | - Thorsten Wolff
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
| | - Olin Silander
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Dirk Eggink
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Chantal Reusken
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Harry Vennema
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Aekyung Park
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
| | | | - Nikita Sahadeo
- University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Michael Carr
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Gabo Gonzalez
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - SEARCH Alliance San Diego
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - National Virus Reference Laboratory
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - SeqCOVID-Spain
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Danish Covid-19 Genome Consortium (DCGC)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Communicable Diseases Genomic Network (CDGN)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Dutch National SARS-CoV-2 surveillance program
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Division of Emerging Infectious Diseases (KDCA)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nuno Faria
- Department of Zoology, University of Oxford, Oxford, UK
- Imperial College London, London, UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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23
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Stufano A, Jahantigh HR, Cagnazzo F, Centrone F, Loconsole D, Chironna M, Lovreglio P. Work-Related Human T-lymphotropic Virus 1 and 2 (HTLV-1/2) Infection: A Systematic Review. Viruses 2021; 13:1753. [PMID: 34578335 PMCID: PMC8472817 DOI: 10.3390/v13091753] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/17/2021] [Accepted: 08/27/2021] [Indexed: 12/22/2022] Open
Abstract
Human T-lymphotropic virus 1 and 2 (HTLV-1/2) belong to the delta group of retroviruses which may cause a life-long infection in humans, HTLV-1 leading to adult T-cell leukemia/lymphoma and other diseases. Different transmission modes have been described, such as breastfeeding, and, as for other blood-borne pathogens, unsafe sexual activity, intravenous drug usage, and blood transfusion and transplantation. The present systematic review was conducted to identify all peer-reviewed studies concerning the work-related infection by HTLV-1/2. A literature search was conducted from January to May 2021, according to the PRISMA methodology, selecting 29 studies: seven related to health care workers (HCWs), five to non-HCWs, and 17 to sex workers (SWs). The findings showed no clear evidence as to the possibility of HTLV-1/2 occupational transmission in HCWs, according to the limited number and quality of the papers. Moreover, non-HCWs showed a higher prevalence in jobs consistent with a lower socioeconomic status or that could represent a familial cluster, and an increased risk of zoonotic transmission from STLV-1-infected non-human primates has been observed in African hunters. Finally, a general increase of HTLV-1 infection was observed in SWs, whereas only one paper described an increased prevalence for HTLV-2, supporting the urgent need for prevention and control measures, including screening, diagnosis, and treatment of HTLV-1/2, to be offered routinely as part of a comprehensive approach to decrease the impact of sexually transmitted diseases in SWs.
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Affiliation(s)
- Angela Stufano
- Interdisciplinary Department of Medicine-Section of Occupational Medicine, University of Bari, 70124 Bari, Italy; (H.R.J.); (F.C.); (P.L.)
| | - Hamid Reza Jahantigh
- Interdisciplinary Department of Medicine-Section of Occupational Medicine, University of Bari, 70124 Bari, Italy; (H.R.J.); (F.C.); (P.L.)
| | - Francesco Cagnazzo
- Interdisciplinary Department of Medicine-Section of Occupational Medicine, University of Bari, 70124 Bari, Italy; (H.R.J.); (F.C.); (P.L.)
| | - Francesca Centrone
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, 70124 Bari, Italy; (F.C.); (D.L.); (M.C.)
| | - Daniela Loconsole
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, 70124 Bari, Italy; (F.C.); (D.L.); (M.C.)
| | - Maria Chironna
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, 70124 Bari, Italy; (F.C.); (D.L.); (M.C.)
| | - Piero Lovreglio
- Interdisciplinary Department of Medicine-Section of Occupational Medicine, University of Bari, 70124 Bari, Italy; (H.R.J.); (F.C.); (P.L.)
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24
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Loconsole D, De Robertis AL, Sallustio A, Centrone F, Morcavallo C, Campanella S, Accogli M, Chironna M. Update on the Epidemiology of Macrolide-Resistant Mycoplasma pneumoniae in Europe: A Systematic Review. Infect Dis Rep 2021; 13:811-820. [PMID: 34562998 PMCID: PMC8482213 DOI: 10.3390/idr13030073] [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: 07/24/2021] [Revised: 08/18/2021] [Accepted: 08/30/2021] [Indexed: 11/16/2022] Open
Abstract
Macrolide-resistant Mycoplasma pneumoniae (MR-MP) infections cause upper and lower respiratory tract infections in both children and adults, and are characterized by a longer duration of symptoms. Here, we undertook a systematic review of studies on MR-MP in Europe. The review meets PRISMA guidelines. The PubMed, Scopus, and Science Direct databases were searched using suitable keywords to identify relevant studies published from 2010 to 2021; 21 studies were included. Overall, a low level of MR-MP spread was reported in Europe. MR-MP spread increased during epidemic waves registered in Europe, particularly in Italy and Scotland, where the highest MR-MP infection rates were registered during the 2010–2011 epidemic. By contrast, no MR-MP infections were reported in Finland and the Netherlands. Continued monitoring of MR-MP in Europe is needed to maintain the low rates of infection. Moreover, a coordinated and structured pan-European surveillance program adequate for public health surveillance is advisable, with the purpose of containing the spread of antimicrobial resistance.
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Affiliation(s)
- Daniela Loconsole
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, 70124 Bari, Italy; (D.L.); (A.L.D.R.); (F.C.); (C.M.); (S.C.); (M.A.)
| | - Anna Lisa De Robertis
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, 70124 Bari, Italy; (D.L.); (A.L.D.R.); (F.C.); (C.M.); (S.C.); (M.A.)
| | - Anna Sallustio
- Hygiene Unit, Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, 70124 Bari, Italy;
| | - Francesca Centrone
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, 70124 Bari, Italy; (D.L.); (A.L.D.R.); (F.C.); (C.M.); (S.C.); (M.A.)
| | - Caterina Morcavallo
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, 70124 Bari, Italy; (D.L.); (A.L.D.R.); (F.C.); (C.M.); (S.C.); (M.A.)
| | - Silvia Campanella
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, 70124 Bari, Italy; (D.L.); (A.L.D.R.); (F.C.); (C.M.); (S.C.); (M.A.)
| | - Marisa Accogli
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, 70124 Bari, Italy; (D.L.); (A.L.D.R.); (F.C.); (C.M.); (S.C.); (M.A.)
| | - Maria Chironna
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, 70124 Bari, Italy; (D.L.); (A.L.D.R.); (F.C.); (C.M.); (S.C.); (M.A.)
- Correspondence: ; Tel.: +39-080-5478498; Fax: +39-080-5593887
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25
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van Summeren JJGT, Rizzo C, Hooiveld M, Korevaar JC, Hendriksen JMT, Dückers MLA, Loconsole D, Chironna M, Bangert M, Demont C, Meijer A, Caini S, Pandolfi E, Paget J. Evaluation of a standardised protocol to measure the disease burden of respiratory syncytial virus infection in young children in primary care. BMC Infect Dis 2021; 21:705. [PMID: 34311699 PMCID: PMC8311415 DOI: 10.1186/s12879-021-06397-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 07/15/2021] [Indexed: 11/24/2022] Open
Abstract
Background A better understanding of the burden of respiratory syncytial virus (RSV) infections in primary care is needed for policymakers to make informed decisions regarding new preventive measures and treatments. The aim of this study was to develop and evaluate a protocol for the standardised measurement of the disease burden of RSV infection in primary care in children aged < 5 years. Methods The standardised protocol was evaluated in Italy and the Netherlands during the 2019/20 winter. Children aged < 5 years who consulted their primary care physician, met the WHO acute respiratory infections (ARI) case definition, and had a laboratory confirmed positive test for RSV (RT-PCR) were included. RSV symptoms were collected at the time of swabbing. Health care use, duration of symptoms and socio-economic impact was measured 14 days after swabbing. Health related Quality of life (HRQoL) was measured using the parent-proxy report of the PedsQL™4.0 generic core scales (2–4 years) and PedsQL™4.0 infant scales (0–2 years) 30 days after swabbing. The standardised protocol was evaluated in terms of the feasibility of patient recruitment, data collection procedures and whether parents understood the questions. Results Children were recruited via a network of paediatricians in Italy and a sentinel influenza surveillance network of general practitioners in the Netherlands. In Italy and the Netherlands, 293 and 152 children were swabbed respectively, 119 and 32 tested RSV positive; for 119 and 12 children the Day-14 questionnaire was completed and for 116 and 11 the Day-30 questionnaire. In Italy, 33% of the children had persistent symptoms after 14 days and in the Netherlands this figure was 67%. Parents had no problems completing questions concerning health care use, duration of symptoms and socio-economic impact, however, they had some difficulties scoring the HRQoL of their young children. Conclusion RSV symptoms are common after 14 days, and therefore, measuring disease burden outcomes like health care use, duration of symptoms, and socio-economic impact is also recommended at Day-30. The standardised protocol is suitable to measure the clinical and socio-economic disease burden of RSV in young children in primary care.
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Affiliation(s)
- J J G T van Summeren
- Nivel, Netherlands Institute for Health Services Research, P.O. Box 1568, 3500BN, Utrecht, Utrecht, The Netherlands.
| | - C Rizzo
- IRCCS, Bambino Gesù Children's Hospital, Rome, Italy
| | - M Hooiveld
- Nivel, Netherlands Institute for Health Services Research, P.O. Box 1568, 3500BN, Utrecht, Utrecht, The Netherlands
| | - J C Korevaar
- Nivel, Netherlands Institute for Health Services Research, P.O. Box 1568, 3500BN, Utrecht, Utrecht, The Netherlands
| | - J M T Hendriksen
- Nivel, Netherlands Institute for Health Services Research, P.O. Box 1568, 3500BN, Utrecht, Utrecht, The Netherlands
| | - M L A Dückers
- Nivel, Netherlands Institute for Health Services Research, P.O. Box 1568, 3500BN, Utrecht, Utrecht, The Netherlands.,University of Groningen, Faculty of Behavioural and Social Sciences, Groningen, The Netherlands
| | - D Loconsole
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, "Aldo Moro", Bari, Italy
| | - M Chironna
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, "Aldo Moro", Bari, Italy
| | | | | | - A Meijer
- Centre for Infectious Diseases Research, Diagnostics and laboratory Surveillance, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - S Caini
- Nivel, Netherlands Institute for Health Services Research, P.O. Box 1568, 3500BN, Utrecht, Utrecht, The Netherlands
| | - E Pandolfi
- IRCCS, Bambino Gesù Children's Hospital, Rome, Italy
| | - J Paget
- Nivel, Netherlands Institute for Health Services Research, P.O. Box 1568, 3500BN, Utrecht, Utrecht, The Netherlands
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26
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Loconsole D, Stea ED, Sallustio A, Fontò G, Pronzo V, Simone S, Centrone F, Accogli M, Gesualdo L, Chironna M. Severe COVID-19 by SARS-CoV-2 Lineage B.1.1.7 in Vaccinated Solid-Organ Transplant Recipients: New Preventive Strategies Needed to Protect Immunocompromised Patients. Vaccines (Basel) 2021; 9:vaccines9080806. [PMID: 34451931 PMCID: PMC8402384 DOI: 10.3390/vaccines9080806] [Citation(s) in RCA: 4] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/15/2021] [Accepted: 07/20/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Solid-organ transplant (SOT) recipients are at a high risk of severe COVID-19, and are priority for vaccination. Here, we describe three cases of severe COVID-19 caused by SARS-CoV-2 B.1.1.7 lineage in vaccinated SOT recipients. METHODS Three SOT patients were hospitalized in the Policlinico Hospital of Bari (southern Italy) and underwent nasopharyngeal swabs for molecular detection of SARS-CoV-2 genes and spike protein mutations by real-time PCR. One sample was subjected to whole-genome sequencing. RESULTS One patient was a heart transplant recipient and two were kidney transplant recipients. All were hospitalized with severe COVID-19 between March and May 2021. Two patients were fully vaccinated and one had received only one dose of the BNT162b2 mRNA vaccine. All the patients showed a high viral load at diagnosis, and molecular typing revealed the presence of B.1.1.7 lineage SARS-CoV-2. In all three cases, prolonged viral shedding was reported. CONCLUSIONS The three cases pose concern about the role of the B.1.1.7 lineage in severe COVID-19 and about the efficacy of COVID-19 vaccination in immunocompromised patients. Protecting immunocompromised patients from COVID-19 is a challenge. SOT recipients show a suboptimal response to standard vaccination, and thus, an additive booster or a combined vaccination strategy with mRNA, protein/subunit, and vector-based vaccines may be necessary. This population should continue to practice strict COVID-19 precautions post-vaccination, until new strategies for protection are available.
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Affiliation(s)
- Daniela Loconsole
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, 70124 Bari, Italy; (D.L.); (F.C.); (M.A.)
| | - Emma Diletta Stea
- Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari, 70124 Bari, Italy; (E.D.S.); (G.F.); (V.P.); (S.S.); (L.G.)
| | - Anna Sallustio
- Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, Hygiene Unit, 70124 Bari, Italy;
| | - Giulia Fontò
- Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari, 70124 Bari, Italy; (E.D.S.); (G.F.); (V.P.); (S.S.); (L.G.)
| | - Virginia Pronzo
- Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari, 70124 Bari, Italy; (E.D.S.); (G.F.); (V.P.); (S.S.); (L.G.)
| | - Simona Simone
- Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari, 70124 Bari, Italy; (E.D.S.); (G.F.); (V.P.); (S.S.); (L.G.)
| | - Francesca Centrone
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, 70124 Bari, Italy; (D.L.); (F.C.); (M.A.)
| | - Marisa Accogli
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, 70124 Bari, Italy; (D.L.); (F.C.); (M.A.)
| | - Loreto Gesualdo
- Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari, 70124 Bari, Italy; (E.D.S.); (G.F.); (V.P.); (S.S.); (L.G.)
| | - Maria Chironna
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, 70124 Bari, Italy; (D.L.); (F.C.); (M.A.)
- Correspondence: ; Tel.: +39-080-5478498; Fax: +39-080-5593887
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27
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O'Toole Á, Hill V, Pybus OG, Watts A, Bogoch II, Khan K, Messina JP, Tegally H, Lessells RR, Giandhari J, Pillay S, Tumedi KA, Nyepetsi G, Kebabonye M, Matsheka M, Mine M, Tokajian S, Hassan H, Salloum T, Merhi G, Koweyes J, Geoghegan JL, de Ligt J, Ren X, Storey M, Freed NE, Pattabiraman C, Prasad P, Desai AS, Vasanthapuram R, Schulz TF, Steinbrück L, Stadler T, Parisi A, Bianco A, García de Viedma D, Buenestado-Serrano S, Borges V, Isidro J, Duarte S, Gomes JP, Zuckerman NS, Mandelboim M, Mor O, Seemann T, Arnott A, Draper J, Gall M, Rawlinson W, Deveson I, Schlebusch S, McMahon J, Leong L, Lim CK, Chironna M, Loconsole D, Bal A, Josset L, Holmes E, St. George K, Lasek-Nesselquist E, Sikkema RS, Oude Munnink B, Koopmans M, Brytting M, Sudha rani V, Pavani S, Smura T, Heim A, Kurkela S, Umair M, Salman M, Bartolini B, Rueca M, Drosten C, Wolff T, Silander O, Eggink D, Reusken C, Vennema H, Park A, Carrington C, Sahadeo N, Carr M, Gonzalez G, de Oliveira T, Faria N, Rambaut A, Kraemer MUG. Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2. Wellcome Open Res 2021; 6:121. [PMID: 34095513 PMCID: PMC8176267 DOI: 10.12688/wellcomeopenres.16661.1] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2021] [Indexed: 12/13/2022] Open
Abstract
Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.
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Affiliation(s)
- Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Alexander Watts
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
| | - Issac I. Bogoch
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
| | - Kamran Khan
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
| | | | - The COVID-19 Genomics UK (COG-UK) consortium
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Network for Genomic Surveillance in South Africa (NGS-SA)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Brazil-UK CADDE Genomic Network
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard R. Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | | | | | | | - Madisa Mine
- National Health Laboratory, Gaborone, Botswana
| | - Sima Tokajian
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Hamad Hassan
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
| | - Tamara Salloum
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Georgi Merhi
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Jad Koweyes
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
| | - Jemma L. Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Joep de Ligt
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Xiaoyun Ren
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Matthew Storey
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - Nikki E. Freed
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Chitra Pattabiraman
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Pramada Prasad
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Anita S. Desai
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Ravi Vasanthapuram
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Thomas F. Schulz
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Lars Steinbrück
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
| | - Swiss Viollier Sequencing Consortium
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Antonio Parisi
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
| | - Angelica Bianco
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
| | - Darío García de Viedma
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
| | - Sergio Buenestado-Serrano
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Sílvia Duarte
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
| | - Neta S. Zuckerman
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Michal Mandelboim
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Orna Mor
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Alicia Arnott
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - Jenny Draper
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - Mailie Gall
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
| | - William Rawlinson
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
| | - Ira Deveson
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
| | - Sanmarié Schlebusch
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
| | - Jamie McMahon
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
| | - Lex Leong
- South Australia Pathology, Adelaide, Australia
| | | | - Maria Chironna
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
| | - Daniela Loconsole
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
| | - Antonin Bal
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | - Laurence Josset
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
| | | | - Kirsten St. George
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | | | - Reina S. Sikkema
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Bas Oude Munnink
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Marion Koopmans
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
| | - Mia Brytting
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
| | - V. Sudha rani
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
| | - S. Pavani
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
| | - Teemu Smura
- Department of Virology, University of Helsinki, Helsinki, Finland
| | - Albert Heim
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Satu Kurkela
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Massab Umair
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Muhammad Salman
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Barbara Bartolini
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
| | - Martina Rueca
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
| | - Christian Drosten
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
| | - Thorsten Wolff
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
| | - Olin Silander
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Dirk Eggink
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Chantal Reusken
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Harry Vennema
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Aekyung Park
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
| | | | - Nikita Sahadeo
- University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Michael Carr
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Gabo Gonzalez
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - SEARCH Alliance San Diego
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - National Virus Reference Laboratory
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - SeqCOVID-Spain
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Danish Covid-19 Genome Consortium (DCGC)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Communicable Diseases Genomic Network (CDGN)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Dutch National SARS-CoV-2 surveillance program
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Division of Emerging Infectious Diseases (KDCA)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Department of Zoology, University of Oxford, Oxford, UK
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- BlueDot, Toronto, Canada
- Department of Medicine, University of Toronto, Toronto, Canada
- Divisions of General Internal Medicine and Infectious Diseases, University Health Network, Toronto, Canada
- Department of Geography, University of Oxford, Oxford, UK
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- National Health Laboratory, Gaborone, Botswana
- Ministry of Health and Wellness, Gaborone, Botswana
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Institute of Environmental Science and Research, Wellington, New Zealand
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias CIBERES, Madrid, Spain
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- South Australia Pathology, Adelaide, Australia
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- University of Sydney, Sydney, Australia
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Department of Virology, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- University of the West Indies, St. Augustine, Trinidad and Tobago
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Imperial College London, London, UK
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nuno Faria
- Department of Zoology, University of Oxford, Oxford, UK
- Imperial College London, London, UK
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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Loconsole D, Sallustio A, Accogli M, Centrone F, Casulli D, Madaro A, Tedeschi E, Parisi A, Chironna M. Symptomatic SARS-CoV-2 Reinfection in a Healthy Healthcare Worker in Italy Confirmed by Whole-Genome Sequencing. Viruses 2021; 13:899. [PMID: 34066205 PMCID: PMC8150928 DOI: 10.3390/v13050899] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/06/2021] [Accepted: 05/11/2021] [Indexed: 12/13/2022] Open
Abstract
This study describes a case of SARS-CoV-2 reinfection confirmed by whole-genome sequencing in a healthy physician who had been working in a COVID-19 hospital in Italy since the beginning of the pandemic. Nasopharyngeal swabs were obtained from the patient at each presentation as part of routine surveillance. Nucleic acid amplification testing was performed on the two samples to confirm SARS-CoV-2 infection, and serological tests were used to detect SARS-CoV-2 IgG antibodies. Comparative genome analysis with whole-genome sequencing was performed on nasopharyngeal swabs collected during the two episodes of COVID-19. The first COVID-19 episode was in March 2020, and the second was in January 2021. Both SARS-CoV-2 infections presented with mild symptoms, and seroconversion for SARS-CoV-2 IgG was documented. Genomic analysis showed that the viral genome from the first infection belonged to the lineage B.1.1.74, while that from the second infection to the lineage B.1.177. Epidemiological, clinical, serological, and genomic analyses confirmed that the second episode of SARS-CoV-2 infection in the healthcare worker met the qualifications for "best evidence" for reinfection. Further studies are urgently needed to assess the frequency of such a worrisome occurrence, particularly in the light of the recent diffusion of SARS-CoV-2 variants of concern.
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Affiliation(s)
- Daniela Loconsole
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, 70124 Bari, Italy; (D.L.); (M.A.); (F.C.)
| | - Anna Sallustio
- Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, 70124 Bari, Italy; (A.S.); (D.C.)
| | - Marisa Accogli
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, 70124 Bari, Italy; (D.L.); (M.A.); (F.C.)
| | - Francesca Centrone
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, 70124 Bari, Italy; (D.L.); (M.A.); (F.C.)
| | - Daniele Casulli
- Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, 70124 Bari, Italy; (A.S.); (D.C.)
| | - Antonino Madaro
- Department of Prevention, Local Health Unit of Bari, 70124 Bari, Italy;
| | - Ersilia Tedeschi
- Covid-Unit, Hospital F. Miulli, Acquaviva delle Fonti, 70124 Bari, Italy;
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy;
| | - Maria Chironna
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, 70124 Bari, Italy; (D.L.); (M.A.); (F.C.)
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Rizzo C, Loconsole D, Pandolfi E, Ciofi Degli Atti ML, van Summeren J, Paget J, Russo L, Campagna I, Croci I, Gesualdo F, Concato C, Linardos G, Bartolucci V, Ciampini S, Muda AO, Raponi M, Chironna M. Sars-Cov2 Not Detected in a Pediatric Population With Acute Respiratory Infection in Primary Care in Central and Southern Italy From November 2019 to Early March 2020. Front Pediatr 2021; 9:620598. [PMID: 34046372 PMCID: PMC8147864 DOI: 10.3389/fped.2021.620598] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 04/12/2021] [Indexed: 02/03/2023] Open
Abstract
Background: In December 2019, a novel coronavirus named SARS-CoV-2 started circulating in China and this led to a major epidemic in Northern Italy between February and May 2020. Young children (aged <5 years) seem to be less affected by this coronavirus disease (COVID-19) compared to adults, although there is very little information on the circulation of this new virus among children in Italy. We retrospectively tested nasopharyngeal swabs for SARS-CoV-2 in samples collected in young children between November, 2019 and March, 2020 in the context of the RSV ComNet study. Methods: Two networks of primary care pediatricians in Lazio (Central Italy) and Puglia (Southern Italy) collected nasopharyngeal swabs from children, aged <5 years, presenting with symptoms for an acute respiratory infection (ARI). The RSV ComNet study is a multicenter study implemented to estimate the burden of RSV in young children (aged <5 years) in the community. Swabs were sent to a central reference laboratory and tested for 14 respiratory viruses through RT-PCR. All collected samples were retrospectively tested for SARS-CoV-2 using RT-PCR (Istituto Superiore di Sanità protocol). Results: A total of 293 children with ARI were identified in the two participating networks. The highest number of cases were recruited in weeks 51/2019 and 3/2020. The majority of patients (57%) came from the Lazio region. All of the 293 samples tested negative for SARS-Cov2. Rhinovirus was the most frequently detected virus (44%), followed by RSV (41%) and influenza viruses (14%). Conclusions: Our study shows that in Lazio (a region of intermediate SARS-COV-2 incidence) and Puglia (a region of low incidence), the SARS-Cov2 virus did not circulate in a sample of ARI pediatric cases consulting primary care pediatricians between November 2019 and March 2020.
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Affiliation(s)
- Caterina Rizzo
- Clinical Pathways and Epidemiology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Daniela Loconsole
- Department of Biomedical Science and Human Oncology, University of Bari, Bari, Italy
| | - Elisabetta Pandolfi
- Multifactorial Disease and Complex Disease Area, Bambino Gesù Children Hospital, Rome, Italy
| | | | | | - John Paget
- Nivel, Netherlands Institute for Health Services Research, Utrecht, Netherlands
| | - Luisa Russo
- Multifactorial Disease and Complex Disease Area, Bambino Gesù Children Hospital, Rome, Italy
| | - Ilaria Campagna
- Multifactorial Disease and Complex Disease Area, Bambino Gesù Children Hospital, Rome, Italy
| | - Ileana Croci
- Multifactorial Disease and Complex Disease Area, Bambino Gesù Children Hospital, Rome, Italy
| | - Francesco Gesualdo
- Multifactorial Disease and Complex Disease Area, Bambino Gesù Children Hospital, Rome, Italy
| | - Carlo Concato
- Virology Unit, Laboratory Department, Bambino Gesù Children's Hospital, Rome, Italy
| | - Giulia Linardos
- Virology Unit, Laboratory Department, Bambino Gesù Children's Hospital, Rome, Italy
| | - Veronica Bartolucci
- Department of Biomedical Science and Human Oncology, University of Bari, Bari, Italy
| | - Sara Ciampini
- Public Health Service, Local Health Authority Rome 1, Rome, Italy
| | - Andrea Onetti Muda
- Department of Laboratories, Bambino Gesù Children's Hospital, Rome, Italy
| | | | - Maria Chironna
- Department of Biomedical Science and Human Oncology, University of Bari, Bari, Italy
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Loconsole D, Centrone F, Morcavallo C, Campanella S, Sallustio A, Accogli M, Fortunato F, Parisi A, Chironna M. Rapid Spread of the SARS-CoV-2 Variant of Concern 202012/01 in Southern Italy (December 2020-March 2021). Int J Environ Res Public Health 2021; 18:ijerph18094766. [PMID: 33947087 PMCID: PMC8125211 DOI: 10.3390/ijerph18094766] [Citation(s) in RCA: 19] [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] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/28/2021] [Accepted: 04/28/2021] [Indexed: 11/18/2022]
Abstract
Epidemiological and virological studies have revealed that SARS-CoV-2 variants of concern (VOCs) are emerging globally, including in Europe. The aim of this study was to evaluate the spread of B.1.1.7-lineage SARS-CoV-2 in southern Italy from December 2020–March 2021 through the detection of the S gene target failure (SGTF), which could be considered a robust proxy of VOC B.1.1.7. SGTF was assessed on 3075 samples from week 52/2020 to week 10/2021. A subset of positive samples identified in the Apulia region during the study period was subjected to whole-genome sequencing (WGS). A descriptive and statistical analysis of the demographic and clinical characteristics of cases according to SGTF status was performed. Overall, 20.2% of samples showed SGTF; 155 strains were confirmed as VOC 202012/01 by WGS. The proportion of SGTF-positive samples rapidly increased over time, reaching 69.2% in week 10/2021. SGTF-positive cases were more likely to be symptomatic and to result in hospitalization (p < 0.0001). Despite the implementation of large-scale non-pharmaceutical interventions (NPIs), such as the closure of schools and local lockdowns, a rapid spread of VOC 202012/01 was observed in southern Italy. Strengthened NPIs and rapid vaccine deployment, first among priority groups and then among the general population, are crucial both to contain the spread of VOC 202012/01 and to flatten the curve of the third wave.
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Affiliation(s)
- Daniela Loconsole
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, 70124 Bari, Italy; (D.L.); (F.C.); (C.M.); (S.C.); (M.A.)
| | - Francesca Centrone
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, 70124 Bari, Italy; (D.L.); (F.C.); (C.M.); (S.C.); (M.A.)
| | - Caterina Morcavallo
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, 70124 Bari, Italy; (D.L.); (F.C.); (C.M.); (S.C.); (M.A.)
| | - Silvia Campanella
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, 70124 Bari, Italy; (D.L.); (F.C.); (C.M.); (S.C.); (M.A.)
| | - Anna Sallustio
- Hygiene Unit, Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, 70124 Bari, Italy;
| | - Marisa Accogli
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, 70124 Bari, Italy; (D.L.); (F.C.); (C.M.); (S.C.); (M.A.)
| | - Francesca Fortunato
- Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy;
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy;
| | - Maria Chironna
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, 70124 Bari, Italy; (D.L.); (F.C.); (C.M.); (S.C.); (M.A.)
- Correspondence: ; Tel.: +39-080-547-8498; Fax: +39-080-559-3887
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Loconsole D, Metallo A, Bruno V, De Robertis AL, Morea A, Quarto M, Chironna M. HIV awareness: a kap study among students in Italy reveals that preventive campaigns still represent a public health priority. Ann Ig 2021; 32:56-64. [PMID: 31713577 DOI: 10.7416/ai.2020.2330] [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] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Improving knowledge about HIV/AIDS among young people is crucial for preventing new infections. The aim of the study was to investigate knowledge, attitudes and practices regarding HIV infection among students attending university courses related to the healthcare professions, in order to better target future preventive and informative HIV campaigns tailored for young people. STUDY DESIGN A knowledge, attitude and practices study was conducted among university students attending the following university courses in Bari (Southern Italy): Medicine and Surgery (MS), Dentistry and Dental Prostheses, Health Assistance, Motor Activities and Sports Sciences, Sciences and Technology of Herbal and Health Products, Nursing, Biomedical Laboratory Techniques, and Dietetics. METHODS Students completed a self-administered questionnaire designed to assess their knowledge/attitudes re/ HIV and their own sexual practices. The general part of the questionnaire requested information about age, gender, nationality, religion and marital status. The second part included questions asking about knowledge, attitude and practices with respect to HIV, which required true/false answers or graduated answers (reported as agree, quite agree, quite disagree, and disagree). RESULTS Four hundred students were invited to fill in the questionnaire. The response rate was 91.2% (n=365). Almost all students were aware that HIV is transmitted through sexual intercourse and blood, but only 34% knew that breastfeeding is a route of transmission. Of the respondents, 86.8% referred to previous sexual intercourse (25.8% reported using a condom in all cases of sexual intercourse, 43.5% in most cases, 18.6% rarely and 12.1 never). Sexual intercourse with casual partners was reported by 37.5% of these students and 63.9% of them did not always use a condom. CONCLUSIONS The results of the study show that knowledge about some aspects of HIV is insufficient even though the students participating in the present study are students attending university courses related to the healthcare professions. Moreover, high-risk behaviors as the lack of the use of condom during sexual intercourse with casual partners are also common among interviewed students. Programs aimed at providing information that can prevent/reduce transmission of HIV in young people and new strategies to improve knowledge should be stressed as a public health priority.
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Affiliation(s)
- D Loconsole
- Department of Biomedical Sciences and Human Oncology, University of Bari "Aldo Moro", Bari, Italy
| | - A Metallo
- Department of Biomedical Sciences and Human Oncology, University of Bari "Aldo Moro", Bari, Italy
| | - V Bruno
- Department of Biomedical Sciences and Human Oncology, University of Bari "Aldo Moro", Bari, Italy
| | - A L De Robertis
- Department of Biomedical Sciences and Human Oncology, University of Bari "Aldo Moro", Bari, Italy
| | - A Morea
- Department of Biomedical Sciences and Human Oncology, University of Bari "Aldo Moro", Bari, Italy
| | - M Quarto
- Department of Biomedical Sciences and Human Oncology, University of Bari "Aldo Moro", Bari, Italy
| | - M Chironna
- Department of Biomedical Sciences and Human Oncology, University of Bari "Aldo Moro", Bari, Italy
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Bianco A, Capozzi L, Monno MR, Del Sambro L, Manzulli V, Pesole G, Loconsole D, Parisi A. Characterization of Bacillus cereus Group Isolates From Human Bacteremia by Whole-Genome Sequencing. Front Microbiol 2021; 11:599524. [PMID: 33510722 PMCID: PMC7835510 DOI: 10.3389/fmicb.2020.599524] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 11/27/2020] [Indexed: 12/18/2022] Open
Abstract
Members of the Bacillus cereus group are spore-forming organisms commonly associated with food poisoning and intestinal infections. Moreover, some strains of the group (i.e., B. cereus sensu stricto and Bacillus thuringiensis) can cause bacteremia in humans, mainly in immunocompromised individuals. Here we performed the genetic characterization of 17 human clinical strains belonging to B. cereus group isolated from blood culture. The whole-genome sequencing (WGS) revealed that the isolates were closely related to B. cereus sensu stricto and B. thuringiensis-type strain. Multilocus sequence typing analysis performed on the draft genome revealed the genetic diversity of our isolates, which were assigned to different sequence types. Based on panC nucleotide sequence, the isolates were grouped in the phylogenetic groups III and IV. The NHE, cer, and inhA gene cluster, entA, entFM, plcA, and plcB, were the most commonly detected virulence genes. Although we did not assess the ability to generate biofilm by phenotypic tests, we verified the prevalence of biofilm associated genes using an in silico approach. A high prevalence of pur gene cluster, xerC, clpY, codY, tasA, sipW, sinI, and sigB genes, was found. Genes related to the resistance to penicillin, trimethoprim, and ceftriaxone were identified in most of the isolates. Intriguingly, the majority of these virulence and AMR genes appeared to be evenly distributed among B. cereus s.s. isolates, as well as closely related to B. thuringiensis isolates. We showed the WGS represents a good approach to rapidly characterize B. cereus group strains, being able to give useful information about genetic epidemiology, the presence of virulence and antimicrobial genes, and finally about the potential hazard related to this underestimated risk.
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Affiliation(s)
- Angelica Bianco
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Loredana Capozzi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Maria Rosa Monno
- Department of Basic Medical Sciences, Neurosciences and Sense Organs, University of Bari "Aldo Moro", Bari, Italy
| | - Laura Del Sambro
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Viviana Manzulli
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Graziano Pesole
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari "A. Moro", Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies of the National Research Council and Consorzio Interuniversitario Biotecnologie, Bari, Italy
| | - Daniela Loconsole
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
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Lanave G, Loconsole D, Centrone F, Catella C, Capozza P, Diakoudi G, Parisi A, Suffredini E, Buonavoglia A, Camero M, Chironna M, Martella V. Astrovirus VA1 in patients with acute gastroenteritis. Transbound Emerg Dis 2021; 69:864-869. [PMID: 33411943 DOI: 10.1111/tbed.13979] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/29/2020] [Accepted: 01/04/2021] [Indexed: 01/22/2023]
Abstract
Human astroviruses (AstVs) are usually associated with acute gastroenteritis. In recent years, atypical animal-like AstVs have been identified, but their pathogenic role in humans has not been determined. Starting from 2010, there has been a growing evidence that AstVs may also be associated with encephalitis in human and animal hosts. Some human atypical AstV strains (VA1, MLB1/MLB2) display neurotropic potential, as they have been repeatedly identified in patients with AstV-related encephalitis, chiefly in immunosuppressed individuals. In this study, a VA1-like AstV was identified from a single stool sample from an outbreak of foodborne acute gastroenteritis occurred in Italy in 2018. On genome sequencing, the virus was related to the VA1-like strain UK1 (99.3% at the nucleotide level). Similar viruses were also found to circulate in paediatric patients hospitalized with AGE in the same time span, 2018, but at low prevalence (0.75%, 3/401). Gathering epidemiological data on atypical AstVs will be useful to assess the risks posed by atypical AstV infections, chiefly in medically fragile patients.
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Affiliation(s)
- Gianvito Lanave
- Department of Veterinary Medicine, University of Bari, Valenzano (Bari), Italy
| | - Daniela Loconsole
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, Bari, Italy
| | - Francesca Centrone
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, Bari, Italy
| | - Cristiana Catella
- Department of Veterinary Medicine, University of Bari, Valenzano (Bari), Italy
| | - Paolo Capozza
- Department of Veterinary Medicine, University of Bari, Valenzano (Bari), Italy
| | - Georgia Diakoudi
- Department of Veterinary Medicine, University of Bari, Valenzano (Bari), Italy
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale di Puglia e Basilicata, Sezione di Putignano, Bari, Italy
| | - Elisabetta Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Alessio Buonavoglia
- Department of Biomedical Sciences and Human Oncology, Unit of Internal Medicine 'Guido Baccelli', University of Bari, Bari, Italy
| | - Michele Camero
- Department of Veterinary Medicine, University of Bari, Valenzano (Bari), Italy
| | - Maria Chironna
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, Bari, Italy
| | - Vito Martella
- Department of Veterinary Medicine, University of Bari, Valenzano (Bari), Italy
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Baggieri M, Morea A, Marchi A, Bucci P, Loconsole D, Chironna M, Magurano F. Measles outbreak in Apulia, southern Italy. J Med Virol 2020; 92:2897-2899. [PMID: 32692403 DOI: 10.1002/jmv.26313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 07/12/2020] [Indexed: 12/01/2023]
Affiliation(s)
- Melissa Baggieri
- Italian National Reference Laboratory for measles and rubella, Departement of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Anna Morea
- Department of Biomedical Science and Human Oncology, Aldo Moro University of Bari, Bari, Italy
| | - Antonella Marchi
- Italian National Reference Laboratory for measles and rubella, Departement of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Paola Bucci
- Italian National Reference Laboratory for measles and rubella, Departement of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Daniela Loconsole
- Department of Biomedical Science and Human Oncology, Aldo Moro University of Bari, Bari, Italy
| | - Maria Chironna
- Department of Biomedical Science and Human Oncology, Aldo Moro University of Bari, Bari, Italy
| | - Fabio Magurano
- Italian National Reference Laboratory for measles and rubella, Departement of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
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Paradiso AV, De Summa S, Loconsole D, Procacci V, Sallustio A, Centrone F, Silvestris N, Cafagna V, De Palma G, Tufaro A, Garrisi VM, Chironna M. Rapid Serological Assays and SARS-CoV-2 Real-Time Polymerase Chain Reaction Assays for the Detection of SARS-CoV-2: Comparative Study. J Med Internet Res 2020; 22:e19152. [PMID: 33031048 PMCID: PMC7641647 DOI: 10.2196/19152] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 07/31/2020] [Accepted: 09/13/2020] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Real-time polymerase chain reaction (RT-PCR) testing for the identification of viral nucleic acid is the current standard for the diagnosis of SARS-CoV-2 infection, but technical issues limit its utilization for large-scale screening. Serological immunoglobulin M (IgM)/IgG testing has been proposed as a useful tool for detecting SARS-CoV-2 exposure. OBJECTIVE The objective of our study was to compare the results of the rapid serological VivaDiag test for SARS-CoV-2-related IgM/IgG detection with those of the standard RT-PCR laboratory test for identifying SARS-CoV-2 nucleic acid. METHODS We simultaneously performed both serological and molecular tests with a consecutive series of 191 symptomatic patients. The results provided by a new rapid serological colorimetric test for analyzing IgM/IgG expression were compared with those of RT-PCR testing for SARS-CoV-2 detection. RESULTS Of the 191 subjects, 70 (36.6%) tested positive for SARS-CoV-2 based on RT-PCR results, while 34 (17.3%) tested positive based on serological IgM/IgG expression. Additionally, 13 (6.8%) subjects tested positive based on serological test results, but also tested negative based on RT-PCR results. The rapid serological test had a sensitivity of 30% and a specificity of 89% compared to the standard RT-PCR assay. Interestingly, the performance of both assays improved 8 days after symptom appearance. After 10 days had passed since symptom appearance, the predictive value of the rapid serological test was higher than that of the standard molecular assay (proportion of positive results: 40% vs 20%). Multivariate analysis showed that age >58 years (P<.01) and period of >15 days after symptom onset (P<.02) were significant and independent factors associated with serological test positivity. CONCLUSIONS The rapid serological test analyzed in this study seems limited in terms of usefulness when diagnosing SARS-CoV-2 infection. However, it may be useful for providing relevant information on people's immunoreaction to COVID-19 exposure.
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Affiliation(s)
| | - Simona De Summa
- Molecular Diagnostics and Pharmacogenetics Unit, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Daniela Loconsole
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, Bari, Italy
| | - Vito Procacci
- Emergency Department, Policlinico Hospital, Bari, Italy
| | - Anna Sallustio
- Regional Epidemiological Observatory, Apulia Region, Bari, Italy
| | - Francesca Centrone
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, Bari, Italy
| | - Nicola Silvestris
- Unit of Internal Medicine Guido Baccelli, Department of Biomedical Sciences and Human Oncology, University of Bari Medical School, Bari, Italy.,Medical Oncology Unit, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Vito Cafagna
- Clinical Pathology Laboratory, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Giuseppe De Palma
- Experimental Oncology and BioBank Management Unit, Institutional BioBank, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Antonio Tufaro
- Experimental Oncology and BioBank Management Unit, Institutional BioBank, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Vito Michele Garrisi
- Clinical Pathology Laboratory, IRCCS Istituto Tumori Giovanni Paolo II, Bari, Italy
| | - Maria Chironna
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, Bari, Italy.,Emergency Department, Policlinico Hospital, Bari, Italy.,Regional Epidemiological Observatory, Apulia Region, Bari, Italy.,Hygeine Unit, Policlinico Hospital, Bari, Italy
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Caselli D, Chironna M, Loconsole D, Aricò M. Response to 'No evidence of SARS-CoV-2 infection by polymerase chain reaction or serology in children with pseudo-chilblain'. Reply from the authors. Br J Dermatol 2020; 183:1156-1157. [PMID: 32974916 PMCID: PMC7537176 DOI: 10.1111/bjd.19563] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- D Caselli
- Pediatric Infectious Diseases, Azienda, Piazza G., 70124, Bari, Italy
| | - M Chironna
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, Piazza G. Cesare 11, 70124, Bari, Italy
| | - D Loconsole
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, Piazza G. Cesare 11, 70124, Bari, Italy
| | - M Aricò
- COVID Emergency Task Force, Giovanni XXIII Children's Hospital, Azienda Ospedaliero Universitaria, Consorziale Policlinico, Bari, Piazza G. Cesare 11, 70124, Bari, Italy
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Loconsole D, Centrone F, Morcavallo C, Campanella S, Sallustio A, Quarto M, Procacci V, Chironna M. The Light and Shadow of Rapid Serological Tests for SARS-CoV-2 Infection: Results from a Study in a Large Emergency Department. Int J Environ Res Public Health 2020; 17:ijerph17186493. [PMID: 32906596 PMCID: PMC7558531 DOI: 10.3390/ijerph17186493] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/27/2020] [Accepted: 09/04/2020] [Indexed: 06/11/2023]
Abstract
A critical point in the management of the SARS-CoV-2 pandemic is the need to promptly identify the greatest number of infected people and to implement strict public health measures. In this study, the performance of a rapid serological test in a clinical setting was evaluated. Samples from 819 consecutive patients (with or without respiratory symptoms) admitted to a large Emergency Department were tested between 23 March and 21 April 2020. Patient samples were tested in a real-time PCR assay and a serological assay. In total, 148/819 patients (18.1%) tested positive for SARS-CoV-2 by real-time PCR. The serological test revealed that 70/819 patients (8.5%) had anti-SARS-CoV-2 IgM and/or IgG. The prevalence of anti-SARS-CoV-2 antibodies was significantly higher in patients with respiratory symptoms lasting for >7 days than in those with respiratory symptoms lasting for 0-7 days (p < 0.001). The serological assay had an overall sensitivity of 35.1% and an overall specificity of 97.3%. A high negative predictive value (96.7%) was reported for patients without respiratory symptoms. The results confirm that rapid serological assays alone are not sufficient for diagnosis of SARS-CoV-2 infection but can be incorporated into large-scale screening programs during periods in which the virus circulation is low.
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Affiliation(s)
- Daniela Loconsole
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy; (D.L.); (F.C.); (C.M.); (S.C.); (M.Q.)
| | - Francesca Centrone
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy; (D.L.); (F.C.); (C.M.); (S.C.); (M.Q.)
| | - Caterina Morcavallo
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy; (D.L.); (F.C.); (C.M.); (S.C.); (M.Q.)
| | - Silvia Campanella
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy; (D.L.); (F.C.); (C.M.); (S.C.); (M.Q.)
| | - Anna Sallustio
- Hygiene Unit, Policlinico Hospital, Piazza G. Cesare 11, 70124 Bari, Italy;
| | - Michele Quarto
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy; (D.L.); (F.C.); (C.M.); (S.C.); (M.Q.)
| | - Vito Procacci
- Emergency Department, Policlinico Hospital, Piazza G. Cesare 11, 70124 Bari, Italy;
| | - Maria Chironna
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy; (D.L.); (F.C.); (C.M.); (S.C.); (M.Q.)
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Baldacci S, Giannico OV, Giorgino A, Buccoliero GB, Desiante F, Fragnelli GR, Rizzi R, Loconsole D, Centrone F, Chironna M, Conversano M. 63 days detection of SARS-CoV-2 RNA from a recovered patient in Southern Italy: A Case Report. Ann Ig 2020; 32:590-592. [PMID: 32744589 DOI: 10.7416/ai.2020.2378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- S Baldacci
- Department of Prevention, Local Health Authority of Taranto, Taranto, Italy
| | - O V Giannico
- Department of Prevention, Local Health Authority of Taranto, Taranto, Italy
| | - A Giorgino
- Department of Prevention, Local Health Authority of Taranto, Taranto, Italy
| | - G B Buccoliero
- Infectious Diseases Unit, "San Giuseppe Moscati" Hospital, Taranto, Italy
| | - F Desiante
- Department of Prevention, Local Health Authority of Taranto, Taranto, Italy
| | - G R Fragnelli
- Department of Prevention, Local Health Authority of Taranto, Taranto, Italy
| | - R Rizzi
- Department of Prevention, Local Health Authority of Taranto, Taranto, Italy
| | - D Loconsole
- Department of Biomedical Sciences and Human Oncology, University of Bari "Aldo Moro", Bari, Italy
| | - F Centrone
- Department of Biomedical Sciences and Human Oncology, University of Bari "Aldo Moro", Bari, Italy
| | - M Chironna
- Department of Biomedical Sciences and Human Oncology, University of Bari "Aldo Moro", Bari, Italy
| | - M Conversano
- Department of Prevention, Local Health Authority of Taranto, Taranto, Italy
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Brindicci G, Santoro CR, Loconsole D, Martinelli D, Prato R, Lonero G, Loperfido P, Buccoliero GB, Chironna M. A Cluster of Cryptic Plasmodium falciparum Malaria in African Migrants in Southern Italy, October 2017. Vector Borne Zoonotic Dis 2020; 20:927-931. [PMID: 32833595 DOI: 10.1089/vbz.2019.2607] [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] [Indexed: 11/12/2022] Open
Abstract
Background: Italy was declared malaria free by the World Health Organization in 1970. Despite this, nonimport malaria cases are on the increase in Italy and throughout the Mediterranean area. In Italy, in the period between 2011 and 2015, seven cases of locally acquired malaria have been reported, including one introduced case of Plasmodium vivax; moreover, the last certain case of introduced malaria (by P. vivax) has been reported in Tuscany in 1997. No case of introduced malaria from Plasmodium falciparum has been reported in Italy since 1970. Case Presentation: A cluster of four cryptic P. falciparum malaria cases were ascertained in migrant farm workers (three from Morocco and one from Sudan) in Apulia (southern Italy) with clinical onset between September 20 and 27, 2017. None of the patients reported a history of a recent trip to malaria-endemic areas or hospitalization or other risk factors. Typing of malaria was also confirmed using molecular biology methods in two different laboratories. There were no cases of severe malaria in our four patients, and only one in need of transfusion. All patients were discharged cured after being treated with mefloquine due to the unavailability of other antimalarials. Conclusions: In recent years, numerous reports of locally acquired malaria have been made in southern Europe. The cases described in this article represent the first cluster of malaria caused by P. falciparum in Europe. Today, clinical presentation in the diagnosis of malaria is more important than ever, since epidemiological criterion cannot be considered unfailing. The mode of transmission has not been proven and further biological and entomological studies are necessary to define our case as cryptic or confirm the presence of mosquitoes capable of transmitting P. falciparum and/or the capacity of Anopheles labranchiae, An. superpictus, or An. plumbeus to transmit it on Italian territory.
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Affiliation(s)
- Gaetano Brindicci
- Operative Unit of Infectious and Tropical Diseases, San Giuseppe Moscati Hospital, Taranto, Italy
| | - Carmen Rita Santoro
- Operative Unit of Infectious and Tropical Diseases, San Giuseppe Moscati Hospital, Taranto, Italy
| | - Daniela Loconsole
- Department of Biomedical Science and Human Oncology, Hospital-University Polyclinic, University of Bari, Bari, Italy
| | - Domenico Martinelli
- Department of Medical and Surgical Science, University of Foggia, Foggia, Italy
| | - Rosa Prato
- Department of Medical and Surgical Science, University of Foggia, Foggia, Italy
| | - Gaetano Lonero
- Operative Unit of Infectious and Tropical Diseases, San Giuseppe Moscati Hospital, Taranto, Italy
| | - Pietro Loperfido
- Operative Unit of Infectious and Tropical Diseases, San Giuseppe Moscati Hospital, Taranto, Italy
| | | | - Maria Chironna
- Department of Biomedical Science and Human Oncology, Hospital-University Polyclinic, University of Bari, Bari, Italy
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Rizzo C, Gesualdo F, Loconsole D, Pandolfi E, Bella A, Orsi A, Guarona G, Panatto D, Icardi G, Napoli C, Orsi GB, Manini I, Montomoli E, Campagna I, Russo L, Alfonsi V, Puzelli S, Reale A, Raucci U, Piccioni L, Concato C, Ciofi Degli Atti ML, Villani A, Chironna M, Tozzi AE. Moderate Vaccine Effectiveness against Severe Acute Respiratory Infection Caused by A(H1N1)pdm09 Influenza Virus and No Effectiveness against A(H3N2) Influenza Virus in the 2018/2019 Season in Italy. Vaccines (Basel) 2020; 8:vaccines8030427. [PMID: 32751584 PMCID: PMC7564262 DOI: 10.3390/vaccines8030427] [Citation(s) in RCA: 12] [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] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/26/2020] [Accepted: 07/28/2020] [Indexed: 01/05/2023] Open
Abstract
Every season, circulating influenza viruses change; therefore, vaccines must be reformulated each year. We aimed to estimate vaccine effectiveness (VE) against severe influenza infection for the 2018/19 season in Italy. We conducted a test-negative design case-control study at five Italian hospitals. We estimated influenza VE against severe acute respiratory infection (SARI) requiring hospitalisation overall, and by virus subtype, vaccine brand, and age. The 2018/19 season was characterised by A(H1N1)pmd09 and A(H3N2) influenza viruses. Vaccine coverage among <18 years recruited SARI cases was very low (3.2%). Seasonal vaccines were moderately effective against type A influenza overall (adjusted VE = 40.5%; 95% confidence interval (CI) = 18.7–56.4%) and subtype A(H1N1)pmd09 viruses (adjusted VE = 55%; 95% CI = 34.5–69.1%), but ineffective against subtype A(H3N2) viruses (adjusted VE = 2.5%; 95% CI = −50.0–36.7%). Both Fluad and Fluarix Tetra vaccines were effective against type A influenza overall and subtype A(H1N1)pdm09 viruses. VE appeared to be similar across age groups (0–64 years, ≥65 years). Seasonal influenza vaccines in the 2018/19 season were moderately effective in preventing SARI caused by A(H1N1)pdm09 influenza but ineffective against A(H3N2).
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Affiliation(s)
- Caterina Rizzo
- IRCCS, Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (F.G.); (E.P.); (I.C.); (L.R.); (A.R.); (U.R.); (L.P.); (C.C.); (M.L.C.D.A.); (A.V.); (A.E.T.)
- Correspondence:
| | - Francesco Gesualdo
- IRCCS, Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (F.G.); (E.P.); (I.C.); (L.R.); (A.R.); (U.R.); (L.P.); (C.C.); (M.L.C.D.A.); (A.V.); (A.E.T.)
| | - Daniela Loconsole
- Department of Biomedical Science and Medical, Oncology of the University of Bari, 70120 Bari, Italy; (D.L.); (M.C.)
| | - Elisabetta Pandolfi
- IRCCS, Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (F.G.); (E.P.); (I.C.); (L.R.); (A.R.); (U.R.); (L.P.); (C.C.); (M.L.C.D.A.); (A.V.); (A.E.T.)
| | - Antonino Bella
- Department of Infectious Diseases, National Institute of Health, 00161 Rome, Italy; (A.B.); (S.P.)
| | - Andrea Orsi
- IRCCS University Hospital San Martino, 16100 Genoa, Italy; (A.O.); (G.G.); (D.P.); (G.I.)
| | - Giulia Guarona
- IRCCS University Hospital San Martino, 16100 Genoa, Italy; (A.O.); (G.G.); (D.P.); (G.I.)
| | - Donatella Panatto
- IRCCS University Hospital San Martino, 16100 Genoa, Italy; (A.O.); (G.G.); (D.P.); (G.I.)
| | - Giancarlo Icardi
- IRCCS University Hospital San Martino, 16100 Genoa, Italy; (A.O.); (G.G.); (D.P.); (G.I.)
| | - Christian Napoli
- Department of Medical-Surgical Sciences and Translational Medicine, University of Rome “Sapienza”, 00185 Rome, Italy;
| | - Giovanni Battista Orsi
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy; (G.B.O.); (I.M.)
| | - Ilaria Manini
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Rome, Italy; (G.B.O.); (I.M.)
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy;
| | - Emanuele Montomoli
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy;
- Vaccine Assessment VisMederi Srl, 53100 Siena, Italy
| | - Ilaria Campagna
- IRCCS, Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (F.G.); (E.P.); (I.C.); (L.R.); (A.R.); (U.R.); (L.P.); (C.C.); (M.L.C.D.A.); (A.V.); (A.E.T.)
| | - Luisa Russo
- IRCCS, Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (F.G.); (E.P.); (I.C.); (L.R.); (A.R.); (U.R.); (L.P.); (C.C.); (M.L.C.D.A.); (A.V.); (A.E.T.)
| | - Valeria Alfonsi
- Medical Direction, University Hospital Sant’Andrea, 00189 Rome, Italy;
| | - Simona Puzelli
- Department of Infectious Diseases, National Institute of Health, 00161 Rome, Italy; (A.B.); (S.P.)
| | - Antonino Reale
- IRCCS, Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (F.G.); (E.P.); (I.C.); (L.R.); (A.R.); (U.R.); (L.P.); (C.C.); (M.L.C.D.A.); (A.V.); (A.E.T.)
| | - Umberto Raucci
- IRCCS, Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (F.G.); (E.P.); (I.C.); (L.R.); (A.R.); (U.R.); (L.P.); (C.C.); (M.L.C.D.A.); (A.V.); (A.E.T.)
| | - Livia Piccioni
- IRCCS, Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (F.G.); (E.P.); (I.C.); (L.R.); (A.R.); (U.R.); (L.P.); (C.C.); (M.L.C.D.A.); (A.V.); (A.E.T.)
| | - Carlo Concato
- IRCCS, Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (F.G.); (E.P.); (I.C.); (L.R.); (A.R.); (U.R.); (L.P.); (C.C.); (M.L.C.D.A.); (A.V.); (A.E.T.)
| | - Marta Luisa Ciofi Degli Atti
- IRCCS, Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (F.G.); (E.P.); (I.C.); (L.R.); (A.R.); (U.R.); (L.P.); (C.C.); (M.L.C.D.A.); (A.V.); (A.E.T.)
| | - Alberto Villani
- IRCCS, Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (F.G.); (E.P.); (I.C.); (L.R.); (A.R.); (U.R.); (L.P.); (C.C.); (M.L.C.D.A.); (A.V.); (A.E.T.)
| | - Maria Chironna
- Department of Biomedical Science and Medical, Oncology of the University of Bari, 70120 Bari, Italy; (D.L.); (M.C.)
| | - Alberto Eugenio Tozzi
- IRCCS, Bambino Gesù Children’s Hospital, 00165 Rome, Italy; (F.G.); (E.P.); (I.C.); (L.R.); (A.R.); (U.R.); (L.P.); (C.C.); (M.L.C.D.A.); (A.V.); (A.E.T.)
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Caselli D, Chironna M, Loconsole D, Nigri L, Mazzotta F, Bonamonte D, Aricò M. No evidence of SARS-CoV-2 infection by polymerase chain reaction or serology in children with pseudo-chilblain. Br J Dermatol 2020; 183:784-785. [PMID: 32613638 PMCID: PMC7361942 DOI: 10.1111/bjd.19349] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2020] [Indexed: 11/30/2022]
Affiliation(s)
- D Caselli
- Pediatric Infectious Diseases, Giovanni XXIII Children Hospital, Azienda Ospedaliero Universitaria Consorziale Policlinico, Bari, Piazza G. Cesare 11, 70124, Bari, Italy
| | - M Chironna
- Department of Biomedical Sciences and Human Oncology - Hygiene Section, University of Bari, Piazza G. Cesare 11, 70124, Bari, Italy
| | - D Loconsole
- Department of Biomedical Sciences and Human Oncology - Hygiene Section, University of Bari, Piazza G. Cesare 11, 70124, Bari, Italy
| | - L Nigri
- Italian Federation of Pediatricians (FIMP), Rome, Italy
| | - F Mazzotta
- Pediatric Dermatology, ASL Barletta, Barletta, Italy
| | - D Bonamonte
- Section of Dermatology, Department of Biomedical Science and Human Oncology, University of Bari, Piazza G. Cesare 11, 70124, Bari, Italy
| | - M Aricò
- COVID Emergency Task Force, Giovanni XXIII Children Hospital, Azienda Ospedaliero Universitaria Consorziale Policlinico, Bari, Piazza G. Cesare 11, 70124, Bari, Italy
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Loconsole D, Giordano M, Centrone F, Accogli M, Casulli D, De Robertis AL, Morea A, Quarto M, Parisi A, Scavia G, Chironna M. Epidemiology of Shiga Toxin-Producing Escherichia coli Infections in Southern Italy after Implementation of Symptom-Based Surveillance of Bloody Diarrhea in the Pediatric Population. Int J Environ Res Public Health 2020; 17:E5137. [PMID: 32708640 PMCID: PMC7400587 DOI: 10.3390/ijerph17145137] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 07/08/2020] [Accepted: 07/14/2020] [Indexed: 12/30/2022]
Abstract
Shiga toxin-producing Escherichia coli (STEC) infections result in a significant public health impact because of the severity of the disease that, in young children especially, can lead to hemolytic-uremic syndrome (HUS). A rise in the number of HUS cases was observed in the Apulia region of Italy from 2013 to 2017, and so, in 2018, a symptom-based surveillance system for children with bloody diarrhea (BD) was initiated in order to detect and manage STEC infections. The objective of the study was to describe the epidemiology of STEC infections in children from June 2018 to August 2019. Children <15 years old with BD were hospitalized and tested for STEC. Real-time PCR for virulence genes (stx1, stx2, eae) and serogroup identification tests were performed on stool samples/rectal swabs of cases. STEC infection was detected in 87 (10.6%) BD cases. The median age of STEC cases was 2.7 years, and 60 (68.9%) were <4. Of these 87 cases, 12 (13.8%) came from households with diarrhea. The reporting rate was 14.2/100,000, with the highest incidence in cases from the province of Bari (24.2/100,000). Serogroups O26 and O111 were both detected in 22/87 (25.3%) cases. Co-infections occurred in 12.6% of cases (11/87). Twenty-nine STEC were positive for stx1, stx2, and eae. Five cases (5.7%) caused by O26 (n = 2), O111 (n = 2), and O45 (n = 1) developed into HUS. A risk-oriented approach based on the testing of children with BD during the summer may represent a potentially beneficial option to improve the sensitivity of STEC surveillance, not only in Italy but also in the context of Europe as a whole.
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Affiliation(s)
- Daniela Loconsole
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy; (D.L.); (F.C.); (M.A.); (D.C.); (A.L.D.R.); (A.M.); (M.Q.)
| | - Mario Giordano
- Pediatric Nephrology and Dialysis Unit, Pediatric Hospital “Giovanni XXIII”, Via Giovanni Amendola, 207, 70126 Bari, Italy;
| | - Francesca Centrone
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy; (D.L.); (F.C.); (M.A.); (D.C.); (A.L.D.R.); (A.M.); (M.Q.)
| | - Marisa Accogli
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy; (D.L.); (F.C.); (M.A.); (D.C.); (A.L.D.R.); (A.M.); (M.Q.)
| | - Daniele Casulli
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy; (D.L.); (F.C.); (M.A.); (D.C.); (A.L.D.R.); (A.M.); (M.Q.)
| | - Anna Lisa De Robertis
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy; (D.L.); (F.C.); (M.A.); (D.C.); (A.L.D.R.); (A.M.); (M.Q.)
| | - Anna Morea
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy; (D.L.); (F.C.); (M.A.); (D.C.); (A.L.D.R.); (A.M.); (M.Q.)
| | - Michele Quarto
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy; (D.L.); (F.C.); (M.A.); (D.C.); (A.L.D.R.); (A.M.); (M.Q.)
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Via Manfredonia, 20, 71121 Foggia, Italy;
| | - Gaia Scavia
- Food Safety, Nutrition and Veterinary Public Health Department, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161 Rome, Italy;
| | - Maria Chironna
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy; (D.L.); (F.C.); (M.A.); (D.C.); (A.L.D.R.); (A.M.); (M.Q.)
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Loconsole D, Accogli M, De Robertis AL, Capozzi L, Bianco A, Morea A, Mallamaci R, Quarto M, Parisi A, Chironna M. Emerging high-risk ST101 and ST307 carbapenem-resistant Klebsiella pneumoniae clones from bloodstream infections in Southern Italy. Ann Clin Microbiol Antimicrob 2020; 19:24. [PMID: 32487201 PMCID: PMC7266126 DOI: 10.1186/s12941-020-00366-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [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: 01/03/2020] [Accepted: 05/25/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Carbapenem-resistant Klebsiella pneumoniae (CR-KP) is an urgent public health issue in Italy. This pattern of resistance is due mainly to dissemination of carbapenemase genes. Molecular characterization of carbapenem-resistant Klebsiella pneumoniae (CR-KP) strains was performed over a three-year period. In-depth analysis was performed on a subset of emerging CR-KP ST101 and ST307 clones. METHODS A prospective study was performed on 691 patients with CR-KP bloodstream infections hospitalized in 19 hospitals located in three large provinces in Southern Italy. Carbapenemase genes were identified via genotyping methods. Multi-locus sequence typing (MLST) and Whole Genome Sequencing (WGS) were carried out on ST101 and ST307 isolates. RESULTS Among the CR-KP isolates, blaKPC was found in 95.6%, blaVIM was found in 3.5%, blaNDM was found in 0.1% and blaOXA-48 was found in 0.1%. The blaKPC-3 variant was identified in all 104 characterized KPC-KP isolates. MLST of 231 representative isolates revealed ST512 in 45.5%, ST101 in 20.3% and ST307 in 18.2% of the isolates. cgMLST of ST307 and ST101 isolates revealed presence of more than one beta-lactam resistance gene. Amino acid substitution in the chromosomal colistin-resistance gene pmrB was found in two ST101 isolates. CONCLUSIONS ST512 is widespread in Southern Italy, but ST101 and ST307 are emerging since they were found in a significant proportion of cases. Aggressive infection control measures and a continuous monitoring of these high-risk clones are necessary to avoid rapid spread of CR-KP, especially in hospital settings.
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Affiliation(s)
- Daniela Loconsole
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Marisa Accogli
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Anna Lisa De Robertis
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Loredana Capozzi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Angelica Bianco
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Anna Morea
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Rosanna Mallamaci
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy
| | - Michele Quarto
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Maria Chironna
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari "Aldo Moro", Bari, Italy.
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Loconsole D, Accogli M, Monaco M, Del Grosso M, De Robertis AL, Morea A, Capozzi L, Del Sambro L, Simone A, De Letteriis V, Quarto M, Parisi A, Chironna M. First detection of autochthonous extensively drug-resistant NDM-1 Pseudomonas aeruginosa ST235 from a patient with bloodstream infection in Italy, October 2019. Antimicrob Resist Infect Control 2020; 9:73. [PMID: 32450907 PMCID: PMC7249406 DOI: 10.1186/s13756-020-00734-5] [Citation(s) in RCA: 3] [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: 03/11/2020] [Accepted: 05/09/2020] [Indexed: 12/15/2022] Open
Abstract
Background Pseudomonas aeruginosa (PA) is one of the most common and serious causes of healthcare-associated bacteremia. The emergence and dissemination of multidrug-resistant (MDR) and extensively drug-resistant (XDR) PA strains pose a major clinical concern. ST235-PA is a high-risk clone which shows a high capacity to acquire antibiotic resistance. Here we describe the first autochthonous New Delhi metallo-β-lactamase (NDM)-producing Pseudomonas aeruginosa ST235 identified in Italy. Case presentation In October 2019, a patient residing in an elderly health care and rehabilitation facility, was hospitalized and died from sepsis caused by an XDR-PA. The strain belonged to the high-risk clone sequence type ST235. Whole genome sequencing (WGS) revealed the presence of genes encoding NDM-1 and multiple β-lactamases, many clinically significant multidrug efflux pump complexes and also the virulence gene ExoU, which is associated with a high cytotoxic phenotype. Conclusions Few strains of NDM-1-PA have been identified worldwide, all belonging to ST235. The combination of ST235 and ExoU is a predictor of highly unfavorable prognosis. The potential spread of these high-risk clones in healthcare settings is worrisome because treatment options are limited. Early identification of high-risk clones could help in outbreaks investigation and infections control.
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Affiliation(s)
- Daniela Loconsole
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari "Aldo Moro", P.zza G. Cesare 11, 70124, Bari, Italy
| | - Marisa Accogli
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari "Aldo Moro", P.zza G. Cesare 11, 70124, Bari, Italy
| | - Monica Monaco
- Department of Infectious Diseases, Istituto Superiore di Sanità, Roma, Italy
| | - Maria Del Grosso
- Department of Infectious Diseases, Istituto Superiore di Sanità, Roma, Italy
| | - Anna Lisa De Robertis
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari "Aldo Moro", P.zza G. Cesare 11, 70124, Bari, Italy
| | - Anna Morea
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari "Aldo Moro", P.zza G. Cesare 11, 70124, Bari, Italy
| | - Loredana Capozzi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Laura Del Sambro
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | | | | | - Michele Quarto
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari "Aldo Moro", P.zza G. Cesare 11, 70124, Bari, Italy
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Maria Chironna
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari "Aldo Moro", P.zza G. Cesare 11, 70124, Bari, Italy.
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Vimercati L, Tafuri S, Chironna M, Loconsole D, Fucilli FIM, Migliore G, Gesualdo L. The COVID-19 hotel for healthcare workers: an Italian best practice. J Hosp Infect 2020; 105:387-388. [PMID: 32425286 PMCID: PMC7229477 DOI: 10.1016/j.jhin.2020.05.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 05/13/2020] [Indexed: 11/26/2022]
Affiliation(s)
- L Vimercati
- Interdisciplinary Department of Medicine, University of Bari, Bari, Italy.,Unit of Occupational Medicine, University Hospital of Bari, Bari, Italy
| | - S Tafuri
- Department of Biomedical Science and Human Oncology, University of Bari, Bari, Italy
| | - M Chironna
- Department of Biomedical Science and Human Oncology, University of Bari, Bari, Italy
| | - D Loconsole
- Department of Biomedical Science and Human Oncology, University of Bari, Bari, Italy
| | - F I M Fucilli
- Prevention-Protection Service, Bari Policlinico General Hospital, Bari, Italy
| | - G Migliore
- Hospital Director, Bari Policlinico General Hospital, Bari, Italy
| | - L Gesualdo
- President, School of Medicine, University Aldo Moro of Bari, Bari, Italy
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46
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Loconsole D, Giordano M, Laforgia N, Torres D, Santangelo L, Carbone V, Parisi A, Quarto M, Scavia G, Chironna M. Correction to: Case-management protocol for bloody diarrhea as a model to reduce the clinical impact of Shiga toxin-producing Escherichia coli infections. Experience from Southern Italy. Eur J Clin Microbiol Infect Dis 2019; 39:549. [PMID: 31858353 DOI: 10.1007/s10096-019-03788-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the originally published article, the name of the 8th author Michele Quarto was inadvertently omitted during typesetting. Author's name is now correctly captured above. Also, the collaborators of the institutional group "Bloody Diarrhea Apulia Working Group" are also given here.
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Affiliation(s)
- Daniela Loconsole
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari Aldo Moro, P.zza G. Cesare 11, 70124, Bari, Italy
| | - Mario Giordano
- Pediatric Nephrology and Dialysis Unit, Pediatric Hospital "Giovanni XXIII", Bari, Italy
| | - Nicola Laforgia
- Department of Biomedical Sciences and Human Oncology, Neonatal Intensive Care Unit, University of Bari Aldo Moro, Bari, Italy
| | - Diletta Torres
- Pediatric Nephrology and Dialysis Unit, Pediatric Hospital "Giovanni XXIII", Bari, Italy
| | - Luisa Santangelo
- Pediatric Nephrology and Dialysis Unit, Pediatric Hospital "Giovanni XXIII", Bari, Italy
| | - Vincenza Carbone
- Pediatric Nephrology and Dialysis Unit, Pediatric Hospital "Giovanni XXIII", Bari, Italy
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Michele Quarto
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari Aldo Moro, P.zza G. Cesare 11, 70124, Bari, Italy
| | - Gaia Scavia
- Food Safety, Nutrition and Veterinary Public Health Department, Istituto Superiore di Sanità, Rome, Italy
| | - Maria Chironna
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari Aldo Moro, P.zza G. Cesare 11, 70124, Bari, Italy.
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Brindicci G, Loconsole D, Carboni D, Genga R, Moschini E, Montorzi G, Viscogliosi F, Pompili M, Agostini M, Ripanti G. Incidence of pertussis in the province of Pesaro-Urbino (Italy). Infez Med 2019; 27:393-397. [PMID: 31846988] [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: 06/10/2023]
Abstract
Pertussis vaccination coverage in the Marche region is one of the lowest in Italy, with the province of Pesaro-Urbino remaining stable below 95% coverage since at least 2013. In this paper, we retrospectively analyzed all whooping cough notification cards arriving at the prevention department of the Area Vasta 1 Health Office in the Marche region and relating to the Pesaro-Urbino province (Italy). Between 2012 and 2017, there were 28 reported cases of pertussis with a peak in 2016 (11 cases, of which seven were in Urbino). The 28 patients were mostly male (65%), and had a mean age of 9 years. Three of these were not Italian. Between 2012 and 2017, the district of Pesaro reported the highest number of cases (almost 46.5% of the total), followed by Urbino (28.5%) and Fano (25%). The average incidence in the province in the period in question, still under 2 cases/100,000 inhabitants, arrived in 2016 at 4 cases/100,000 inhabitants. In particular, in Urbino there was an unforeseen incidence >8 cases/100,000 inhabitants. There were no deaths, although two children (both under 12 months of age) were hospitalized. Our data confirm that in 2016 there was a pertussis epidemic in Urbino (Italy).
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Affiliation(s)
- Gaetano Brindicci
- U.O. Pediatria e Neonatologia, Ospedale Santa Maria della Misericordia, Urbino (PU), Italy
| | - Daniela Loconsole
- Dipartimento di Scienze Biomediche e Oncologia Umana - Sezione di Igiene, AOU Consorziale Policlinico di Bari, Bari, Italy
| | - Danilo Carboni
- U.O. Pediatria e Neonatologia, Ospedale Santa Maria della Misericordia, Urbino (PU), Italy
| | - Roberto Genga
- U.O. Pediatria e Neonatologia, Ospedale Santa Maria della Misericordia, Urbino (PU), Italy
| | - Eleonora Moschini
- U.O. Pediatria e Neonatologia, Ospedale Santa Maria della Misericordia, Urbino (PU), Italy
| | - Giulia Montorzi
- U.O. Pediatria e Neonatologia, Ospedale Santa Maria della Misericordia, Urbino (PU), Italy
| | - Felicetta Viscogliosi
- U.O. Pediatria e Neonatologia, Ospedale Santa Maria della Misericordia, Urbino (PU), Italy
| | - Marco Pompili
- Dipartimento di Prevenzione Area Vasta 1, Azienda Sanitaria Unica Regione Marche, Fano (PU), Italy
| | - Massimo Agostini
- Dipartimento di Prevenzione Area Vasta 1, Azienda Sanitaria Unica Regione Marche, Fano (PU), Italy
| | - Gabriele Ripanti
- U.O. Pediatria e Neonatologia, Ospedale Santa Maria della Misericordia, Urbino (PU), Italy
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Loconsole D, Giordano M, Laforgia N, Torres D, Santangelo L, Carbone V, Parisi A, Quarto M, Scavia G, Chironna M. Case-management protocol for bloody diarrhea as a model to reduce the clinical impact of Shiga toxin-producing Escherichia coli infections. Experience from Southern Italy. Eur J Clin Microbiol Infect Dis 2019; 39:539-547. [PMID: 31776873 PMCID: PMC7040055 DOI: 10.1007/s10096-019-03755-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 10/27/2019] [Indexed: 01/19/2023]
Abstract
To describe an operating protocol for bloody diarrhea (BD) in a pediatric population as a rapid response to a public health threat represented by an excess of pediatric HUS cases in the Apulia region (Southern Italy) starting from 2013. The protocol was set up with the goal of correct clinical management of Shiga toxin-producing Escherichia coli (STEC) infections, reductions in subsequent cases of hemolytic uremic syndrome (HUS), and improved short- and long-term disease outcomes. The protocol consisted of rapid hospitalization of children with bloody diarrhea (BD), hematochemical laboratory tests every 12–24 hours, and prompt laboratory diagnosis of STEC. No antibiotics were recommended until diagnosis. Children positive for STEC infections underwent early vigorous volume expansion. In June–December 2018, 438 children with BD were hospitalized, of which 53 (12.1%) had a STEC infection. The most common serogroups were O26 (36.1%), O111 (23.0%), and O157 (14.8%). Thirty-one samples carried the stx2 gene. Four cases evolved into HUS (7.5%), all with favorable outcome despite neurological involvement in two cases. Prompt and accurate laboratory diagnosis of STEC infections is of the utmost importance in patients with BD for correct clinical management. The strict adherence to the protocol could reduce the progression rate of STEC infections to HUS and prevents complications. Enhanced BD surveillance may help reduce cases of pediatric HUS in Southern Italy.
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Affiliation(s)
- Daniela Loconsole
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari Aldo Moro, P.zza G. Cesare 11, 70124, Bari, Italy
| | - Mario Giordano
- Pediatric Nephrology and Dialysis Unit, Pediatric Hospital "Giovanni XXIII", Bari, Italy
| | - Nicola Laforgia
- Department of Biomedical Sciences and Human Oncology, Neonatal Intensive Care Unit, University of Bari Aldo Moro, Bari, Italy
| | - Diletta Torres
- Pediatric Nephrology and Dialysis Unit, Pediatric Hospital "Giovanni XXIII", Bari, Italy
| | - Luisa Santangelo
- Pediatric Nephrology and Dialysis Unit, Pediatric Hospital "Giovanni XXIII", Bari, Italy
| | - Vincenza Carbone
- Pediatric Nephrology and Dialysis Unit, Pediatric Hospital "Giovanni XXIII", Bari, Italy
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Michele Quarto
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari Aldo Moro, P.zza G. Cesare 11, 70124, Bari, Italy
| | - Gaia Scavia
- Food Safety, Nutrition and Veterinary Public Health Department, Istituto Superiore di Sanità, Rome, Italy
| | - Maria Chironna
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari Aldo Moro, P.zza G. Cesare 11, 70124, Bari, Italy.
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Loconsole D, De Robertis AL, Morea A, Casulli D, Mallamaci R, Baldacci S, Centrone F, Bruno V, Quarto M, Accogli M, Chironna M. High Public-Health Impact in an Influenza-B-Mismatch Season in Southern Italy, 2017-2018. Biomed Res Int 2019; 2019:4643260. [PMID: 31531353 PMCID: PMC6720359 DOI: 10.1155/2019/4643260] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 08/01/2019] [Indexed: 12/25/2022]
Abstract
BACKGROUND Yearly influenza epidemics have considerable effects on public health worldwide. The 2017-2018 influenza season in Italy was of greater severity than previous seasons. The aim of this study was to describe the 2017-2018 influenza season in Southern Italy and the molecular characteristics of the circulating viral strains. METHODS The incidence of influenza-like illness (ILI) was analysed. Nasopharyngeal swabs collected from patients with ILI from week 46/2017 to week 17/2018 were tested to identify influenza A viruses (IAV) and influenza B viruses (IBV). Sequencing and phylogenetic analysis of haemagglutinin genes were also performed on 73 positive samples (35 IBV, 36 IAV H1, and 2 IAV H3 strains). RESULTS During the 2017-2018 season, the peak incidence was 14.32 cases per 1,000 inhabitants. IBV strains were identified in 71.0% of cases. The 35 characterised IBV strains belonged to Yamagata lineage clade 3, the 36 A/H1N1pdm09 strains clustered with the genetic subgroup 6B.1, and the 2 A/H3N2 strains clustered with the genetic subgroup 3C.2a. Intensive-care unit (ICU) admission was required in 50 cases of acute respiratory distress syndrome (ARDS). Among the >64-year age group, 18 out of 26 ICU-ARDS cases (69.2%) were caused by IBV, and 14 of these (77.8%) were B/Yamagata lineage. CONCLUSIONS The 2017-2018 influenza season was one of the most severe in a decade in Southern Italy. IBV mismatch between the trivalent vaccine and the circulating strains occurred. The high number of ICU-ARDS cases caused by B/Yamagata strains in the >64-year age group suggests that further data on the effectiveness of the available influenza vaccines are needed to determine the best way to protect the elderly against both IBV lineages.
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Affiliation(s)
- Daniela Loconsole
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Anna Lisa De Robertis
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Anna Morea
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Daniele Casulli
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Rosanna Mallamaci
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Via Orabona 4, 70124 Bari, Italy
| | - Simona Baldacci
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Francesca Centrone
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Viviana Bruno
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Michele Quarto
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Marisa Accogli
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
| | - Maria Chironna
- Department of Biomedical Sciences and Human Oncology-Hygiene Section, University of Bari, Piazza G. Cesare 11, 70124 Bari, Italy
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Diakoudi G, Lanave G, Catella C, Medici MC, De Conto F, Calderaro A, Loconsole D, Chironna M, Bonura F, Giammanco GM, Bányai K, Tohma K, Parra GI, Martella V, De Grazia S. Analysis of GII.P7 and GII.6 noroviruses circulating in Italy during 2011-2016 reveals a replacement of lineages and complex recombination history. Infect Genet Evol 2019; 75:103991. [PMID: 31394293 DOI: 10.1016/j.meegid.2019.103991] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 08/01/2019] [Accepted: 08/02/2019] [Indexed: 01/22/2023]
Abstract
Noroviruses are important human enteric pathogens and monitoring their genetic diversity is important for epidemiological surveillance, vaccine development, and understanding of RNA viruses evolution. Epidemiological investigations have revealed that genogroup II, genotype 6 noroviruses (GII.6) are common agents of gastroenteritis. Upon sequencing of the ORF2 (encoding the viral capsid), GII.6 viruses have been distinguished into three variants. Sentinel hospital-based surveillance in Italy revealed that GII.6 noroviruses were the second most common capsid genotype in 2015, mostly in association with a GII.P7 ORF1 (encoding the viral polymerase). Upon molecular characterization of the ORF1 and ORF2, the GII.P7_GII.6 epidemic viruses circulating in 2014-2015 (variant GII.6b) were different from those that circulated sporadically in 2011-2013 (variant GII.6a). Analysis of the ORF1 (GII.P7) and ORF2 (GII.6) sequences available in the databases unveiled marked genetic diversity and peculiarities in the phylogenetic segregation patterns, suggesting multiple recombination events. Phylogenetic analyses suggest that recent GII.P7_GII.6b viruses were circulating as early as 2008, and formed a genetically homogenous group that emerged globally.
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Affiliation(s)
- Georgia Diakoudi
- Dipartimento di Medicina Veterinaria, Università Aldo Moro di Bari, Italy
| | - Gianvito Lanave
- Dipartimento di Medicina Veterinaria, Università Aldo Moro di Bari, Italy
| | - Cristiana Catella
- Dipartimento di Medicina Veterinaria, Università Aldo Moro di Bari, Italy
| | | | - Flora De Conto
- Dipartimento di Medicina e Chirurgia, Università degli Studi di Parma, Italy
| | - Adriana Calderaro
- Dipartimento di Medicina e Chirurgia, Università degli Studi di Parma, Italy
| | - Daniela Loconsole
- Dipartimento di Scienze Biomediche e Oncologia Umana, Università Aldo Moro di Bari, Italy
| | - Maria Chironna
- Dipartimento di Scienze Biomediche e Oncologia Umana, Università Aldo Moro di Bari, Italy
| | - Floriana Bonura
- Dipartimento di Medicina Veterinaria, Università Aldo Moro di Bari, Italy
| | - Giovanni Maurizio Giammanco
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Italy
| | - Kristián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Kentaro Tohma
- Division of Viral Products, Food and Drug Administration, Silver Spring, MD, USA
| | | | - Vito Martella
- Dipartimento di Medicina Veterinaria, Università Aldo Moro di Bari, Italy.
| | - Simona De Grazia
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Italy
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