1
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Braeye T, Proesmans K, Van Cauteren D, Brondeel R, Hens N, Vermeiren E, Hammami N, Rosas A, Taame A, André E, Cuypers L. Personal characteristics and transmission dynamics associated with SARS-CoV-2 semi-quantitative PCR test results: an observational study from Belgium, 2021-2022. Front Public Health 2024; 12:1429021. [PMID: 39319296 PMCID: PMC11420023 DOI: 10.3389/fpubh.2024.1429021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 08/20/2024] [Indexed: 09/26/2024] Open
Abstract
Introduction Following harmonization efforts by the Belgian National Reference Center for SARS-CoV-2, semi-quantitative PCR test (SQ-PCR) results, used as a proxy for viral load, were routinely collected after performing RT-qPCR tests. Methods We investigated both the personal characteristics associated with SQ-PCR results and the transmission dynamics involving these results. We used person-level laboratory test data and contact tracing data collected in Belgium from March 2021 to February 2022. Personal characteristics (age, sex, vaccination, and laboratory-confirmed prior infection) and disease stage by date of symptom onset were analyzed in relation to SQ-PCR results using logistic regression. Vaccine effectiveness (VE) against a high viral load (≥107 copies/mL) was estimated from the adjusted probabilities. Contact tracing involves the mandatory testing of high-risk exposure contacts (HREC) after contact with an index case. Odds ratios for test positivity and high viral load in HREC were calculated based on the SQ-PCR result of the index case using logistic regression models adjusted for age, sex, immunity status (vaccination, laboratory-confirmed prior infection), variant (Alpha, Delta, Omicron), calendar time, and contact tracing covariates. Results We included 909,157 SQ-PCR results of COVID-19 cases, 379,640 PCR results from index cases, and 72,052 SQ-PCR results of HREC. High viral load was observed more frequently among recent cases, symptomatic cases, cases over 25 years of age, and those not recently vaccinated (>90 days). The vaccine effectiveness (VE) of the primary schedule in the first 30 days after vaccination was estimated at 47.3% (95%CI 40.8-53.2) during the Delta variant period. A high viral load in index cases was associated with an increased test positivity in HREC (OR 2.7, 95%CI 2.62-2.79) and, among those testing positive, an increased likelihood of a high viral load (OR 2.84, 95%CI 2.53-3.19).
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Affiliation(s)
- Toon Braeye
- Epidemiology of Infectious Diseases, Sciensano, Brussels, Belgium
- I-BioStat, Data Science Institute, Hasselt University, Hasselt, Belgium
| | - Kristiaan Proesmans
- Faculty of Pharmaceutical Sciences, Department of Bio-analysis, Ghent University, Ghent, Belgium
| | | | - Ruben Brondeel
- Epidemiology of Infectious Diseases, Sciensano, Brussels, Belgium
| | - Niel Hens
- I-BioStat, Data Science Institute, Hasselt University, Hasselt, Belgium
- Centre for Health Economic Research and Modelling Infectious Diseases, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Elias Vermeiren
- Epidemiology of Infectious Diseases, Sciensano, Brussels, Belgium
| | - Naïma Hammami
- Department of Care, Infection Prevention and Control, Flemish Community, Brussels, Belgium
| | - Angel Rosas
- Direction Surveillance des Maladies Infectieuses, Agence out une Vie de Qualité (AVIQ), Charleroi, Belgium
| | - Adrae Taame
- Cellule de médecine préventive- Direction santé et aide aux personnes – Vivalis/Cocom, Brussels, Belgium
| | - Emmanuel André
- Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical Microbiology, KU Leuven, Leuven, Belgium
| | - Lize Cuypers
- Department of Laboratory Medicine, National Reference Centre for Respiratory Pathogens, University Hospitals Leuven, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical Microbiology, KU Leuven, Leuven, Belgium
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2
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Demey M, Bruyneel A, Chatzis O, Christiaens C, Cossey V, De Crombrugghe G, De Lille L, Goetghebuer T, Gueulette E, Hainaut M, Heijmans C, Hubinont H, Lé PQ, Lecomte L, Mattijs I, Mignon C, Mondovits B, Rodesch M, Rooze S, Schelstraete P, Stroobant D, Thielemans L, Thomas I, Valbona SK, Van Damme E, Van der Linden D, Van Praet J, Vermeulen F, Weynants D, Tilmanne A. SARS-CoV-2 Infection in Children Less Than Forty Days Hospitalized in Belgium Between 2020 and 2022. Pediatr Infect Dis J 2024; 43:e307-e309. [PMID: 38754003 DOI: 10.1097/inf.0000000000004400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Our study aimed to assess the severity of severe acute respiratory syndrome coronavirus 2 infection in hospitalized infants under 40 days old, across 21 Belgian hospitals between 2020 and 2022. Of the 365 infants studied, 14.2% needed respiratory support. The median hospital stay was 3 days (interquartile range, 2-4), and there were no deaths. Infection severity was similar during the Omicron and Alpha/Delta periods.
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Affiliation(s)
- Milena Demey
- From the Department of Paediatrics, Université libre de Bruxelles, Brussels, Belgium
| | - Arnaud Bruyneel
- Infection Prevention and Control Nurse (HOST)|Réseau Helora, CHU Tivoli, La Louvière, Belgium
- Health Economics, Hospital Management and Nursing Research Department, School of Public Health, Université libre de Bruxelles
| | - Olga Chatzis
- Paediatric Infectious Diseases Unit, Specialized Paediatrics Service, Department of Paediatrics, Cliniques universitaires Saint-Luc, UCLouvain, Brussels, Belgium
| | | | - Veerle Cossey
- Neonatal Intensive Care Unit, Infection Control Department, University Hospitals Leuven, Leuven, Belgium
| | | | - Lieve De Lille
- Department of Paediatrics, O.L.V. van Lourdes Ziekenhuis Waregem, Waregem, Belgium
| | - Tessa Goetghebuer
- Department of Paediatrics, CHU Saint-Pierre, Université libre de Bruxelles, Brussels, Belgium
| | | | - Marc Hainaut
- Department of Paediatrics, CHU Saint-Pierre, Université libre de Bruxelles, Brussels, Belgium
| | - Catherine Heijmans
- Department of Paediatrics, Hôpital de La Louvière - Site Jolimont - HELORA, La Louvière, Belgium
| | - Hortense Hubinont
- Department of Paediatrics, Hôpital Civil Marie Curie, Charleroi, Belgium
| | - Phu-Quoc Lé
- Department of Paediatrics, Hôpital IRIS Sud, Site Etterbeek-Ixelles, Brussels, Belgium
| | - Laurie Lecomte
- Department of Paediatrics, Hôpital de La Louvière - Site Jolimont - HELORA, La Louvière, Belgium
| | - Inge Mattijs
- Department of Paediatrics, AZ Delta, Roeselare, Belgium
| | - Céline Mignon
- Department of Paediatric Infectious Diseases, HUB Hôpital Universitaire des Enfants Reine Fabiola (HUDERF), Université libre de Bruxelles
| | | | - Marine Rodesch
- Department of Paediatrics, HUB Hôpital Erasme, Université libre de Bruxelles
| | - Shancy Rooze
- Pediatric Intensive Care Unit, HUB Hôpital Universitaire des Enfants Reine Fabiola (HUDERF), Université libre de Bruxelles, Brussels, Belgium
| | - Petra Schelstraete
- Department of Internal Medicine and Paediatrics, Ghent University Hospital, Ghent, Belgium
| | - Diane Stroobant
- Department of Paediatrics, Grand Hôpital de Charleroi, Charleroi, Belgium
| | | | - Ingrid Thomas
- Department of Paediatrics, CHU Ambroise Paré, Mons, Belgium
| | | | - Emmi Van Damme
- Department of Paediatrics, ZNA Jan Palfijn, Merksem, Belgium
| | - Dimitri Van der Linden
- Paediatric Infectious Diseases Unit, Specialized Paediatrics Service, Department of Paediatrics, Cliniques universitaires Saint-Luc, UCLouvain, Brussels, Belgium
| | - Jens Van Praet
- Department of Nephrology and Infectious Diseases, AZ Sint-Jan Brugge-Oostende AV, Brugge, Belgium
| | - Françoise Vermeulen
- Pediatric Intensive Care Unit, HUB Hôpital Universitaire des Enfants Reine Fabiola (HUDERF), Université libre de Bruxelles, Brussels, Belgium
| | - David Weynants
- Department of Paediatrics, CHU UCL Namur - Site Saint Elisabeth, Namur, Belgium
| | - Anne Tilmanne
- Department of Paediatrics, Hôpital Civil Marie Curie, Charleroi, Belgium
- Department of Paediatrics, ZNA Jan Palfijn, Merksem, Belgium
- Department of Infectious Diseases, CHU Tivoli, La Louvière, Belgium
- Department of Infectious Diseases, Université libre de Bruxelles, Brussels, Belgium
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3
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El Moussaoui M, Bontems S, Meex C, Hayette MP, Lejeune M, Hong SL, Dellicour S, Moutschen M, Cambisano N, Renotte N, Bours V, Darcis G, Artesi M, Durkin K. Intrahost evolution leading to distinct lineages in the upper and lower respiratory tracts during SARS-CoV-2 prolonged infection. Virus Evol 2024; 10:veae073. [PMID: 39399151 PMCID: PMC11470753 DOI: 10.1093/ve/veae073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 07/18/2024] [Accepted: 08/29/2024] [Indexed: 10/15/2024] Open
Abstract
Accumulating evidence points to persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in immunocompromised individuals as a source of novel lineages. While intrahost evolution of the virus in chronically infected patients has previously been reported, existing knowledge is primarily based on samples from the nasopharynx. In this study, we investigate the intrahost evolution and genetic diversity that accumulated during a prolonged SARS-CoV-2 infection with the Omicron BF.7 sublineage, which is estimated to have persisted for >1 year in an immunosuppressed patient. Based on the sequencing of eight samples collected at six time points, we identified 87 intrahost single-nucleotide variants, 2 indels, and a 362-bp deletion. Our analysis revealed distinct viral genotypes in the nasopharyngeal (NP), endotracheal aspirate, and bronchoalveolar lavage samples. This suggests that NP samples may not offer a comprehensive representation of the overall intrahost viral diversity. Our findings not only demonstrate that the Omicron BF.7 sublineage can further diverge from its already exceptionally mutated state but also highlight that patients chronically infected with SARS-CoV-2 can develop genetically specific viral populations across distinct anatomic compartments. This provides novel insights into the intricate nature of viral diversity and evolution dynamics in persistent infections.
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Affiliation(s)
- Majdouline El Moussaoui
- Department of Infectious Diseases and General Internal Medicine, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium
| | - Sebastien Bontems
- Department of Microbiology, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium
| | - Cecile Meex
- Department of Microbiology, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium
| | - Marie-Pierre Hayette
- Department of Microbiology, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium
| | - Marie Lejeune
- Department of Hematology, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium
| | - Samuel L Hong
- Department of Microbiology, Immunology and Transplantation, Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, 49 Herestraat, Leuven 3000, Belgium
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, 49 Herestraat, Leuven 3000, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 50 Avenue Franklin Roosevelt, Bruxelles 1050, Belgium
| | - Michel Moutschen
- Department of Infectious Diseases and General Internal Medicine, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium
| | - Nadine Cambisano
- Department of Human Genetics, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium
- Laboratory of Human Genetics, GIGA Institute, University of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium
| | - Nathalie Renotte
- Department of Human Genetics, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium
- Laboratory of Human Genetics, GIGA Institute, University of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium
| | - Vincent Bours
- Department of Human Genetics, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium
- Laboratory of Human Genetics, GIGA Institute, University of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium
| | - Gilles Darcis
- Department of Infectious Diseases and General Internal Medicine, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium
| | - Maria Artesi
- Department of Human Genetics, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium
- Laboratory of Human Genetics, GIGA Institute, University of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium
| | - Keith Durkin
- Department of Human Genetics, University Hospital of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium
- Laboratory of Human Genetics, GIGA Institute, University of Liège, 1 Avenue de l'Hôpital, Liège 4000, Belgium
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4
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De Muylder G, Laisnez V, Stefani G, Boulouffe C, Faes C, Hammami N, Hubin P, Molenberghs G, Sans J, van de Konijnenburg C, Van der Borght S, Brondeel R, Stassijns J, Lernout T. Translating the COVID-19 epidemiological situation into policies and measures: the Belgian experience. Front Public Health 2024; 12:1306361. [PMID: 38645450 PMCID: PMC11026715 DOI: 10.3389/fpubh.2024.1306361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 03/20/2024] [Indexed: 04/23/2024] Open
Abstract
The COVID-19 pandemic led to sustained surveillance efforts, which made unprecedented volumes and types of data available. In Belgium, these data were used to conduct a targeted and regular assessment of the epidemiological situation. In addition, management tools were developed, incorporating key indicators and thresholds, to define risk levels and offer guidance to policy makers. Categorizing risk into various levels provided a stable framework to monitor the COVID-19 epidemiological situation and allowed for clear communication to authorities. Although translating risk levels into specific public health measures has remained challenging, this experience was foundational for future evaluation of the situation for respiratory infections in general, which, in Belgium, is now based on a management tool combining different data sources.
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Affiliation(s)
| | - Valeska Laisnez
- Department of Epidemiology and Public Health, Sciensano, Brussels, Belgium
| | - Giulietta Stefani
- Department of Epidemiology and Public Health, Sciensano, Brussels, Belgium
| | | | - Christel Faes
- Data Science Institute, I-BioStat, Hasselt University, Hasselt, Belgium
| | - Naïma Hammami
- Department of Care, Team Infection Prevention and Vaccination, Brussels, Belgium
| | - Pierre Hubin
- Department of Epidemiology and Public Health, Sciensano, Brussels, Belgium
| | - Geert Molenberghs
- Data Science Institute, I-BioStat, Hasselt University, Hasselt, Belgium
- Faculty of Medicine, Department of Public Health and Primary Care, L-BioStat, Leuven, Belgium
| | - Jasper Sans
- Department of Infectious Disease Prevention, Brussels, Belgium
| | | | | | - Ruben Brondeel
- Department of Epidemiology and Public Health, Sciensano, Brussels, Belgium
| | | | - Tinne Lernout
- Department of Epidemiology and Public Health, Sciensano, Brussels, Belgium
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5
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Janssen R, Cuypers L, Laenen L, Keyaerts E, Beuselinck K, Janssenswillen S, Slechten B, Bode J, Wollants E, Van Laethem K, Rector A, Bloemen M, Sijmons A, de Schaetzen N, Capron A, Van Baelen K, Pascal T, Vermeiren C, Bureau F, Vandesompele J, De Smet P, Uten W, Malonne H, Kerkhofs P, De Cock J, Matheeussen V, Verhasselt B, Gillet L, Detry G, Bearzatto B, Degosserie J, Henin C, Pairoux G, Maes P, Van Ranst M, Lagrou K, Dequeker E, André E. Nationwide quality assurance of high-throughput diagnostic molecular testing during the SARS-CoV-2 pandemic: role of the Belgian National Reference Centre. Virol J 2024; 21:40. [PMID: 38341597 PMCID: PMC10858549 DOI: 10.1186/s12985-024-02308-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Since the onset of the coronavirus disease (COVID-19) pandemic in Belgium, UZ/KU Leuven has played a crucial role as the National Reference Centre (NRC) for respiratory pathogens, to be the first Belgian laboratory to develop and implement laboratory developed diagnostic assays for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) and later to assess the quality of commercial kits. To meet the growing demand for decentralised testing, both clinical laboratories and government-supported high-throughput platforms were gradually deployed across Belgium. Consequently, the role of the NRC transitioned from a specialised testing laboratory to strengthening capacity and coordinating quality assurance. Here, we outline the measures taken by the NRC, the national public health institute Sciensano and the executing clinical laboratories to ensure effective quality management of molecular testing throughout the initial two years of the pandemic (March 2020 to March 2022).
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Affiliation(s)
- Reile Janssen
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000, Leuven, Belgium.
| | - Lize Cuypers
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000, Leuven, Belgium
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000, Leuven, Belgium
| | - Lies Laenen
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000, Leuven, Belgium
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000, Leuven, Belgium
| | - Els Keyaerts
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000, Leuven, Belgium
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000, Leuven, Belgium
| | - Kurt Beuselinck
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000, Leuven, Belgium
| | - Sunita Janssenswillen
- Federal Testing Platform COVID-19, Department of Laboratory Medicine, University Hospitals Leuven, 3000, Leuven, Belgium
| | - Bram Slechten
- Federal Testing Platform COVID-19, Department of Laboratory Medicine, University Hospitals Leuven, 3000, Leuven, Belgium
| | - Jannes Bode
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000, Leuven, Belgium
| | - Elke Wollants
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
| | - Kristel Van Laethem
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
| | - Annabel Rector
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
| | - Mandy Bloemen
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
| | - Anke Sijmons
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000, Leuven, Belgium
| | - Nathalie de Schaetzen
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000, Leuven, Belgium
| | - Arnaud Capron
- Quality of Laboratories Unit, Scientific Directorate of Biological Health Risks, Sciensano, 1000, Brussels, Belgium
| | - Kurt Van Baelen
- Janssen Pharmaceutica N.V, Johnson & Johnson, 2340, Beerse, Belgium
| | | | | | - Fabrice Bureau
- Laboratory of Cellular and Molecular Immunology, GIGA Institute, University of Liège, 4000, Liège, Belgium
| | - Jo Vandesompele
- Biogazelle, a CellCarta Company, Technologiepark Zwijnaarde, 9052, Zwijnaarde, Belgium
| | | | | | - Hugues Malonne
- Federal Agency for Medicines and Health Products (FAGG-AFMPS), 1210, Brussels, Belgium
- Department of Pharmacology, Pharmacotherapy and Pharmaceutical Care, Faculty of Pharmacy, Université Libre de Bruxelles, 1070, Brussels, Belgium
- Department of Biomedical Sciences, Namur Research Institute for Life Sciences, University of Namur, 5000, Namur, Belgium
| | - Pierre Kerkhofs
- Federal Public Service Public Health, Safety of the Food Chain and the Environment, 1210, Brussels, Belgium
| | - Jo De Cock
- National Institute for Health and Disability Insurance (RIZIV/INAMI), 1150, Brussels, Belgium
| | - Veerle Matheeussen
- Federal Testing Platform COVID-19, University Hospitals Antwerp, 2650, Edegem, Belgium
| | - Bruno Verhasselt
- Federal Testing Platform COVID-19, Department of Laboratory Medicine, Ghent University and Ghent University Hospital, 9000, Ghent, Belgium
| | - Laurent Gillet
- Federal Testing Platform COVID-19, University of Liège, 4000, Liège, Belgium
| | - Gautier Detry
- Federal Testing Platform COVID-19, Laboratory of Clinical Biology, Pole Hospitalier Jolimont, 7100, La Louvière, Belgium
| | - Bertrand Bearzatto
- Federal Testing Platform COVID-19, Centre Des Technologies Moléculaires Appliquées (CTMA), Institute of Experimental and Clinical Research (IREC), Cliniques Universitaires Saint-Luc and Université Catholique de Louvain (UCLouvain), 1200, Brussels, Belgium
| | - Jonathan Degosserie
- Federal Testing Platform COVID-19, Department of Laboratory Medicine, CHU UCL Namur, 5530, Yvoir, Belgium
| | - Coralie Henin
- Federal Testing Platform COVID-19, Université Libre de Bruxelles, 1070, Brussels, Belgium
| | - Gregor Pairoux
- Quality of Laboratories Unit, Scientific Directorate of Biological Health Risks, Sciensano, 1000, Brussels, Belgium
| | - Piet Maes
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
| | - Marc Van Ranst
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000, Leuven, Belgium
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
| | - Katrien Lagrou
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000, Leuven, Belgium
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000, Leuven, Belgium
| | - Elisabeth Dequeker
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000, Leuven, Belgium
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, University of Leuven, 3000, Leuven, Belgium
| | - Emmanuel André
- National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000, Leuven, Belgium
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000, Leuven, Belgium
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6
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Kremer C, Willem L, Boone J, Arrazola de Oñate W, Hammami N, Faes C, Hens N. Key performance indicators of COVID-19 contact tracing in Belgium from September 2020 to December 2021. PLoS One 2023; 18:e0292346. [PMID: 37862313 PMCID: PMC10588862 DOI: 10.1371/journal.pone.0292346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 09/18/2023] [Indexed: 10/22/2023] Open
Abstract
The goal of tracing, testing, and quarantining contacts of infected individuals is to contain the spread of infectious diseases, a strategy widely used during the COVID-19 pandemic. However, limited research exists on the effectiveness of contact tracing, especially with regard to key performance indicators (KPIs), such as the proportion of cases arising from previously identified contacts. In our study, we analyzed contact tracing data from Belgium collected between September 2020 and December 2021 to assess the impact of contact tracing on SARS-CoV-2 transmission and understand its characteristics. Among confirmed cases involved in contact tracing in the Flemish and Brussels-Capital regions, 19.1% were previously identified as close contacts and were aware of prior exposure. These cases, referred to as 'known' to contact tracing operators, reported on average fewer close contacts compared to newly identified individuals (0.80 versus 1.05), resulting in fewer secondary cases (0.23 versus 0.28). Additionally, we calculated the secondary attack rate, representing infections per contact, which was on average lower for the 'known' cases (0.22 versus 0.25) between December 2020 and August 2021. These findings indicate the effectiveness of contact tracing in Belgium in reducing SARS-CoV-2 transmission. Although we were unable to quantify the exact number of prevented cases, our findings emphasize the importance of contact tracing as a public health measure. In addition, contact tracing data provide indications of potential shifts in transmission patterns among different age groups associated with emerging variants of concern and increasing vaccination rates.
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Affiliation(s)
- Cécile Kremer
- Interuniversity Institute for Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, Hasselt, Belgium
| | - Lander Willem
- Centre for Health Economics Research and Modelling Infectious Diseases, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- Family Medicine and Population Health, University of Antwerp, Antwerp, Belgium
| | - Jorden Boone
- KPMG Advisory, Public Sector Practice, Zaventem, Belgium
| | - Wouter Arrazola de Oñate
- Belgian Lung and Tuberculosis Association, Brussels, Belgium
- Flemish Association for Respiratory Health and Tuberculosis, Leuven, Belgium
| | - Naïma Hammami
- Department of Infectious Disease Prevention and Control, Department of Care, Flemish Region, Brussels, Belgium
| | - Christel Faes
- Interuniversity Institute for Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, Hasselt, Belgium
| | - Niel Hens
- Interuniversity Institute for Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, Hasselt, Belgium
- Centre for Health Economics Research and Modelling Infectious Diseases, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
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7
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Denayer S, Dufrasne FE, Monsieurs B, van Eycken R, Houben S, Seyler L, Demuyser T, van Nedervelde E, Bourgeois M, Delaere B, Magerman K, Jouck D, Lissoir B, Sion C, Reynders M, Petit E, Dauby N, Hainaut M, Laenen L, Maes P, Baele G, Dellicour S, Cuypers L, André E, Couvreur S, Brondeel R, Barbezange C, Bossuyt N, van Gucht S. Genomic monitoring of SARS-CoV-2 variants using sentinel SARI hospital surveillance. Influenza Other Respir Viruses 2023; 17:e13202. [PMID: 37840842 PMCID: PMC10570899 DOI: 10.1111/irv.13202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 10/17/2023] Open
Abstract
Background To support the COVID-19 pandemic response, many countries, including Belgium, implemented baseline genomic surveillance (BGS) programs aiming to early detect and characterize new SARS-CoV-2 variants. In parallel, Belgium maintained a sentinel network of six hospitals that samples patients with severe acute respiratory infections (SARI) and integrated SARS-CoV-2 detection within a broader range of respiratory pathogens. We evaluate the ability of the SARI surveillance to monitor general trends and early signals of viral genetic evolution of SARS-CoV-2 and compare it with the BGS as a reference model. Methods Nine-hundred twenty-five SARS-CoV-2 positive samples from patients fulfilling the Belgian SARI definition between January 2020 and December 2022 were sequenced using the ARTIC Network amplicon tiling approach on a MinION platform. Weekly variant of concern (VOC) proportions and types were compared to those that were circulating between 2021 and 2022, using 96,251 sequences of the BGS. Results SARI surveillance allowed timely detection of the Omicron (BA.1, BA.2, BA.4, and BA.5) and Delta (B.1.617.2) VOCs, with no to 2 weeks delay according to the start of their epidemic growth in the Belgian population. First detection of VOCs B.1.351 and P.1 took longer, but these remained minor in Belgium. Omicron BA.3 was never detected in SARI surveillance. Timeliness could not be evaluated for B.1.1.7, being already major at the start of the study period. Conclusions Genomic surveillance of SARS-CoV-2 using SARI sentinel surveillance has proven to accurately reflect VOCs detected in the population and provides a cost-effective solution for long-term genomic monitoring of circulating respiratory viruses.
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Affiliation(s)
- Sarah Denayer
- Viral Diseases, National Influenza Centre, Scientific Directorate of Infectious Diseases in HumansSciensanoUkkelBelgium
| | - François E. Dufrasne
- Viral Diseases, National Influenza Centre, Scientific Directorate of Infectious Diseases in HumansSciensanoUkkelBelgium
| | - Bert Monsieurs
- Viral Diseases, National Influenza Centre, Scientific Directorate of Infectious Diseases in HumansSciensanoUkkelBelgium
| | - Reinout van Eycken
- Viral Diseases, National Influenza Centre, Scientific Directorate of Infectious Diseases in HumansSciensanoUkkelBelgium
| | - Sarah Houben
- Observational Clinical Trials, Scientific Directorate of infectious Diseases in HumansSciensanoUkkelBelgium
| | - Lucie Seyler
- Department of Internal Medicine and Infectiology, Universitair Ziekenhuis Brussel (UZB)Vrije Universiteit Brussel (VUB)BrusselsBelgium
| | - Thomas Demuyser
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel (UZB)Vrije Universiteit Brussel (VUB)BrusselsBelgium
- AIMS Lab, Center for Neurosciences, Faculty of Medicine and PharmacyVrije Universiteit Brussel (VUB)BrusselsBelgium
| | - Els van Nedervelde
- Department of Internal Medicine and Infectiology, Universitair Ziekenhuis Brussel (UZB)Vrije Universiteit Brussel (VUB)BrusselsBelgium
| | | | | | - Koen Magerman
- Infection Control and Clinical LaboratoryJessa ZiekenhuisHasseltBelgium
- Department of Immunology and InfectionHasselt UniversityHasseltBelgium
| | - Door Jouck
- Infection ControlJessa ZiekenhuisHasseltBelgium
| | | | - Catherine Sion
- Laboratory Site St‐JosephGrand Hôpital de CharleroiGillyBelgium
| | | | - Evelyn Petit
- Laboratory MedicineAZ Sint‐Jan Brugge‐Oostende AVBrugesBelgium
| | - Nicolas Dauby
- Department of Infectious Diseases, Centre Hospitalier Universitaire Saint‐PierreUniversité Libre de Bruxelles (ULB)BrusselsBelgium
- Institute for Medical Immunology, ULB Center for Research in Immunology (U‐CRI)Université Libre de Bruxelles (ULB)BrusselsBelgium
- School of Public HealthUniversité Libre de Bruxelles (ULB)BrusselsBelgium
| | - Marc Hainaut
- Pediatrics Department, CHU Saint‐PierreUniversité Libre de Bruxelles (ULB)BrusselsBelgium
| | - Lies Laenen
- National Reference Center for Respiratory Pathogens, UZ LeuvenUniversity Hospitals LeuvenLeuvenBelgium
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and TransplantationKU LeuvenLeuvenBelgium
| | - Piet Maes
- Department of Microbiology, Immunology and Transplantation, Rega InstituteKU LeuvenLeuvenBelgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega InstituteKU LeuvenLeuvenBelgium
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega InstituteKU LeuvenLeuvenBelgium
- Spatial Epidemiology Lab (SpELL)Université Libre de BruxellesBrusselsBelgium
| | - Lize Cuypers
- National Reference Center for Respiratory Pathogens, UZ LeuvenUniversity Hospitals LeuvenLeuvenBelgium
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and TransplantationKU LeuvenLeuvenBelgium
| | - Emmanuel André
- National Reference Center for Respiratory Pathogens, UZ LeuvenUniversity Hospitals LeuvenLeuvenBelgium
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and TransplantationKU LeuvenLeuvenBelgium
| | - Simon Couvreur
- Epidemiology and public Health, Epidemiology of Infectious DiseasesSciensanoBrusselsBelgium
| | - Ruben Brondeel
- Epidemiology and public Health, Epidemiology of Infectious DiseasesSciensanoBrusselsBelgium
| | - Cyril Barbezange
- Viral Diseases, National Influenza Centre, Scientific Directorate of Infectious Diseases in HumansSciensanoUkkelBelgium
| | - Nathalie Bossuyt
- Epidemiology and public Health, Epidemiology of Infectious DiseasesSciensanoBrusselsBelgium
| | - Steven van Gucht
- Viral Diseases, National Influenza Centre, Scientific Directorate of Infectious Diseases in HumansSciensanoUkkelBelgium
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Di Lorenzo A, Mangone I, Colangeli P, Cioci D, Curini V, Vincifori G, Mercante MT, Di Pasquale A, Iannetti S. One health system supporting surveillance during COVID-19 epidemic in Abruzzo region, southern Italy. One Health 2023; 16:100471. [PMID: 36507072 PMCID: PMC9726647 DOI: 10.1016/j.onehlt.2022.100471] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/06/2022] [Accepted: 12/06/2022] [Indexed: 12/12/2022] Open
Abstract
The Istituti Zooprofilattici Sperimentali (IZSs) are public health institutes dealing with the aetiology and pathogenesis of infectious diseases of domestic and wild animals. During Coronavirus Disease 2019 epidemic, the Italian Ministry of Health appointed the IZSs to carry out diagnostic tests for the detection of SARS-CoV-2 in human samples. In particular, the IZS of Abruzzo and Molise (IZS-Teramo) was involved in the diagnosis of SARS-CoV-2 through testing nasopharyngeal swabs by Real Time RT-PCR. Activities and infrastructures were reorganised to the new priorities, in a "One Health" framework, based on interdisciplinary, laboratory promptness, accreditation of the test for the detection of the RNA of SARS-CoV-2 in human samples, and management of confidentiality of sensitive data. The laboratory information system - SILAB - was implemented with a One Health module for managing data of human origin, with tools for the automatic registration of information improving the quality of the data. Moreover, the "National Reference Centre for Whole Genome Sequencing of microbial pathogens - database and bioinformatics analysis" - GENPAT - formally established at the IZS-Teramo, developed bioinformatics workflows and IT dashboard with ad hoc surveillance tools to support the metagenomics-based SARS-CoV-2 surveillance, providing molecular sequencing analysis to quickly intercept the variants circulating in the area. This manuscript describes the One Health system developed by adapting and integrating both SILAB and GENPAT tools for supporting surveillance during COVID-19 epidemic in the Abruzzo region, southern Italy. The developed dashboard permits the health authorities to observe the SARS-CoV-2 spread in the region, and by combining spatio-temporal information with metagenomics provides early evidence for the identification of emerging space-time clusters of variants at the municipality level. The implementation of the One Health module was designed to be easily modelled and adapted for the management of other diseases and future hypothetical events of pandemic nature.
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9
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Maschietto C, Otto G, Rouzé P, Debortoli N, Bihin B, Nyinkeu L, Denis O, Huang TD, Mullier F, Bogaerts P, Degosserie J. Minimal requirements for ISO15189 validation and accreditation of three next generation sequencing procedures for SARS-CoV-2 surveillance in clinical setting. Sci Rep 2023; 13:6934. [PMID: 37117393 PMCID: PMC10140720 DOI: 10.1038/s41598-023-34088-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 04/24/2023] [Indexed: 04/30/2023] Open
Abstract
Rapid and recurrent breakthroughs of new SARS-CoV-2 strains (variants) have prompted public health authorities worldwide to set up surveillance networks to monitor the circulation of variants of concern. The use of next-generation sequencing technologies has raised the need for quality control assessment as required in clinical laboratories. The present study is the first to propose a validation guide for SARS-CoV-2 typing using three different NGS methods fulfilling ISO15189 standards. These include the assessment of the risk, specificity, accuracy, reproducibility, and repeatability of the methods. Among the three methods used, two are amplicon-based involving reverse transcription polymerase chain reaction (Artic v3 and Midnight v1) on Oxford Nanopore Technologies while the third one is amplicon-based using reverse complement polymerase chain reaction (Nimagen) on Illumina technology. We found that all methods met the quality requirement (e.g., 100% concordant typing results for accuracy, reproducibility, and repeatability) for SARS-CoV-2 typing in clinical setting. Additionally, the typing results emerging from each of the three sequencing methods were compared using three widely known nomenclatures (WHO, Pangolineage, and Nextclade). They were also compared regarding single nucleotide variations. The outcomes showed that Artic v3 and Nimagen should be privileged for outbreak investigation as they provide higher quality results for samples that do not meet inclusion criteria for analysis in a clinical setting. This study is a first step towards validation of laboratory developed NGS tests in the context of the new European regulation for medical devices and in vitro diagnostics.
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Affiliation(s)
- Céline Maschietto
- Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium
- COVID-19 Federal Testing Platform Bis, CHU UCL Namur & UNamur, 5530, Yvoir, Belgium
| | - Gaëtan Otto
- Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium
- COVID-19 Federal Testing Platform Bis, CHU UCL Namur & UNamur, 5530, Yvoir, Belgium
| | - Pauline Rouzé
- Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium
- Laboratory of Microbiology, CHU UCL Namur, 5530, Yvoir, Belgium
| | - Nicolas Debortoli
- Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium
- Namur Molecular Tech, CHU UCL Namur, 5530, Yvoir, Belgium
| | - Benoît Bihin
- Scientific Support Unit, CHU UCL Namur, 5530, Yvoir, Belgium
| | - Lesly Nyinkeu
- Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium
- COVID-19 Federal Testing Platform Bis, CHU UCL Namur & UNamur, 5530, Yvoir, Belgium
- Namur Molecular Tech, CHU UCL Namur, 5530, Yvoir, Belgium
| | - Olivier Denis
- Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium
- COVID-19 Federal Testing Platform Bis, CHU UCL Namur & UNamur, 5530, Yvoir, Belgium
- Laboratory of Microbiology, CHU UCL Namur, 5530, Yvoir, Belgium
| | - Te-Din Huang
- Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium
- COVID-19 Federal Testing Platform Bis, CHU UCL Namur & UNamur, 5530, Yvoir, Belgium
- Laboratory of Microbiology, CHU UCL Namur, 5530, Yvoir, Belgium
| | - François Mullier
- Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium
- COVID-19 Federal Testing Platform Bis, CHU UCL Namur & UNamur, 5530, Yvoir, Belgium
| | - Pierre Bogaerts
- Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium
- Laboratory of Microbiology, CHU UCL Namur, 5530, Yvoir, Belgium
| | - Jonathan Degosserie
- Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium.
- COVID-19 Federal Testing Platform Bis, CHU UCL Namur & UNamur, 5530, Yvoir, Belgium.
- Namur Molecular Tech, CHU UCL Namur, 5530, Yvoir, Belgium.
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