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Genomic monitoring of SARS-CoV-2 variants using sentinel SARI hospital surveillance.
Denayer, Sarah; Dufrasne, François E; Monsieurs, Bert; van Eycken, Reinout; Houben, Sarah; Seyler, Lucie; Demuyser, Thomas; van Nedervelde, Els; Bourgeois, Marc; Delaere, Bénédicte; Magerman, Koen; Jouck, Door; Lissoir, Bénédicte; Sion, Catherine; Reynders, Marijke; Petit, Evelyn; Dauby, Nicolas; Hainaut, Marc; Laenen, Lies; Maes, Piet; Baele, Guy; Dellicour, Simon; Cuypers, Lize; André, Emmanuel; Couvreur, Simon; Brondeel, Ruben; Barbezange, Cyril; Bossuyt, Nathalie; van Gucht, Steven.
Afiliação
  • Denayer S; Viral Diseases, National Influenza Centre, Scientific Directorate of Infectious Diseases in Humans Sciensano Ukkel Belgium.
  • Dufrasne FE; Viral Diseases, National Influenza Centre, Scientific Directorate of Infectious Diseases in Humans Sciensano Ukkel Belgium.
  • Monsieurs B; Viral Diseases, National Influenza Centre, Scientific Directorate of Infectious Diseases in Humans Sciensano Ukkel Belgium.
  • van Eycken R; Viral Diseases, National Influenza Centre, Scientific Directorate of Infectious Diseases in Humans Sciensano Ukkel Belgium.
  • Houben S; Observational Clinical Trials, Scientific Directorate of infectious Diseases in Humans Sciensano Ukkel Belgium.
  • Seyler L; Department of Internal Medicine and Infectiology, Universitair Ziekenhuis Brussel (UZB) Vrije Universiteit Brussel (VUB) Brussels Belgium.
  • Demuyser T; Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel (UZB) Vrije Universiteit Brussel (VUB) Brussels Belgium.
  • van Nedervelde E; AIMS Lab, Center for Neurosciences, Faculty of Medicine and Pharmacy Vrije Universiteit Brussel (VUB) Brussels Belgium.
  • Bourgeois M; Department of Internal Medicine and Infectiology, Universitair Ziekenhuis Brussel (UZB) Vrije Universiteit Brussel (VUB) Brussels Belgium.
  • Delaere B; CHU UCL Namur, site Mont-Godinne Yvoir Belgium.
  • Magerman K; CHU UCL Namur, site Mont-Godinne Yvoir Belgium.
  • Jouck D; Infection Control and Clinical Laboratory Jessa Ziekenhuis Hasselt Belgium.
  • Lissoir B; Department of Immunology and Infection Hasselt University Hasselt Belgium.
  • Sion C; Infection Control Jessa Ziekenhuis Hasselt Belgium.
  • Reynders M; Laboratory Site St-Joseph Grand Hôpital de Charleroi Gilly Belgium.
  • Petit E; Laboratory Site St-Joseph Grand Hôpital de Charleroi Gilly Belgium.
  • Dauby N; Laboratory Medicine AZ Sint-Jan Brugge-Oostende AV Bruges Belgium.
  • Hainaut M; Laboratory Medicine AZ Sint-Jan Brugge-Oostende AV Bruges Belgium.
  • Laenen L; Department of Infectious Diseases, Centre Hospitalier Universitaire Saint-Pierre Université Libre de Bruxelles (ULB) Brussels Belgium.
  • Maes P; Institute for Medical Immunology, ULB Center for Research in Immunology (U-CRI) Université Libre de Bruxelles (ULB) Brussels Belgium.
  • Baele G; School of Public Health Université Libre de Bruxelles (ULB) Brussels Belgium.
  • Dellicour S; Pediatrics Department, CHU Saint-Pierre Université Libre de Bruxelles (ULB) Brussels Belgium.
  • Cuypers L; National Reference Center for Respiratory Pathogens, UZ Leuven University Hospitals Leuven Leuven Belgium.
  • André E; Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation KU Leuven Leuven Belgium.
  • Couvreur S; Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven Leuven Belgium.
  • Brondeel R; Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven Leuven Belgium.
  • Barbezange C; Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven Leuven Belgium.
  • Bossuyt N; Spatial Epidemiology Lab (SpELL) Université Libre de Bruxelles Brussels Belgium.
  • van Gucht S; National Reference Center for Respiratory Pathogens, UZ Leuven University Hospitals Leuven Leuven Belgium.
Influenza Other Respir Viruses ; 17(10): e13202, 2023 10.
Article em En | MEDLINE | ID: mdl-37840842
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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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Pneumonia / COVID-19 Idioma: En Ano de publicação: 2023 Tipo de documento: Article

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Pneumonia / COVID-19 Idioma: En Ano de publicação: 2023 Tipo de documento: Article