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Genomic monitoring of SARS-CoV-2 variants using sentinel SARI hospital surveillance |
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| Authors: | Sarah Denayer François E Dufrasne Bert Monsieurs Reinout van Eycken Sarah Houben Lucie Seyler Thomas Demuyser Els van Nedervelde Marc Bourgeois Bénédicte Delaere Koen Magerman Door Jouck Bénédicte Lissoir Catherine Sion Marijke Reynders Evelyn Petit Nicolas Dauby Marc Hainaut Lies Laenen Piet Maes Guy Baele Simon Dellicour Lize Cuypers Emmanuel André Simon Couvreur Ruben Brondeel Cyril Barbezange Nathalie Bossuyt Steven van Gucht |
| Institution: | 1. Viral Diseases, National Influenza Centre, Scientific Directorate of Infectious Diseases in Humans, Sciensano, Ukkel, Belgium;2. Viral Diseases, National Influenza Centre, Scientific Directorate of Infectious Diseases in Humans, Sciensano, Ukkel, Belgium
Contribution: Methodology (lead), Supervision (supporting), Writing - original draft (supporting), Writing - review & editing (equal);3. Viral Diseases, National Influenza Centre, Scientific Directorate of Infectious Diseases in Humans, Sciensano, Ukkel, Belgium Contribution: ?Investigation (equal);4. Observational Clinical Trials, Scientific Directorate of infectious Diseases in Humans, Sciensano, Ukkel, Belgium Contribution: Visualization (supporting);5. Department of Internal Medicine and Infectiology, Universitair Ziekenhuis Brussel (UZB), Vrije Universiteit Brussel (VUB), Brussels, Belgium Contribution: Resources (equal), Writing - review & editing (equal);6. Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel (UZB), Vrije Universiteit Brussel (VUB), Brussels, Belgium AIMS Lab, Center for Neurosciences, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), Brussels, Belgium Contribution: Resources (equal), Writing - review & editing (equal);7. CHU UCL Namur, site Mont-Godinne, Yvoir, Belgium Contribution: Resources (equal), Writing - review & editing (equal);8. CHU UCL Namur, site Mont-Godinne, Yvoir, Belgium;9. Infection Control and Clinical Laboratory, Jessa Ziekenhuis, Hasselt, Belgium Department of Immunology and Infection, Hasselt University, Hasselt, Belgium Contribution: Resources (equal), Writing - review & editing (equal);10. Infection Control, Jessa Ziekenhuis, Hasselt, Belgium Contribution: Resources (equal), Writing - review & editing (equal);11. Laboratory Site St-Joseph, Grand Hôpital de Charleroi, Gilly, Belgium Contribution: Resources (equal), Writing - review & editing (equal);12. Laboratory Medicine, AZ Sint-Jan Brugge-Oostende AV, Bruges, Belgium Contribution: Resources (equal), Writing - review & editing (equal);13. Department of Infectious Diseases, Centre Hospitalier Universitaire Saint-Pierre, Université Libre de Bruxelles (ULB), Brussels, Belgium Institute for Medical Immunology, ULB Center for Research in Immunology (U-CRI), Université Libre de Bruxelles (ULB), Brussels, Belgium School of Public Health, Université Libre de Bruxelles (ULB), Brussels, Belgium Contribution: Resources (equal), Writing - review & editing (equal);14. Pediatrics Department, CHU Saint-Pierre, Université Libre de Bruxelles (ULB), Brussels, Belgium Contribution: Resources (equal), Writing - review & editing (equal);15. National Reference Center for Respiratory Pathogens, UZ Leuven, University Hospitals Leuven, Leuven, Belgium Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium Contribution: Writing - review & editing (equal);16. Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium Contribution: Writing - review & editing (equal);17. Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium Contribution: Writing - review & editing (equal);18. Epidemiology and public Health, Epidemiology of Infectious Diseases, Sciensano, Brussels, Belgium Contribution: Resources (equal);19. Epidemiology and public Health, Epidemiology of Infectious Diseases, Sciensano, Brussels, Belgium Contribution: Conceptualization (supporting), Writing - review & editing (equal);20. Viral Diseases, National Influenza Centre, Scientific Directorate of Infectious Diseases in Humans, Sciensano, Ukkel, Belgium Contribution: Conceptualization (supporting), Writing - original draft (supporting), Writing - review & editing (equal) |
| Abstract: | BackgroundTo 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.MethodsNine-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.ResultsSARI 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.ConclusionsGenomic 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. |
| Keywords: | genomic surveillance influenza pandemic preparedness respiratory viruses SARI surveillance SARS-CoV-2 |