Genomic monitoring of SARS-CoV-2 variants using sentinel SARI hospital surveillance

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 MaesGuy Baele, Simon Dellicour, Lize Cuypers, Emmanuel André, Simon Couvreur, Ruben Brondeel, Cyril Barbezange, Nathalie Bossuyt, Steven Van Gucht

Research output: Contribution to journalArticlepeer-review


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.

Keywords: SARI surveillance; SARS‐CoV‐2; genomic surveillance; influenza; pandemic preparedness; respiratory viruses
Original languageEnglish
Article numbere13202
Pages (from-to)e13202
Number of pages12
JournalInfluenza and other Respiratory Viruses
Issue number10
Publication statusPublished - 13 Oct 2023

Bibliographical note

Publisher Copyright:
© 2023 Sciensano and The Authors. Influenza and Other Respiratory Viruses published by John Wiley & Sons Ltd.


  • SARI
  • SARI surveillance
  • SARS-CoV-2
  • Genomic surveillance
  • influenza
  • Pandamic preparedness
  • Respiratory viruses


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