Two Years of Genomic Surveillance in Belgium during the SARS-CoV-2 Pandemic to Attain Country-Wide Coverage and Monitor the Introduction and Spread of Emerging Variants

Lize Cuypers; Simon Dellicour; Samuel L Hong; Barney I Potter; Bruno Verhasselt; Nick Vereecke; Laurens Lambrechts; Keith Durkin; Vincent Bours; Sofieke Klamer; Guillaume Bayon-Vicente; Carl Vael; Kevin K Ariën; Ricardo De Mendonca; Oriane Soetens; Charlotte Michel; Bertrand Bearzatto; Reinout Naesens; Jeremie Gras; Anne Vankeerberghen; Veerle Matheeussen; Geert Martens; Dagmar Obbels; Ann Lemmens; Bea Van den Poel; Ellen Van Even; Klara De Rauw; Luc Waumans; Marijke Reynders; Jonathan Degosserie; COVID-19 Genomics Belgium Consortium; Piet Maes; Emmanuel André; Guy Baele

doi:10.3390/v14102301

Two Years of Genomic Surveillance in Belgium during the SARS-CoV-2 Pandemic to Attain Country-Wide Coverage and Monitor the Introduction and Spread of Emerging Variants

Viruses. 2022 Oct 20;14(10):2301. doi: 10.3390/v14102301.

Authors

Lize Cuypers¹, Simon Dellicour^{2

3}, Samuel L Hong³, Barney I Potter³, Bruno Verhasselt⁴, Nick Vereecke⁵, Laurens Lambrechts^{6

7}, Keith Durkin⁸, Vincent Bours^{8

9}, Sofieke Klamer¹⁰, Guillaume Bayon-Vicente¹¹, Carl Vael¹², Kevin K Ariën^{13

14}, Ricardo De Mendonca¹⁵, Oriane Soetens¹⁶, Charlotte Michel¹⁷, Bertrand Bearzatto¹⁸, Reinout Naesens¹⁹, Jeremie Gras²⁰, Anne Vankeerberghen²¹, Veerle Matheeussen²², Geert Martens²³, Dagmar Obbels²⁴, Ann Lemmens²⁵, Bea Van den Poel²⁶, Ellen Van Even²⁷, Klara De Rauw²⁸, Luc Waumans²⁹, Marijke Reynders³⁰, Jonathan Degosserie^{31

32}; COVID-19 Genomics Belgium Consortium; Piet Maes³, Emmanuel André^{1

33

34}, Guy Baele³

Affiliations

¹ National Reference Centre for Respiratory Pathogens, Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium.
² Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1000 Brussels, Belgium.
³ Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium.
⁴ Department of Diagnostic Sciences, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium.
⁵ PathoSense BV, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium.
⁶ HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium.
⁷ BioBix, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium.
⁸ Laboratory of Human Genetics, GIGA Research Institute, 4000 Liège, Belgium.
⁹ Department of Human Genetics, University Hospital of Liège, 4000 Liège, Belgium.
¹⁰ Scientific Directorate of Epidemiology and Public Health, Sciensano, 1050 Brussels, Belgium.
¹¹ Department of Proteomic and Microbiology, Research Institute for Biosciences, University of Mons, 7000 Mons, Belgium.
¹² Clinical Laboratory, AZ Klina, 2930 Brasschaat, Belgium.
¹³ Virology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine Antwerp, 2000 Antwerp, Belgium.
¹⁴ Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, Department of Biomedical Sciences, University of Antwerp, 2000 Antwerp, Belgium.
¹⁵ Department of Microbiology, CUB-Hôpital Erasme, Université Libre de Bruxelles, 1000 Brussels, Belgium.
¹⁶ Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, 1090 Brussels, Belgium.
¹⁷ Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles (LHUB-ULB), 1000 Brussels, Belgium.
¹⁸ Center for Applied Molecular Technologies (CTMA), Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain (UCLouvain), 1000 Brussels, Belgium.
¹⁹ Department of Medical Microbiology, Ziekenhuis Netwerk Antwerpen, 2020 Antwerp, Belgium.
²⁰ Institute of Pathology and Genetics (IPG), 6041 Gosselies, Belgium.
²¹ Laboratory of Molecular Biology, Campus Aalst-Asse-Ninove, Onze-Lieve-Vrouwziekenhuis, 9300 Aalst, Belgium.
²² Laboratory of Medical Microbiology, Department of Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, 2610 Wilrijk, Belgium.
²³ Department of Laboratory Medicine, AZ Delta General Hospital, 8800 Roeselare, Belgium.
²⁴ Clinical Laboratory, Imelda Hospital, 2820 Bonheiden, Belgium.
²⁵ Laboratory of Clinical Biology, AZ Sint-Maarten Hospital, 2800 Mechelen, Belgium.
²⁶ Clinical Laboratory, General Hospital Jan Portaels, 1800 Vilvoorde, Belgium.
²⁷ Clinical Laboratory of Microbiology, HH Hospital Lier, 2500 Lier, Belgium.
²⁸ Laboratory of Clinical Biology, AZ Sint Lucas Hospital, 9000 Ghent, Belgium.
²⁹ Clinical Laboratory, Jessa Hospital, 3500 Hasselt, Belgium.
³⁰ Department of Laboratory Medicine, Medical Microbiology, AZ Sint-Jan Bruges-Ostend AV, 8000 Bruges, Belgium.
³¹ Federal Testing Platform COVID-19, Department of Laboratory Medicine, CHU UCL Namur, 5530 Yvoir, Belgium.
³² Next Generation Sequencing Platform, Molecular Diagnostic Center, CHU UCL Namur, 5530 Yvoir, Belgium.
³³ Federal Testing Platform COVID-19, Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium.
³⁴ Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium.

Abstract

An adequate SARS-CoV-2 genomic surveillance strategy has proven to be essential for countries to obtain a thorough understanding of the variants and lineages being imported and successfully established within their borders. During 2020, genomic surveillance in Belgium was not structurally implemented but performed by individual research laboratories that had to acquire the necessary funds themselves to perform this important task. At the start of 2021, a nationwide genomic surveillance consortium was established in Belgium to markedly increase the country's genomic sequencing efforts (both in terms of intensity and representativeness), to perform quality control among participating laboratories, and to enable coordination and collaboration of research projects and publications. We here discuss the genomic surveillance efforts in Belgium before and after the establishment of its genomic sequencing consortium, provide an overview of the specifics of the consortium, and explore more details regarding the scientific studies that have been published as a result of the increased number of Belgian SARS-CoV-2 genomes that have become available.

Keywords: Belgium; COVID-19; SARS-CoV-2; genomic surveillance; next-generation sequencing; variants of concern.

Publication types

Review
Research Support, Non-U.S. Gov't

MeSH terms

Belgium / epidemiology
COVID-19* / epidemiology
Genome, Viral
Genomics
High-Throughput Nucleotide Sequencing
Humans
Pandemics*
SARS-CoV-2 / genetics

Grants and funding

S.D. acknowledges support from the Fonds National de la Recherche Scientifique (F.R.S.-FNRS, Belgium; grant F.4515.22), and from the European Union Horizon 2020 project MOOD (grant agreement 874850). S.L.H. and G.B. acknowledge support from the Research Foundation—Flanders (Fonds voor Wetenschappelijk Onderzoek—Vlaanderen, G0E1420N). B.I.P. and G.B. acknowledge support from the Internal Funds KU Leuven (Grant C14/18/094). S.D. and G.B. acknowledge support from the Research Foundation—Flanders (Fonds voor Wetenschappelijk Onderzoek—Vlaanderen, G098321N). K.K.A. acknowledges support from the Research Foundation—Flanders (Fonds voor Wetenschappelijk Onderzoek—Vlaanderen, G0G4220N). N.V. is supported by the Flemish Agency for Innovation and Entrepreneurship (Baekeland Mandate HBC.2020.2889). This work and the sequencing capacity were supported in part by a COVID19 research grant of Fonds Wetenschappelijk Onderzoek/Research Foundation Flanders (G0H4420N). UZ Leuven, as national reference center for respiratory pathogens, is supported by Sciensano, which is gratefully acknowledged.