Article (Scientific journals)
Exploiting genomic surveillance to map the spatio-temporal dispersal of SARS-CoV-2 spike mutations in Belgium across 2020.
Bollen, Nena; Artesi, Maria; Durkin, Keith et al.
2021In Scientific Reports, 11 (1), p. 18580
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Keywords :
Belgium; Epidemiological Monitoring; Genome, Viral; Humans; Mutation; SARS-CoV-2/genetics; Spike Glycoprotein, Coronavirus/genetics
Abstract :
[en] At the end of 2020, several new variants of SARS-CoV-2-designated variants of concern-were detected and quickly suspected to be associated with a higher transmissibility and possible escape of vaccine-induced immunity. In Belgium, this discovery has motivated the initiation of a more ambitious genomic surveillance program, which is drastically increasing the number of SARS-CoV-2 genomes to analyse for monitoring the circulation of viral lineages and variants of concern. In order to efficiently analyse the massive collection of genomic data that are the result of such increased sequencing efforts, streamlined analytical strategies are crucial. In this study, we illustrate how to efficiently map the spatio-temporal dispersal of target mutations at a regional level. As a proof of concept, we focus on the Belgian province of Liège that has been consistently sampled throughout 2020, but was also one of the main epicenters of the second European epidemic wave. Specifically, we employ a recently developed phylogeographic workflow to infer the regional dispersal history of viral lineages associated with three specific mutations on the spike protein (S98F, A222V and S477N) and to quantify their relative importance through time. Our analytical pipeline enables analysing large data sets and has the potential to be quickly applied and updated to track target mutations in space and time throughout the course of an epidemic.
Disciplines :
Genetics & genetic processes
Author, co-author :
Bollen, Nena
Artesi, Maria ;  Université de Liège - ULiège > Département des sciences biomédicales et précliniques > Génétique humaine
Durkin, Keith  ;  Université de Liège - ULiège > GIGA Cancer - Human Genetics
Hong, Samuel L.
Potter, Barney
Boujemla, Bouchra ;  Université de Liège - ULiège > GIGA Cancer - Human Genetics
Vanmechelen, Bert
Martí-Carreras, Joan
Wawina-Bokalanga, Tony
Meex, Cécile ;  Université de Liège - ULiège > Département des sciences cliniques > Département des sciences cliniques
Bontems, Sébastien ;  Université de Liège - ULiège > Département des sciences biomédicales et précliniques > Bact., mycologie, parasitologie, virologie, microbio.
Hayette, Marie-Pierre ;  Université de Liège - ULiège > Département des sciences biomédicales et précliniques > Bact., mycologie, parasitologie, virologie, microbio.
André, Emmanuel
Maes, Piet
Bours, Vincent ;  Université de Liège - ULiège > Département des sciences biomédicales et précliniques > Génétique humaine
Baele, Guy
Dellicour, Simon
More authors (7 more) Less
Language :
English
Title :
Exploiting genomic surveillance to map the spatio-temporal dispersal of SARS-CoV-2 spike mutations in Belgium across 2020.
Publication date :
2021
Journal title :
Scientific Reports
eISSN :
2045-2322
Publisher :
Nature Publishing Group, London, United Kingdom
Volume :
11
Issue :
1
Pages :
18580
Peer reviewed :
Peer Reviewed verified by ORBi
Commentary :
© 2021. The Author(s).
Available on ORBi :
since 10 November 2021

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