Article (Scientific journals)
A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages
Dellicour, Simon; Durkin, Keith; Hong, Samuel et al.
2021In Molecular Biology and Evolution
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Keywords :
COVID-19; SARS-CoV-2; phylodynamic; phylogeography; Nextstrain; phylogenetic clusters
Abstract :
[en] Since the start of the COVID-19 pandemic, an unprecedented number of genomic sequences of the causative virus (SARS-CoV-2) have been publicly released. The resulting volume of available genetic data presents a unique opportunity to gain real-time insights into the pandemic, but also a daunting computational hurdle if analysed with gold-standard phylogeographic methods. We here describe and apply an analytical pipeline that is a compromise between fast and rigorous analytical steps. As a proof of concept, we focus on Belgium, one of the countries with the highest spatial density of sequenced SARS-CoV-2 genomes. At the global scale, our analyses confirm the importance of external introduction events in establishing transmission chains in the country. At the country scale, our spatially-explicit phylogeographic analyses highlight an impact of the national lockdown of mid-March on the dispersal velocity of viral lineages. Our pipeline has the potential to be quickly applied to other countries or regions, with key benefits in complementing epidemiological analyses in assessing the impact of intervention measures or their progressive easement.
Disciplines :
Immunology & infectious disease
Laboratory medicine & medical technology
Author, co-author :
Dellicour, Simon
Durkin, Keith  ;  Université de Liège - ULiège > Cancer-Human Genetics
Hong, Samuel
Vanmechelen, Bert
Marti-Carreras, Joan
Gill, Mandev
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 > Département des sciences biomédicales et précliniques
André, Emmanuel
Gilbert, Marius
Walker, Conor
De Maio, Nicola
Hadfield, James
Hayette, Marie-Pierre  ;  Université de Liège - ULiège > Département des sciences biomédicales et précliniques > Bactériologie, mycologie, parasitologie, virologie
Wawina-Bokalanga, Tony
Artesi, Maria ;  Université de Liège - ULiège > Cancer-Human Genetics
Baele, Guy
Maes, Piet
Faria, Nuno R
More authors (10 more) Less
Language :
English
Title :
A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages
Alternative titles :
[en] Un workflow phylodynamique pour obtenir rapidement un aperçu de l'historique de la dispersion et de la dynamique des lignées SARS-CoV-2
Publication date :
2021
Journal title :
Molecular Biology and Evolution
ISSN :
0737-4038
eISSN :
1537-1719
Publisher :
Oxford University Press, United Kingdom
Peer reviewed :
Peer Reviewed verified by ORBi
Available on ORBi :
since 13 May 2020

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