A Phylodynamic Workflow to Rapidly Gain Insights into the Dispersal History and Dynamics of SARS-CoV-2 Lineages.
COVID-19
SARS-CoV-2
lockdown measures
phylodynamic
phylogenetic clusters
phylogeography
Journal
Molecular biology and evolution
ISSN: 1537-1719
Titre abrégé: Mol Biol Evol
Pays: United States
ID NLM: 8501455
Informations de publication
Date de publication:
13 04 2021
13 04 2021
Historique:
pubmed:
15
12
2020
medline:
24
4
2021
entrez:
14
12
2020
Statut:
ppublish
Résumé
Since the start of the COVID-19 pandemic, an unprecedented number of genomic sequences of SARS-CoV-2 have been generated and shared with the scientific community. The unparalleled volume of available genetic data presents a unique opportunity to gain real-time insights into the virus transmission during the pandemic, but also a daunting computational hurdle if analyzed with gold-standard phylogeographic approaches. To tackle this practical limitation, we here describe and apply a rapid analytical pipeline to analyze the spatiotemporal dispersal history and dynamics of SARS-CoV-2 lineages. As a proof of concept, we focus on the Belgian epidemic, which has had one of the highest spatial densities of available SARS-CoV-2 genomes. 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.
Identifiants
pubmed: 33316043
pii: 5952687
doi: 10.1093/molbev/msaa284
pmc: PMC7665608
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1608-1613Subventions
Organisme : Medical Research Council
ID : MC_PC_19012
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/S019510/1
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/S0195/1
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/R015600/1
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 204311/Z/16/Z
Pays : United Kingdom
Informations de copyright
© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Références
Lancet. 2020 Feb 22;395(10224):565-574
pubmed: 32007145
Virus Evol. 2018 Jun 08;4(1):vey016
pubmed: 29942656
Proc Natl Acad Sci U S A. 2012 Sep 11;109(37):15066-71
pubmed: 22927414
N Engl J Med. 2020 Feb 20;382(8):727-733
pubmed: 31978945
Virus Evol. 2018 Jan 08;4(1):vex042
pubmed: 29340210
Nat Med. 2020 Apr;26(4):450-452
pubmed: 32284615
Elife. 2020 May 11;9:
pubmed: 32392129
Lancet Psychiatry. 2020 Jun;7(6):547-560
pubmed: 32304649
Mol Biol Evol. 2010 Aug;27(8):1877-85
pubmed: 20203288
BMC Bioinformatics. 2018 Dec 18;19(1):532
pubmed: 30563445
Syst Biol. 2019 Nov 1;68(6):1052-1061
pubmed: 31034053
Virus Evol. 2020 Apr 10;6(1):veaa027
pubmed: 32296544
Nature. 2020 Mar;579(7798):270-273
pubmed: 32015507
Curr Opin Virol. 2018 Aug;31:24-32
pubmed: 30248578
Nat Med. 2020 May;26(5):640-642
pubmed: 32273610
Bioinformatics. 2018 Dec 1;34(23):4121-4123
pubmed: 29790939
Euro Surveill. 2017 Mar 30;22(13):
pubmed: 28382917
Cell. 2020 May 28;181(5):997-1003.e9
pubmed: 32359424
PLoS Comput Biol. 2009 Sep;5(9):e1000520
pubmed: 19779555