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Tytuł:
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A Phylodynamic Workflow to Rapidly Gain Insights into the Dispersal History and Dynamics of SARS-CoV-2 Lineages.
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Autorzy:
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Dellicour S; Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium.; Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.
Durkin K; Department of Human Genetics, CHU Liège, and Medical Genomics, GIGA Research Center, University of Liège, Liège, Belgium.
Hong SL; Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.
Vanmechelen B; Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.
Martí-Carreras J; Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.
Gill MS; Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.
Meex C; Department of Clinical Microbiology, University of Liège, Liège, Belgium.
Bontems S; Department of Clinical Microbiology, University of Liège, Liège, Belgium.
André E; Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.
Gilbert M; Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium.
Walker C; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom.
Maio N; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom.
Faria NR; Department of Zoology, University of Oxford, Oxford, United Kingdom.; MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, United Kingdom.
Hadfield J; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA.
Hayette MP; Department of Clinical Microbiology, University of Liège, Liège, Belgium.
Bours V; Department of Human Genetics, CHU Liège, and Medical Genomics, GIGA Research Center, University of Liège, Liège, Belgium.
Wawina-Bokalanga T; Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.
Artesi M; Department of Human Genetics, CHU Liège, and Medical Genomics, GIGA Research Center, University of Liège, Liège, Belgium.
Baele G; Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.
Maes P; Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.
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Źródło:
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Molecular biology and evolution [Mol Biol Evol] 2021 Apr 13; Vol. 38 (4), pp. 1608-1613.
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Typ publikacji:
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Journal Article; Research Support, Non-U.S. Gov't
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Język:
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English
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Imprint Name(s):
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Publication: 2003- : New York, NY : Oxford University Press
Original Publication: [Chicago, Ill.] : University of Chicago Press, [c1983-
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MeSH Terms:
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Genome, Viral*
Phylogeography*
COVID-19/*transmission
COVID-19/*virology
SARS-CoV-2/*genetics
Belgium ; COVID-19/epidemiology ; Evolution, Molecular ; Genomics ; Humans ; Likelihood Functions ; Mutation ; Patient Isolation ; Phylogeny ; Physical Distancing ; Spatio-Temporal Analysis ; Workflow
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References:
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Grant Information:
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MC_PC_19012 United Kingdom MRC_ Medical Research Council; MR/S019510/1 United Kingdom MRC_ Medical Research Council; MR/S0195/1 United Kingdom MRC_ Medical Research Council; MR/R015600/1 United Kingdom MRC_ Medical Research Council; 204311/Z/16/Z United Kingdom WT_ Wellcome Trust
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Contributed Indexing:
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Keywords: COVID-19; SARS-CoV-2; lockdown measures; phylodynamic; phylogenetic clusters; phylogeography
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Entry Date(s):
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Date Created: 20201214 Date Completed: 20210423 Latest Revision: 20211117
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Update Code:
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20240104
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PubMed Central ID:
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PMC7665608
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DOI:
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10.1093/molbev/msaa284
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PMID:
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33316043
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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.
(© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)
