About: A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages

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About: A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages
Creator	Maes, Piet Gilbert, Marius Baele, Guy Dellicour, Simon Vanmechelen, Bert Faria, Nuno Hadfield, James André, Emmanuel Artesi, Maria Bontems, Sébastien Bours, Vincent Durkin, Keith Gill, Mandev Hayette, Marie-Pierre Meex, Cécile Martí-Carreras, Joan Wawina-Bokalanga, Tony Hong, Samuel De Maio, Nicola Walker, Conor
source	BioRxiv
abstract	Since the start of the COVID-19 pandemic, an unprecedented number of genomic sequences of the causative virus (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 analysed with gold-standard phylogeographic approaches. 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 the Belgium epidemic, with one of the highest spatial density of available SARS-CoV-2 genomes. At the global scale, our analyses confirm the importance of external introduction events in establishing multiple transmission chains in the country. At the country scale, our spatially-explicit phylogeographic analyses highlight that the national lockdown had a relatively low impact on both the lineage dispersal velocity and the long-distance dispersal events within Belgium. 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.
has issue date	2020-07-09(xsd:dateTime)
bibo:doi	10.1101/2020.05.05.078758
has license	biorxiv
sha1sum (hex)	d551696043d51ecd652f4f19ea22d1b2c65ba069
schema:url	https://doi.org/10.1101/2020.05.05.078758
resource representing a document's title	A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages
schema:publication	bioRxiv
resource representing a document's body	covid:d551696043d51ecd652f4f19ea22d1b2c65ba069#body_text
is schema:about of	named entity 'SARS-CoV-2' named entity 'hurdle' named entity 'SARS-CoV-2' named entity 'GOLD' named entity 'DISTANCE' named entity 'EXTERNAL' named entity 'SCIENTIFIC' named entity 'DENSITY' named entity 'IS A' named entity 'MULTIPLE' named entity 'RAPIDLY' named entity 'HISTORY' named entity 'DISPERSAL' named entity 'long-distance dispersal' named entity 'start' named entity 'causative' named entity 'transmission' named entity 'generated' named entity 'genomes' named entity 'number' named entity 'gain' named entity 'global' named entity 'confirm' named entity 'pipeline' named entity 'phylogeographic' named entity 'velocity' named entity 'long-distance dispersal' named entity 'phylogeographic' named entity 'virus' named entity 'national lockdown' named entity 'Italy' named entity 'phylogeographic' named entity 'random walk' named entity 'genetic data' named entity 'gold standard' named entity 'epidemic' named entity 'virus' named entity 'epidemiological' named entity 'phylogeographic' named entity 'inference' named entity 'Belgian' named entity 'Belgium' named entity 'virus' named entity 'Markov chain' named entity 'Belgian' named entity 'GISAID' named entity 'clade' named entity 'genomes' named entity 'phylogeographic' named entity 'sampling' named entity 'Belgium' named entity 'maximum-likelihood' named entity 'data set' named entity 'sequencing data' named entity 'genomes' named entity 'R package' named entity 'University of Ghent' named entity 'carnival holidays' named entity 'phylogeographic' named entity '1.1' named entity 'SARS-CoV-2' named entity 'Belgium' named entity 'Belgian' named entity 'virus' named entity 'epidemiology'

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