Imperial College London
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Professor Nuno R. Faria

Faculty of Medicine, School of Public Health

Professor in Virus Genomic Epidemiology
 
 
 
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Contact

 

+44 (0)20 7594 3560n.faria

 
 
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Location

 

Sir Alexander Fleming BuildingSouth Kensington Campus

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Summary

 

Publications

Citation

BibTex format

@unpublished{Dellicour:2020:10.1101/2020.05.05.078758,
author = {Dellicour, S and Durkin, K and Hong, SL and Vanmechelen, B and Martí-Carreras, J and Gill, MS and Meex, C and Bontems, S and André, E and Gilbert, M and Walker, C and De, Maio N and Faria, NR and Hadfield, J and Hayette, M-P and Bours, V and Wawina-Bokalanga, T and Artesi, M and Baele, G and Maes, P},
doi = {10.1101/2020.05.05.078758},
title = {A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages},
url = {http://dx.doi.org/10.1101/2020.05.05.078758},
year = {2020}
}
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RIS format (EndNote, RefMan)

TY  - UNPB
AB  - <jats:p>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.</jats:p>
AU  - Dellicour,S
AU  - Durkin,K
AU  - Hong,SL
AU  - Vanmechelen,B
AU  - Martí-Carreras,J
AU  - Gill,MS
AU  - Meex,C
AU  - Bontems,S
AU  - André,E
AU  - Gilbert,M
AU  - Walker,C
AU  - De,Maio N
AU  - Faria,NR
AU  - Hadfield,J
AU  - Hayette,M-P
AU  - Bours,V
AU  - Wawina-Bokalanga,T
AU  - Artesi,M
AU  - Baele,G
AU  - Maes,P
DO  - 10.1101/2020.05.05.078758
PY  - 2020///
TI  - A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages
UR  - http://dx.doi.org/10.1101/2020.05.05.078758
ER  -
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