Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2

Philippe Lemey; Samuel L. Hong; Verity Hill; Guy Baele; Chiara Poletto; Vittoria Colizza; Áine O’Toole; John T. McCrone; Kristian G. Andersen; Michael Worobey; Martha I. Nelson; Andrew Rambaut; Marc A. Suchard

doi:10.1038/s41467-020-18877-9

Nature Communications (Oct 2020)

Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2

Philippe Lemey,
Samuel L. Hong,
Verity Hill,
Guy Baele,
Chiara Poletto,
Vittoria Colizza,
Áine O’Toole,
John T. McCrone,
Kristian G. Andersen,
Michael Worobey,
Martha I. Nelson,
Andrew Rambaut,
Marc A. Suchard

Affiliations

Philippe Lemey: Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Laboratory of Clinical and Evolutionary Virology
Samuel L. Hong: Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Laboratory of Clinical and Evolutionary Virology
Verity Hill: Institute of Evolutionary Biology, University of Edinburgh
Guy Baele: Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Laboratory of Clinical and Evolutionary Virology
Chiara Poletto: INSERM, Sorbonne Université, Institut Pierre Louis d’Epidémiologie et de Santé Publique IPLESP
Vittoria Colizza: INSERM, Sorbonne Université, Institut Pierre Louis d’Epidémiologie et de Santé Publique IPLESP
Áine O’Toole: Institute of Evolutionary Biology, University of Edinburgh
John T. McCrone: Institute of Evolutionary Biology, University of Edinburgh
Kristian G. Andersen: Department of Immunology and Microbiology, Scripps Research
Michael Worobey: Department of Ecology and Evolutionary Biology, University of Arizona
Martha I. Nelson: Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health
Andrew Rambaut: Institute of Evolutionary Biology, University of Edinburgh
Marc A. Suchard: Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles

DOI: https://doi.org/10.1038/s41467-020-18877-9
Journal volume & issue: Vol. 11, no. 1
pp. 1 – 14

Abstract

Read online

Spatiotemporal sampling gaps in existing pathogen genomic data limits their use in understanding epidemiological patterns. Here, the authors apply a phylogeographic approach with SARS-CoV-2 genomes to accurately reproduce pathogen spread by accounting for spatial biases and travel history of the individual.

Published in Nature Communications

ISSN: 2041-1723 (Online)
Publisher: Nature Portfolio
Country of publisher: United Kingdom
LCC subjects: Science
Website: https://www.nature.com/ncomms/

About the journal