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 and Marc A. Suchard ()
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Philippe Lemey: Laboratory of Clinical and Evolutionary Virology
Samuel L. Hong: Laboratory of Clinical and Evolutionary Virology
Verity Hill: University of Edinburgh
Guy Baele: 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: University of Edinburgh
John T. McCrone: University of Edinburgh
Kristian G. Andersen: Scripps Research
Michael Worobey: University of Arizona
Martha I. Nelson: National Institutes of Health
Andrew Rambaut: University of Edinburgh
Marc A. Suchard: University of California Los Angeles

Nature Communications, 2020, vol. 11, issue 1, 1-14

Abstract: Abstract Spatiotemporal bias in genome sampling can severely confound discrete trait phylogeographic inference. This has impeded our ability to accurately track the spread of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, despite the availability of unprecedented numbers of SARS-CoV-2 genomes. Here, we present an approach to integrate individual travel history data in Bayesian phylogeographic inference and apply it to the early spread of SARS-CoV-2. We demonstrate that including travel history data yields i) more realistic hypotheses of virus spread and ii) higher posterior predictive accuracy compared to including only sampling location. We further explore methods to ameliorate the impact of sampling bias by augmenting the phylogeographic analysis with lineages from undersampled locations. Our reconstructions reinforce specific transmission hypotheses suggested by the inclusion of travel history data, but also suggest alternative routes of virus migration that are plausible within the epidemiological context but are not apparent with current sampling efforts.

Date: 2020
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DOI: 10.1038/s41467-020-18877-9

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