Details

Autor(en) / Beteiligte

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

Titel

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

Ist Teil von

• Nature communications, 2020-10, Vol.11 (1), p.5110-5110, Article 5110

Ort / Verlag

England: Nature Publishing Group

Erscheinungsjahr

2020

Quelle

MEDLINE

Beschreibungen/Notizen

• 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.