About: Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study

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About: Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study Goto Sponge NotDistinct Permalink

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study
Creator	Colizza, Vittoria Poletto, Chiara Rambaut, Andrew Lemey, Philippe Baele, Guy Nelson, Martha Andersen, Kristian Mccrone, John Suchard, Marc Hill, Verity Worobey, Michael Hong, Samuel O'toole, Áine
source	BioRxiv; Medline
abstract	Spatiotemporal bias in genome sequence sampling can severely confound phylogeographic inference based on discrete trait ancestral reconstruction. This has impeded our ability to accurately track the emergence and spread of SARS-CoV-2, the virus responsible for the COVID-19 pandemic. Despite the availability of unprecedented numbers of SARS-CoV-2 genomes on a global scale, evolutionary reconstructions are hindered by the slow accumulation of sequence divergence over its relatively short transmission history. When confronted with these issues, incorporating additional contextual data may critically inform phylodynamic reconstructions. Here, we present a new approach to integrate individual travel history data in Bayesian phylogeographic inference and apply it to the early spread of SARS-CoV-2, while also including global air transportation data. We demonstrate that including travel history data for each SARS-CoV-2 genome yields more realistic reconstructions of virus spread, particularly when travelers from undersampled locations are included to mitigate sampling bias. We further explore methods to ameliorate the impact of sampling bias by augmenting the phylogeographic analysis with lineages from undersampled locations in the analyses. 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. Although further research is needed to fully examine the performance of our travel-aware phylogeographic analyses with unsampled diversity and to further improve them, they represent multiple new avenues for directly addressing the colossal issue of sample bias in phylogeographic inference.
has issue date	2020-06-23(xsd:dateTime)
bibo:doi	10.1101/2020.06.22.165464
bibo:pmid	32596695
has license	biorxiv
sha1sum (hex)	cf162f18bef0530f30fc336929b540873c3c7fa4
schema:url	https://doi.org/10.1101/2020.06.22.165464
resource representing a document's title	Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study
has PubMed identifier	32596695
schema:publication	bioRxiv
resource representing a document's body	covid:cf162f18bef0530f30fc336929b540873c3c7fa4#body_text
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