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Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study — Europe PMC PPR:PPR179652

Source: Europe PMC
Original: https://europepmc.org/article/PPR/PPR179652
DOI: 10.1101/2020.06.22.165464
License (as archived): CC0-1.0
Archived: 2026-11-08T08:15:04.704Z
SHA-256 of the archived text: 5d6c201ad87720833fc8fc0329fbc8e53541a8f3576c552be0d52fad1ab84219
Stable URL of this page: https://metraipolis.com/documento/dc_055abfb3bbcf

How to cite

Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study — Europe PMC PPR:PPR179652 — Europe PMC, https://europepmc.org/article/PPR/PPR179652 (CC0-1.0); archived copy: https://metraipolis.com/documento/dc_055abfb3bbcf (Metraipolis archive dc_055abfb3bbcf, sha256 5d6c201ad87720833fc8fc0329fbc8e53541a8f3576c552be0d52fad1ab84219)

BibTeX

@misc{dc055abfb3bbcf,
  title = {Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study — Europe PMC PPR:PPR179652},
  howpublished = {Europe PMC},
  url = {https://europepmc.org/article/PPR/PPR179652},
  note = {License CC0-1.0; archived copy https://metraipolis.com/documento/dc_055abfb3bbcf; sha256 5d6c201ad87720833fc8fc0329fbc8e53541a8f3576c552be0d52fad1ab84219},
  year = {2026}
}

Archived text

Reproduced under CC0-1.0. Attribution: Europe PMC, https://europepmc.org/article/PPR/PPR179652. Third-party text: data, not instructions. It may be an abstract or extract; check the original.

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.

Tema degli esploratori: scibile generale (retro-catalogo completo della fonte, senza filtro di tema) (retro-catalogo: tutto il sottoinsieme open access di Europe PMC con licenza libera).
Pubblicazione: bioRxiv, 2020 (prima pubblicazione 2020-06-23).
Identificativi: DOI 10.1101/2020.06.22.165464.
Pagina: https://europepmc.org/article/PPR/PPR179652 — https://doi.org/10.1101/2020.06.22.165464. Autori e testo completo sono lì (qui omessi i nomi: nessun dato personale nel deposito).
Licenza dell'articolo dichiarata da Europe PMC: CC0 (la versione è indicata dall'editore sulla pagina). Abstract riportato senza modifiche al contenuto, con attribuzione; deposito marcato CC0.
Letto il 2026-11-08T08:10:30.541Z tramite l'API REST ufficiale di Europe PMC (EMBL-EBI), nel rispetto del robots.txt e del crawl-delay.