Cargando…
Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study.
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 avai...
Autores principales: | , , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cold Spring Harbor Laboratory
2020
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7315996/ https://www.ncbi.nlm.nih.gov/pubmed/32596695 http://dx.doi.org/10.1101/2020.06.22.165464 |
_version_ | 1783550360998117376 |
---|---|
author | Lemey, Philippe Hong, Samuel 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. |
author_facet | Lemey, Philippe Hong, Samuel 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. |
author_sort | Lemey, Philippe |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-7315996 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Cold Spring Harbor Laboratory |
record_format | MEDLINE/PubMed |
spelling | pubmed-73159962020-06-26 Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study. Lemey, Philippe Hong, Samuel 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. bioRxiv Article 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. Cold Spring Harbor Laboratory 2020-06-23 /pmc/articles/PMC7315996/ /pubmed/32596695 http://dx.doi.org/10.1101/2020.06.22.165464 Text en https://creativecommons.org/publicdomain/zero/1.0/This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license (https://creativecommons.org/publicdomain/zero/1.0/) . |
spellingShingle | Article Lemey, Philippe Hong, Samuel 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. Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study. |
title | Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study. |
title_full | Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study. |
title_fullStr | Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study. |
title_full_unstemmed | Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study. |
title_short | Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study. |
title_sort | accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a sars-cov-2 case study. |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7315996/ https://www.ncbi.nlm.nih.gov/pubmed/32596695 http://dx.doi.org/10.1101/2020.06.22.165464 |
work_keys_str_mv | AT lemeyphilippe accommodatingindividualtravelhistoryglobalmobilityandunsampleddiversityinphylogeographyasarscov2casestudy AT hongsamuel accommodatingindividualtravelhistoryglobalmobilityandunsampleddiversityinphylogeographyasarscov2casestudy AT hillverity accommodatingindividualtravelhistoryglobalmobilityandunsampleddiversityinphylogeographyasarscov2casestudy AT baeleguy accommodatingindividualtravelhistoryglobalmobilityandunsampleddiversityinphylogeographyasarscov2casestudy AT polettochiara accommodatingindividualtravelhistoryglobalmobilityandunsampleddiversityinphylogeographyasarscov2casestudy AT colizzavittoria accommodatingindividualtravelhistoryglobalmobilityandunsampleddiversityinphylogeographyasarscov2casestudy AT otooleaine accommodatingindividualtravelhistoryglobalmobilityandunsampleddiversityinphylogeographyasarscov2casestudy AT mccronejohnt accommodatingindividualtravelhistoryglobalmobilityandunsampleddiversityinphylogeographyasarscov2casestudy AT andersenkristiang accommodatingindividualtravelhistoryglobalmobilityandunsampleddiversityinphylogeographyasarscov2casestudy AT worobeymichael accommodatingindividualtravelhistoryglobalmobilityandunsampleddiversityinphylogeographyasarscov2casestudy AT nelsonmarthai accommodatingindividualtravelhistoryglobalmobilityandunsampleddiversityinphylogeographyasarscov2casestudy AT rambautandrew accommodatingindividualtravelhistoryglobalmobilityandunsampleddiversityinphylogeographyasarscov2casestudy AT suchardmarca accommodatingindividualtravelhistoryglobalmobilityandunsampleddiversityinphylogeographyasarscov2casestudy |