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

Author

Listed:
  • 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
    University of California Los Angeles
    University of California Los Angeles)

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.

Suggested Citation

  • 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 Ramb, 2020. "Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2," Nature Communications, Nature, vol. 11(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-18877-9
    DOI: 10.1038/s41467-020-18877-9
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    Cited by:

    1. Edyth Parker & Catelyn Anderson & Mark Zeller & Ahmad Tibi & Jennifer L. Havens & Geneviève Laroche & Mehdi Benlarbi & Ardeshir Ariana & Refugio Robles-Sikisaka & Alaa Abdel Latif & Alexander Watts & , 2022. "Regional connectivity drove bidirectional transmission of SARS-CoV-2 in the Middle East during travel restrictions," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    2. Jordan Douglas & David Winter & Andrea McNeill & Sam Carr & Michael Bunce & Nigel French & James Hadfield & Joep Ligt & David Welch & Jemma L. Geoghegan, 2022. "Tracing the international arrivals of SARS-CoV-2 Omicron variants after Aotearoa New Zealand reopened its border," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    3. Santiago Justo Arevalo & Carmen Sofia Uribe Calampa & Cinthy Jimenez Silva & Mauro Quiñones Aguilar & Remco Bouckaert & Joao Renato Rebello Pinho, 2023. "Phylodynamic of SARS-CoV-2 during the second wave of COVID-19 in Peru," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    4. Tiago Gräf & Alexander A. Martinez & Gonzalo Bello & Simon Dellicour & Philippe Lemey & Vittoria Colizza & Mattia Mazzoli & Chiara Poletto & Vanessa Leiko Oikawa Cardoso & Alexandre Freitas Silva & Fe, 2024. "Dispersion patterns of SARS-CoV-2 variants Gamma, Lambda and Mu in Latin America and the Caribbean," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    5. Andrew Holtz & Guy Baele & Hervé Bourhy & Anna Zhukova, 2023. "Integrating full and partial genome sequences to decipher the global spread of canine rabies virus," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    6. Benjamin Faucher & Chiara E. Sabbatini & Peter Czuppon & Moritz U. G. Kraemer & Philippe Lemey & Vittoria Colizza & François Blanquart & Pierre-Yves Boëlle & Chiara Poletto, 2024. "Drivers and impact of the early silent invasion of SARS-CoV-2 Alpha," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    7. Tamara Kaleta & Lisa Kern & Samuel Leandro Hong & Martin Hölzer & Georg Kochs & Julius Beer & Daniel Schnepf & Martin Schwemmle & Nena Bollen & Philipp Kolb & Magdalena Huber & Svenja Ulferts & Sebast, 2022. "Antibody escape and global spread of SARS-CoV-2 lineage A.27," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    8. Egon A. Ozer & Lacy M. Simons & Olubusuyi M. Adewumi & Adeola A. Fowotade & Ewean C. Omoruyi & Johnson A. Adeniji & Oluseyi A. Olayinka & Taylor J. Dean & Janet Zayas & Pavan P. Bhimalli & Michelle K., 2022. "Multiple expansions of globally uncommon SARS-CoV-2 lineages in Nigeria," Nature Communications, Nature, vol. 13(1), pages 1-13, December.

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