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Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework

Author

Listed:
  • Simon Dellicour

    (Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles
    Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven)

  • Sebastian Lequime

    (Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven)

  • Bram Vrancken

    (Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven)

  • Mandev S. Gill

    (Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven)

  • Paul Bastide

    (Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven)

  • Karthik Gangavarapu

    (Department of Immunology and Microbiology, The Scripps Research Institute)

  • Nathaniel L. Matteson

    (Department of Immunology and Microbiology, The Scripps Research Institute)

  • Yi Tan

    (Vanderbilt University Medical Center
    Infectious Diseases Group, J. Craig Venter Institute)

  • Louis Plessis

    (University of Oxford)

  • Alexander A. Fisher

    (University of California)

  • Martha I. Nelson

    (Fogarty International Center, National Institutes of Health)

  • Marius Gilbert

    (Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles)

  • Marc A. Suchard

    (University of California
    University of California
    University of California)

  • Kristian G. Andersen

    (Department of Immunology and Microbiology, The Scripps Research Institute
    Scripps Research Translational Institute)

  • Nathan D. Grubaugh

    (Yale School of Public Health)

  • Oliver G. Pybus

    (University of Oxford)

  • Philippe Lemey

    (Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven)

Abstract

Computational analyses of pathogen genomes are increasingly used to unravel the dispersal history and transmission dynamics of epidemics. Here, we show how to go beyond historical reconstructions and use spatially-explicit phylogeographic and phylodynamic approaches to formally test epidemiological hypotheses. We illustrate our approach by focusing on the West Nile virus (WNV) spread in North America that has substantially impacted public, veterinary, and wildlife health. We apply an analytical workflow to a comprehensive WNV genome collection to test the impact of environmental factors on the dispersal of viral lineages and on viral population genetic diversity through time. We find that WNV lineages tend to disperse faster in areas with higher temperatures and we identify temporal variation in temperature as a main predictor of viral genetic diversity through time. By contrasting inference with simulation, we find no evidence for viral lineages to preferentially circulate within the same migratory bird flyway, suggesting a substantial role for non-migratory birds or mosquito dispersal along the longitudinal gradient.

Suggested Citation

  • Simon Dellicour & Sebastian Lequime & Bram Vrancken & Mandev S. Gill & Paul Bastide & Karthik Gangavarapu & Nathaniel L. Matteson & Yi Tan & Louis Plessis & Alexander A. Fisher & Martha I. Nelson & Ma, 2020. "Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
  • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-19122-z
    DOI: 10.1038/s41467-020-19122-z
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    Cited by:

    1. Raphaëlle Klitting & Liana E. Kafetzopoulou & Wim Thiery & Gytis Dudas & Sophie Gryseels & Anjali Kotamarthi & Bram Vrancken & Karthik Gangavarapu & Mambu Momoh & John Demby Sandi & Augustine Goba & F, 2022. "Predicting the evolution of the Lassa virus endemic area and population at risk over the next decades," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    2. 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.
    3. Mark P. Khurana & Jacob Curran-Sebastian & Neil Scheidwasser & Christian Morgenstern & Morten Rasmussen & Jannik Fonager & Marc Stegger & Man-Hung Eric Tang & Jonas L. Juul & Leandro Andrés Escobar-He, 2024. "High-resolution epidemiological landscape from ~290,000 SARS-CoV-2 genomes from Denmark," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    4. Giulia Mencattelli & Marie Henriette Dior Ndione & Andrea Silverj & Moussa Moise Diagne & Valentina Curini & Liana Teodori & Marco Di Domenico & Rassoul Mbaye & Alessandra Leone & Maurilia Marcacci & , 2023. "Spatial and temporal dynamics of West Nile virus between Africa and Europe," Nature Communications, Nature, vol. 14(1), pages 1-11, December.

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