Emerging dynamics from high-resolution spatial numerical epidemics

  1. Olivier Thomine  Is a corresponding author
  2. Samuel Alizon  Is a corresponding author
  3. Corentin Boennec  Is a corresponding author
  4. Marc Barthelemy  Is a corresponding author
  5. Mircea Sofonea  Is a corresponding author
  1. Aix-Marseille Université / CNRS LIS, France
  2. IRD/MIVEGEC, France
  3. Institut de physique théorique, France
  4. Montpellier University, France

Abstract

Simulating nationwide realistic individual movements with a detailed geographical structure can help optimize public health policies. However, existing tools have limited resolution or can only account for a limited number of agents. We introduce Epidemap, a new framework that can capture the daily movement of more than 60 million people in a country at a building-level resolution in a realistic and computationally efficient way. By applying it to the case of an infectious disease spreading in France, we uncover hitherto neglected effects, such as the emergence of two distinct peaks in the daily number of cases or the importance of local density in the timing of arrival of the epidemic. Finally, we show that the importance of super-spreading events strongly varies over time.

Data availability

The raw data associated with the 100 simulations performed and the Rscripts used to generate the figures are available from theZenodo repository at https://zenodo.org/record/5542171 ( results.zip ).

The following data sets were generated

Article and author information

Author details

  1. Olivier Thomine

    Aix-Marseille Université / CNRS LIS, Marseille, France
    For correspondence
    olivier.thomine@protonmail.com
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4847-3224
  2. Samuel Alizon

    IRD/MIVEGEC, Montpellier, France
    For correspondence
    samuel.alizon@ird.fr
    Competing interests
    The authors declare that no competing interests exist.
  3. Corentin Boennec

    IRD/MIVEGEC, Montpellier, France
    For correspondence
    corentin.boennec@ird.fr
    Competing interests
    The authors declare that no competing interests exist.
  4. Marc Barthelemy

    Institut de physique théorique, Saclay, France
    For correspondence
    marc.barthelemy@ipht.fr
    Competing interests
    The authors declare that no competing interests exist.
  5. Mircea Sofonea

    Montpellier University, Montpellier, France
    For correspondence
    mircea.sofonea@umontpellier.fr
    Competing interests
    The authors declare that no competing interests exist.

Funding

Région Occitanie Pyrénées-Méditerranée

  • Samuel Alizon

Agence Nationale de la Recherche (PhyEpi project)

  • Samuel Alizon

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Talía Malagón, McGill University, Canada

Publication history

  1. Received: June 18, 2021
  2. Accepted: October 7, 2021
  3. Accepted Manuscript published: October 15, 2021 (version 1)
  4. Version of Record published: November 4, 2021 (version 2)

Copyright

© 2021, Thomine et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Olivier Thomine
  2. Samuel Alizon
  3. Corentin Boennec
  4. Marc Barthelemy
  5. Mircea Sofonea
(2021)
Emerging dynamics from high-resolution spatial numerical epidemics
eLife 10:e71417.
https://doi.org/10.7554/eLife.71417