Epidemiological monitoring and control perspectives: application of a parsimonious modelling framework to the COVID-19 dynamics in France

  1. Mircea T. Sofonea
  2. Bastien Reyné
  3. Baptiste Elie
  4. Ramsès Djidjou-Demasse
  5. Christian Selinger
  6. Yannis Michalakis
  7. Samuel Alizon

Reviewed by

Read the full article See related articles

Listed in

Log in to save this article

Abstract

SARS-Cov-2 virus has spread over the world creating one of the fastest pandemics ever. The absence of immunity, asymptomatic transmission, and the relatively high level of virulence of the COVID-19 infection it causes led to a massive flow of patients in intensive care units (ICU). This unprecedented situation calls for rapid and accurate mathematical models to best inform public health policies. We develop an original parsimonious model that accounts for the effect of the age of infection on the natural history of the disease. Analysing the ongoing COVID-19 in France, we estimate the value of the key epidemiological parameters, such as the basic reproduction number , and the efficiency of the national control strategy. We then use our deterministic model to explore several scenarios posterior to lock-down lifting and compare the efficiency of non pharmaceutical interventions (NPI) described in the literature.

Article activity feed

  1. ScreenIT

    SciScore for 10.1101/2020.05.22.20110593: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    No key resources detected.

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    This limitation can become strong if the epidemic grows in size to infect a large proportion of the population. Second, there is no specification of the public health control measures implemented: all the options (quarantine of confirmed cases, adoption of barrier measures, social distancing: closing of schools and universities, banning of gatherings, etc.) are combined to reduce the contact rate. We also neglected fomite transmission (see Ferretti et al. (2020) for an example) and assumed perfect and lifelong immunity against reinfection due to currently insufficient data on immunity. One simplifying assumption we made is that mortality probabilities do not vary over time, whereas in practice hospital saturation could affect mortality, whether related to COVID-19 or not. In terms of outlook, this work lays the foundation for an online application soon to be released, as an update of the earlier version COVIDSIM-FR (ETE Modelling Team, 2020a). Next challenges include taking to account for possible changes in parameter values with time, mainly detecting and estimating seasonal effects. If these are of significant impact, model fitting could be adapted, either by estimating parameters within defined time windows or by left-censoring the data as time goes by. Lastly, the NPI analysis exposed in this work sets the ground for the exploration of finely tuned public health measures accounting for spatial heterogeneity and combining advantages of adaptive, periodic and group-differen...

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  2. Version published to 10.1101/2020.05.22.20110593v1 on medRxiv