SIR model for assessing the impact of the advent of Omicron and mitigating measures on infection pressure and hospitalization needs

  1. Jan-Diederik van Wees
  2. Martijn van der Kuip
  3. Sander Osinga
  4. Bart Keijser
  5. David van Westerloo
  6. Maurice Hanegraaf
  7. Maarten Pluymaekers
  8. Olwijn Leeuwenburgh
  9. Logan Brunner
  10. Marceline Tutu van Furth

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Abstract

Background

On 26 November 2021, the world health organization (WHO) designated the coronavirus SARS-CoV-2 B.1.1.529 a variant of concern, named Omicron (WHO, 2021a). As of December 16, Omicron has been detected in 89 countries (WHO, 2021b). The thread posed by Omicron is highly uncertain.

Methods and findings

For the analysis of the impact of Omicron on infection pressure and hospitalization needs we developed an open-source stochastic SIR (Susceptible-Infectious-Removed) fast-model for simulating the transmission in the transition stage from the prevailing variant (most often Delta) to Omicron. The model is capable to predict trajectories of infection pressure and hospitalization needs, considering (a) uncertainties for the (Omicron) parametrization, (b) pre-existing vaccination and/or partial immunity status of the population, and demographic specific aspects regarding reference hospitalization needs, (c) effects of mitigating measures including social distancing and accelerated vaccination (booster) campaigns.

Conclusions

The SIR model approach yields results in fair agreement with Omicron transmission characteristics observed in South Africa and prognosis results in Europe (UK and Netherlands). The equations underlying the SIR formulation allows to effectively explore the effect of Omicron parametrization on anticipated infection growth rates and hospitalization rates relative to the prevailing variant. The models are online available as open source on GitHub.

One Sentence Summary

fast-model for the impact of Omicron

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  1. Version published to 10.1101/2021.12.25.21268394v2 on medRxiv
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    SciScore for 10.1101/2021.12.25.21268394: (What is this?)

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

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    No key resources detected.

    Results from OddPub: Thank you for sharing your code and data.

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    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.

    Results from scite Reference Check: We found no unreliable references.

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  3. Version published to 10.1101/2021.12.25.21268394v1 on medRxiv