Correcting the reproduction number for time-varying tests: A proposal and an application to COVID-19 in France

  1. Christelle Baunez
  2. Mickaël Degoulet
  3. Stéphane Luchini
  4. Matteo L. Pintus
  5. Patrick A. Pintus
  6. Miriam Teschl

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Abstract

We provide a novel way to correct the effective reproduction number for the time-varying amount of tests, using the acceleration index (Baunez et al., 2021) as a simple measure of viral spread dynamics. Not correcting results in the reproduction number being a biased estimate of viral acceleration and we provide a formal decomposition of the resulting bias, involving the useful notions of test and infectivity intensities. When applied to French data for the COVID-19 pandemic (May 13, 2020—October 26, 2022), our decomposition shows that the reproduction number, when considered alone, characteristically underestimates the resurgence of the pandemic, compared to the acceleration index which accounts for the time-varying volume of tests. Because the acceleration index aggregates all relevant information and captures in real time the sizable time variation featured by viral circulation, it is a more parsimonious indicator to track the dynamics of an infectious disease outbreak in real time, compared to the equivalent alternative which would combine the reproduction number with the test and infectivity intensities.

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  1. Version published to 10.1371/journal.pone.0281943
  2. Version published to 10.1101/2020.12.01.20241570v5 on medRxiv
  3. Version published to 10.1101/2020.12.01.20241570v4 on medRxiv
  4. Version published to 10.1101/2020.12.01.20241570v3 on medRxiv
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    SciScore for 10.1101/2020.12.01.20241570: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    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: 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.

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  6. Version published to 10.1101/2020.12.01.20241570v1 on medRxiv
  7. Version published to 10.1101/2020.12.01.20241570v2 on medRxiv