Viral mutation, contact rates and testing: a DCM study of fluctuations

  1. Karl J. Friston
  2. Anthony Costello
  3. Guillaume Flandin
  4. Adeel Razi

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Abstract

This report considers three mechanisms that might underlie the course of the secondary peak of coronavirus infections in the United Kingdom. It considers: (i) fluctuations in transmission strength; (ii) seasonal fluctuations in contact rates and (iii) fluctuations in testing. Using dynamic causal modelling, we evaluated the contribution of all combinations of these three mechanisms using Bayesian model comparison. We found overwhelming evidence for the combination of all mechanisms, when explaining 16 types of data. Quantitatively, there was clear evidence for an increase in transmission strength of 57% over the past months (e.g., due to viral mutation), in the context of increased contact rates (e.g., rebound from national lockdowns) and increased test rates (e.g., due to the inclusion of lateral flow tests). Models with fluctuating transmission strength outperformed models with fluctuating contact rates. However, the best model included all three mechanisms suggesting that the resurgence during the second peak can be explained by an increase in effective contact rate that is the product of a rebound of contact rates following a national lockdown and increased transmission risk due to viral mutation.

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  1. ScreenIT

    SciScore for 10.1101/2021.01.10.21249520: (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: Thank you for sharing your code.

    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.

    About SciScore

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  2. Version published to 10.1101/2021.01.10.21249520 on medRxiv