Statistical and agent-based modelling of the transmissibility of different SARS-CoV-2 variants in England and impact of different interventions

  1. J. Panovska-Griffiths
  2. B. Swallow
  3. R. Hinch
  4. J. Cohen
  5. K. Rosenfeld
  6. R. M. Stuart
  7. L. Ferretti
  8. F. Di Lauro
  9. C. Wymant
  10. A. Izzo
  11. W. Waites
  12. R. Viner
  13. C. Bonell
  14. C. Fraser
  15. D. Klein
  16. C. C. Kerr
  17. The COVID-19 Genomics UK (COG-UK) Consortium

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Abstract

The English SARS-CoV-2 epidemic has been affected by the emergence of new viral variants such as B.1.177, Alpha and Delta, and changing restrictions. We used statistical models and the agent-based model Covasim, in June 2021, to estimate B.1.177 to be 20% more transmissible than the wild type, Alpha to be 50–80% more transmissible than B.1.177 and Delta to be 65–90% more transmissible than Alpha. Using these estimates in Covasim (calibrated 1 September 2020 to 20 June 2021), in June 2021, we found that due to the high transmissibility of Delta, resurgence in infections driven by the Delta variant would not be prevented, but would be strongly reduced by delaying the relaxation of restrictions by one month and with continued vaccination.

This article is part of the theme issue ‘Technical challenges of modelling real-life epidemics and examples of overcoming these’.

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  1. Version published to 10.1098/rsta.2021.0315
  2. ScreenIT

    SciScore for 10.1101/2021.12.30.21267090: (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

    Software and Algorithms
    SentencesResources
    In this study, we used Covasim’s default parameters and the “hybrid” network structure for England (see Section 2.4 of [9] for details), with the default data included in the model for English population age structure and household sizes.
    Covasim’s
    suggested: None
    Using Covasim version 3.0.7, we generated a population of 100,000 agents interacting over the four contact-network layers (households, workplaces, schools, and communities).
    Covasim
    suggested: None
    (ii) Modelling different SARS-CoV-2 variants: In our previous work we either modelled a single strain (wild type) of SARS-CoV-2 [15,17], or implicitly modelled the effect of two strains (wild type and Alpha variant) [18].
    SARS-CoV-2
    suggested: (BioLegend Cat# 946101, RRID:AB_2892515)
    These were necessary since the mobility changes in the Google reports stratify society in different ways to how we stratify society in the layers depicted in Figure 2(c).
    Google
    suggested: (Google, RRID:SCR_017097)
    ) hyperparameter optimisation framework in Python to search the 9-dimensional parameter space for optimal values that minimised the absolute difference between the model’s estimates of daily cases, deaths, and severe infections (representing hospitalisations), and the corresponding data on cumulative and daily infections by date reported, deaths within 28 days, and admissions to hospital by date reported between September 1, 2020 and June 20, 2021.
    Python
    suggested: (IPython, RRID:SCR_001658)

    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 10.1101/2021.12.30.21267090v1 on medRxiv