Quantifying pupil-to-pupil SARS-CoV-2 transmission and the impact of lateral flow testing in English secondary schools

  1. Trystan Leng
  2. Edward M. Hill
  3. Alex Holmes
  4. Emma Southall
  5. Robin N. Thompson
  6. Michael J. Tildesley
  7. Matt J. Keeling
  8. Louise Dyson

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Abstract

A range of measures have been implemented to control within-school SARS-CoV-2 transmission in England, including the self-isolation of close contacts and twice weekly mass testing of secondary school pupils using lateral flow device tests (LFTs). Despite reducing transmission, isolating close contacts can lead to high levels of absences, negatively impacting pupils. To quantify pupil-to-pupil SARS-CoV-2 transmission and the impact of implemented control measures, we fit a stochastic individual-based model of secondary school infection to both swab testing data and secondary school absences data from England, and then simulate outbreaks from 31st August 2020 until 23rd May 2021. We find that the pupil-to-pupil reproduction number, R s c h o o l , has remained below 1 on average across the study period, and that twice weekly mass testing using LFTs has helped to control pupil-to-pupil transmission. We also explore the potential benefits of alternative containment strategies, finding that a strategy of repeat testing of close contacts rather than isolation, alongside mass testing, substantially reduces absences with only a marginal increase in pupil-to-pupil transmission.

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  1. Version published to 10.1038/s41467-022-28731-9
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    SciScore for 10.1101/2021.07.09.21260271: (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
    We performed the model fitting, model simulations, and visualisation of results using MATLAB 2019b.
    MATLAB
    suggested: (MATLAB, RRID:SCR_001622)
    As such infections that are confirmed by PRC but where the S-gene is not detected (often termed as ‘S-gene failures’) provide a key indicator for the geographic spread of the Alpha variant.
    PRC
    suggested: None

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

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    Accordingly, our study has several limitations. Regarding transmission, our model captures the impact of community prevalence on within-school transmission, but does not capture the impact of within-school transmission on community prevalence. In reality, within-school epidemics may increase community prevalence in extremely local areas (smaller than that of an LTLA), which would then be expected to increase transmission in schools as a damped feed-back loop. Our study assumes homogeneous onwards transmission rates from infected pupils within a given secondary school. In reality, onwards transmission rates are likely heterogeneous between pupils, with transmission rates likely a function of viral load 57 which is heterogeneous both in time and between individuals. Previous studies accounting for this heterogeneity, through the incorporation of within-host viral dynamics 28 obtained similar results to our previous study 27, though the inclusion of heterogeneity may impact the cluster sizes of epidemics in schools 58. Regarding testing, our model assumes that the proportion of pupils taking an LFT test on a given day is equivalent to the local proportion of 10-19 year olds in that school’s LTLA taking an LFT test on a given day, i.e. we assume uptake is homogeneous across schools within a region. In reality, there may be significant heterogeneity between schools even within a local area. Further, we assume that pupils have a given probability of taking an LFT test to satisfy a ...

    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 10.1101/2021.07.09.21260271v1 on medRxiv