Fig. 4: Overview of the individual-based model components.

a A schematic of the modelled within-school mixing structure. Within a school, pupils interact with close contacts in their year at baseline rate α₀ = 1, with other pupils within their year at a relative rate α₁, and interact with other pupils in other years at a relative rate α₂, where 0 ≤ α₁, α₂ ≤ 1. b England divided by LTLA, with an example LTLA highlighted in purple. Each school is situated within an LTLA, which determines its probability of infection from the community, its relative frequency of the B.1.1.7 (Alpha) variant, and LFT uptake. Each LTLA contains multiple secondary schools, shown as blue dots (the number of blue dots shown is illustrative rather than an accurate depiction of the number of secondary schools in the highlighted LTLA). c A time-series of the percentage of that LTLA’s population testing positive on a PCR test on that day. A pupil’s probability of external infection on day t depends upon prevalence in the community, which we assume to be proportional to the proportion of the population in that LTLA testing PCR positive on day t + 5. d A time-series of the fitted estimate of the relative frequency of the B.1.1.7 variant in the example LTLA. The expected number of secondary infections from infected pupils depends upon the proportion of cases that are of the (more transmissible) B.1.1.7 variant, which varies through time and is dependent on the LTLA the school is situated within. Cross markers indicate the percentage of PCR tests from an LTLA that return an S-gene negative result out of those that return an S-gene status. Our model does not consider the impact of the B.1.617.2 (Delta) variant, which became the dominant variant in circulation during late May 2021, i.e. occurring beyond the time horizon of our analyses.