Fig. 3: Temporal and geographical distribution of SARS-CoV-2 swab positivity.

Comparison of an exponential model fit to SARS-CoV-2 swab-positivity data in round 17 (n = 102,174 participants with valid RT-PCR test results, in red), and a P-spline model fit to all rounds of REACT-1 (black, shown here only for rounds 14, 15, 16 and 17) (A). The solid red line represents the posterior mean estimate from the exponential growth model, and the shaded red region the 95% posterior credible interval for the exponential models. The solid black line represents the posterior mean smoothed estimate of the weighted prevalence and the shaded grey region shows 50% (dark grey) and 95% (light grey) posterior credible interval for the P-spline model. Results are presented for each day (X axis) of sampling for round 14, round 15, round 16 and round 17 and the weighted prevalence of swab-positivity is shown (Y axis) on a log scale. Weighted observations (black dots) and their 95% credible intervals (vertical lines) are also shown. Results from similar P-spline models for those aged 17 years and under (n = 10,638 participants with valid RT-PCR test results, in red), those aged 18 to 54 years inclusive (n = 39,676 participants with valid RT-PCR test results, in blue) and those aged 55 years and over (n = 51,860 participants with valid RT-PCR test results, in green) (B). Results are presented for round 16 and 17. Solid lines represent the posterior mean estimate of the smoothed weighted prevalence, and shaded regions represent the 50% (dark color) and 95% (light color) posterior credible interval of the smoothed prevalence. Weighted observations (dots) and 95% credible intervals (vertical lines) are also represented. Neighbourhood smoothed average SARS-CoV-2 swab-positivity prevalence by lower-tier local authority area for round 16 (C) and round 17 (D) in England. Neighbourhood prevalence calculated from nearest neighbours (the median number of neighbours within 30 km in the study). We represent the (jittered) location where we first detected BA.1 and sub-lineages (N = 56) in round 16 (C) and BA.2 and sub-lineages (N = 19) in round 17 (D). Regions: NE North East, NW North West, YH Yorkshire and The Humber, EM East Midlands, WM West Midlands, EE East of England, L London, SE South East, SW South West.