Rapid increase in Omicron infections in England during December 2021: REACT-1 study

Abstract

The unprecedented rise in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections during December 2021 was concurrent with rapid spread of the Omicron variant in England and globally. We analyzed the prevalence of SARS-CoV-2 and its dynamics in England from the end of November to mid-December 2021 among almost 100,000 participants in the REACT-1 study. Prevalence was high with rapid growth nationally and particularly in London during December 2021, with an increasing proportion of infections due to Omicron. We observed large decreases in swab positivity among mostly vaccinated older children (12 to 17 years) relative to unvaccinated younger children (5 to 11 years), and in adults who received a third (booster) vaccine dose versus two doses. Our results reinforce the importance of vaccination and booster campaigns, although additional measures have been needed to control the rapid growth of the Omicron variant.

Fig. 1.. Dynamics of the prevalence of SARS-CoV-2 swab positivity in England.

(A) Comparison of exponential model fits to round 16 overall (green), round 16 from 23-30 November (blue) and from 1 December onwards (red) in addition to a P-spline model fit to all rounds of REACT-1 (black, shown here only for rounds 14, 15 and 16). Shaded blue and red regions show the 95% posterior credible interval for the exponential models, 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 and round 16 and the prevalence of swab positivity is shown (Y axis) on a log scale. Weighted observations (black dots) and 95% confidence intervals (vertical lines) are also shown. (B) P-spline models for those aged 17 years and under (red), 18 to 54 years (blue) and 55 years and over (green). (C) Weighted prevalence of swab positivity by age group for round 15 and round 16. Bars show the prevalence point estimates (grey for round 15 and orange for round 16), and the vertical lines represent the 95% confidence intervals.

Fig. 2.. Spatio-temporal distribution of SARS-CoV-2 prevalence in England.

(A) Weighted prevalence of swab positivity by region for round 15 and round 16 . Bars represent prevalence point estimates (grey for round 15 and orange for round 16), and the vertical lines the corresponding 95% confidence intervals. (B) P-spline models fit to all rounds of REACT-1 for each of the nine regions separately. Shown here only for the period of round 14, round 15 and round 16. Shaded regions show 50% (dark shade) and 95% (light shade) posterior credible interval for the P-spline models. (C) Neighborhood smoothed average prevalence by lower-tier local authority area for round 16. Neighborhood prevalence calculated from nearest neighbors (the median number of neighbors within 30 km in the study). Average neighborhood prevalence displayed for individual lower-tier local authorities for the whole of England and for South West and London. 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.

Fig. 3.. Geographical and temporal distribution of Delta and Omicron variants in England.

The geographical distribution was based on the postcode of the participant’s home address (jittered to protect personal data) of the (N = 756) positive swabs with determined lineages and at least 50% genome coverage. Delta infections are presented in green, and Omicron infections in orange. Results are presented for (A) the (N=378) infections obtained from 23 November to 30 November 2021, (B) the (N=197) infections obtained in swabs from 1 December to 6 December 2021, (C) the (N=118) infections obtained in swabs from 7 December to 12 December 2021 and (D) for the (N=63) infections obtained in swabs from 13 to 17 December 2021. (E) Daily proportion of Omicron infections among positive swabs with determined lineage and at least 50% genome coverage in round 16. Point estimates are represented (dots) along with 95% confidence intervals (vertical lines). Smoothed estimates of the proportion are also shown (solid line) together with their 95% credible intervals (shaded regions). 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.