Trends in SARS-CoV-2 infection prevalence during England’s roadmap out of lockdown, January to July 2021

PLoS Computational Biology 18(11): e1010724

Abstract

Background

Following rapidly rising COVID-19 case numbers, England entered a national lockdown on 6 January 2021, with staged relaxations of restrictions from 8 March 2021 onwards.

Aim

We characterise how the lockdown and subsequent easing of restrictions affected trends in SARS-CoV-2 infection prevalence.

Methods

On average, risk of infection is proportional to infection prevalence. The REal-time Assessment of Community Transmission-1 (REACT-1) study is a repeat cross-sectional study of over 98,000 people every round (rounds approximately monthly) that estimates infection prevalence in England. We used Bayesian P-splines to estimate prevalence and the time-varying reproduction number (R_t) nationally, regionally and by age group from round 8 (beginning 6 January 2021) to round 13 (ending 12 July 2021) of REACT-1. As a comparator, a separate segmented-exponential model was used to quantify the impact on R_t of each relaxation of restrictions.

Results

Following an initial plateau of 1.54% until mid-January, infection prevalence decreased until 13 May when it reached a minimum of 0.09%, before increasing until the end of the study to 0.76%. Following the first easing of restrictions, which included schools reopening, the reproduction number R_t increased by 82% (55%, 108%), but then decreased by 61% (82%, 53%) at the second easing of restrictions, which was timed to match the Easter school holidays. Following further relaxations of restrictions, the observed R_t increased steadily, though the increase due to these restrictions being relaxed was offset by the effects of vaccination and also affected by the rapid rise of Delta. There was a high degree of synchrony in the temporal patterns of prevalence between regions and age groups.

Conclusion

High-resolution prevalence data fitted to P-splines allowed us to show that the lockdown was effective at reducing risk of infection with school holidays/closures playing a significant part.

Author Summary

Throughout the COVID-19 pandemic in England there has been a high rate of testing. However, the case data obtained from this mass testing is prone to many biases due to changing testing rates and behaviours. The REal-time Assessment of Community Transmission-1 (REACT-1) study instead tests random subsets of the population of England for SARS-CoV-2, providing a relatively unbiased signal of infection prevalence over time. Here we present the temporal analysis of rounds 8–13 of REACT-1, running from January to July 2021. During this period a national lockdown was introduced in England, followed by the staged relaxation of restrictions. We find that the lockdown was highly effective at reducing levels of infection prevalence in England, with prevalence declining until mid-May. However, as restrictions were gradually relaxed the reproduction number, R, increased to greater than 1 (the threshold for epidemic growth) and infection prevalence once more entered a phase of growth. Analysis of the step-changes in R after each restriction relaxation highlighted the significant effect that school holidays/closures likely had on R over this period. Additionally, we found that increases in R were likely offset by the high rates of vaccination that were achieved by July 2021.

Citation

Eales O, Wang H, Haw D, Ainslie KEC, Walters CE, Atchison C, et al. (2022) Trends in SARS-CoV-2 infection prevalence during England’s roadmap out of lockdown, January to July 2021. PLoS Comput Biol 18(11): e1010724. [DOI]