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High prevalence of SARS-CoV-2 swab positivity in England during September 2020: interim report of round 5 of REACT-1 study

By Steven Riley, Kylie E. C. Ainslie, Oliver Eales, Caroline E. Walters, Haowei Wang, Christina Atchison, Claudio Fronterre, Peter J. Diggle, Deborah Ashby, Christl Donnelly, Graham Cooke, Wendy S Barclay, Helen Ward, Ara Darzi, Paul Elliott

Posted 02 Oct 2020
medRxiv DOI: 10.1101/2020.09.30.20204727

BackgroundREACT-1 is a community survey of PCR confirmed swab-positivity for SARS-CoV-2 among random samples of the population in England. This interim report includes data from the fifth round of data collection currently underway for swabs sampled from the 18th to 26th September 2020. MethodsRepeated cross-sectional surveys of random samples of the population aged 5 years and over in England with sample size ranging from 120,000 to 160,000 people in each round of data collection. Collection of self-administered nose and throat swab for PCR and questionnaire data. Prevalence of swab-positivity by round and by demographic variables including age, sex, region, ethnicity. Estimation of reproduction number (R) between and within rounds, and time trends using exponential growth or decay model. Assessment of geographical clustering based on boundary-free spatial model. ResultsOver the 9 days for which data are available, we find 363 positives from 84,610 samples giving a weighted prevalence to date of 0.55% (0.47%, 0.64%) in round 5. This implies that 411,000 (351,000, 478,000) people in England are virus-positive under the assumption that the swab assay is 75% sensitive. Using data from the most recent two rounds, we estimate a doubling time of 10.6 (9.4, 12.0) days covering the period 20th August to 26th September, corresponding to a reproduction number R of 1.47 (1.40, 1.53). Using data only from round 5 we estimate a reproduction number of 1.06 (0.74, 1.46) with probability of 63% that R is greater than 1. Between rounds 4 and 5 there was a marked increase in unweighted prevalence at all ages. In the most recent data, prevalence was highest in the 18 to 24 yrs age group at 0.96% (0.68%, 1.36%). At 65+ yrs prevalence increased [~]7-fold between rounds 4 and 5 from 0.04% (0.03%, 0.07%) to 0.29% (0.23%, 0.37%). Prevalence increased in all regions between rounds 4 and 5, giving the highest unweighted prevalence in round 5 in the North West at 0.86% (0.69%, 1.06%). In London, prevalence increased [~]5-fold from 0.10% (0.06%, 0.17%) to 0.49% (0.36%, 0.68%). Regional R values ranged from 1.32 (1.16,1.50) in Yorkshire and the Humber to 1.63 (1.42, 1.88) in the East Midlands over the same period. In the most recent data, there was extensive clustering in the North West, Midlands and in and around London with pockets of clustering in other regions including the South West, North East and East of England. Odds of swab-positivity were [~]2-fold higher in people of Asian and Black ethnicity compared with white participants. ConclusionRapid growth has led to high prevalence of SARS-CoV-2 virus in England among all regions and age groups, including those age groups at highest risk. Although there is evidence of a recent deceleration in the epidemic, current levels of prevalence will inevitably result in additional hospitalisations and mortality in coming weeks. A re-doubling of public health efforts is needed to return to a declining phase of the epidemic.

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