Dynamics of a national Omicron SARS-CoV-2 epidemic during January 2022 in England
Paul Elliott, Oliver Eales, Barbara Bodinier, David Tang, Haowei Wang, Jakob Jonnerby, David Haw, Joshua Elliott, Matthew Whitaker, Caroline E. Walters, Christina Atchison, Peter J. Diggle, Andrew J. Page, Alexander J. Trotter, Deborah Ashby, William Barclay, Graham P. Taylor, Helen Ward, Ara Darzi, Graham Cooke, Marc Chadeau‐Hyam, Christl A. Donnelly
Abstract
Rapid transmission of the SARS-CoV-2 Omicron variant has led to record-breaking case incidence rates around the world. Since May 2020, the REal-time Assessment of Community Transmission-1 (REACT-1) study tracked the spread of SARS-CoV-2 infection in England through RT-PCR of self-administered throat and nose swabs from randomly-selected participants aged 5 years and over. In January 2022, we found an overall weighted prevalence of 4.41% (n = 102,174), three-fold higher than in November to December 2021; we sequenced 2,374 (99.2%) Omicron infections (19 BA.2), and only 19 (0.79%) Delta, with a growth rate advantage for BA.2 compared to BA.1 or BA.1.1. Prevalence was decreasing overall (reproduction number R = 0.95, 95% credible interval [CrI], 0.93, 0.97), but increasing in children aged 5 to 17 years (R = 1.13, 95% CrI, 1.09, 1.18). In England during January 2022, we observed unprecedented levels of SARS-CoV-2 infection, especially among children, driven by almost complete replacement of Delta by Omicron.