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, Wendy Barclay, Graham Taylor, Helen Ward, Ara Darzi, Graham S. Cooke, Marc Chadeau-Hyam () and Christl A. Donnelly ()
Additional contact information
Paul Elliott: School of Public Health, Imperial College London
Oliver Eales: School of Public Health, Imperial College London
Barbara Bodinier: School of Public Health, Imperial College London
David Tang: School of Public Health, Imperial College London
Haowei Wang: School of Public Health, Imperial College London
Jakob Jonnerby: School of Public Health, Imperial College London
David Haw: School of Public Health, Imperial College London
Joshua Elliott: Imperial College Healthcare NHS Trust
Matthew Whitaker: School of Public Health, Imperial College London
Caroline E. Walters: School of Public Health, Imperial College London
Christina Atchison: School of Public Health, Imperial College London
Peter J. Diggle: Lancaster University, UK and Health Data Research
Andrew J. Page: Quadram Institute
Alexander J. Trotter: Quadram Institute
Deborah Ashby: School of Public Health, Imperial College London
Wendy Barclay: Imperial College London
Graham Taylor: Imperial College London
Helen Ward: School of Public Health, Imperial College London
Ara Darzi: Imperial College Healthcare NHS Trust
Graham S. Cooke: Imperial College Healthcare NHS Trust
Marc Chadeau-Hyam: School of Public Health, Imperial College London
Christl A. Donnelly: School of Public Health, Imperial College London

Nature Communications, 2022, vol. 13, issue 1, 1-10

Abstract: 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.

Date: 2022
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DOI: 10.1038/s41467-022-32121-6

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