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Dynamics of a national Omicron SARS-CoV-2 epidemic during January 2022 in England

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  • Paul Elliott
  • Oliver Eales
  • Barbara Bodinier
  • David Tang
  • Haowei Wang
  • Jakob Jonnerby
  • David Haw
  • Joshua Elliott
  • Matthew Whitaker
  • Caroline E Walters
  • Christina Atchison
  • Andrew J Page
  • Alexander J Trotter
  • Deborah Ashby
  • Wendy Barclay
  • Graham Taylor
  • Helen Ward
  • Ara Darzi
  • Graham S Cooke
  • Marc Chadeau-Hyam
  • Christl A Donnelly
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Article number4500
<mark>Journal publication date</mark>3/08/2022
<mark>Journal</mark>Nature Communications
Issue number1
Volume13
Publication StatusPublished
<mark>Original language</mark>English

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. [Abstract copyright: © 2022. The Author(s).]