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

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  • Paul Elliott

    (School of Public Health, Imperial College London
    MRC Centre for Environment and Health, School of Public Health, Imperial College London
    Imperial College Healthcare NHS Trust
    National Institute for Health Research Imperial Biomedical Research Centre)

  • Oliver Eales

    (School of Public Health, Imperial College London
    MRC Centre for Global infectious Disease Analysis
    Imperial College London)

  • Barbara Bodinier

    (School of Public Health, Imperial College London
    MRC Centre for Environment and Health, School of Public Health, Imperial College London)

  • David Tang

    (School of Public Health, Imperial College London
    MRC Centre for Environment and Health, School of Public Health, Imperial College London)

  • Haowei Wang

    (School of Public Health, Imperial College London
    MRC Centre for Global infectious Disease Analysis
    Imperial College London)

  • Jakob Jonnerby

    (School of Public Health, Imperial College London
    National Heart and Lung Institute, Imperial College Healthcare NHS Trust)

  • David Haw

    (School of Public Health, Imperial College London
    MRC Centre for Global infectious Disease Analysis
    Imperial College London)

  • Joshua Elliott

    (Imperial College Healthcare NHS Trust
    Imperial College London)

  • Matthew Whitaker

    (School of Public Health, Imperial College London
    MRC Centre for Environment and Health, School of Public Health, Imperial College London)

  • Caroline E. Walters

    (School of Public Health, Imperial College London
    MRC Centre for Global infectious Disease Analysis
    Imperial College London)

  • Christina Atchison

    (School of Public Health, Imperial College London
    Imperial College Healthcare NHS Trust)

  • 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
    Imperial College Healthcare NHS Trust
    National Institute for Health Research Imperial Biomedical Research Centre
    MRC Centre for Global infectious Disease Analysis)

  • Ara Darzi

    (Imperial College Healthcare NHS Trust
    National Institute for Health Research Imperial Biomedical Research Centre
    Institute of Global Health Innovation, Imperial College London)

  • Graham S. Cooke

    (Imperial College Healthcare NHS Trust
    National Institute for Health Research Imperial Biomedical Research Centre
    Imperial College London)

  • Marc Chadeau-Hyam

    (School of Public Health, Imperial College London
    MRC Centre for Environment and Health, School of Public Health, Imperial College London)

  • Christl A. Donnelly

    (School of Public Health, Imperial College London
    MRC Centre for Global infectious Disease Analysis
    Imperial College London
    University of Oxford)

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.

Suggested Citation

  • 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 , 2022. "Dynamics of a national Omicron SARS-CoV-2 epidemic during January 2022 in England," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-32121-6
    DOI: 10.1038/s41467-022-32121-6
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