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 Diggle; 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

doi:10.1038/s41467-022-32121-6

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 Diggle, Andrew J. Page, Alexander J. Trotter, Deborah Ashby, Wendy Barclay, Graham Taylor, Helen Ward, Ara Darzi, Graham S. CookeMarc Chadeau-Hyam, Christl A. Donnelly

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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.

Original language	English
Article number	4500
Journal	Nature Communications
Volume	13
Issue number	1
DOIs	https://doi.org/10.1038/s41467-022-32121-6
Publication status	Published - 1 Dec 2022
Externally published	Yes

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Elliott, P., Eales, O., Bodinier, B., Tang, D., Wang, H., Jonnerby, J., Haw, D., Elliott, J., Whitaker, M., Walters, C. E., Atchison, C., Diggle, P., Page, A. J., Trotter, A. J., Ashby, D., Barclay, W., Taylor, G., Ward, H., Darzi, A., ... Donnelly, C. A. (2022). Dynamics of a national Omicron SARS-CoV-2 epidemic during January 2022 in England. Nature Communications, 13(1), Article 4500. https://doi.org/10.1038/s41467-022-32121-6

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title = "Dynamics of a national Omicron SARS-CoV-2 epidemic during January 2022 in England",

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.",

author = "Paul Elliott and Oliver Eales and Barbara Bodinier and David Tang and Haowei Wang and Jakob Jonnerby and David Haw and Joshua Elliott and Matthew Whitaker and Walters, \{Caroline E.\} and Christina Atchison and Peter Diggle and Page, \{Andrew J.\} and Trotter, \{Alexander J.\} and Deborah Ashby and Wendy Barclay and Graham Taylor and Helen Ward and Ara Darzi and Cooke, \{Graham S.\} and Marc Chadeau-Hyam and Donnelly, \{Christl A.\}",

year = "2022",

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doi = "10.1038/s41467-022-32121-6",

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Elliott, P, Eales, O, Bodinier, B, Tang, D, Wang, H, Jonnerby, J, Haw, D, Elliott, J, Whitaker, M, Walters, CE, Atchison, C, Diggle, P, Page, AJ, Trotter, AJ, Ashby, D, Barclay, W, Taylor, G, Ward, H, Darzi, A, Cooke, GS, Chadeau-Hyam, M & Donnelly, CA 2022, 'Dynamics of a national Omicron SARS-CoV-2 epidemic during January 2022 in England', Nature Communications, vol. 13, no. 1, 4500. https://doi.org/10.1038/s41467-022-32121-6

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T1 - Dynamics of a national Omicron SARS-CoV-2 epidemic during January 2022 in England

AU - Elliott, Paul

AU - Eales, Oliver

AU - Bodinier, Barbara

AU - Tang, David

AU - Wang, Haowei

AU - Jonnerby, Jakob

AU - Haw, David

AU - Elliott, Joshua

AU - Whitaker, Matthew

AU - Walters, Caroline E.

AU - Atchison, Christina

AU - Diggle, Peter

AU - Page, Andrew J.

AU - Trotter, Alexander J.

AU - Ashby, Deborah

AU - Barclay, Wendy

AU - Taylor, Graham

AU - Ward, Helen

AU - Darzi, Ara

AU - Cooke, Graham S.

AU - Chadeau-Hyam, Marc

AU - Donnelly, Christl A.

PY - 2022/12/1

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N2 - 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.

AB - 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.

U2 - 10.1038/s41467-022-32121-6

DO - 10.1038/s41467-022-32121-6

M3 - Article

SN - 2041-1723

VL - 13

JO - Nature Communications

JF - Nature Communications

IS - 1

M1 - 4500

ER -

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

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