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

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Dynamics of a national Omicron SARS-CoV-2 epidemic during January 2022 in England. / Elliott, Paul; Eales, Oliver; Bodinier, Barbara et al.
In: Nature Communications, Vol. 13, No. 1, 4500, 03.08.2022.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Harvard

Elliott, P, Eales, O, Bodinier, B, Tang, D, Wang, H, Jonnerby, J, Haw, D, Elliott, J, Whitaker, M, Walters, CE, Atchison, C, Diggle, PJ, 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

APA

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. J., 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

Vancouver

Elliott P, Eales O, Bodinier B, Tang D, Wang H, Jonnerby J et al. Dynamics of a national Omicron SARS-CoV-2 epidemic during January 2022 in England. Nature Communications. 2022 Aug 3;13(1):4500. doi: 10.1038/s41467-022-32121-6

Author

Elliott, Paul ; Eales, Oliver ; Bodinier, Barbara et al. / Dynamics of a national Omicron SARS-CoV-2 epidemic during January 2022 in England. In: Nature Communications. 2022 ; Vol. 13, No. 1.

Bibtex

@article{63aa1726c4db4b9a921d9e4dc39824e9,
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. [Abstract copyright: {\textcopyright} 2022. The Author(s).]",
keywords = "England - epidemiology, COVID-19 - epidemiology, Child, Specimen Handling, Humans, SARS-CoV-2, Base Sequence",
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 Diggle, {Peter J} 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",
month = aug,
day = "3",
doi = "10.1038/s41467-022-32121-6",
language = "English",
volume = "13",
journal = "Nature Communications",
issn = "2041-1723",
publisher = "Nature Publishing Group",
number = "1",

}

RIS

TY - JOUR

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 J

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 - 2022/8/3

Y1 - 2022/8/3

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

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

KW - England - epidemiology

KW - COVID-19 - epidemiology

KW - Child

KW - Specimen Handling

KW - Humans

KW - SARS-CoV-2

KW - Base Sequence

U2 - 10.1038/s41467-022-32121-6

DO - 10.1038/s41467-022-32121-6

M3 - Journal article

C2 - 35922409

VL - 13

JO - Nature Communications

JF - Nature Communications

SN - 2041-1723

IS - 1

M1 - 4500

ER -