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Twin peaks: the Omicron SARS-CoV-2 BA.1 and BA.2 epidemics in England

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Title: Twin peaks: the Omicron SARS-CoV-2 BA.1 and BA.2 epidemics in England
Authors: Elliott, P
Eales, O
Steyn, N
Tang, D
Bodinier, B
Wang, H
Elliott, J
Whitaker, M
Atchison, C
Diggle, P
Trotter, A
Ashby, D
Barclay, W
Taylor, G
Ward, H
Darzi, A
Cooke, G
Donnelly, C
Chadeau-Hyam, M
Item Type: Working Paper
Abstract: BACKGROUND Rapid transmission of the SARS-CoV-2 Omicron variant has led to record-breaking incidence rates around the world. Sub-lineages have been detected in many countries with BA.1 replacing Delta and BA.2 replacing BA.1. METHODS The REal-time Assessment of Community Transmission-1 (REACT-1) study has tracked SARS-CoV-2 infection in England using RT-PCR results from self-administered throat and nose swabs from randomly-selected participants aged 5+ years. Rounds of data collection were approximately monthly from May 2020 to March 2022. RESULTS In March 2022, weighted prevalence was 6.37% (N=109,181), more than twice that in February 2022 following an initial Omicron peak in January 2022. Of the lineages determined by viral genome sequencing, 3,382 (99.97%) were Omicron, including 346 (10.2%) BA.1, 3035 (89.7%) BA.2 and one (0.03%) BA.3 sub-lineage; the remainder (1, 0.03%) was Delta AY.4. The BA.2 Omicron sub-lineage had a growth rate advantage (compared to BA.1 and sub-lineages) of 0.11 (95% credible interval [CrI], 0.10, 0.11). Prevalence was increasing overall (reproduction number R=1.07, 95% CrI, 1.06, 1.09), with the greatest increase in those aged 55+ years (R=1.12, 95% CrI, 1.09, 1.14) among whom estimated prevalence on March 31, 2022 was 8.31%, nearly 20-fold the median prevalence since May 1, 2020. CONCLUSIONS We observed unprecedented levels of SARS-CoV-2 infection in England in March 2022 and an almost complete replacement of Omicron BA.1 by BA.2. The high and increasing prevalence in older adults may increase hospitalizations and deaths despite high levels of vaccination. (Funded by the Department of Health and Social Care in England.)
Issue Date: 6-Apr-2022
URI: http://hdl.handle.net/10044/1/96170
Copyright Statement: © 2022 The Author(s).
Keywords: SARS-CoV-2 coronavirus research
Publication Status: Published
Appears in Collections:Faculty of Medicine
Institute of Global Health Innovation
School of Public Health