Dynamics of competing SARS-CoV-2 variants during the Omicron epidemic in England

The SARS-CoV-2 pandemic has been characterised by the regular emergence of genomic variants. With natural and vaccine-induced population immunity at high levels, evolutionary pressure favours variant able to evade SARS-CoV-2 neutralising antibodies. The Omicron variant (first detected in November 2021) exhibited a high degree of immune evasion, leading to increased infection rates worldwide. However, estimates of the magnitude of this Omicron wave have relied on routine testing data, which are prone to several biases. Using data from the Real-time Assessment of Community Transmission-1 (REACT-1) study, a series of cross-sectional surveys assessing prevalence of SARS-CoV-2 infection in England, we estimated the dynamics of England’s Omicron wave (from 9 September 2021 to 1 March 2022). We estimate an initial peak in national Omicron prevalence of 6.89% (5.34%, 10.61%) during January 2022, followed by a resurgence in SARS-CoV-2 infections as the more transmissible Omicron sub-lineage, BA.2 replaced B.1 and BA.1. Assuming the emergence of further distinct variants, intermittent episodes of similar magnitudes may become the ‘new normal’.

Oliver Eales, Leonardo de Oliveira Martins, Andrew J. Page, Haowei Wang, Barbara Bodnier, David Tang, David Haw, Jakob Jonnerby, Christina Atchison, Deborah Ashby, Wendy Barclay, Graham Taylor, Graham Cooke, Helen Ward, Ara Darzi, Steven Riley, Paul Elliott, Christl A. Donnelly, Marc Chadeau-Hyam