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

  1. Oliver Eales
  2. Leonardo de Oliveira Martins
  3. Andrew J. Page
  4. Haowei Wang
  5. Barbara Bodinier
  6. David Tang
  7. David Haw
  8. Jakob Jonnerby
  9. Christina Atchison
  10. Deborah Ashby
  11. Wendy Barclay
  12. Graham Taylor
  13. Graham Cooke
  14. Helen Ward
  15. Ara Darzi
  16. Steven Riley
  17. Paul Elliott
  18. Christl A. Donnelly
  19. Marc Chadeau-Hyam

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Abstract

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 variants better 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 often 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 BA.1 and BA.1.1. Assuming the emergence of further distinct variants, intermittent epidemics of similar magnitudes may become the ‘new normal’.

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  1. Version published to 10.1038/s41467-022-32096-4
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  3. Version published to 10.1101/2022.03.29.22273042 on medRxiv