The rapid replacement of the Delta variant by Omicron (B.1.1.529) in England

The emergence of the B.1.1.529 (Omicron) variant caused international concern due to its rapid spread in Southern Africa. It was unknown whether this variant would replace or co-exist with (either transiently or long-term) the then-dominant Delta variant on its introduction to England. We developed a set of hierarchical logistic growth models to describe changes in the frequency of S gene target failure (SGTF) PCR tests, which was a proxy for Omicron. The doubling time of SGTF cases peaked at 1.56 days (95% CI: 1.49, 1.63) on the 5(th) of December, while triple positive cases were halving every 5.82 days (95% CI: 5.11, 6.67) going into Christmas 2021. We were unable to characterize the replacement of Delta by Omicron with a single rate. The replacement rate decreased by 53.56% (95% CrI: 45.38, 61.01) between the 14(th) and 15(th) of December, meaning the competitive advantage of Omicron approximately halved. Preceding the changepoint, Omicron was replacing Delta 16.24% (95% CrI: 9.72, 23.41) faster in those with two or more vaccine doses, indicative of vaccine escape being a substantial component of the competitive advantage. Despite the slowdown, Delta had almost entirely been replaced in England within a month of the first sequenced domestic case. The synchrony of changepoints across regions at various stages of Omicron epidemics suggests that the growth rate advantage was not attenuated due to biological mechanisms related to strain competition. The step-change in replacement could have resulted from behavioral changes, potentially elicited by public health messaging or policies, that differentially affected Omicron.