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. 2022 Jul 28;13:4375. doi: 10.1038/s41467-022-32096-4

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 3 — a Modelled proportion of Omicron lineages that are BA.1, BA.1.1 and BA.2, estimated for using a Bayesian multinomial logistic regression model. Estimates of proportion are shown with a central estimate (solid line) and 95% (shaded region) credible intervals. Point estimates of mean proportion (points) are shown with 95% confidence intervals (error bars) for each half round of REACT-1 with x-axis value set by the median date (jittered for all lineages for visualisation). b Modelled prevalence of BA.2 and non-BA.2 Omicron in England estimated using a mixed-effects Bayesian P-spline model. Estimates of prevalence are shown with a central estimate (solid line) and 95% (shaded region) credible intervals. Daily weighted estimates of mean prevalence (points) are shown with 95% credible intervals (error bars). c Rolling two-week average (prior two weeks) Reproduction number for BA.2 and non-BA.2 Omicron in England as inferred from the mixed-effects Bayesian P-spline model. Estimates are shown with a central estimate (solid line) and 50% (dark shaded region) and 95% (light shaded region) credible intervals. Dashed line shows R = 1 the threshold for epidemic growth. d Multiplicative advantage in the two-week average reproduction number for BA.2 vs non-BA.2 Omicron in England as inferred from the mixed-effects Bayesian P-spline model. Estimates are shown with a central estimate (solid line) and 50% (dark shaded region) and 95% (light shaded region) credible intervals.