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 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’.


Supplementary
: Apple mobility indices Rolling 7-day average apple mobility indices in England, calculated from phone location data, for driving (red), transit (blue) and walking (green). Mobility indices have been scaled so that the maximum value reached in the period shown takes a value of 100.

Supplementary Figure 10: Maximum prevalence and date of maximum prevalence
The maximum prevalence of Omicron reached and the date at which it was reached inferred from the mixed-effects Bayesian P-spline model fitted to all data, and for the models fit to subsets of data by region and age-group. Estimates are shown for the median value (points) with 95% credible intervals (error-bars).

Supplementary Figure 11: Omicron vs Delta R t by region
Rolling two-week average (prior two weeks) Reproduction number for Omicron (blue) and Delta (red) in each region of England as inferred from mixed-effects Bayesian P-spline models. 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. Estimates for each lineage are only displayed for the period over which the lineage was detected in REACT-1 samples. Figure 12: Omicron vs Delta R t by age-group Rolling two-week average (prior two weeks) Reproduction number for Omicron (blue) and Delta (red) for each age-group in England as inferred from mixed-effects Bayesian P-spline models. 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. Estimates for each lineage are only displayed for the period over which the lineage was detected in REACT-1 samples. Figure 13: BA.2 vs non-BA.2 National growth rate and proportion graph A) Daily growth rate of BA.2 (purple), non-BA.2 Omicron (orange) and their additive difference (green) estimated from the mixed-effects Bayesian P-spline model fitted to rounds 17 and 18 of the data. Estimates are shown with a central estimate (solid line) and 95% credible intervals (shaded region). B) Modelled proportion of lineages identified as BA.2 in England estimated using a mixed-effects Bayesian P-spline model. Estimates are shown with a central estimate (solid line) and 95% credible intervals (shaded region). Daily estimates of the mean proportion of lineages BA.2 (points) are shown with 95% confidence intervals (error bars). Figure 14: BA.2 vs non-BA.2 prevalence by region Modelled prevalence of BA.2 (pink), non-BA.2 Omicron (green) and total prevalence (grey) in each region of England for rounds 17 and 18 estimated using mixed-effects Bayesian P-spline models. 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). (pink), non-BA.2 Omicron (green) and total prevalence (grey) for each age-group in England for rounds 17 and 18 estimated using mixed-effects Bayesian P-spline models. 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). Figure 18: BA.2 vs non-BA.2 proportion by age-group Modelled proportion of lineages identified as BA.2 by age-groups in England for rounds 17 and 18 estimated using mixed-effects Bayesian P-spline models. Estimates are shown with a central estimate (solid line) and 95% credible intervals (shaded region). Daily estimates of the mean proportion of lineages BA.2 (points) are shown with 95% confidence intervals (error bars). Figure 19: BA.2 vs non-BA.2 growth rate by age-group Daily growth rate of BA.2 (purple), non-BA.2 Omicron (orange) and their additive difference (green) estimated from mixed-effects Bayesian P-spline models fitted by age-group in England to rounds 17 and 18 of the data. Estimates are shown with a central estimate (solid line) and 95% credible intervals (shaded region).

R t by region
Rolling two-week average (prior two weeks) Reproduction number for BA.2 (red) and non-BA.2 Omicron (blue) in each region of England as inferred from mixed-effects Bayesian P-spline models fitted to rounds 17 and 18 of the data. 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.

Supplementary Figure 22: BA.2 vs non-BA.2 R t by age-group
Rolling two-week average (prior two weeks) Reproduction number for BA.2 (red) and non-BA.2 Omicron (blue) for each age-group in England as inferred from mixed-effects Bayesian P-spline models fitted to rounds 17 and 18 of the data. 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.   Odds ratio for N-gene Ct is relative to a change in Ct of +5 Odds ratio for round 18 is relative to round 17 Supplementary