Fig. 1: Population-level transmission of SARS-CoV-2 between March 2020 and February 2022 in England.

a Infection positivity amongst individuals 15 years and older in the community through the national PCR testing programme (Pillar 2). b Infection prevalence (PCR) in representative samples of households from the REACT-1 study. Panels a and b show data in green (lines and point, with binomial 95% confidence intervals in error bars) and model trajectory in red (average and 95% credible interval (95% CrI)). Grey shading indicates periods of non-pharmaceutical interventions (NPIs) of interest for the analysis; see in f. For a complete list of modelled change points in contact rates see Supplement Table S11 and Figs. S28 and S29. c Model-inferred average frequency of daily infections by variant and type of infection (either primary or re-infection following any prior infection, “reinf”). d Intrinsic basic reproduction number (R0) estimates by variant (mean and 95% CrI). e Model trajectory of vaccine status of the national population (all ages as denominator), as informed by official data of daily doses administered (see sources in Table S1); transition between vaccination classes was modelled stochastically (Supplement section 3.2) to capture smooth changes in population-level immunity over time. f Model trajectories of the instantaneous reproduction number in the absence of the effect of immunity (Rt) or accounting for immunity (effective Rt). Legends and grey areas specify date and duration of official NPIs in England over the study period. g Inferred effective levels of immunity in the population (all ages as denominator). Lines correspond to the effective immunity against specific variants, with colour scheme as in c and d, whereas areas indicate overall effective immunity by type of immunity (vacc: vaccine-induced, inf: from prior infection, or hybrid). Note that the coloured areas corresponding to the different types of immunity cover different periods of variant dominance and should be interpreted in the context of the circulating variants (see Supplement section 4.8). During periods of variant replacement (e.g. Alpha to Delta) the effective immunity transitions from the levels associated with the variant being replaced to the level of the variant that becomes dominant.