Fig. 3: Key model-inference system estimates.
Left column (a, d, g) shows estimated real-time reproduction number Rt, middle column (b, e, h) shows estimated transmissibility, and right column (c, f, i) shows estimated population susceptibility for each week during the study period, for the three countries. For comparison, estimated weekly infection rates are superimposed in each plot (right y axis). Blue lines and surrounding areas show the estimated mean, 50% (dark) and 95% (light) CrIs. Boxes (middle bar = mean; edges = 50% CrIs) and whiskers (=95% CrIs) show the estimated weekly infection rates. Gray shaded areas indicate the timing of lockdowns or key periods of restricted activity; horizontal arrows indicate the timing of variant identification and vaccination rollout. Note that the transmissibility estimates (b, e, h) have removed the effects of changing population susceptibility, NPIs, and disease seasonality; thus, the trends are more stable than the reproduction number (Rt; a, d, g) and reflect changes in variant-specific properties. Model estimates (mean, 50% and 95% CrIs) are summarized over n = 100 model-inference runs (500 model replica each, totaling 50,000 model realizations).
