Fig. 3. Incidence reconstruction based on sequencing data.

The graphic depicts the genome-based incidence reconstruction in blue using the proposed method (left axis) vs. the 7 days rolling average of newly reported cases in red (right axis). Blue dots depict ϕ_b point estimates of the incidence correlate, where the size of the dot is related to the number of sequences used to infer ϕ_b. The solid and dashed blue lines denote the median smoothed trajectories and their 5th and 95th percentiles. The black markers on the x-axis depict the collected sequences at the given dates. a Denmark (n = 40.575 sequences) b Scotland (n = 30.258 sequences), c Switzerland (n = 25.779 sequences), d Victoria (n = 10.710 sequences).