EpiFusion: Joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle filtering
Fig 6
Inferred Rt from EpiFusion using only case incidence (orange), only the phylogenetic tree (purple) and both data types combined (green) for the three scenarios tested (rows). True Rt is represented by the solid black line. 95%, 80% and 66% highest posterior density intervals are represented by increasingly dark shaded regions. Times of step-changes are marked by vertical dotted lines: a 10-fold increase in case and genomic sequence sampling rates on day 35 for the ‘Sampling’ step-change scenario, and a 3-fold increase in transmission rate on day 100 for the ‘Transmission’ step-change scenario. An Rt of 1 is marked by the dashed horizontal line. The true Rt fluctuates at the end of the sampling step-change scenario due to very low prevalence as the outbreak ends.