EpiFusion: Joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle filtering
Fig 9
(a) Phylogenetic tree of Ebola virus sequences in Sierra Leone consisting of a subclade of the MCC tree obtained from Dellicour et. al [50], with tips coloured by region at a 1st administrative unit level. (b) Weekly case incidence of Ebola virus disease in Sierra Leone obtained from Fang et. al [49], stratified by region. (c) Inferred median effective reproduction number (solid line) of Ebola virus disease in Sierra Leone from an EpiFusion combined model. 95%, 80% and 66% highest posterior density intervals are represented by increasingly dark shaded regions. Two key dates in the epidemic are labelled: (i) Declaration of a national state of emergency on August 6th 2014, and (ii) national three day quarantine beginning on September 19th 2014.