Fig. 2.
Effective reproductive number (Re) of ZIKV of the Asian lineage through time. The effective reproductive number (Re) was estimated using a birth–death skyline approach implemented in BEAST 2 with ZIKVs identified since 2013. An uncorrelated log-normal relaxed clock model and the GTR + Γ nucleotide substitution model were used. A Markov chain Monte Carlo was run with one hundred million steps and the first 10% were removed as burn-in. In the serially sampled birth–death skyline model, the priors for the molecular clock rate, Re, the sampling proportion, and the rate at which patients recover were set according to a previous study, which were also supported by an alternative approach allowing for sampling heterogeneity (data not shown) (Thézé et al.2018). The red line and lighter shading represented the median posterior estimate of Re and its 95% highest posterior density credible intervals, respectively. This figure was created using the R-package bdskytools (available at https://github.com/laduplessis/bdskytools).