Fig. 5: Phylodynamic modeling of regional outbreaks informs regional outbreak dynamics before and after government interventions.
From: Revealing fine-scale spatiotemporal differences in SARS-CoV-2 introduction and spread
Bayesian phylodynamic modeling of cumulative incidence up to 26 April for outbreaks in a Dane county and b Milwaukee county under low (left), medium (center), and high (right) transmission heterogeneity conditions. Model parameters for low, medium, and high transmission heterogeneity were fixed such that 20%, 10%, and 5% of superspreading events contribute 80% of cumulative infections, respectively. Median cumulative incidence (solid black line) is bound by the 95% confidence intervals (CI; gray ribbon). Dots represent reported cumulative positive tests in Dane county (red) and Milwaukee county (blue). Estimated median reproductive numbers (R0) with 95% HDI are listed for the period before the Wisconsin “Safer at Home” order was issued on 25 March 2020. Percent reduction in R0 with 95% HDI is provided for the period after 25 March 2020. Each analysis presented here was run in duplicate for at least 3 million states in BEAST2 (see “Methods” for more details). Source data to replicate this figure can be found in the Source Data file.
