Table 1.

Overview of models used in this study.

Phylodynamic model	Parameter	Value	Evolutionary model	Clock model
Birth–death skyline model with serial sampling (BD)	Effective reproductive number (Re)	Estimated; 3, 4, 6 intervals (3 × Re, 4 × Re, 6 × Re) with LN prior with various parameterizations	HKY+Γ	Relaxed clock
	Become uninfectious rate (δ)	Fixed; $\delta \in \{14.26,18.25,23.40\}$		Strict clock
	Sampling probability (P)	Estimated; with prior Beta(1, 700)
Coalescent Bayesian skyline plot (Coal)	Effective population size (Ne)	Estimated; 3, 4, 6 intervals (3 × Ne, 4 × Ne, 6 × Ne); with prior on first interval $Unif(0,{10}^7)$, following intervals: Γ with mean population size of previous interval	HKY+Γ	Relaxed clock Strict clock

The abbreviations used in Figs 3 and 4 and Supplementary Figs S3 and S4 refer to this scheme. For example, BD: 3×R_e∼LN(0, 1), $\delta =18.25$ refers to the birth–death skyline model with serial sampling which allows for three intervals for R_e, each with LN(0, 1) distributed prior, and the become uninfectious rate δ = 18.25.