Table 1.

Explanation of notation used in the description of the mathematical model, together with priors (in the case of estimated parameters) and values (in the case of fixed parameters) used in the main analysis

Notation	Definition	Prior or value (main analysis)
$R_0^{(c)}$	Basic reproductive number for outbreak $c$	$\text{LogN}(0.8,0.5)$
$R_e^{\mathit{DP}}$	Post-quarantine effective reproductive number for Diamond Princess outbreak	$\text{LogN}(0.8,0.5)$
$s^{(c)}$	Case sequencing probability for outbreak $c$	$\text{Beta}(1,4)$
$b$	Become-uninfectious rate (per year)	36.5
$t_{\mathit{or}}^{(c)}$	Time of origin for outbreak $c$ in years	$\text{LogN}(-2,0.8)$
$A^{(c)}$	SARS-CoV-2 genome alignment for outbreak $c$	–
$T^{(c)}$	Phylogenetic tree for outbreak $c$	BDSKY (19)
$\mu$	SARS-CoV-2 substitution rate (per site per year)	$8\times {10}^{-4}$
$\kappa$	Transition-transversion substitution rate ratio of HKY model	$\text{LogN}(1,1.25)$
$\gamma$	Shape parameter for $\mathrm{\Gamma }$-distributed site-site rate variation	$\text{Exp}(0.5)$