<p>Key differences in phylodynamic model assumptions across simulation scenarios. Scenario abbreviations are as follows: HDT = hospital-driven transmission, ET = equal transmission, and CDT = community-driven transmission. All scenarios were simulated using the same values for the rate of becoming non-infectious (), hospital admission rate (), and discharge rate (). For phylodynamic inference, either a two-deme model (<i>bdmm</i>) or a one-deme model (<i>bdsky</i>) was applied. Genomic evolution in all scenarios was simulated using the HKY substitution model with <i>κ</i> = 4.04 and nucleotide frequencies A: 0.34, C: 0.16, G: 0.16, and T: 0.34. For each scenario, parameters of the sequence evolution model were inferred using default prior distributions during Bayesian analysis. Results for the main scenarios are provided in Tables 2, </p>

Key differences in phylodynamic model assumptions across simulation scenarios. Scenario abbreviations are as follows: HDT = hospital-driven transmission, ET = equal transmission, and CDT = community-driven transmission. All scenarios were simulated using the same values for the rate of becoming non-infectious (), hospital admission rate (), and discharge rate (). For phylodynamic inference, either a two-deme model (bdmm) or a one-deme model (bdsky) was applied. Genomic evolution in all scenarios was simulated using the HKY substitution model with κ = 4.04 and nucleotide frequencies A: 0.34, C: 0.16, G: 0.16, and T: 0.34. For each scenario, parameters of the sequence evolution model were inferred using default prior distributions during Bayesian analysis. Results for the main scenarios are provided in Tables 2,