Figure 3

Assessments of network consistency. Data from simulations conducted on the transmission networks inferred for (A, B) hospital A and (C, D) hospital B. Simulations used the evolutionary model for the Delta variant of SARS-CoV-2 used to infer transmission networks. Simulated data were assessed to measure the total number of independent SNPs arising across the course of the transmission network, and the number of individuals in the network with SNPs that were unique to themselves. Histograms show distributions of each statistic across simulations, while the vertical dashed line shows the statistic calculated for the inferred network. A high value within the inferred network suggests the likely presence of missing data. Thus, data from the networks inferred for hospital A were consistent with the statistics of the simulations, though the data from hospital B showed  a significant outlier in terms of the number of individuals in the network with unique SNPs. These results provide evidence that the networks derived for hospital B is affected by missing data, though no such conclusion could be made for the networks derived for hospital B.