Table 2 Performance of geometric-Poisson distribution
Performance measureMutation rate (Embedded Image)
Proportion of true infection sources identified by maximum likelihood0.270.320.33
Proportion of true infection sources identified by closest genotypea0.190.270.29
Proportion of potential links ruled out at 5% level0.100.210.24
Proportion of true infection sources ruled out at 5% level0.040.070.07
Proportion of cases identified as source by both maximum likelihood and genetic similarity found to be correct0.270.330.35
  • SIR outbreaks with 30 initial susceptibles were simulated and a single genome sample was generated for each infective. Simulations with a final size <20 were discarded. For each infective, the maximum-likelihood source was calculated, and the genetically closest hosts were selected. All previously infected individuals were considered potential sources, regardless of removal times. Simulations for each scenario were repeated 100 times. Baseline parameters were infection rate 0.002, removal rate 0.001, and effective population size 5000.

  • a If the true source and other hosts are genetically equidistant, the true host is assumed to be identified with probability 1/(no. equidistant closest hosts).