Appendix 1—figure 3. Sensitivity analysis varying model parameters across biologically-reasonable parameter ranges.

(A, B) Probability of a detectable infection per inoculation of an experienced host. (C, D) Probability of a detectable new variant infections per inoculation of an experienced host. (E, F) Fraction of detectable infections of experienced hosts that are new variant infections. Points colored according to whether new variant infections were more frequently caused by de novo generated (purple) or inoculated (green) new variant viruses. Each point represents a random parameter set; 10 random parameter sets generated for each bottleneck value shown, and 50,000 inoculations of an experienced host simulated for each parameter set. Two regimes of simulated parameter set shown: (A, C, E) an immediate recall response regime, in which $t_M$ varied from 0 to 1, and (B, D, F) a realistically-timed response regime, in which $t_M$ varied from 2 to 4.5. All other parameters varied across the same ranges in both regimes (see Table 2 for ranges). Parameters Latin Hypercube sampled from within ranges for each regime and bottleneck size.