Figure 3

Examples of dynamic solutions with different strain structures at equilibrium. Dynamic solutions obtained from MANTIS, using three levels of cross-immunity γ=0.10(left), γ=0.75(centre) and γ=0.95(right), within an antigenic system with structure {3,2} and 6 strains. The level of immune selection is here seen to structure the pathogen population into NSS, CSS, and DSS. Examples are initialized with the same initial conditions and parameters are β=292, σ=(1/5)∗365 and μ=1/50, resulting in a basic reproduction number (R0) of ≈4. Grey shaded areas highlight the dynamics at equilibrium. The beginning of the dynamic series is discarded for visualization purposes. Letters were arbitrarily chosen to build figurative strain sequences (locus 1: A, B; locus 2: X and Y). The minimal R code required to replicate these dynamics can be found in the Additional file 1.