Text S1 - Antigenic Diversity, Transmission Mechanisms, and the Evolution of Pathogens

In this appendix we present an extension of our within-host model regarding the implementation of cross-immunity. We include the acquisition of immunity from antigenically similar strains and re-calculate Fig. 2 and relevant parts of Fig. 3. We obtain very similar results compared to our original model by only adjusting the strength of cross-immunity with respect to the antigenic distance while keeping all other model parameters unchanged. This demonstrates the robustness of our original formulation, where cross-immunity is implemented in a more simplified way. In the total absence of tradeoffs between cross-immunity and peak pathogen load, we show that ChD-like infections are excluded. We also illustrate the relation between infectiousness and within-host replication for type C infections. Supplementary to Fig. 3, we plot the cumulative strain number over pathogen space. This allows us to identify infection-type B as the only candidate where, due to our model limitations, exhaustion of strains might impose an implicit artifactual limit on the duration of an infection.
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