Four types of immunity-adapted variants.

Solid lines depict the growth rate of the population of infected individuals for the wild type (blue) and for a variant (red) as a function of the fraction of the population that has been primed against infection by vaccination, previous infection, or both. Priming decreases the growth rate of the wild type (rN>rP). Quantities ΔrN and ΔrP are the differences in growth rate between the variant and the wild type in naïve and primed hosts, respectively. Colored shading indicates which type prevails evolutionarily: the wild type (light blue shading) or the variant (light red shading). Panels (a) and (b) show generalists; the variant is also better adapted to naive hosts (ΔrN>0). Generalist variants will outcompete the wild type even in the absence of priming. Panels (c) and (d) show specialists; the variant is maladapted to naïve hosts (ΔrNa) and (c) show immunity-inhibited variants; the growth rate of the variant decreases with increasing fractions of primed hosts. As a result, the growth rate of infections after adaptation (i.e., after fixation of the fittest type) in a fully primed population (black dot) is always lower than that in a fully naïve population (white dot and dashed line). Panels (b) and (d) are immunity-facilitated variants; the growth rate of the variant increases with increasing fractions of primed hosts. As a result, the growth rate of infections after adaptation in a fully primed population (black dot) is always higher than that in a fully naïve population (white dot) for generalist variants (panel (c)) but it can go either way for specialists (panel (d); only the case where it is lower is shown). Panel (e) show a plot of the growth rate of variants in a fully naïve (ri,N) and a fully primed (ri,P) population. Blue dot indicates location of the wild type. Uncolored region corresponds to variants whose growth rate in primed hosts is less than that of the wild type and so are immunity-maladapted (and so ignored in our discussion). Different colored regions correspond to the 4 types of variants from panels (a–d). Finer distinctions within these types are presented in S1 Fig. See S2 Appendix for a discussion of alternative ways to visualize variants.