Understanding co-infection systems with multiple interacting strains remains difficult. High dimensionality and complex nonlinear feedbacks make the analytical study of such systems very challenging. When strains are similar, we can model trait variation as perturbations in parameters, which simplifies analysis. Applying singular perturbation theory to such multi-strain system we have obtained the explicit collective dynamics in terms of: a fast (neutral) dynamics, and a slow (non-neutral) dynamics. The slow dynamics are given by the replicator equation for strain frequencies, a key equation in evolutionary game theory, which in our case governs selection among N strains. In this talk, I will highlight some key features of this derivation, the use of the replicator equation to better understand such multi-strain system, and discuss links with diversity data both in epidemiology and ecology.