Bacteria and archaea defend themselves against viruses using CRISPR-Cas immunity, which lets them store short genetic “spacers” from past infections and recognize matching phages in the future. Some theoretical work assumes each host can only keep one spacer at a time. In this setting, coexistence depends critically on viral diversity: a host can defend against only a single strain, so whether hosts and viruses survive together is determined by how many viral strains circulate and how quickly they turn over. Using deterministic equations and stochastic simulations, we find that viral diversity stabilizes at a predictable level, set by a balance of extinction and invasion events. Analytic results further connect diversity to ecological parameters such as burst size, adsorption rate, and mutation probability, providing a quantitative description of how viral richness emerges from ecological and evolutionary pressures. We then extend the model to allow hosts to store more than one spacer. Preliminary results point to a counterintuitive outcome: instead of simply increasing immune pressure and driving viruses extinct, extra spacers actually promote the coexistence of a larger number of viral strains. This happens because having more immune memories makes host populations more heterogeneous, not only broadening overall coverage but also leaving space for viral lineages to persist. These results suggest that multi-spacer CRISPR arrays may not only strengthen host defense but also regulate viral diversity at the community scale.
Inci et al. (Sun,) studied this question.