Figure 6. Model shows trailer-end conservation protecting hosts against blooms of old viral sequences.

The model is extended to allow a parameterized fraction of (single) spacer additions in host CRISPR loci to occur with deletions of randomly-sized blocks of spacers from random locus positions. The lower panels in (A) and (B) plot host immunity (blue) against maximum viral strain frequency (red) in each iteration. (A) When 5% of additions occur with deletions, trailer-end memory and clonality are preserved. Only new-end spacers target current viruses and CRISPR's antiviral immunity is maintained at high levels across thousands of model iterations. (B) When 50% of spacer additions occur with deletions, trailer-end memory and clonality are purged. Depletions in host immunity occur (lower panel), indicating viral blooms due to the large fraction of interactions in which CRISPR fails to provide immunity (i.e., host and virus do not share spacers). During the predicted bloom at iteration 768, immunity against the top 300 viral strains is conferred by two older spacers, which are lost from most host lines prior to the bloom (Figure S8).