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The coevolutionary dynamics of lytic viruses and microbes with CRISPR-Cas immunity exhibit alternations between sustained host control of viral proliferation and major viral epidemics in previous computational models. Thesealternatingdynamics have yet to be observed in other host–pathogen systems. Here, we address the breakdown of control and transition to large outbreaks with a stochastic eco-evolutionary model. We establish the role of host density-dependent competition in punctuated virus-driven succession and associated diversity trends that concentrate escape pathways during control phases. Using infection and escape networks, we derive the viral emergence probability whose fluctuations of increasing size and frequency characterize the approach to large outbreaks. We explore alternation probabilities as a function of non-dimensional parameters related to the probability of viral escape and host competition. Our results demonstrate how emergent feedbacks between host competition and viral diversification render the host immune structure fragile, potentiating a dynamical transition to large epidemics. 

ABSTRACT Microbial host populations evolve traits conferring specific resistance to viral predators via various defence mechanisms, while viruses reciprocally evolve traits to evade these defences. Such coevolutionary dynamics often involve diversification promoted by negative frequency‐dependent selection. However, microbial traits conferring competitive asymmetries can induce directional selection, opposing diversification. Despite extensive research on microbe–virus coevolution, the combined effect of both host trait types and associated selection remains unclear. Using a CRISPR‐mediated coevolutionary system, we examine how the co‐occurrence of both trait types impacts viral evolution and persistence, previously shown to be transient and nonstationary in computational models. A stochastic model incorporating host competitive asymmetries via variation of intrinsic growth rates reveals that competitively advantaged host clades generate the majority of immune diversity. Greater asymmetries extend viral extinction times, accelerate viral adaptation locally in time and augment long‐term local adaptation. These findings align with previous experiments and provide further insights into long‐term coevolutionary dynamics.