“Nothing in biology makes sense except in the light of evolution”[1] and this is no less true for viral pathogens than it is for their host species. To appreciate the full extent of the challenges posed by current and future emerging infectious diseases (EIDs), I believe it is insightful to take a coevolutionary perspective. Coevolution comprises the reciprocal, adaptive genetic changes that occur when two species interact. During coevolution, the direction and intensity of natural selection is constantly changing because adaptations in one species provoke counter-adaptations in the coevolving species. Despite continuous adaptations, none of the interacting species gain a sustained fitness advance, making antagonistic coevolution a zero-sum game [2–4]. This is also why coevolution has been likened to the character of the Red Queen in Lewis Carroll’s “Through the Looking Glass”, who said: “ … it takes all the running you can do, to keep in the same place”. But what would happen if one of the parties (our livestock and crops) lacked the coevolutionary means to run, whilst the other party (their parasites) had just received a significant fitness performance-enhancing boost? Here, I will discuss how recent changes in interactions between the evolutionary forces have fundamentally altered the Red Queen dynamics between parasites and their hosts. I believe we have created the perfect coevolutionary storm, and the question is: what can we do about it now?..