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Mathematical disease modelling has long operated under the assumption thatany one infectious disease is caused by one transmissible pathogen spreadingamong a population. This paradigm has been useful in simplifying the biologicalreality of epidemics and has allowed the modelling community to focus on thecomplexity of other factors such as population structure and interventions.However, there is an increasing amount of evidence that the strain diversity ofpathogens, and their interplay with the host immune system, can play a largerole in shaping the dynamics of epidemics. Here, we introduce a disease modelwith an underlying genotype network to account for two important mechanisms.One, the disease can mutate along network pathways as it spreads in a hostpopulation. Two, the genotype network allows us to define a genetic distanceacross strains and therefore to model the transcendence of immunity oftenobserved in real world pathogens. We study the emergence of epidemics in thismodel, through its epidemic phase transitions, and highlight the role of thegenotype network in driving cyclicity of diseases, large scale fluctuations,sequential epidemic transitions, as well as localization around specificstrains of the associated pathogen. More generally, our model illustrates therichness of behaviours that are possible even in well-mixed host populationsonce we consider strain diversity and go beyond the "one disease equals onepathogen" paradigm.

Localization, epidemic transitions, and unpredictability of multistrain epidemics with an underlying genotype network