Whole-System Pandemic Modelling Including Pathogen Evolution

During the SARS-CoV-2 pandemic models played a prominent role in predicting the near- and mid-term course of the pandemic as well as in helping governments to evaluate the effect of interventions or the lack thereof. While usually a number of different models and modelling approaches were used, in most cases the various aspects that affect the system dynamics, such as disease and transmission properties, immunity due to infection and vaccination, behaviour changes in the population due to the spread of official and unofficial information as well as government interventions and the evolution of the pathogen itself were only modelled in subsets. Here we show that interactions between interventions, behaviour and evolution can lead to substantially different dynamics than any subset of these factors. We use a prototype co-evolutionary simulation in which a simulated virus continually evolves as the agent population alters its behaviour in response to the perceived threat posed by the virus as well as to government interventions. Both intra-host and inter-host evolution are simulated. The model shows that evolution can dramatically alter the effect of individual behaviour and policies on the spread of a pandemic. In particular only a small proportion of non-compliance with policies is sufficient to render countermeasures ineffective and lead to the spread of highly infectious variants.