Figure 1.

Multi-scale model schematic. We model an epidemic in which infected individuals with given variants (e.g. red) are introduced into a susceptible population (e.g. yellow). Individual viral load trajectories are tracked, and viral load is assumed to influence infection probability as a dose–response type function. Contacts occur stochastically over time and are drawn from a distribution in which potential SSEs (greater than five infections) are possible but not common. As incidence increases, additional variants each with potentially different transmissibility can emerge, though the depletion of susceptible individuals may influence these onward dynamics.