Cross-scale dynamics and the evolutionary emergence of infectious diseases

Sebastian J. Schreiber; Ruian Ke; Claude Loverdo; Miran Park; Priyanna Ahsan; James O. Lloyd-Smith

Overall, by explicitly modeling the cross-scale dynamics, our model simultaneously tracks the number of infected hosts and the viral loads within each infected host ( Fig 1D) . The structure of our stochastic model is similar to Peck et al. [16] 's stochastic model of molecular viral evolution along transmission chains. However, our model accounts for stochastic transmission dynamics rather than conditioning on a chain of transmission, and explicitly accounts for the dynamics of competing viral strains. It also has similarities with Geoghegan et al. [17] 's cross-scale, stochastic model of a single transmission event from a donor host to a recipient host. Like our model, Geoghegan et al. [17] 's model has constant transmission bottlenecks, multinomial sampling from donor to host, and explicit within host dynamics with exponential growth and ceiling phases. Their model, however, focuses on a single transmission event and assumes that all virions are equally likely to be transmitted from donor to host, i.e. it assumes no selection based on transmissibility.