Toronto, December 6 - 9, 2019
We simulate the within-host evolution using a compartmental model with a latent reservoir and stochastically simulate the transmission bottleneck. As the virus evolves within-host, this increased evolution is coupled to between-host fitness by allowing transmission fitness to drift. i.e. there is greater variance of transmission fitness when the virus is a member of a more evolved within-host compartment.
Linking the within- and between-host scales through a stochastic, competitive transmission bottleneck, our results suggest that both the HIV latent reservoir and bottleneck effects contribute to the observed rate of between-host evolution, over the epidemic.