The antigenic archive of pathogens plays an important role in within-host infections. Antigenically varying pathogens escape host immunity by switching expression of different variants. The timing of this process and the number of antigenic variants expressed over the course of an infection are often stochastic and spontaneous, independent of host immune pressure.

They result mainly from genetic properties of the antigenic archive of the pathogen. However, their subsequent interaction with dynamic host immune mechanisms determines the outcome of an infection: its peak, duration, and nature of chronicity.

African Trypanosomes are a prominent example of such pathogens exploiting antigenic variation to establish chronic infection in their hosts. With increasing availability of parasite genomic data, more realistic within- host models are now possible, through the integration of features of the antigenic archive. This integration has the potential to significantly improve our understanding of the fundamental mechanisms of parasite immune evasion. Here we study the within-host dynamics of trypanosomes. We use a delay-differential equation model to investigate how antigenic archive properties modulate the balance between specific and general control of the

pathogen. We show that introducing stochasticity has important implications for the comparisons between infections across hosts of different size and for understanding the architecture of the genetic archive of the parasite.