Abstract for: Modelling the effect of within-host dynamics on the diversity of a multi-strain pathogen

Multi-strain pathogens cause millions of infections annually. Control of multi-strain pathogens is complicated by the high strain diversity. It is not well understood how high strain diversity is maintained in populations given that strains compete with each other both directly (within an individual host) and indirectly (via host immunity). Previous studies have investigated how indirect competition affects strain diversity. However, these studies tend to make simplifying assumptions about direct competition. There is little data available to validate these assumptions and there is a need to clarify how sensitive model outputs are to these assumptions. In this study, we propose an agent-based model to compare the dynamics of multi-strain pathogens under different assumptions about direct competition between strains. We find that direct competition can affect epidemiological dynamics. Our results suggest that while direct and indirect competition can each decrease strain diversity when they act in isolation, they may increase strain diversity when they act together. We argue that studies using multi-strain transmission models should examine sensitivity to assumptions about direct competition. Omitting consideration of direct competition can lead to inaccurate estimates of the effectiveness of control strategies as changes in strain diversity shift the level of direct strain competition.