Kim Pepin

I study fundamental mechanisms of adaptation and their significance in driving the dynamics of pathogen populations and infectious disease. I am particularly interested in understanding mechanisms of host switching and immune escape, and how these processes determine the genetic variation and distribution of pathogen populations.

I use experimental techniques (past and future) and data-driven simulation modeling (current) to understand the cross-scale interplay of pathogen genetics, fitness and population dynamics. I aim to measure and understand the following complexities (in order from the genetic level of the pathogen to population-level processes within and between hosts):

• Genotype-to-phenotype map for pathogen fitness components
• Phenotypic characteristics of emerging pathogens
• Contribution of within-host strain dynamics to between-host strain distributions
• Difference between population dynamics and genetic variation in reservoirs and novel hosts

Some current modeling projects include

• Effects of variability in transmission patterns and within-host population dynamics on strain dynamics in host populations
• Mechanisms of immune escape in acute viral infections using an evolutionary model of quasispecies dynamics across scales (within and between hosts)
• Relative contribution of intrinsic factors and external forcing to leptospirosis incidence in California Sea Lions
• Role of transovarial transmission and competition between strains in vector populations on strain persistence