Supervised by Matthew Osmond, Faculty of Arts & Science and Nicole Mideo, Faculty of Arts & Science
Project Title: Using signatures of recombination in present-day genomes to identify dangerous viral reservoirs and predict pandemic risk
Project Summary: Where will the next pandemic come from? Pandemic readiness requires identifying the reservoirs (e.g., bats, birds, rodents, primates, swine) that are likely to harbor dangerous viruses, and the aspects of their biology that make them so. Mathematical models have been crucial in developing understanding of the ways in which hosts influence the potential of their pathogens to spill over into humans, and sustain human-human transmission. For example, our recent work has shown that certain bat species, due to their exceptionally long lives and ability to tolerate infection, are dangerous in that recombination between pathogen genotypes––which can generate novel combinations of pathogen genes and proteins––is more pronounced than in, e.g., rodents and other reservoir species with short life histories. The aspects of host biology that shape pathogen evolution in the reservoir also leave signatures in present-day genomes. We will use a growing collection of such genomes to predict in which hosts recombination between pathogen genotypes is most frequent, and the reservoir-pathogen pairs that are most dangerous to humans. This work, at the nexus of mathematics, evolutionary epidemiology, and genomics, will offer unique insights for the global surveillance, control, and forecasting of emerging pathogens.