The evolutionary and mechanistic basis of pathogen host shifts

A major source of emerging infectious disease are virus host shifts, where a pathogen jumps into a new host species (e.g. HIV, Ebola, SARS-CoV-2). Research to date has focused on the role of host genetics. Here I will examine the role pathogen genetics (relatedness) and ecology (interactions between microbes) play in emerging infectious diseases, which will be critical to predict future host shifts. The first goal is to understand how patterns of susceptibility correlate amongst different pathogen taxa. I will infect hosts with different viruses and other pathogens to test the importance of the host phylogeny in determining susceptibility for each pathogen. For example, if a host is susceptible to one virus, are they also susceptible to other types of virus, or is susceptibility pathogen specific? This is critical for understanding whether the characteristics of an emerging pathogen can be predicted based on our knowledge of other related pathogens. Next, I will investigate how interactions between microbes can alter the likelihood of pathogen emergence. I will examine whether the outcomes of co-infection and microbiome-pathogen interactions are the same or different across host species. This has important consequences for understanding how biotic interactions could alter the outcomes of pathogen host shifts.