We study the consequences of pathogen-driven evolution on cells and host immunity factors. Protein surfaces at these interfaces often evolve in a manner resembling molecular arms races. We are also interested in cases where pathogens use molecular mimicry to gain advantages against hosts. In addition, we use experimental evolution to determine the evolutionary potential of viruses and understand the rules by which they adapt.
Protein surfaces at host-pathogen interfaces often evolve in ways that resemble arms races. This phenomenon of genetic conflict has been described by the Red Queen hypothesis, which posits that antagonistic entities vie for dominance in seesawing battles of ongoing adaptations. Molecular arms races often play out repeatedly at the same interfaces and leave behind some of the strongest signals of natural selection in the genome. These arms races can be discerned using phylogenetic analysis, which can provide novel insights for studying the dynamics of host-pathogen interactions.
We are interested in cases where pathogens use mimicry to disrupt host processes. Mimicry is observed widely in nature (e.g. Batesian mimicry among butterfly species). However, little is known about how molecular mimicry impacts host-pathogen interactions. Pathogens use the strategy of mimicry to interfere with immunity and co-opt a wide variety of host processes to their advantage. This poses a conundrum for hosts to maintain critical activities while not being exploited by pathogenic mimics honed to divert host functions. What then are the evolutionary prospects for hosts to counteract mimics?
While experiments based on phylogenetic reconstructions, provide a powerful means of retrospectively studying host-pathogen interactions, experimental evolution offers a prospective view of virus evolution where potential adaptations can be monitored in real-time. Recent advances in deep sequencing coupled with recombinant tools make it possible to quickly determine the genetic basis of a variety of adaptations. We are using experimental evolution to address open questions related to virus evolution, such as mechanisms of rapid evolution and the trade-offs between host range and virulence.