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The Roossinck lab has long been fascinated by the evolution and ecology of RNA viruses. Using Cucumber mosaic virus as a model system for experimental evolution, we have studied various aspects of virus evolution including population structures, bottlenecks during systemic infection and transmission, and recombination frequencies. We have also studied the biodiversity of viruses in wild plants, and this research led to the realization that although almost all of the well-characterized plant viruses have an acute lifestyle, persistent viruses are more common and found in many plants, including many crop plants. These viruses remain in their plants for many generations, and at least in some cases for thousands of years. Fungi are also often infected with persistent viruses, and studying a persistent fungal virus from Yellowstone National Park uncovered a complex relationship among a virus, a fungus and a plant: the holobiont is highly thermotolerant, growing in soils well over 50 °C. This led to a gradual shift towards more studies in virus ecology, and currently the lab uses both plant and fungal viruses to understand virus ecology and evolution.

Currently we are using Cucumber mosaic virus to analyze the host role in recombination frequencies, and the in planta fidelity of the viral RNA dependent RNA polymerase. Other research in the lab focuses on persistent virus ecology and evolution. We use peppers as a plant model system because there is widespread infection of Bell pepper endornavirus and Pepper cryptic virus 1. We are also studying a persistent virus in maize.

We have two projects on the ecology of fungal viruses. One study continues are interest in viruses of endophytic fungi and we are focusing on a novel ecosystem at a coal fire site in Pennsylvania that has been burning for over 50 years. Plants survive the high temperatures as well as the presence of toxic compounds produced by the burning coal. Unlike Yellowstone, which is an ecosystem about 600,000 years old, this system is helping us understand how the mutualistic plant-fungal-viral interactions become established. The second fungal virus project involves characterization of viruses from Pseudogymnoascus destructans, the presumed causal agent of White-nosed syndrome in North American bats. We are looking at the diversity and dispersal of viruses and studying their roles in the biology of the fungus.