Feline infectious peritonitis (FIP) is a viral disease that occurs in cats and is caused by particular strains or variants of feline coronavirus (FCoV-1). FIP is usually fatal in cats and although there are increasingly available treatment options once a cat becomes infected. This grant proposal seeks funding to challenge the prevailing notion that feline coronavirus (FCoV) is an enteric pathogen. We have evidence that long term infections with the virus can result in shedding of the virus from the respiratory tract, notable the conjunctiva. Sequencing of these viruses often reveals the presence of spike proteins with furin cleavage-activation loops that are predicted to be upregulated, which in turn results in more ‘up’ conformations of controls the receptor binding properties of the virus, promoting transmission events The goal of our research is to explore the conjunctiva as a potential transmission route of FCoV-1. We propose a pilot surveillance study of shelter and other community-based cats to monitor baseline FVoV-1 genomic sequences, and evaluate whether spike is being upregulated or downregulated, along with the functional role that furin cleavage site might have in those spike proteins. Our overall goal is to unravel the intricate dynamics of FCoV’s genomic changes - by examining viral evolution, including parallel evolution within different body compartments, and to determine the role of transmission events that occur outside of the enteric tract. We hypothesize that such disease dynamics are critical in understanding the dynamics of this complex viral disease, especially in shelter situations. Through this research, we hope to contribute significantly to a more refined understanding of FCoV epidemiology.