Feline coronavirus and FIP remains one of the most important infectious diseases in the cat population, yet remains poorly understood and without good diagnostics. While anti-viral treatment for FIP is now advancing at a rapid pace, this is largely unregulated and present a dilemma in terms of AMR stewardship—as it is becoming increasingly apparent that FCoV-related disease extends far beyond the traditional FECV–wet-dry FIP paradigm. Our primary objective in this project is to expand our clinical sample collection pipeline to focus on: i) cats with documented FCoV infection that do not fit the traditional FECV-FIPV criteria, ii) cats that show disease signs not traditionally linked to FCoV infection; e.g., to include cats with IBD, cardiac problems and pancreatitis, and iii) cats that are undergoing FIP anti-viral treatment protocols with their owners. Our experimental focus is to develop NGS technologies to analyze FCoV sequences, with a focus on the spike gene and its FCS, which we predict are present at low levels in “sanctuary sites” or reservoirs during long-term persistent infection—linking to clinical outcome and the use of novel, highly sensitive ISH techniques to identify cell types in certain tissues. We believe that disease signs are driven by “short-sighted” evolution of the virus as it replicates as a persistent infection, possibly over the life-time of the animal. This process of evolution selects viral variants in key genomic regions that may span the viral genome, but are concentrated in the spike protein—in particular, the structural loop connecting the S1 and S2 domains that serves as a furin cleavage site (FCS) that is a regulator of spike protein function and thereby viral pathogenesis, tropism, and transmissibility. We have two specific aims 1) to perform next-generation sequence analysis feline coronavirus-1 (FCoV-1) to understand emergence and selection of highly pathogenic viral variants, and 2) to develop feline coronavirus-1 (FCov-1) as a model for understanding persistent coronavirus infections and the identification of “sanctuary sites".