The coronavirus spike protein is a critical determinant of cell tropism and pathogenicity. It is expressed on the viral surface and is responsible for binding the host cell receptor and initiating fusion of the viral and host cell membranes. The work presented herein is an investigation into the genetic and biochemical properties of spike that influence the in vivo pathogenesis of feline and canine coronaviruses. A targeted sequencing approach was undertaken to identify mutations in a key viral activation site that correlate with the development of systemic disease after feline coronavirus infection. A similar strategy was used to characterize the spike proteins of canine coronaviruses associated with fatal enteritis in dogs and a thorough histopathologic characterization was performed in an attempt to independently confirm reports pantropic canine coronavirus variants.