Molecular detection using hybridization capture and next-generation sequencing reveals cross-species transmission of feline coronavirus type-1 between a domestic cat and a captive wild felid

Feline coronavirus (FCoV) is highly prevalent in domestic cats worldwide and has also been reported in wild felids, including endangered species, in which it has caused substantial population declines. Characterizing the genetic diversity of FCoV is crucial due to recent reports of novel pathogenic recombinant variants causing high mortality in feral cats in Cyprus. In this retrospective molecular epidemiology study, we used archived samples collected in a zoological institution in the U.S. in which a domestic and a wild felid succumbed to FCoV. Using hybridization capture (HC) and next-generation sequencing, we show for the first time that FCoV can be naturally transmitted between domestic and wild felids. We demonstrate the efficacy of HC for detecting and sequencing the whole genome of FCoV, which is essential to characterize its different genotypes.