Longitudinal detection and genetic characterization of feline coronavirus in a captive cheetah population

Feline coronavirus (FCoV) infections, including fatal feline infectious peritonitis (FIP), have been documented in captive cheetahs ( Acinonyx jubatus ), but longitudinal data on viral circulation and genetic diversity in this species remain limited. In this study, we performed a 3.5-year molecular epidemiological investigation of a closed captive cheetah cohort at a single zoological facility in Japan. Non-invasive monitoring of 17 individually identified cheetahs by reverse-transcription quantitative PCR of faecal samples revealed long-term maintenance of FCoV in the population, with highly variable individual-specific viral RNA detection patterns over time. Phylogenetic analysis of near-complete genomes recovered from an asymptomatic shedder and an FIP-affected individual placed the cheetah-derived viruses within the type I FCoV clade. Targeted sequencing of the partial nucleocapsid gene identified 17 nt haplotypes and revealed viral sequence diversity and temporal changes in the dominant consensus haplotypes detected within individual cheetahs. These temporal changes could not distinguish reinfection from within-host evolution or undetected within-sample viral diversity. Analysis of the spike (S) gene showed marked regional differences in sequence diversity: the S1/S2 cleavage site region contained 16 nt haplotypes, whereas the S2 1058/1060 region contained only 4 nt haplotypes and showed lower diversity. Tissue-derived sequences from the FIP-affected cheetah were assigned to defined haplotypes within the population-level haplotype framework. Together, these data show that FCoV was maintained for multiple years in this closed cheetah cohort and that faecal surveillance combined with targeted sequencing can track temporal changes in the dominant FCoV sequences detected in captive non-domestic felids.