Molecular epidemiological surveillance of the feline coronavirus reveals novel recombinant FCoV strains with evidence of ongoing viral evolution.

Feline Infectious Peritonitis Virus (FIPV) is a virulent biotype of feline coronavirus (FCoV) that causes fatal systemic disease in cats and continues to emerge through mutation and recombination. We conducted demographic data collection, molecular surveillance and genomic characterization of FCoV circulating in feral and shelter cats. Among 139 cats screened, 22.3% tested positive for FCoV. Lower weight and Body Condition Scores indicate higher likelihood for FCoV. Whole-genome sequencing identified three novel FCoV (FIPV-170, FIPV-193, and FIPV-246) belonging to FCoV type I. The viral genomes shared ≈90% nucleotide similarity among themselves and ≈83% similarity with local type II strains. Spike gene analysis revealed 76 amino acid substitutions in the S1 region, including 12 mutations in the receptor-binding domain. Accessory gene mutations included a premature stop codon in NSP-3a and truncation of NSP-7a. Recombination analysis identified mosaic genomes derived from feline coronavirus types I and II and canine coronavirus lineages, with breakpoints in ORF1b, spike, and NSP-3abc regions, resembling patterns reported during the recent 2023 FCoV outbreak in Cyprus (FCoV-23). Continued regional molecular and genomic surveillance is advised.