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

Abstract

Highlights • Whole-genome sequencing identified three FCoV viral genomes (FIPV-170, FIPV-193, and FIPV-246) that belong to FCoV type-I.• These FCoV viral genomes shared about 90% nucleotide similarity with FCoV type-I strains and approximately 83% similarity with FCoV type-II strains, indicating substantial genomic drift.• Substantial amino acid substitutions were found in the S1 region of the spike glycoprotein, suggesting potential changes in viral attachment and pathogenicity.• The Recombination pattern in these isolates closely resembles that reported in the recent Cyprus FIP outbreak, supporting the possibility of continued emergence of recombination FCoV strains in the United States.