First molecular detection and genetic characterization of feline coronavirus from India

Feline coronavirus (FCoV), the etiological agent of feline infectious peritonitis (FIP), represents a major clinical and economic challenge in feline populations worldwide. However, molecular prevalence and genetic diversity data from India remain limited, and the relatedness of circulating strains to vaccine isolates is poorly defined. In this study, 24 suspected feline cases from Chennai were screened by RT-PCR targeting a 698 bp fragment of the spike (S) gene, and FCoV was detected in 10 cats (41.7%), with a case fatality rate of 40%. Molecular characterization of a circulating FCoV strain (FCoV/ABT/MVC/2024/001) revealed 95.8-100% nucleotide identity with Asian and European isolates and 95.6% identity with canine coronavirus (CCoV). Key nucleotide substitutions (22,508, 22,549, 22,371, 23,105) and amino acid changes (I739T, R764K, N773D, S781K) suggested evolutionary relationships influencing spike protein folding, glycosylation, and immune recognition. Phylogenetic analysis showed that the Indian strain clustered with field isolates from China, Japan, Thailand, Italy, Australia, and the USA, but was distinct from Japanese vaccine strains and CCoV, confirming species-specific divergence. B-cell epitope prediction identified nine major epitopes, with conserved regions at positions 58, 77-88, 134, 161-164, 166, and 190 as potential immunogenic targets. In contrast, notable antigenic variability was observed, including extended epitopes at 99-132 and substitutions at 139-147 and 168-173, indicating antigenic drift that may reduce vaccine cross-protection. This study provides the first molecular characterization of Indian FCoV, demonstrating genetic diversity and antigenic variation, and underscores the need for comparative genomics to inform surveillance and vaccine design.