Abstract
BACKGROUND AND AIM: Feline coronavirus (FeCoV) is a widely circulating Alphacoronavirus that causes mild enteric infections and, in some cases, progresses to Feline infectious peritonitis, a fatal systemic disease. FeCoV consists of two genotypes (I and II) and two biotypes (FeCoV and feline infectious peritonitis virus [FIPV]). Despite its importance, whole-genome data, particularly for FeCoV genotype II, remain limited in Thailand. This study aimed to determine the prevalence of FeCoV in domestic cats and to genetically characterize circulating strains using whole-genome and S gene sequencing. MATERIALS AND METHODS: A total of 471 rectal swabs were collected from domestic cats presented to private small animal hospitals in Bangkok and neighboring provinces from October 2022 to October 2023. FeCoV detection and genotyping were performed using one-step reverse transcription polymerase chain reaction targeting the 3'UTR and S gene, respectively. Selected FeCoV-positive samples were subjected to whole-genome sequencing (WGS) (n = 4) and complete S gene sequencing (n = 6) using Oxford Nanopore technology with Minimap2, Racon, and Medaka pipelines. Phylogenetic and genetic analyses were conducted using MEGA program. RESULTS: FeCoV positivity was 21.87% (103/471), with higher detection in young cats (<6 months; 28.46%), though age, clinical status, and season showed no significant association (p > 0.05). Genotype I was overwhelmingly predominant (99.03%), whereas genotype II was rare (0.97%). Phylogenetic analysis revealed that Thai FeCoV-I strains clustered closely with Chinese and Dutch FeCoV-I strains, while the FeCoV-II strain grouped with Chinese FeCoV-II. Whole-genome pairwise comparisons showed high nucleotide and amino acid identities with their respective genotype references. No mutations were detected in the S1/S2 or S2 cleavage sites of Thai FeCoV-I, indicating conserved spike characteristics typical of FECoV biotypes. FeCoV-II exhibited the characteristic deletion and insertion patterns known for this genotype. No evidence of recombination with other coronaviruses was observed. CONCLUSION: This study provides updated molecular epidemiology of FeCoV in Thailand and reports the first complete FeCoV-II genome sequences from the country. The predominance of FeCoV-I and the detection of conserved spike regions highlight the need for genotype-specific surveillance and the reconsideration of vaccine strategies that currently target FeCoV-II. Expanded nationwide monitoring and detailed recombination analyses are warranted to better understand FeCoV evolution and transmission in feline populations.