Detection and Genetic Analysis of Feline Coronavirus in Clinically Suspected Cats

Feline coronavirus (FCoV) is a common infection in cats, producing outcomes that differ from mild intestinal disease to the fatal form known as feline infectious peritonitis (FIP). Accurate antemortem diagnosis is challenging, and reverse transcription-quantitative polymerase chain reaction (RT-qPCR) targeting the nucleocapsid (N) gene offers high sensitivity and specificity, while phylogenetic analysis reveals viral variation. The present study aimed to detect FCoV in clinically suspected cats using RT-qPCR and to analyze the phylogenetic relationships of local isolates from Yogyakarta, Indonesia. A total of 45 clinical samples, consisting of 14 ascitic fluid and 31 blood samples, were collected from cats of different breeds (mixed, domestic shorthair, and Persian), aged 0.5-4 years, including 22 males and 23 females, that were presented to seven veterinary clinics in Yogyakarta with clinical signs such as vomiting, diarrhea, abdominal effusion, uveitis, and ataxia. The RT-qPCR revealed 62.2% (28/45) positive cases, with detection rates of 100% (14/14) in ascitic fluid and 45.2% (14/31) in blood. The most frequent clinical findings among FCoV-positive cats were abdominal distension (50%), uveitis (32.1%), ataxia (21.4%), and rhinitis (17.9%). Most infected cats (71.4%) were under two years of age, with a slightly higher prevalence in males (57.1%). Phylogenetic analysis of three isolates from ascitic fluid demonstrated a close genetic relationship with strains from Italy, the United Kingdom, and China, clustering into two distinct clades. The present study highlighted the utility of RT-qPCR targeting the N gene as a reliable diagnostic tool for clinical cases, while providing new clinicopathological and molecular data on naturally occurring FCoV infection in Indonesia. These findings contribute to the global understanding of FCoV molecular epidemiology and support future surveillance and control strategies for coronavirus infections in domestic cats.