Vet World   Vol.18   December-2025  Article - 16 

Whole-genome characterization and molecular epidemiology of Feline coronavirus (FeCoV) circulating in domestic cats in Thailand: First report of FeCoV-II whole genomes

Yu Nandi Thaw¹ , Kamonpan Charoenkul^1,2 , Chanakarn Nasamran^1,2 , Ekkapat Chamsai³ , Waleemas Jairak³ , Eaint Min Phyu³ , Hnin Wai Phyu³ , Supassama Chaiyawong^1,2 , Somsak Pakpinyo³ , and Alongkorn Amonsin^1,2

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. 

Keywords: domestic cats, FeCov, genotype I and II, molecular epidemiology, phylogenetic analysis, spike (S) gene, Thailand, whole-genome sequencing.

How to cite this article: Thaw YN, Charoenkul K, Nasamran C, Chamsai E, Jairak W, Phyu EM, Phyu HW, Chaiyawong S, Pakpinyo S, and Amonsin A (2025) Whole-genome characterization and molecular epidemiology of Feline coronavirus (FeCoV) circulating in domestic cats in Thailand: First report of FeCoV-II whole genomes, Veterinary World, 18(12): 3888–3901.

Received: 26-06-2025   Accepted: 14-11-2025   Published online: 14-12-2025

Corresponding author: Alongkorn Amonsin    E-mail: alongkorn.a@chula.ac.th

DOI: 10.14202/vetworld.2025.3888-3901

Copyright: Thaw, et al. This article is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http:// creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.