Genomic and phylogenetic characterization of severe fever with thrombocytopenia syndrome virus in companion animals in Korea, 2023–2024

Background Severe fever with thrombocytopenia syndrome virus (SFTSV) is a tick-borne Phlebovirus with high fatality rates in humans and expanding geographic distribution in East Asia. Companion animals, including dogs and cats, are increasingly recognized as susceptible hosts that may contribute to viral maintenance and spillover. However, genomic information on SFTSV strains circulating in companion animals in Korea remains limited. Methodology/principal findings Between April 2023 and June 2024, 63 SFTSV-positive clinical specimens from dogs and cats were collected across the Republic of Korea. Whole-genome sequencing using a multiplex tiling RT-PCR and next-generation sequencing approach yielded 39 complete viral genomes. Phylogenetic analysis revealed that most viruses clustered within genotype B, including 10 viruses classified as the highly virulent B2 subtype. Five reassortant viruses (12.8%) were identified, comprising four intra-genotypic (B1/B2/B2) and one inter-genotypic (B2/C/B2) reassortants. Multiple amino acid substitutions linked to increased human case fatality, such as RdRp-T1433A (94.9%) and Gn-Q341P (97.4%), were prevalent among companion animal viruses. In addition, mutations within neutralizing antibody epitopes (Y83F, K113R, G218S, P222A, F225L, V323I, and S340N) were detected, several of which significantly reduced antibody binding affinity in silico (G218S, P222A, F225L, and S340N). Conclusions/significance This study provides nationwide genomic characterization of SFTSV in companion animals in Korea. The detection of highly virulent subtypes, frequent reassortment, and epitope-altering mutations highlights the evolutionary potential of SFTSV in non-human hosts. The close genetic relationship between animal- and human-derived viruses underscores the risk of cross-species transmission. These findings emphasize the need for integrated One Health surveillance systems linking veterinary and human health sectors to enable early detection, risk assessment, and mitigation of emerging SFTSV threats.