Whole-genome characterization and phylogenetic analysis of Equine Rotavirus A isolated from Jeju Island, Korea.

Abstract

Importance: Equine Rotavirus A (ERVA) is a major cause of acute diarrhea in neonatal foals, leading to significant economic losses. Genetic variation and global transmission complicate disease control efforts.

Objective: To analyze the complete genome of an ERVA strain from Jeju Island, Korea, and assess its genetic and phylogenetic relationships with global ERVA strains.

Methods: Twenty-five fecal and swab samples were collected from diarrheic horses in Jeju during spring and summer 2025. Samples were screened using antigen testing and RT-PCR. One PCR-positive, antigen-test-positive sample was selected for whole-genome sequencing. All 11 segments were amplified using segment-specific primers and sequenced by the Sanger method.

Results: The Jeju isolate exhibited a G14-P[12]-I2-R2-C2-M3-A10-N2-T3-E2-H7 genome constellation, matching the globally prevalent ERVA genotypes. Most segments showed > 99% identity to a South African strain (SA1), while the VP4 segment showed higher similarity to a Japanese BI strain, suggesting a reassortment event. Phylogenetic analysis grouped the Jeju strain with isolates from South Africa and Ireland, but distinct from recent Japanese strains, indicating independent transmission patterns.

Conclusions and relevance: This is the first full-genome report of ERVA from Korea. The findings confirm the presence of globally related ERVA in Korean horses and suggest complex, international transmission dynamics. Continuous molecular surveillance is essential to support effective prevention and vaccine strategies.