Whole-genome characterization and zoonotic potential of Alphacoronavirus from greater horseshoe bats (Rhinolophus ferrumequinum) collected on Jeju Island, Republic of Korea, 2009–2014

The genus Alphacoronavirus (α-CoV), belonging to the family Coronaviridae , comprises positive-sense RNA viruses that infect a broad spectrum of mammalian hosts, often facilitating cross-species transmission. Bats are recognized as the ancestral reservoirs for numerous α-CoVs that infect various mammals, including raccoon dogs and rodents. In the Republic of Korea (ROK), the existence of genetically distinct bat populations underscores the need for continuous viral surveillance to comprehensively understand CoV diversity and evaluate its zoonotic potential. Between 2009 and 2014, a total of 434 bat samples representing 15 species were collected across eight provinces in the Republic of Korea (ROK). The samples were screened for CoV RNA using nested reverse-transcription PCR (RT-PCR). Positive samples were further analyzed using metagenomic next-generation sequencing (mNGS) to obtain complete coding sequences, followed by phylogenetic classification and genome-based preliminary risk prioritization. CoV RNA was detected in 7 of 434 (1.6%) bat samples, all of which originated from Rhinolophus ferrumequinum on Jeju Island. Two complete coding sequences of CoVs were successfully characterized and classified within the Decacovirus subgenus of α-CoVs. Phylogenetic analyses revealed that these isolates share a recent common ancestor with bat CoVs identified in China. Furthermore, predictive spillover scoring and structural analyses classified these viruses as a medium priority for potential spillover risk. These findings highlight the circulation of α-CoVs, even in geographically isolated bat populations on Jeju Island. Furthermore, they contribute to a broader understanding of the genetic and geographic diversity of bat-borne coronaviruses in East Asia. Given their preliminary risk prioritization, continuous surveillance is necessary to anticipate and mitigate future spillover risks.