Epidemiological surveillance and genomic characterisation of betacoronavirus in Apodemus agrarius from Gyeonggi and Gangwon Provinces, Republic of Korea, 2017–2019

Coronaviruses (CoVs) infect a broad range of hosts and cause illnesses of varying severity, ranging from the common cold to severe acute respiratory syndrome, posing significant public health concerns. Although rodents are recognized as natural reservoirs of CoVs, genomic surveillance of rodent-borne Betacoronavirus (β-CoV) has not been conducted in the Republic of Korea (ROK). 511 Apodemus agrarius specimens collected in Gyeonggi and Gangwon Provinces between 2017 and 2019 were examined, with CoV RNA detected in 6.7% (34/511) of the intestinal tissue samples using reverse transcription polymerase chain reaction. This study represents the first molecular evidence of β-CoV in A. agrarius in the ROK. Phylogenetic analysis revealed two distinct genetic groups: A. agrarius CoV 1 (AaCoV-1) and AaCoV-2. The complete coding genome sequence of AaCoV-1 revealed the highest genomic similarity to China rat CoV HKU24, species B. ratti , and the subgenus Embecovirus . AaCoV-1 is predicted to have a high level of zoonotic potential, highlighting the need for epidemiological and pathogenic studies to assess its potential for human transmission. This report provides substantial insights into the molecular epidemiology, geographic distribution, and zoonotic potential of rodent-borne β-CoVs, contributing to a unified one health framework for the enhanced surveillance and risk control of emerging CoVs.