Whole-Genome Characterization of Rodent Coronaviruses (RCoVs) in Thailand, 2024-2025

Rodents are recognized as important reservoirs of coronaviruses, contributing to viral diversity and potential zoonotic emergence. However, data on rodent coronaviruses (RCoVs) in Thailand remained limited. This study aimed to determine the prevalence, genetic characteristics, and phylogenetic relationships of RCoVs circulating in rodent populations across Thailand. A total of 435 rodents were captured in 26 provinces across five geographic regions of Thailand between January 2024 and April 2025. Paired oral and rectal swabs (n = 870) from 435 rodents were collected and screened for RCoVs using one-step RT-PCR targeting the RNA-dependent RNA polymerase (RdRp) gene. RCoVs were detected in 2.07% (9/435) of rodents or 1.15% (10/870) of swab samples, with higher detection in rectal swabs than oral swabs. All positive specimens were found exclusively in Bandicota indica. Of 10 positive swab samples, 5 were subjected to whole-genome sequencing, and the rest to RdRp gene sequencing (n = 5). Phylogenetic and comparative genomic analyses were performed to determine genetic relationships and potential host adaptation. Our results showed that all Thai RCoVs belonged to the genus Betacoronavirus, subgenus Embecovirus, species Betacoronavirus muris, and exhibited conserved genomic organization and clustering with previously reported RCoVs from Asia. Thai RCoVs showed high nucleotide identity (up to ~97%) with RCoVs from China, Thailand, and Vietnam, indicating regional circulation and shared evolutionary origins. Analysis of the spike (S) protein revealed conserved receptor-binding motifs associated with 9-O-acetylated sialic acid binding, alongside variability in key functional regions, including the S1/S2 cleavage site, suggesting adaptive evolution. In summary, this study demonstrated a low frequency of detection of genetically diverse RCoVs in three provinces of Thailand. RCoV genomic diversity and variability in S proteins warranted further investigation and underscored the importance of maintaining ongoing One Health surveillance to improve early detection and mitigate potential emerging coronavirus threats.