Myanmar is one of the most biodiverse countries from a species perspective in Southeast Asia, yet there is minimal published data on zoonotic viruses in small mammals. From July 2017 to August 2018, wildlife sampling was conducted at human-animal interfaces at sites in the Yangon Region and Kayin State. To investigate virus diversity of commensal rodents and shrew, rectal swabs were collected from mice (Mus sp., N = 3), rats (Rattus norvegicus, N = 80; Rattus rattus, N = 6), and Southeast Asian shrews (Crocidura fuliginosa, N = 8). RNA was extracted from rectal swabs, made into cDNA, and subjected to metagenomic next-generation sequencing followed by phylogenetic analysis for virus identification and taxonomic placement. The study provides the first detection of Wencheng shrew virus (WESV) in Myanmar and the first report in C. fuliginosa. A novel member of the genus Cardiovirus was also detected in R. norvegicus and clustered with Cardiovirus theileri sequences previously identified in wild rats from China. Further characterization of viruses circulating in small mammals will help inform public health officials of potential zoonotic risks in a region with virus surveillance gaps and ongoing land use change which may be increasing the risk of zoonotic disease emergence.
Supplementary Information: The online version contains supplementary material available at 10.1038/s41598-026-38406-w.
Keywords: Alphacoronavirus; Cardiovirus; Commensal rodents; Metagenomics; Myanmar; Shrews.