Genomic analysis and evolutionary insights of betacoronaviruses in wild Peromyscus mice and other terrestrial small mammals

Coronaviruses (CoVs) are diverse RNA viruses infecting a wide range of hosts; many are important pathogens of humans and domestic animals. Certain human and livestock CoVs are thought to have rodent origins. We surveyed wild rodents and eulipotyphlans in Ontario, Canada. We detected four species of beta-CoVs across host species and geographic location suggesting potentially low barriers to cross-species transmission. Whole Peromyscus CoV (PCoV) genomes were recovered from Peromyscus mice, which were highly related to important human and animal Betacoronavirus gravedinis viruses (e.g., human coronavirus OC43, bovine coronavirus [BCoV]). We identified at least three PCoV genotypes resulting from recombination with other B. gravedinis viruses, suggesting cross-species transmission events have occurred. We found high similarity of predicted sialoglycan-binding sites on the spike glycoprotein structure for PCoV, OC43, and BCoV. This study highlights the need for continued virus genomic characterization to support the investigation of CoV evolution and ecology in North American terrestrial small mammals.