Viruses and Parasites in Swamp Rabbits (Sylvilagus aquaticus): A Baseline Survey to Aid Conservation Efforts.

Technical advancements have enabled the discovery of potential pathogens in an ever-broadening range of wildlife taxa. To further the scope of this body of knowledge and to inform conservation efforts, we examined potential disease agents present in swamp rabbits (Sylvilagus aquaticus) of southeastern Missouri, USA, during winter 2023. This region represents the northernmost portion of the species' range and is characterized by an intermixed landscape of preferred bottomland hardwood forest and agricultural landcover. Concerns about infectious disease threats to swamp rabbits have increased since the emergence of rabbit hemorrhagic disease, caused by rabbit hemorrhagic disease virus 2 (RHDV2; Caliciviridae, Lagovirus europaeus), that has spread to domestic, wild, and feral rabbits and hares, predominantly in the western and midwestern USA. We applied metagenomic and metabarcoding methods, designed to characterize communities of viruses and parasites, to noninvasively collected rabbit fecal samples. We identified seven viruses and eight parasite genera that probably infect mammals. Although some relatives of these agents cause disease, none are unexpected in lagomorphs, and none are considered a health concern. Notably, RHDV2 was not detected. These results provide baseline data for future conservation and management efforts, especially if RHDV2 or other pathogens become a concern for swamp rabbits.