Non‐invasive surveys of mammalian viruses using environmental DNA

Environmental DNA (eDNA) and invertebrate‐derived DNA (iDNA) are used to survey biodiversity non‐invasively to mitigate difficulties in obtaining wildlife samples, particularly in remote areas or for rare species. Recently, eDNA/iDNA were used to monitor known wildlife pathogens; however, most wildlife pathogens are unknown and often evolutionarily divergent. To detect and identify known and novel mammalian viruses from eDNA/iDNA, we used a curated set of RNA oligonucleotides as viral baits in a hybridization capture system coupled with high‐throughput sequencing. We detected multiple known and novel mammalian RNA and DNA viruses from multiple viral families from both waterhole eDNA and leech‐derived iDNA. Congruence was found between detected hosts and viruses identified in leeches and waterholes. Our results demonstrate that eDNA/iDNA samples represent an effective non‐invasive resource for studying wildlife viral diversity and for detecting novel potentially zoonotic viruses prior to their emergence.