%0 Journal Article %A Niccolo Alfano %A Anisha Dayaram %A Jan Axtner %A Kyriakos Tsangaras %A Marie-Louise Kampmann %A Azlan Mohamed %A Seth T. Wong %A M. Thomas P. Gilbert %A Andreas Wilting %A Alex D. Greenwood %T Non-invasive surveys of mammalian viruses using environmental DNA %D 2020 %R 10.1101/2020.03.26.009993 %J bioRxiv %P 2020.03.26.009993 %X Environmental DNA (eDNA) and its subdiscipline, invertebrate-derived DNA (iDNA) have been used to survey biodiversity non-invasively [1,2]. Water is ubiquitous in most ecosystems, and, among invertebrates, terrestrial haematophagous leeches are abundant and can be easily collected in many tropical rainforests [3,4]. Such non-invasive nucleic acid sources can mitigate difficulties of obtaining wildlife samples, particularly in remote areas or for rare species. Recently, eDNA/iDNA sources have been applied to monitoring specific wildlife pathogens [5,6]. However, previous studies have focused on known pathogens, whereas most wildlife pathogens are uncharacterized and unknown. Non-invasive approaches to monitoring known and novel pathogens may be of particular benefit in ecosystems prone to viral emergence, many of which occur in areas where invasive sampling is challenging, such as tropical rainforests. Here, we show that both eDNA from natural waterholes, and iDNA from terrestrial haematophagous leeches, can be used to detect unknown viruses circulating in mammalian hosts (Figure 1). Using a curated set of RNA oligonucleotides based on the ViroChip microarray assay [7] as baits in a hybridization capture system, multiple mammalian RNA and DNA viruses were detected from both eDNA and iDNA samples. Congruence was found between host DNA assignment and viruses identified in leeches, and between animals observed visiting the waterholes and the viruses detected. Our results demonstrate that eDNA/iDNA samples may represent an effective non-invasive resource for studying wildlife viral diversity. Several of the detected viruses were novel, highlighting the potential of eDNA/iDNA for epidemiological analysis of emerging viruses prior to their emergence.HighlightsEnvironmental DNA (water and blood-sucking leeches) provided a non-invasive method of screening wildlife for virusesA comprehensive viral RNA oligonucleotide bait set was developed to capture known and unknown mammalian virus diversityLeech blood meal host determination and viruses identified were congruentViruses determined from water correlated with known and observed species visiting the water sourcesIn brief Alfano, Dayaram, et al. demonstrate that environmental DNA from southeast Asian leech bloodmeals and waterholes from Africa and Mongolia can be used as to detect viruses circulating in wildlife. These nucleic acid sources may represent an effective non-invasive resource for studying wildlife viral diversity and emerging viruses pre-emergence. %U https://www.biorxiv.org/content/biorxiv/early/2020/03/29/2020.03.26.009993.full.pdf