Non-invasive surveys of mammalian viruses using environmental DNA

Niccolo Alfano; Anisha Dayaram; Jan Axtner; Kyriakos Tsangaras; Marie-Louise Kampmann; Azlan Mohamed; Seth Timothy Wong; M. Thomas P. Gilbert; Andreas Wilting; Alex Daivd Greenwood

The authors declare no competing interests. Figure 1 : Viral screening of vertebrate viruses from leech iDNA and waterholes eDNA using RNA olignonucleotide based hybridization capture. In the upper panel the left photo shows a leech feeding on a frog in a rainforest of Vietnam (courtesy Andrew Tilker; Leibniz-IZW) and the right photo shows an African waterhole in Tanzania (courtesy Peter Seeber; Leibniz-IZW). The middle panel depicts the hybridization capture protocol. Briefly, Illumina libraries were produced from reverse transcribed RNA and DNA from leech bloodmeals or from waterhole surface water and sediments. Biotinylated viral RNA baits were hybridized to the libraries and non-target DNA was washed away. The remaining DNA was sequenced, reads assembled into contigs and mapped to reference viral genomes. These contigs were further analyzed to determine viral identity. Viral identity was paired with host identity determined either by mammalian metabarcoding of the leech samples, or by observation of waterhole usage.