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

Five waterholes from Tanzania and six from Mongolia were tested. From each waterhole, one water filtrate and one sediment sample were collected (except for one waterhole where only a sediment sample was collected), for a total of twenty-one samples. Five samples (two water and three sediment samples) in total were positive for viral sequences (23.8%). Four viral families were identified including: Retroviridae, Herpesviridae, Adenoviridae and Papillomaviridae. In filtered water and sediment samples collected from the same waterhole, only one virus per sample was generally identified and in one location (WM20 and SM20) contigs from different viral families were isolated based on sample type. Differences between sediment and water are not unexpected as the sediment likely represents a longer-term accumulation of biomaterial and the water represents more acute contamination at the surface and variable mixing throughout.