Non‐invasive surveys of mammalian viruses using environmental DNA

Abstract

1. Environmental DNA (eDNA) and invertebrate-derived DNA (iDNA) have been used to survey biodiversity non-invasively to mitigate difficulties of obtaining wildlife samples, particularly in remote areas or for rare species. Recently, eDNA/iDNA have been applied to monitor known wildlife pathogens, however, most wildlife pathogens are unknown and often evolutionarily divergent.2. To detect and identify known and novel mammalian viruses from eDNA/iDNA sources, we used a curated set of RNA oligonucleotides as viral baits in a hybridization capture system coupled with high throughput sequencing.3. 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. 4. 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.

Challenges to Implementing Environmental-DNA Monitoring in Namibia

“…Bioinformatic processing artefacts can be generated in the clustering of read data, to simplify ultra-complex datasets (Rossberg et al, 2014). For identifying individual species, we advocate informatic extraction ("fishing out") by means of baits (Alfano, et al, 2021) for target sequences to confirm presence and sequence diversity.…”

Viral diversity and zoonotic risk in endangered species

“…Collection of non-lethal samples such as oral and rectal swabs, or whole blood or sera, could help further characterize viral assemblages in threatened species—in addition to bolstering voucher collections and providing other conservation-relevant data, like estimates of species’ genetic diversity. In cases where direct sampling still presents logistical or ethical challenges, non-invasive sampling through testing of feces or urine—as sometimes already used for pathogen surveillance in bats and primates (Köndgen et al 2010; Giles et al 2021)—represents another avenue to characterize viral communities and their zoonotic potential in these species; recent diagnostic advances also now allow for pathogen risk to be evaluated from environmental DNA (eDNA) or invertebrate-based DNA (iDNA) (Alfano et al 2021). Lastly, analyses of previously collected voucher specimens and individual samples in museum collections could represent another means to improve research effort of these undertested species (Thompson et al 2021).…”

A Review of Non-Invasive Sampling in Wildlife Disease and Health Research: What’s New?

“…Kvapil and colleagues [206] used medicinal leeches (Hirudo medicinalis) as an alternative to more complex and invasive methods for blood sampling for preventive medicine and epidemiological studies in zoo animals looking for antibodies to tick-borne encephalitic virus. Alfano and colleagues [207] collected leech-derived iDNA (terrestrial leeches: Haemadipsa picta, H. zeylanica) in the forests of the Malaysian Borneo to detect and identify known and novel mammalian viruses. In this study, iDNA was also paired with eDNA from waterholes to study wildlife viral diversity and to detect novel potentially zoonotic viruses prior to their emergence.…”

“…The detection of viral infections can also be conducted collecting samples from the environment where the targeted wildlife live. The study previously mentioned by Alfano and colleagues [207] paired the iDNA analyses with those of the eDNA collected from waterholes in Tanzania and Mongolia. The indirect transmission of beak and feather disease virus, which is of global concern and can cause lethal infections, was tested by Martens and colleagues [212] using nest swabs.…”