Non-invasive surveys of mammalian viruses using environmental DNA

Abstract

SummaryEnvironmental 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 briefAlfano, 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.

Towards an ecosystem model of infectious disease

“…Upscaling to landscapes, where the effects of environmental filtering and dispersal on host and vector populations are greatest, observational studies conducted using remote monitoring devices along gradients of human activity (such as the 'Biome Health Project' https://www.biomehealthproject.com/) can be used to estimate how anthropogenic environmental change impacts the spatial distribution of host and vector populations (e.g., ungulate wildlife, livestock, mosquitos, ticks) 66 . When paired with metagenomic and metatranscriptomic sequencing, associations between hosts and their environment can be related to pathogens and their functional roles within parasite communities, through blood-meal or gut content analysis 67 .…”

Measuring protected-area outcomes with leech iDNA: large-scale quantification of vertebrate biodiversity in Ailaoshan nature reserve

“…We further propose that iDNA may be used to survey other dimensions of biodiversity, such as zoonotic disease. Recent work has demonstrated the exciting possibility of using leech-derived bloodmeals, sampled from the wild, to screen for both viruses and their vertebrate hosts [34, 102]. The 2020 SARS-CoV-2 pandemic has underscored the urgency of better understanding zoonotic disease in wildlife reservoirs – a need that is likely to become even more pressing as global land use changes continue [103].…”

“…iDNA is vertebrate DNA collected by invertebrate 'samplers,' including haematophagous parasites (leeches, mosquitoes, biting flies, ticks) and dung visitors (flies, dung beetles) [26][27][28]. iDNA methods are rapidly improving, with research focused on documenting the ranges of vertebrate species and their diseases that can be efficiently detected via iDNA [29][30][31][32][33][34], plus comparisons with camera trapping and other survey methods [35][36][37], and pipeline development [38,39].…”

Non‐invasive surveys of mammalian viruses using environmental DNA

“…The consensus sequences of the viral contigs obtained in this study were deposited in GenBank under the accession numbers MT444451-MT444487. Supplementary data for this publication can be found on Dryad Digital Repository https:// doi.org/10.5061/dryad.2v6ww pznc (Alfano et al, 2021).…”