eDNA from Air Yields Data for Social Distancing, Disease Transmission and More
British researchers succeeded in extracting environmental DNA (eDNA) from the air, opening up more possibilities for identifying microbes, pathogen, pollens and fungal spores; mapping disease transmission; and establishing more accurate social distancing guidelines during the COVID-19 pandemic. The technology also has intriguing potential in DNA forensics, even without the presence of other physical samples.
This study from researchers at Queen Mary University of London provides “proof of concept that we can collect, extract and analyze airDNA using readily available tools and analysis pipeline,” with sampling times as short as five minutes, according to the research paper. The paper appeared recently in PeerJ, an open access peer-reviewed journal covering life, biology, medicine, and environmental sciences.
Lead researcher Elizabeth L. Clare has, as she said, “a background working with bats in remote places.” Co-lead Chris Faulkes has expertise in burrowing animals.
“We thought we could use this to assess what animals were present in a cave or burrow when we couldn’t easily see or capture them,” Clare said in an online discussion of the work.
Traditionally in the environmental field, the paper notes, “eDNA is increasingly being used for bio-surveillance, species occupancy studies, and the detection of endangered and invasive species, particularly in aquatic ecosystems. Assay development has focused on single species qPCR for targets of interest.”
Clare and colleagues’ work notably expands those applications, with potential opportunities for human-focused biotech companies and for public health.
In forensics, airDNA could enable recovery of forensic traces of recent activity “even when no physical traces (such as blood or hair) have been left, for non-invasive DNA collection or in forensic anthropology,” the paper noted.
In the human health arena, it could “help us map the transmission of infectious diseases or allergen, for example,” Clare said, by identifying microbes, pathogen, pollens and fungal spores from the air.
With development, the technology also has potential to serve as an early warning system, similar to the Biological Aerosol Sentry and Information System (BASIS) developed at Los Alamos National Laboratory and deployed in several metropolitan areas in 2003.
Currently, it could help refine social distancing guidelines.
“The key is determining what concentration of viable viral particles is sufficient to constitute an infectious dose and over what distance that volume can be delivered,” the authors wrote.
Methods similar to those used by Clare and colleagues may be used to quantify specific targets and thereby to define more accurate safety guidelines.
The team performed the airDNA tests in a dedicated animal housing room that for more than one year had contained only naked mole rats (Heterocephalus glaber). The 225 animals were housed in 15 colonies in the 4m x 3m room.
The test began by “sucking air through a filter from the artificial burrows of naked mole rats and then in the room where the burrows are housed,” Clare said. “We then extracted eDNA from the filters.”
The DNA was amplified using primers designed for mammals, targeting the 16S mitochondrial region. Another set of DNA from the same filters was amplified using vertebrate primers commonly used to with aquatic eDNA, targeting the 12S mitochondrial region. Because amplification was greatest when using the mammalian primers, only those were sequenced.
“We sequenced a piece of DNA and compared that to reference samples. This let us identify the naked mole rats, and also humans who cared for them,” Clare said.
In the four samples sequenced, only the one taken from the room was clear. It was 100% human. The other three showed competing DNA signals, as expected. All the bases that could be called, however, were identical to those of the mole rat reference DNA. A handful of samples from the facility room also detected dog DNA, the paper noted.
“We found the naked mole rat DNA where we expected in the burrows, but also in the room, which shows the DNA is moving away from the source,” she said.
Finding human DNA mixed in with the naked mole rat DNA samples was unanticipated, and the team at first considered it a contaminant.
“Then we realized it opened some interesting questions about how this could be used,” Clare added. “We’re discussing what we can do with this technology.”
The biggest challenge to applying this research is determining the optimal size of the space to be monitored to return actionable results.
“The potential is that air DNA extracted in large spaces might be too dilute for detection…” she said, possibly mixing into a “meaningless soup.”
That has proven not to be the case in aquatic environments, which gives the researchers hope. None-the-less, it ultimately may be most effective in smaller spaces.
The team’s initial applications likely will be to monitor species in the wild without disturbing them by getting too close, and possibly as a tool to measure biodiversity. Currently, the researchers are working to determine how far airborne DNA can travel and how large the space can be for the technology to detect the animal.