Detection of emerging diseases: environmental DNA, a miracle tool?

Detection of emerging diseases environmental DNA a miracle tool

The level of detail is impressive for such an old world. A study published in early December in the review Nature meticulously describes the ecosystem of northern Greenland two million years ago (Ma). A record obtained by the formidable time machine represented by DNA, whose oldest fragment used by scientists dates back to 1 mA. Thanks to this work, we know better the region, which was populated by a very different fauna and flora under ten additional degrees: ancestors of hares and reindeer or even lemmings surveyed forests of birches, poplars and cedars. Another more surprising discovery: the presence in these territories of mastodons, distant relatives of elephants and mammoths. While paleoecology specialists greedily detail this new panorama of Greenland’s prehistoric biodiversity, they are especially pleased with the tremendous potential of the tool that made such a discovery possible: environmental DNA (eDNA).

All living organisms leave traces in their wake. Humans, especially during cell renewal processes or during secretions (saliva) and excretions (urine, faeces), but also plants, bacteria or viruses. All this DNA released in nature can be sampled and analyzed using molecular biology techniques (PCR, sequencing) that are ever more efficient and less and less expensive. And, beyond the study of the very ancient (palaeobiology), they have known for ten years a dazzling rise in varied and contemporary fields.

“In 2014, there were only about twenty scientific articles with eDNA, compared to several tens of thousands in 2022”, assures Sébastien Brosse, head of the “aquatic ecology and global changes” research team at the Evolution laboratory. and biological diversity (Toulouse III-Paul-Sabatier University). The method has become safe enough to be applied to the entire current living world, from the inventory of species to monitoring the evolution of biodiversity, and also for the detection and monitoring of emerging infectious diseases.

“Very promising” approach

There are two approaches in this area. The first is already known and used “just about everywhere in the world”, notes Marine Combe, researcher at the Research Institute for Development (IRD). This is the use of eDNA in urban wastewater, a reflection of what is carried by the population. “This essentially consists of monitoring the potential re-emergence of diseases such as polio, hepatitis A, influenza, the pathogens responsible for gastrointestinal epidemics such as noroviruses. This technique has been widely deployed to monitor the epidemic of Sars-Cov- 2 and all the specific infectious diseases that we know quite well”, she continues.

The tool turns out, on the other hand, to be less developed for circulation in nature, like freshwater environments, and for diseases of “less interest”. This approach is however “very promising”, assures the researcher. Via regular water samples in a defined environment, eDNA, whose molecules are then extracted, amplified, then compared to existing databases, makes it possible to observe the presence or absence of pathogens and their concentration… and thus detect an emergence and possibly a risk of infection.

“Cheaper and faster” technique

In France, this “sentinel” tool was first used in Guyana, where the team of Rodolphe Gozlan, research director at the IRD, worked on Buruli ulcer and leptospirosis, mapping the presence of these two bacterial diseases in fresh waters and sediments. The approach is now duplicated in Cambodia, Guinea, Madagascar, etc., because eDNA-based studies have a double advantage: “They are cheaper and faster”, summarizes Rodolphe Gozlan, who also mentions an “important taxonomic resolution “. “For the inventory of species, one hour in the field with eDNA is five years of classic sampling”, image Sébastien Brosse. Marine Combe confirms the time saving, and adds the “non-invasive” nature of these approaches: “We won’t need to collect animals or invertebrates.” The monitoring of a medium is then facilitated and accelerated.

However, eDNA extraction technology is not immune to some biases. “One of them is the availability of DNA in the environment where it is going to be taken. It happens that several samples are collected to look for a rare pathogen and that it is not detected. This does not necessarily mean that it is not present, only that its threshold is above the detection limit of the technology”, explains Marine Combe. DNA can also be degraded (more rapidly in water than in sediment, for example), to the point of no longer being identifiable. “And where does it come from? Upstream of the river, from a nearby field, from even further away, asks Rodolphe Gozlan? You have to take into account the aspect of displacement in sampling.”

Despite these limitations, “eDNA is revolutionizing the potential for monitoring a territory for zoonotic pathogens”, assures the research director at IRD. It offers a network, an unprecedented possibility of inventory, but above all a “broad approach, while science often remains too compartmentalized”. Building bridges between research fields is not the least advantage of this technology. In the Amazonian forest or in the heart of our cities, eDNA has not finished opening up new paths.

lep-sports-01