Environmental DNA – How a tool used to detect endangered wildlife ended up helping fight the COVID-19 pandemic

Imagine discovering that an animal species that you thought was extinct was still alive – without looking at it. This was the case with the Brazilian frog species. Megaelosia bocainensis, whose complete disappearance in 1968 led scientists to believe it was extinct. But thanks to a new genetic detection technique, it was rediscovered in 2020.

Such discoveries are now possible thanks to a new approach that collects and reads traces of DNA released into the environment by animals. It’s called environmental DNA, or DNA – and it takes advantage of the fact that each animal sheds DNA into its environment through skin, hair, scales, feces, or bodily fluids. when he travels around the world.

As wildlife biologists at the University of Florida’s Whitney Laboratory for Marine Bioscience & Sea Turtle Hospital, we use eDNA to track a virus responsible for a marine turtle pandemic called fibropapillomatosis, which causes debilitating tumors. We also use eDNA to detect sea turtles in the wild.

But in 2020, human health researchers began to reuse electronic DNA techniques to track the COVID-19 pandemic. This is a prime example of how research in one area – wildlife conservation – can be adapted to another area – mitigation of human disease. In the future, we believe that eDNA will prove to be an essential tool for monitoring human and animal health.

From soil microbes to sea turtles

In the 1980s, scientists started looking for microbial DNA in soil samples. Over the next 20 years, the technique was adapted for use with air and water samples, and scientists began using eDNA to detect larger animals and plants.

Scientists can now detect traces of DNA in many different environments.
Liam Whitmore, University of Limerick, CC BY-ND

Although the science behind eDNA techniques is complex, the actual process of collecting and testing a sample is relatively straightforward. Samples are filtered through very fine paper, which traps loose cells and DNA strands. The techniques for reading the DNA present are the same as those used for tissue or blood samples, typically quantitative polymerase chain reaction or whole genome sequencing. Scientists can either read all the DNA present from each organism – or target only the DNA of the species of interest.

Scientists now regularly use eDNA to detect endangered wildlife and invasive species. The ability to tell if an animal is present without ever needing to lay an eye or a lens on it is an incredible leap forward, reducing the time, resources and human effort required to monitor and protect vulnerable species.

A sea turtle on its back in an examination room.  One of its fins is severely deformed.
Routine imaging of a juvenile green sea turtle patient with virus-triggered fibropapillomatosis at Florida Whitney Sea Turtle Hospital.
Devon Rollinson-Ramia, CC BY-ND

However, to truly protect endangered species, it’s not just animals that need to be watched, but pathogens that threaten their survival. Environmental DNA is able to monitor parasites, fungi and viruses that can cause disease in wildlife.

COVID-19 monitoring

While scientists originally applied eDNA to the detection of human pathogens over a decade ago, it was not until the onset of the current human COVID-19 pandemic that the reuse of the DNA has taken off on a large scale, allowing technology to make staggering advancements in a short period of time.

The genomes of the coronavirus are not made up of DNA, but rather of its cousin molecule, RNA. So the researchers quickly optimized a variant of eDNA – eRNA – to detect coronavirus RNA in human air and wastewater.

For example, at Shands Hospital at the University of Florida, researchers took air samples from the hospital room of two patients with COVID-19. Using eRNA, they successfully isolated and sequenced the virus. Confirmation of air as a key transmission route directly influenced public health guidelines.

A gloved hand holds a sealed plastic bottle of cloudy water.
Collecting wastewater samples to test for SARS-CoV-2 at Utah State University in September 2020.
AP Photo / Rick Bowmer

When scientists apply eRNA to archived wastewater samples, the actual dates of SARS-CoV-2 onset can be detected. The concentration of SARS-CoV-2 in wastewater in Valencia, Spain peaked on March 9, 2020, but the number of clinical cases did not peak until early April 2020 due to the lag between infection and symptoms serious clinics.

This type of predictive surveillance has profound implications for healthcare systems, allowing time to prepare – not just for COVID-19, but for any future disease outbreaks that threaten human populations.

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Intersection of diseases

It is essential that human and animal diseases are studied together. Sixty percent of emerging human pathogens come from animals – many of which (42%) come from populations of wild animals, including Ebola, Zika, West Nile and Marburg viruses. Humans can also transmit pathogens to animals.

SARS-CoV-2 has already infected monkeys at a San Diego zoo, large cats at a New York zoo, and minks on farms in Europe – the latter has given rise to new variants that may constitute a new one. threat to humans.

Doctors, veterinarians and scientists call this convergence of human, animal and environmental well-being OneHealth or EcoHealth. The study and treatment of human and wildlife diseases together recognize their commonalities and often lead to breakthroughs.

With eDNA, all pathogens can be monitored in an environment, regardless of their origin. An integrated electronic DNA surveillance program could cost-effectively provide early warning of human, animal and wild diseases.


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