Pulling lifesaving data out of thin air, literally

In rural Cambodia, two hours outside of the capital, Phnom Penh, scientists navigate to the bottom of a cliff face. Above them is a canopy of teak trees, their shining leaves swaying gently. The heat is stifling. Kampot pepper plants scattered here and there nearly block the narrow pathway.

Filip Claes and Erik Karlsson, the scientists leading this expedition, walk for 20 minutes before they enter a barely noticeable cave entrance perhaps a metre and a half in diameter. It is shrouded in shrubs and vines.

This venture into one of Cambodia’s lost caves is part of an innovative mission for disease surveillance conducted as part of a joint project between the Food and Agriculture Organization of the United Nations (FAO) through its Emergency Centre for Transboundary Animal Diseases (ECTAD) and the Institut Pasteur du Cambodge (IPC).

Their goal today is to collect bat DNA samples. Utilizing a non-invasive technique, the team employs drones to pull environmental DNA (eDNA) — traces of genetic material from hair, feathers, saliva and even pollen — from the air itself. 

The Government of Cambodia is at the forefront of this visionary approach aimed at protecting animals and humans alike from disease. The team works wherever there could be an interface between humans and animals or between wild and domesticated animals, including in places like poultry farms and live animal markets. The aim is to create an early warning system to prevent the transmission of diseases from wild to domestic animals, safeguarding livestock health across the country and stopping the zoonotic transmission of animal diseases to humans.

In Asia, poultry and pig farms are often close to wildlife environments. Hence, the risk of zoonotic diseases spreading to wider populations has become a concern. “Three to four new zoonotic diseases emerge every year throughout the world,” says Karlsson. “And two out of three of current human diseases are zoonotic in origin.”

In the shadow of recent global outbreaks like African swine fever and avian influenza, this project is more than just a scientific endeavour; it is a crucial step towards global preparedness. The technology enables quicker, safer and more cost-effective surveillance compared to traditional methods.

“We live in a world where the boundaries between wildlife, humans and livestock are increasingly blurred,” says Vincent Martin, Director of FAO’s Office of Innovation, who is himself an epidemiologist. “This novel approach to the early detection of zoonotic diseases doesn’t just solve a problem, it can help to prevent an epidemic in both animals and humans.”

FAO supports the effort as part of ELEVATE, an incubator programme run out of its Office of Innovation, to develop and work on cutting edge ideas related to agriculture and farming. The programme sponsors about a dozen different groups, providing them a space to test new ideas related to agrifood systems. “The idea of the incubator is to ignite novel solutions to promote innovation and intrapreneurship,” says Martin.

Drones out for DNA

Back in the cave, the team members pull out their drones from the portable cases that they carry on their shoulders. Each drone has an air sampler attached to it.

Normally sampling missions like this would mean that the team would have to capture a large number of wild animals, take swabs or blood and bring the samples to a lab for testing. With this new system, however, they can collect whatever virus the animals may be shedding into the air.

“When we enter these environments, we are looking for any disease that could jump from bats to pigs and chickens to humans,” says Claes.

The team is also accelerating the process of identifying pathogens. With the portable PCR and DNA sequencers they can search for the presence of everything from avian flu, zika, novel strains of coronavirus, African swine fever, rabies, nipah or even new unknown pathogens.

Known diseases can be diagnosed within hours, directly in the field. Sequencing requires a bit more time, but field sequencing can now speed up the process from weeks to days.

The data they collect can contribute to developing a comprehensive picture of the health landscape. By collecting samples over time, the project seeks to have a better understanding of which diseases are present in the environment and during what periods.

Reaction time is key. The faster the reaction time, the greater the ability to contain the spread of a deadly pathogen. The implications of the project extend beyond issues of livestock and human health. Airborne sampling and remote testing of environmental DNA samples can be used also to monitor wildlife in fragile ecosystems and has great potential for applications in ecology and biodiversity management.

With the world increasingly vulnerable to zoonotic diseases due to climate change, urbanization and deforestation, this initiative is helping countries stay on top of emerging health threats and their vast repercussions.