Environmental swabs reveal hidden avian viral diversity

Scientists at Duke-NUS Medical School have found that viruses circulating in live poultry markets can be detected more effectively by sampling the surrounding environment than by testing individual birds. The study, published in Nature Communications, shows that environmental sampling can uncover a broader range of poultry viruses-including highly pathogenic avian influenza strains that traditional surveillance may miss.

Live poultry markets are widely used across Asia, supplying fresh food and supporting livelihoods. However, there are also settings where humans and animals interact closely, increasing the risk of viruses crossing from birds to people. Effective surveillance is therefore critical to preventing outbreaks.

Current monitoring methods typically involve capturing birds and collecting a swab from their throat or digestive tract. This process is slow, labour-intensive, can pose safety risks to workers, and may fail to detect viruses if the birds sampled are not infected at the time.

In this study, researchers instead analysed the environment shared by animals and humans. Between January 2022 and April 2023, they collected air samples, swabbed cages, and sampled water used in poultry processing from two live poultry markets in Cambodia. These samples were analysed using metagenomic sequencing, which identifies all viral genetic material present in a sample without targeting specific viruses.

We showed that direct animal testing is not always necessary to detect pathogenic viruses in live-bird markets. Instead, sampling air, water, cages, and surfaces can reveal a wide range of poultry viruses, including avian influenza, even when those same viruses are not detected in the birds at the time."

Dr. Peter Cronin, Study First Author and Research Fellow, Duke-NUS Medical School

The team compared the results from environmental sampling with traditional swabs taken from chickens and ducks at the same markets, and detected genetic material from 40 different poultry viruses, including influenza viruses and coronaviruses. The air samples consistently captured the greatest diversity.

Notably, the researchers identified highly pathogenic avian influenza H5N1 in environmental samples even when it was not detected in the birds tested concurrently. Some of these viruses belonged to specific genetic lineages known to pose significant risks to poultry and humans, suggesting that relying solely on bird testing may underestimate the true level of viral circulation.

Professor Gavin Smith, Director of the Emerging Infectious Diseases Signature Research Programme and co-senior author, added:

"This study provides a more comprehensive view of viral circulation in live poultry markets than is possible through single-animal testing alone. By applying unbiased metagenomic sequencing to environmental samples, we capture viral material shed across shared air and surfaces, enabling broader detection in a cost-effective and scalable manner while reducing the need for close animal contact."

The team also found that air samples collected near slaughter and holding areas contained viral material from multiple poultry pathogens. This indicates that workers and customers may be exposed through shared air, underscoring the importance of ventilation and market design in risk reduction.

The researchers emphasised that environmental surveillance should complement, not replace, animal testing. Some viruses, particularly those carried by ducks present in smaller numbers, were more reliably detected through direct swabbing. Combining environmental surveillance with targeted animal sampling provides the most comprehensive surveillance strategy.

Professor Lok Sheemei, Interim Vice-Dean for Research at Duke-NUS Medical School, said:


"These findings show that surveillance in high-risk animal-human interfaces can be strengthened though more efficient and safer approaches. Improving early detection ultimately supports stronger outbreak preparedness."

The team is now exploring how environmental surveillance can be applied in other high-risk settings, including pig slaughterhouses and wildlife environments. Refining these methods could improve preparedness for emerging infectious diseases across Southeast Asia and beyond.