Environmental Sampling Outperforms Traditional Bird Testing for Virus Detection in Live Poultry Markets

Scientists at Duke-NUS Medical School have identified that environmental sampling is more effective than individual bird testing for detecting circulating viruses in live poultry markets. The study, published in Nature Communications, indicates that this method can uncover a broader range of poultry viruses, including highly pathogenic avian influenza strains, that traditional surveillance might miss. Live poultry markets are common in Asia, providing food and supporting livelihoods, but they also represent settings where close human-animal interaction increases the risk of zoonotic virus transmission, making effective surveillance critical.

The Limitations of Traditional Surveillance

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

A Novel Approach: Sampling the Environment

In this study, researchers focused on the shared environment of animals and humans. From January 2022 to April 2023, air samples, cage swabs, and water samples from poultry processing were collected from two live poultry markets in Cambodia. These samples underwent metagenomic sequencing, a technique that identifies all viral genetic material present without targeting specific viruses.

Key Findings: Broader Detection and Hidden Threats

"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, First Author, Duke-NUS Emerging Infectious Diseases Signature Research Programme

The team compared these environmental sampling results with traditional swabs from chickens and ducks in the same markets. They detected genetic material from 40 different poultry viruses, including influenza viruses and coronaviruses, with air samples consistently showing the highest diversity.

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

"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."
— Professor Gavin Smith, Director of the Emerging Infectious Diseases Signature Research Programme and Co-Senior Author

Implications for Public Health and Market Safety

Additionally, the study found that air samples near slaughter and holding areas contained viral material from multiple poultry pathogens. This indicates potential exposure risks for workers and customers through shared air, emphasizing the importance of ventilation and market design in risk reduction.

Towards a Comprehensive Surveillance Strategy

The researchers highlighted that environmental surveillance should supplement, rather than replace, animal testing. Certain viruses, especially those carried by ducks in smaller numbers, were more reliably detected via direct swabbing. Combining environmental surveillance with targeted animal sampling offers the most comprehensive strategy.

"These findings show that surveillance in high-risk animal-human interfaces can be strengthened through more efficient and safer approaches. Improving early detection ultimately supports stronger outbreak preparedness."
— Professor Lok Sheemei, Interim Vice-Dean for Research at Duke-NUS Medical School

Future Directions

The team plans to explore the application of environmental surveillance in other high-risk settings, such as pig slaughterhouses and wildlife environments, to enhance preparedness for emerging infectious diseases across Southeast Asia and beyond.