Scientists at Duke-NUS Medical School have discovered a more effective method to detect poultry viruses by sampling the environment rather than testing individual birds. The study, published in Nature Communications, reveals that environmental sampling can uncover a broader range of poultry viruses, including highly pathogenic avian influenza strains that traditional surveillance might overlook. This breakthrough is particularly significant in live poultry markets, which are prevalent in Asia, where humans and animals interact closely, heightening the risk of viral transmission. Current monitoring methods, such as capturing birds and collecting swabs, are slow, labor-intensive, and may not detect viruses if the birds are not infected at the time. In contrast, the new approach involves analyzing the environment shared by animals and humans. Between January 2022 and April 2023, researchers collected air samples, swabbed cages, and sampled water from two live poultry markets in Cambodia. They used metagenomic sequencing to identify all viral genetic material present in the samples without targeting specific viruses. Dr. Peter Cronin, the study's first author, emphasizes that direct animal testing is not always necessary to detect pathogenic viruses. 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. The team compared environmental sampling results with traditional swabs taken from chickens and ducks and detected genetic material from 40 different poultry viruses, including influenza viruses and coronaviruses. Notably, the researchers identified highly pathogenic avian influenza H5N1 in environmental samples even when it was not detected in the birds tested concurrently. This suggests that relying solely on bird testing may underestimate the true level of viral circulation. Professor Gavin Smith, the study's co-senior author, highlights the comprehensive view of viral circulation in live poultry markets that this method provides. By applying unbiased metagenomic sequencing to environmental samples, they 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, indicating that workers and customers may be exposed through shared air. This underscores the importance of ventilation and market design in risk reduction. The researchers emphasize 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, the Interim Vice-Dean for Research at Duke-NUS Medical School, emphasizes the importance of improving early detection to support 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. Duke-NUS is a global leader in medical education and biomedical research, combining scientific discovery with real-world impact to improve health outcomes in Singapore and around the world.
