Metagenomic assessment of airborne and surface viral signals and worker acceptability during a partial-lid intervention in a Cambodian live bird market

Mechanical defeathering can disperse viral material in live poultry markets, but interventional machine modifications must fit routine work. This nonrandomized field study evaluated partial lids on defeathering machines at Orussey Market, Cambodia, across six sampling days, three with lids and three without. Targeted RT-qPCR and target-enriched metagenomics characterised viral RNA in air samples collected during a three-hour air-sampling period and in nearby surface samples collected before and after that period, while work questionnaires assessed usability. Sequencing detected 73 poultry-associated viral taxa. Influenza A virus, avian coronavirus and rotavirus G together accounted for over 80% of relative metagenomic abundance in 14 of 18 air samples. In air samples, RT-qPCR cycle thresholds correlated inversely with metagenomic relative abundance for avian influenza virus and Newcastle disease virus (Spearman’s ρ = −0.645 and − 0.684, respectively). Airborne richness was descriptively lower on days with lids, but targeted viral detections did not change consistently, and composition profiles overlapped. Surface profiles changed from before to after the air-sampling period on days with and without lids; the study did not establish a lid-associated difference in these changes. All five workers reported discomfort and perceived slower work; none wanted to use the lid in its tested form, although three would continue if it were permanently integrated into the machine. With only three sampling days per condition, the study did not establish a consistent reduction in airborne or surface viral contamination associated with lid use. Future studies should evaluate lids redesigned with workers alongside complementary measures addressing ventilation, hygiene, and clean water and waste management to reduce occupational exposure.