Untargeted viral metagenomics of indoor air as a novel surveillance tool for respiratory, enteric and skin viruses

Conventional hospital-based infectious disease surveillance struggles to detect mild or asymptomatic infections and incurs high costs for large-scale testing during outbreaks. In contrast, environmental surveillance can effectively monitor viral circulation and capture asymptomatic or mildly symptomatic infections that may otherwise go unnoticed. This longitudinal study explores the use of indoor air, in combination with targeted qPCR panels and untargeted viral metagenomics, as a novel virus surveillance tool. Indoor air samples were collected weekly from a daycare center in Leuven, Belgium, over a 12-month period using active indoor air sampling, followed by screening using respiratory and enteric qPCR panels, as well as untargeted viral metagenomics. Human-associated viruses were detected in 95.2% (40/42) of samples, with MW polyomavirus being the most prevalent at 80.9%. Several other respiratory viruses (e.g., rhinoviruses, RSV-B) and enteric viruses (e.g.. rotavirus, astrovirus, adenovirus) were identified, correlating with their known epidemiological circulation patterns. Metagenomics resulted in multiple complete viral genome reconstructions, allowing discrimination of viral subtypes and the identification of coinfections with closely related virus variants. Finally, a plethora of animal, insect, fungal and plant-infecting viruses could be detected, representing the indoor and outdoor environment. Indoor air surveillance can be a robust complementary tool for virus surveillance.