Shotgun metagenomics on indoor air for surveillance of respiratory, enteric, and skin viruses in a Belgian daycare setting, January to December 2022

BACKGROUNDHospital-based communicable disease surveillance may be costly during large outbreaks and often misses mild or asymptomatic infections. It can be enhanced by environmental surveillance, which monitors circulating pathogens, even from asymptomatic carriers.AIMWe investigated if tracking viruses in indoor air could be used for their surveillance in a community setting. We also tested the value of untargeted metagenomics to identify viruses in air samples.METHODSWeekly indoor air samples were collected with active air samplers from January until December 2022 from a daycare centre in Leuven, Belgium. Samples were analysed using respiratory and enteric quantitative (q)PCR panels, as well as with untargeted metagenomics, enabling both targeted and agnostic viral detections.RESULTSHuman-associated viruses were detected in 40 of 42 samples across the study period, with MW polyomavirus being most prevalent (33 samples). Respiratory agents such as rhinoviruses and RSV-B and enteric viruses including rotavirus A, astrovirus, and adenovirus appeared at epidemiologically expected times. Skin-associated viruses were also observed, notably Merkel cell polyomavirus and STL polyomavirus. Metagenomics enabled reconstructing multiple complete genomes, distinguishing viral subtypes and detecting copresence of closely related variants. Additionally, several animal, insect, fungal, and plant viruses were found, reflecting both indoor and outdoor environmental exposure.CONCLUSIONIndoor air monitoring, combined with untargeted metagenomics, demonstrates a potential to support virus surveillance. This approach can allow monitoring circulation of viruses in community settings, including those causing asymptomatic or mild infections. By enabling to reconstruct complete viral genomes, it allows detailed variant tracking, facilitating adapted public health responses.