Hospital air sampling enables surveillance of respiratory virus infections and genomes

There is an urgent need for early detection and comprehensive surveillance of respiratory pathogens. Environmental surveillance may be key to timely responses for newly emerging pathogens and infections that are unreported or underreported. Here, we employed air sampling in a large urban hospital. Air samples (n=358) were collected weekly at five locations, including two in the emergency department, two in hospital common areas and one in a storage room, for two respiratory virus seasons (November 2022 to June 2024). Air samples were tested for eight respiratory pathogens by qPCR, including RNA and DNA viruses and a bacterium. Air samples had an average of four detected pathogens per sample and 97% samples contained SARS-CoV-2. Air sample pathogen positivity and quantity were strongly correlated with clinical surveillance for four seasonal respiratory pathogens: influenza A and B, respiratory syncytial virus, and human metapneumovirus. Targeted sequencing of SARS-CoV-2 showed that lineages detected in air samples reflected those in contemporaneous regional clinical specimens. Metagenomic sequencing with viral enrichment detected myriad human pathogens, including respiratory-associated viruses with recovery of full viral genomes. Detection of viral pathogens correlated well between metagenomic sequencing and qPCR. Overall, this suggests air sampling can be an agile and effective tool for pathogen early warning, surveillance and genome characterization.