Citywide indoor air sampling mirrors wastewater and clinical case surveillance of respiratory viruses

Wastewater surveillance of respiratory pathogens can provide timely estimates of viral activity and disease trends in a population. Indoor air surveillance could be used similarly with some advantages but remains largely unvalidated at the community-scale. Here, an indoor air surveillance program was employed as part of public health environmental surveillance in Chicago, Illinois, USA. Ten air samplers were placed in healthcare and congregate living settings across the city. Weekly air samples were evaluated for influenza A, influenza B, respiratory syncytial virus, and SARS-CoV-2 over two respiratory virus seasons. Citywide, aggregated air sample positivity and viral load were closely correlated with local clinical case and wastewater surveillance data across all respiratory viruses. Virus trends in air data often preceded clinical and wastewater, although this varied across pathogens and respiratory virus seasons. Further, whole-genome sequencing of SARS-CoV-2 showed close correlation of variant proportions across all datasets. At the building-scale, air samples obtained from a single sampling device provided efficient respiratory virus surveillance, with well-correlated estimates of respiratory pathogens. These data demonstrate that air surveillance can provide accurate estimates of respiratory virus infections and variants at a building or community-scale, serving as an alternative or complementary tool for public health environmental surveillance.