Abstract
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 (2023-2025). 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 respiratory pathogen levels mirroring citywide clinical surveillance data. These data demonstrate that air surveillance can provide respiratory virus case and variant trend data at a building or community-scale, serving as an alternative or complementary tool for public health environmental surveillance.
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Acknowledgements
We thank our colleagues at the Chicago Department of Public Health for their invaluable support and review of this work, specifically Peter DeJonge, PhD; Michelle Funk, DVM, MPH; Colin Korban, MPH; Peter Ruestow, PhD; and Haifa Wahbeh, MBA, CFFE. We thank the Genomics and Microbiome Core Facility at Rush University Medical Center for laboratory processing of air samples, qPCR analysis and SARS-CoV-2 library preparation and sequencing, especially Kevin Kunstman, Giancarlo Balangue, Felix Araujo-Perez, Jeremy Kahsen, and Marisol Dominguez. We thank Drs. David and Shelby O’Connor at the University of Wisconsin Madison for sharing air sampling expertise in support of this study. We acknowledge the Illinois Department of Public Health, Metropolitan Water Reclamation District of Greater Chicago and Chicago Department of Water Management for their contributions and support of wastewater surveillance in Chicago and Cook County. Finally, we gratefully thank air sampling sites for weekly cartridge exchanges, and support of the program, specifically Larry K. Kociolek, MD and Megan E. Reyna, BA at the Division of Pediatric Infectious Diseases, Ann & Robert H. Lurie Children’s Hospital of Chicago; Nidhi S. Undevia, M.D. and Lisa A. Duffner, BA, BS at RML Specialty Hospital Office of Clinical Research, Hinsdale, IL; Priscilla Ware, MD at Cermak Health Services and Juvenile Temporary Detention Center; Annie Chambers, B.A. at the Cook County Sheriff’s Office; Chad Zawitz, MD at Cook County Health; Allison H. Bartlett, MD, MS and David Zhang, MD at Comer Children’s Hospital, University of Chicago Medicine; Michael Gottlieb, MD, at the Department of Emergency Medicine, Rush University Medical Center; and the staff at the Chicago Department of Public Health Lakeview Sexual Health Clinic.
Funding
S.R.B discloses support for this work from the Centers for Disease Control and Prevention of the U.S. Department of Health and Human Services as part of a financial assistance award totaling $800,000 with 100% funded by CDC/HHS. The contents are those of the author(s) and do not necessarily represent the official views of, nor an endorsement, by CDC/HHS, or the U.S. Government. M.K.H. discloses support in part for this research by cooperative agreement NU50CK000556 from CDC. Its contents are solely the responsibility of the authors and do not necessarily represent the official views of CDC. H.J.B discloses support for this research from Rush University Medical Center through an award from the Center for Emerging Infectious Diseases (1 GE1HS45832-01-00).
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Barbian, H.J., Newcomer, E.P., Bobrovska, S. et al. Citywide indoor air sampling mirrors wastewater and clinical case surveillance of respiratory viruses. Nat Commun (2026). https://doi.org/10.1038/s41467-026-72919-2
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DOI: https://doi.org/10.1038/s41467-026-72919-2
