SARS-CoV-2 and other respiratory pathogens are detected in continuous air samples from congregate settings

Mitchell D. Ramuta, Christina M. Newman, Savannah F. Brakefield, Miranda R. Stauss, Roger W. Wiseman, Amanda Kita-Yarbro, Eli J. O’Connor, Neeti Dahal, Ailam Lim, Keith P. Poulsen, Nasia Safdar, John A. Marx, Molly A. Accola, William M. Rehrauer, Julia A. Zimmer, Manjeet Khubbar, Lucas J. Beversdorf, Emma C. Boehm, David Castañeda, Clayton RushfordDevon A. Gregory, Joseph D. Yao, Sanjib Bhattacharyya, Marc C. Johnson, Matthew T. Aliota, Thomas C. Friedrich, David H. O’Connor, Shelby L. O’Connor

Research output: Contribution to journalArticlepeer-review

14 Scopus citations

Abstract

Two years after the emergence of SARS-CoV-2, there is still a need for better ways to assess the risk of transmission in congregate spaces. We deployed active air samplers to monitor the presence of SARS-CoV-2 in real-world settings across communities in the Upper Midwestern states of Wisconsin and Minnesota. Over 29 weeks, we collected 527 air samples from 15 congregate settings. We detected 106 samples that were positive for SARS-CoV-2 viral RNA, demonstrating that SARS-CoV-2 can be detected in continuous air samples collected from a variety of real-world settings. We expanded the utility of air surveillance to test for 40 other respiratory pathogens. Surveillance data revealed differences in timing and location of SARS-CoV-2 and influenza A virus detection. In addition, we obtained SARS-CoV-2 genome sequences from air samples to identify variant lineages. Collectively, this shows air sampling is a scalable, high throughput surveillance tool that could be used in conjunction with other methods for detecting respiratory pathogens in congregate settings.

Original languageEnglish (US)
Article number4717
JournalNature communications
Volume13
Issue number1
DOIs
StatePublished - Dec 2022

Bibliographical note

Funding Information:
This work was made possible by financial support through Rockefeller Regional Accelerator for Genomic Surveillance (133 AAJ4558 D.H.O., S.L.O., and T.C.F.), Wisconsin Department of Health Services Epidemiology and Laboratory Capacity funds (144 AAJ8216 D.H.O. and T.C.F.), and National Institutes of Health grant (U01DA053893 M.C.J.). M.D.R. is supported by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health under Award Number T32AI55397. We would like to thank all of the participating congregate settings for their partnership during this study. We would like to thank Thermo Fisher Scientific, Inc. for donating 4 of the AerosolSense samplers used in the data described in this work. We would like to acknowledge Elizabeth Durkes and Hannah Kraussel, Public Health Emergency Response Planning Coordinators, Lindor Schmidt, Environmental & Disease Control Specialist, and Dr. Nicholas Tomaro, Emergency Preparedness Environmental Health Director at the City of Milwaukee Health Department for their assistance in coordinating site selection, sampling, cartridge replacement, and unit decontamination processes. We would also like to acknowledge Dr. Arun Ramaiah, Bioinformatician at MHD lab, for depositing air sample sequencing data in SRA.

Publisher Copyright:
© 2022, The Author(s).

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