In the air tonight: COVID testing spaces, not faces.

Developing alternative environmental testing strategies to improve viral surveillance.
Published in Microbiology
In the air tonight: COVID testing spaces, not faces.

The COVID-19 pandemic has emphasized that we are underprepared to respond against (re)emerging respiratory pathogens. As of August 2022, there have been more than 578 million confirmed COVID-19 cases and 6 million deaths worldwide. Over two and a half years into the pandemic, we are still experiencing surges of COVID-19 cases due to the emergence of Variants of Concern (VOC). Despite this, there has been a shift in public sentiment toward the pandemic. Many individuals around the world are pushing for daily life to return to “pre-pandemic times” with reduced COVID-19 precautions that are important for controlling community spread. Highlighting this shift in public sentiment, several States around the United States of America have scaled back testing efforts by closing mass testing sites. As society moves forward, putting the COVID-19 pandemic in the rear-view mirror, we must be careful not to ignore the blind spots ahead that could leave us vulnerable to current and future pandemics. 

Viral testing and surveillance have played an integral role in the pandemic response. Accurate COVID-19 case counts and monitoring of VOC in a community help guide public health response. To date, surveillance efforts have mainly focused on individual testing of clinical samples to estimate disease burden and monitor VOC. However, existing surveillance networks for COVID-19 have provided crude estimates for disease burden and transmission risk. Furthermore, estimates of community infection rates are likely to become less accurate in the future as mass testing sites close and more people rely on antigen testing, possibly leaving communities vulnerable to future waves of COVID-19 cases and VOC. There remains a need to develop surveillance strategies that circumvent the limitations of individual testing to help build the nation’s capacity to provide population-wide surveillance through space and time.

Alternative environmental testing strategies that circumvent challenges associated with individualized testing could help provide a more rapid and efficient assessment of SARS-CoV-2 infection risk in communities. To date, environmental testing strategies have predominantly focused on wastewater surveillance for SARS-CoV-2. Wastewater surveillance has increased the nation’s capacity to provide population-wide surveillance data for large geographic regions. However, wastewater surveillance that relies on sample collection from treatment plants does not capture communities with decentralized systems, leaving these communities vulnerable in the future as individual testing decreases. In February 2021, our lab was talking with Dr. Marc Johnson at the University of Missouri about their work with wastewater surveillance, and we asked if the same methods could be used on concentrated air collected from congregate settings. This conversation led our lab to explore air surveillance strategies that could be used in conjunction with wastewater testing to provide hyperlocal data with high spatial resolution within a community. 

Air surveillance is an alternative form of environmental sampling that has recently gained attention for detecting SARS-CoV-2 in congregate settings considered to be high-risk for close-contact transmission. While the idea of pulling viruses out of thin air to detect their presence in an indoor environment may seem far-fetched, this is not a new practice. For almost a century, passive and active air sampling techniques have been used to survey viruses, bacteria, and fungi that are released in large respiratory droplets and aerosols when infected individuals cough, sneeze, breath, or talk. Active air samplers pull air in from the environment to collect aerosol particles from a larger surrounding area. This is important because pathogen-containing aerosols are quickly dispersed in the environment after being released. The United States Department of Homeland Security established the BioWatch Program in 2003 to use active air samplers as routine environmental monitoring systems to detect pathogens of concern and combat bioterrorism. We pursued air sampling as an approach for enabling virus detection that bypasses challenges associated with individual testing. Air samples contain a mixture of exhaled components from many individuals, including individuals who might be shedding infectious viruses while they are asymptomatic. Furthermore, air samplers can detect SARS-CoV-2 in the community independent of test-seeking behavior and testing access in the area. Unlike wastewater surveillance strategies, air samplers can be easily moved around to collect data with spatial resolution throughout a community, even down to a single room in a building. 

In collaboration with the University of Minnesota-Twin Cities, City of Milwaukee Health Department, and Mayo Clinic, we deployed active air samplers in various congregate settings to monitor the presence of SARS-CoV-2 and other respiratory pathogens across communities in the Upper Midwestern states of Wisconsin and Minnesota. Our study aimed to (1) Evaluate the utility of routine air surveillance of SARS-CoV-2 in real-world congregate settings. (2) Develop a workflow to allow task-shifting cartridge management to individuals with no scientific training. (3) Expand surveillance efforts to track the prevalence of VOC and other respiratory pathogens in the community. (4) Design a framework for using air surveillance to improve risk mitigation strategies and public health response.

Over 29 weeks, we demonstrated that SARS-CoV-2 could be detected in continuous air samples collected from a variety of real-world settings at daily and weekly sampling intervals. Furthermore, we expanded the utility of air surveillance to test for 40 other respiratory pathogens. Air samples were able to capture perennial respiratory viruses commonly associated with illness in school-aged children. Surveillance data also revealed differences in timing and location of SARS-CoV-2 and influenza A virus detection within Dane County, Wisconsin. Lastly, we obtained SARS-CoV-2 genome sequences from air samples to identify circulating variant lineages over time. 

Air surveillance could be used to complement surveillance methods to improve public health awareness and response. Similar to the National Wastewater Surveillance System recently established by the CDC, expansion of air surveillance efforts could provide additional safeguards for congregate settings and improve resilience to future respiratory virus threats. Much like the 1992 United States men’s Olympic basketball team that pulled together players from across the National Basketball Association to create the Dream Team and change the course of basketball on an international scale forever, we believe that using air sampling in conjunction with wastewater surveillance and individual testing to monitor disease threats could allow Public Health to form a “Disease Surveillance Dream Team” to improve public health response now and in the future.

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