NCM 2023 Houston: Metagenomic sequencing of air samples to identify human viral pathogens

The phase-out of community testing programs and minimal reporting of at-home test results have resulted in a slow decline in the availability of genome surveillance for SARS-CoV-2. Environmental surveillance can fill the gaps left by community testing programs with the added benefit of being able to collect anonymous data from multiple individuals at once. In addition, environmental surveillance can provide information about other potential pathogens in a community such as respiratory syncytial virus (RSV) or influenza viruses. As a proof of concept, we used environmental air sampling in combination with unbiased metagenomic sequencing to study a household outbreak of SARS-CoV-2 and to detect diverse human viruses in community settings. This community level data can be especially useful for monitoring populations where virus outbreaks are of especially high consequence such as in long-term care facilities or to identify emerging threats in transportation hubs such as airports.