Multimodal genomic surveillance for respiratory pathogens at four U.S. international airports: A comparison of air, wastewater, clinical, and national surveillance data

Abstract

Early detection of outbreaks and emerging pathogens is critical for public health and global biosecurity. Airports, as major international travel hubs with dense, enclosed populations, are high-risk settings for disease transmission and potential pathogen introduction. The U.S. Centers for Disease Control and Prevention, in collaboration with Ginkgo Biosecurity and the University of Wisconsin–Madison, implemented air monitoring for pathogen surveillance in congregate areas at four U.S. international airports. From October 2023 to August 2024, SARS-CoV-2 was detected by PCR in 98.3% of air samples and influenza A in 17.2%. Influenza A positivity in air samples correlated with aviation wastewater (r = 0.48), traveler nasal swab positivity (r = 0.73), and national clinical surveillance (r = 0.86), whereas SARS-CoV-2 measurements did not correlate significantly across these modalities. Targeted amplicon sequencing of SARS-CoV-2 from air samples identified contemporaneous lineages also detected in wastewater collected from the same airports. Targeted enrichment sequencing detected 30 viral species and recovered high-quality genomes for SARS-CoV-2, influenza, bocavirus, and seasonal coronaviruses. Together, these findings demonstrate that air sampling can complement aviation wastewater surveillance at ports of entry, although performance and concordance vary by pathogen and sample type.