Efficient detection of SARS-CoV-2 from exhaled breath.

Duan, Chaorui; Buerer, Luke; Wang, Jing; Kaplan, Samuel; Sabalewski, Gavin; Jay, Gregory D.; Monaghan, Sean; Arena, Andrea E.; Fairbrother, William G.

SARS-CoV-2 is transmitted through airborne particles in exhaled breath, causing severe respiratory disease. SARS-CoV-2 is typically collected by nasopharyngeal swab and detected by PCR; however, patients can test positive for 3 months after infection. Without the ability to assay SARS-CoV-2 in human breath, it is not possible to learn the transmission risk from infected individuals. To detect virus in breath, the Bubbler - a breathalyzer that reverse transcribes RNA from airborne SARS-CoV-2 particles into a sample-specific barcoded cDNA was developed. Tests of the Bubbler on 70 patients admitted to Rhode Island Hospital showed that it was both more predictive of lower respiratory track involvement (i.e. abnormal chest X-rays) and less invasive than alternatives. In addition, the Bubbler sample of exhaled air was 3 times more enriched for SARS-CoV-2 RNA than tongue swabs implying viral particles were being directly sampled. The demonstration of how barcode-enabled Bubblers can simultaneously diagnose large batches of pooled samples at a detection limit of 334 genomic copies/sample was given. Diagnosis by sequencing can provide additional information such as viral load and strain identity. Finally, the Bubbler was configured to sample nucleic acids in water droplets circulating in air, demonstrating this device’s potential for environmental monitoring and the protective effect of adequate ventilation.