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Collection of SARS-CoV-2 Virus from the Air in a University Student Health Care Center and Analyses of its Viral Genomic Sequence
John Lednicky, SRIPRIYA NANNU SHANKAR, Maha Adel El Badry, Julia C. Gibson, MD Mahbubul Alam, Caroline J Stephenson, Arantzazu Eiguren Fernandez, John Glenn Morris, Carla Nartuhi Mavian, Marco Salemi, James R Clugston, Chang-Yu Wu, University of Florida
Abstract Number: 311
Working Group: The Role of Aerosol Science in the Understanding of the Spread and Control of COVID-19 and Other Infectious Diseases
Abstract
Tracking the progression of COVID-19 worldwide can be achieved by identifying mutations within the genomic sequence of SARS-CoV-2 that occur as a function of time. Currently, such efforts rely on genomic sequencing of SARS-CoV-2 in patient specimens (direct sequencing) or of virus isolated from patient specimens in cell cultures. We conducted a pilot air sampling study at a clinic within a university student health care center in late March, 2020, and detected the virus RNA (vRNA) with an estimated concentration of 0.87 virus genomes/L of air. Attempts were made to isolate the virus in cell cultures to determine whether the virus detected was viable (‘live’). Virus-induced cytopathic effects (CPE) were observed within two days post-inoculation of Vero E6 cells with collection media from air samples; however, rRT-PCR tests for SARS-CoV-2 vRNA from cell culture were negative. Instead, three other fast-growing human respiratory viruses were isolated and subsequently identified (Human coronavirus OC43, and Influenza A H1N1 and H3N2 viruses), illustrating the challenge in isolating SARS-CoV-2 when multiple viruses are present in a test sample. The complete SARS-CoV-2 genomic sequence was determined by Sanger sequencing of vRNA extracted from the aerosol sample and deposited as SARS-CoV-2/ENV/USA/UF-3/2020 in GenBank (accession no. MT324684.1). Maximum likelihood (ML) phylogenetic tree analysis revealed that this virus’ genome exactly matches (100% identity) a SARS-CoV-2 genome previously described in Georgia, USA. Results of this study illustrate the feasibility of tracking progression of the COVID-19 pandemic using environmental aerosol samples instead of human specimens. Collection of a positive sample from a distance 3 m away from the nearest patient traffic implies the virus was in an aerosol.