Host, Viral, and Environmental Transcriptome Profiles of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

Daniel J Butler; Christopher Mozsary; Cem Meydan; David C Danko; Jonathan Foox; Joel Rosiene; Alon Shaiber; Ebrahim Afshinnekoo; Matthew MacKay; Fritz J Sedlazeck; Nikolay A Ivanov; Maria A Sierra; Diana Pohle; Michael Zeitz; Vijendra Ramlall; Undina Gisladottir; Craig D Westover; Krista Ryon; Benjamin Young; Chandrima Bhattacharya; Phyllis Ruggiero; Bradley W Langhorst; Nathan A Tanner; Justyn Gawrys; Dmitry Meleshko; Dong Xu; Jenny Xiang; Angelika Iftner; Daniela Bezdan; John Sipley; Lin Cong; Arryn Craney; Priya Velu; Ari Melnick; Iman A Hajirasouliha; Thomas Iftner; Mirella Salvatore; Massimo Loda; Lars F Westblade; Shawn Levy; Melissa Cushing; Nicholas P Tatonetti; Marcin Imielinski; Hanna Rennert; Christopher Mason

Having validated a rapid LAMP assay and shotgun metratranscriptomics platform, we deployed both to investigate the environmental distribution of SARS-CoV-2 in high-transit areas of the NYC subway antecedent to the dawn of the NYC pandemic. We collected 86 samples from handrails, kiosks, and floors in Grand Central and Times Square subway stations between March 6 and 13th, 2020. Each sample was collected using a sterile and DNA/RNA free swab, following the MetaSUB sampling protocols for nucleic acid stabilization (Danko et al., 2020) . None of these 86 samples reached significant levels of LAMP fluorescence, suggesting that these high transit surfaces were likely free of SARS-CoV-2 virions.