Author: 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
Title: Host, Viral, and Environmental Transcriptome Profiles of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Document date: 2020_4_20
ID: kyoa5gsf_15
Snippet: To further investigate these 86 environmental samples for the presence of SARS-CoV-2, we generated total RNA-seq libraries and investigated the distribution of non-human sequences. These samples demonstrated a mix of fungal and archaeal species that was consistent with underground subway origin (Danko et al., 2020) (Supp . Table 1 ). However, we did not observe significant counts or proportions (Figure 2a ) of SARS-CoV-2 reads, which was particul.....
Document: To further investigate these 86 environmental samples for the presence of SARS-CoV-2, we generated total RNA-seq libraries and investigated the distribution of non-human sequences. These samples demonstrated a mix of fungal and archaeal species that was consistent with underground subway origin (Danko et al., 2020) (Supp . Table 1 ). However, we did not observe significant counts or proportions (Figure 2a ) of SARS-CoV-2 reads, which was particularly clear with dual-index library preparations (Supp Figure 8) . However, a broad range of other bacterial and viral species was found, including a large set of phages (e.g. Streptomyces phage VWB), desiccation-tolerant bacteria (e.g Deinococcus radiodurans), and more abundant bacterial and archaeal RNA than the clinical samples (Supp . Table 1 ). Of note, these were checked against a database of putative false positives (Supp . Table 2) , which was created from in silico fragmentation of the SARS-CoV-2 genome and mapping against the same database. Taken together, these results indicate that high transit surfaces were not likely to harbor significant levels of SARS-CoV-2 in the early phases of the NYC epidemic.
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