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

Primers were compared with a list of sequences from organism from the same genetic family as SARS-CoV-2 and other high-priority organisms listed in the United States Food and Drug Administration's Emergency Use Authorization Template (https://www.fda.gov/media/135900/download). Using the sequence names in the EUA template, the NCBI taxonomy database was queried to find the highest quality representative sequences for more detailed analysis. Primers were compared to this database using Blast 2.8.1 and the following parameters (word size: 7, match score: 2, mismatch score: -3, gap open cost: 5, gap extend cost: 2). Up to 1000 hits with e-value > 10 were reported.