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

During a large-scale pandemic with exponential spread, such as COVID-19, scalable methods for diagnosis and screening are crucial for both mitigation and containment (Lan et al., 2020 . While hospital-grade, core lab devices can achieve massive throughput (thousands of samples per day), a key limitation of these assays is accessibility of testing facilities (even roadside testing stations) to patients and the logistics of sample transport and timely test reporting. These limitations become even more stark in the context of widespread quarantines and nationwide lockdowns, where requiring patients to travel (even for viral testing) incurs significant personal and public health risks. The most urgent diagnostic need in this situation is for scalable rapid point-of-care tests that can be potentially implemented in the home. Our validation of a rapid one-tube colorimetric SARS-CoV-2 assay with both qRT-PCR and total RNA-seq provides a potential solution to this problem. Further work will be needed to assess whether this LAMP assay can detect the presence of SARS-CoV-2 at lower (but clinically relevant) viral concentrations in specimen types that are less cumbersome to collect than naso-/ oro-pharyngeal swabs (e.g. saliva, stool). As we demonstrate, this LAMP SARS-CoV2 can be also applied for environmental sampling, which may be crucial in the containment phase of this pandemic. Specifically, LAMP positivity may quickly indicate if an area is infectious and a negative result (with appropriate confirmation) will possibly represent a lower risk. Indeed, these tools and methods can help create a viral "weather report" if broadly used and partnered with continual validation.