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 optimized the LAMP assay, we next evaluated its efficacy as a diagnostic across the 201 clinically-annotated samples. Quantitative LAMP fluorescence data were used to build a Receiver Operator Characteristic (ROC) plot and evaluate the clinical sensitivity and specificity of the assay. At the optimal threshold based on the reading from the Quantifluor relative fluorescence units (RFUs, 11, 140) , we observed an overall sensitivity of 95.6% and specificity of 99.4% (Figure 1e) . With increasing viral load, as measured by qRT-PCR Ct values, the LAMP assay showed an increased diagnostic sensitivity (Supp. Fig. 4) . The highest viral load (Ct <20) showed 100.0% sensitivity and 97.4% specificity, compared with the sensitivity at the lowest viral load at 80.0% (Ct >28, RFU below 7010). These same LAMP assay thresholds yielded consistent test positivity for synthetic RNA positive controls (Twist Biosciences) as well as clinical spike-in carrier RNAs (20/20) (Supp. Fig. 4) , and consistent signal from clinical viral positives in Vero 6 cells (100.0%, 12/12) and blank clinical buffer negatives (100.0% 8/8).