Fig. 2: Evaluation of an automated and condensed mCARMEN workflow.

a, Schematic of the streamlined mCARMEN workflow for testing of 188 patient specimens using a panel of 9 human respiratory viruses, RVP (SARS-CoV-2, HCoV-HKU1, HCoV-OC43, HCoV-NL63, FLUAV, FLUBV, HPIV-3, HRSV, HMPV) and a human internal control (RNase P). b, Concordance of RVP and RT–qPCR results. Top, RT–qPCR results were obtained from concurrent testing with mCARMEN. Bottom, RT–qPCR results were obtained from the original testing. c, Scaled normalized fluorescence at 1 h post-reaction initiation for 525 NP swabs ranked by increasing SARS-CoV-2 signal (blue); the respective RNase P signal (gray) is also shown. Normalized fluorescence signal (FAM/ROX) scaled from 0 to 1. The NTC-noMg signal was set as 0 and the maximum normalized fluorescence value at 1 h was set as 1. Dashed horizontal line: threshold for RVP positivity, calculated by multiplying the NTC-extract fluorescence value by 1.8; NTC-extract: no template control taken through the entire workflow. Gray X represents a failed sample excluded from concordance calculations and other analyses. d, Scatter plot of the scaled normalized fluorescence values from b compared to viral Ct values obtained from concurrent testing with the CDC 2019-nCoV Kit. Green: positive SARS-CoV-2 signal detected by both RVP and RT–qPCR; gray: inconclusive RT–qPCR result indicating that one or two of the three technical replicates were undetermined; black: undetermined RT–qPCR result indicating that all three technical replicates were negative for SARS-CoV-2. Dashed horizontal lines: threshold for RVP positivity. Solid vertical line: Ct value of 40 (CDC positivity cutoff).