Performance characteristics of a high throughput automated transcription mediated amplification test for SARS-CoV-2 detection

Pham, J.; Meyer, S.; Nguyen, C.; Williams, A.; Hunsicker, M.; McHardy, I.; Gendlina, I.; Goldstein, D. Y.; Fox, A. S.; Hudson, A.; Darby, P.; Hovey, P.; Morales, J.; Mitchell, J.; Harrington, K.; Majlessi, M.; Moberly, J.; Shah, A.; Worlock, A.; Walcher, M.; Eaton, B.; Getman, D.; Clark, C.

The COVID19 pandemic caused by the new SARSCoV2 coronavirus has imposed severe challenges on laboratories in their effort to achieve sufficient diagnostic testing capability for identifying infected individuals. In this study we report the analytical and clinical performance characteristics of a new, high throughput, fully automated nucleic acid amplification test system for the detection of SARSCoV2. The assay utilizes target capture, transcription mediated amplification, and acridinium ester labeled probe chemistry on the automated Panther System to directly amplify and detect two separate target sequences in the ORF1ab region of the SARSCoV2 RNA genome. The probit 95% limit of detection of the assay was determined to be 0.004 TCID50/ml using inactivated virus, and 25 c/ml using synthetic in vitro transcript RNA targets. Analytical sensitivity (100% detection) was confirmed to be 83 to 194 c/ml using three commercially available SARSCoV2 nucleic acid controls. No cross reactivity or interference was observed with testing six related human coronaviruses, as well as 24 other viral, fungal, and bacterial pathogens, at high titer. Clinical nasopharyngeal swab specimen testing (N=140) showed 100%, 98.7%, and 99.3% positive, negative, and overall agreement, respectively, with a validated reverse transcription PCR NAAT for SARSCoV2 RNA. These results provide validation evidence for a sensitive and specific method for pandemic-scale automated molecular diagnostic testing for SARSCoV2.