Performance Characteristics of a High-Throughput Automated Transcription-Mediated Amplification Test for SARS-CoV-2 Detection

• Published in: Journal of clinical microbiology Vol. 58; no. 10
• Main Authors: Pham, Jimmykim, Meyer, Sarah, Nguyen, Catherine, Williams, Analee, Hunsicker, Melissa, McHardy, Ian, Gendlina, Inessa, Goldstein, D Yitzchak, Fox, Amy S, Hudson, Angela, Darby, Paul, Hovey, Paul, Morales, Jose, Mitchell, James, Harrington, Karen, Majlessi, Mehrdad, Moberly, Joshua, Shah, Ankur, Worlock, Andrew, Walcher, Marion, Eaton, Barbara, Getman, Damon, Clark, Craig
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 22-09-2020
• Subjects: Automation, Laboratory; Betacoronavirus - genetics; Betacoronavirus - isolation & purification; Clinical Laboratory Techniques; Coronavirus Infections - diagnosis; COVID-19 Testing; Humans; Molecular Diagnostic Techniques; Nasopharynx - virology; Nucleic Acid Amplification Techniques; Reproducibility of Results; RNA, Viral - genetics; SARS-CoV-2; Sensitivity and Specificity; Viral Proteins - genetics; Virology; TMA; SARS-CoV-2; Aptima; automation; high throughput
• ISSN: 0095-1137; 1098-660X
• DOI: 10.1128/JCM.01669-20

The COVID-19 pandemic caused by the new SARS-CoV-2 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 SARS-CoV-2. 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 open reading frame 1ab (ORF1ab) region of the SARS-CoV-2 RNA genome. The probit 95% limit of detection of the assay was determined to be 0.004 50% tissue culture infective dose (TCID
)/ml using inactivated virus and 25 copies/ml (c/ml) using synthetic
transcript RNA targets. Analytical sensitivity (100% detection) was confirmed to be 83 to 194 c/ml using three commercially available SARS-CoV-2 nucleic acid controls. No cross-reactivity or interference was observed with testing of six related human coronaviruses, as well as 24 other viral, fungal, and bacterial pathogens, at high titers. Clinical nasopharyngeal swab specimen testing (
 = 140) showed 100%, 98.7%, and 99.3% positive, negative, and overall agreement, respectively, with a validated reverse transcription-PCR nucleic acid amplification test (NAAT) for SARS-CoV-2 RNA. These results provide validation evidence for a sensitive and specific method for pandemic-scale automated molecular diagnostic testing for SARS-CoV-2.