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

Jimmykim Pham, Sarah Meyer, Catherine Nguyen, Analee Williams, Melissa Hunsicker, Ian McHardy, Inessa Gendlina, D. Yitzchak Goldstein, Amy S. Fox, Angela Hudson, Paul Darby, Paul Hovey, Jose Morales, James Mitchell, Karen Harrington, Mehrdad Majlessi, Joshua Moberly, Ankur Shah, Andrew Worlock, Marion WalcherBarbara Eaton, Damon Getman, Craig Clark

Research output: Contribution to journalArticle

Abstract

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 (TCID50)/ml using inactivated virus and 25 copies/ml (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 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 (n = 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.

Original languageEnglish (US)
Article numbere0166920
JournalJournal of Clinical Microbiology
Volume58
Issue number10
DOIs
StatePublished - Oct 2020

Keywords

  • Aptima
  • Automation
  • High throughput
  • SARS-CoV-2
  • TMA

ASJC Scopus subject areas

  • Microbiology (medical)

Fingerprint Dive into the research topics of 'Performance characteristics of a high-throughput automated transcription-mediated amplification test for SARS-CoV-2 detection'. Together they form a unique fingerprint.

  • Cite this

    Pham, J., Meyer, S., Nguyen, C., Williams, A., Hunsicker, M., McHardy, I., Gendlina, I., Yitzchak Goldstein, D., Fox, A. S., Hudson, A., Darby, P., Hovey, P., Morales, J., Mitchell, J., Harrington, K., Majlessi, M., Moberly, J., Shah, A., Worlock, A., ... Clark, C. (2020). Performance characteristics of a high-throughput automated transcription-mediated amplification test for SARS-CoV-2 detection. Journal of Clinical Microbiology, 58(10), [e0166920]. https://doi.org/10.1128/JCM.01669-20