Clinical Performance of SARS-CoV-2 Molecular Tests

  1. Daniel A. Green
  2. Jason Zucker
  3. Lars F. Westblade
  4. Susan Whittier
  5. Hanna Rennert
  6. Priya Velu
  7. Arryn Craney
  8. Melissa Cushing
  9. Dakai Liu
  10. Magdalena E. Sobieszczyk
  11. Amelia K. Boehme
  12. Jorge L. Sepulveda

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Abstract

Molecular testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the gold standard for diagnosis of coronavirus disease 2019 (COVID-19), but the clinical performance of these tests is still poorly understood, particularly with regard to disease course, patient-specific factors, and viral shedding. From 10 March to 1 May 2020, NewYork-Presbyterian laboratories performed 27,377 SARS-CoV-2 molecular assays from 22,338 patients. Repeat testing was performed for 3,432 patients, of which 2,413 had initial negative and 802 had initial positive results.

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  1. Version published to 10.1128/jcm.00995-20
  2. ScreenIT

    SciScore for 10.1101/2020.05.06.20093575: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Institutional Review Board StatementIRB: This study was approved by the Institutional Review Boards of Columbia and Cornell Universities.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    From 4/3/2020 thereafter other platforms were introduced in the NYP laboratories, including the Xpert Xpress SARS-CoV-2 test analyzed on the GeneXpert (N=265) and Infinity (N=5954) platforms (Cepheid, Sunnyvale, CA), the ID Now (N=53), (Abbott, Chicago, IL) and the Panther Fusion (N=26) (Hologic Inc., San Diego, CA) instruments.
    Abbott
    suggested: (Abbott, RRID:SCR_010477)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    Limitations of the study: This is an observational study without selection bias for the laboratory data, as all results were included in the analysis. However, the clinical data was restricted to a subset of patients seen at Columbia University Irving Medical Center campuses. Nevertheless, rates of positivity and demographic variables captured in the laboratory dataset were not significantly different between the other campuses, suggesting that the population in the clinical dataset is generally representative of the New York City patients tested for COVID-19. Other limitations of the study of repeat-tested patients include: 1) only 15% of the total patient’s tested had repeat testing done and 2) ordering of repeat testing was at the discretion of the health care providers and not performed according to a standard protocol, although test ordering was mostly accomplished through standardized electronic medical record order sets.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  3. Version published to 10.1101/2020.05.06.20093575 on medRxiv