Occurrence and Timing of Subsequent Severe Acute Respiratory Syndrome Coronavirus 2 Reverse-transcription Polymerase Chain Reaction Positivity Among Initially Negative Patients

  1. Dustin R Long
  2. Saurabh Gombar
  3. Catherine A Hogan
  4. Alexander L Greninger
  5. Vikas O’Reilly-Shah
  6. Chloe Bryson-Cahn
  7. Bryan Stevens
  8. Arjun Rustagi
  9. Keith R Jerome
  10. Christina S Kong
  11. James Zehnder
  12. Nigam H Shah
  13. Noel S Weiss
  14. Benjamin A Pinsky
  15. Jacob E Sunshine

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Abstract

Using data for 20 912 patients from 2 large academic health systems, we analyzed the frequency of severe acute respiratory syndrome coronavirus 2 reverse-transcription polymerase chain reaction test discordance among individuals initially testing negative by nasopharyngeal swab who were retested on clinical grounds within 7 days. The frequency of subsequent positivity within this window was 3.5% and was similar across institutions.

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  1. ScreenIT

    SciScore for 10.1101/2020.05.03.20089151: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: The University of Washington Institutional Review Board determined this study to be exempt (STUDY00009931).
    Consent: This study received approval by the Stanford Institutional Review Board (Protocol #48973) and individual consent was not required.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    No key resources detected.

    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:
    Results from each research group have limitations. Neither team is able to calculate a true clinical sensitivity or false negative proportion due to the absence of retesting in all initially negative patients and the lack of a gold standard confirmatory mechanism. Additionally, it cannot be ruled out that some discordant test results in this cohort may be due to newly acquired infection. By limiting the scope of retesting considered to a 7-day period, the likelihood of this scenario is minimized, but not eliminated. Finally, we were unable to ascertain the disease status of the individuals who initially tested negative for COVID-19 but did not undergo repeat testing; in most cases this likely reflects the absence of an indication for retesting (e.g. alternative diagnosis or resolution of symptoms), but could also be the result of limited access to care. The intention of this report is not to definitively quantify the clinical performance of NP SARS-CoV-2 RT-PCR testing, which will likely require orthogonal approaches such as serology. Rather, by characterizing the experience of two large US health systems on the short-term occurrence of newly positive SARS-CoV-2 results among initially test-negative patients, we provide data on a topic of practical significance that should be used in combination with other reports to guide the use and interpretation of this common testing modality.

    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.
    • Thank you for including a protocol registration statement.

    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.

  2. Version published to 10.1093/cid/ciaa722
  3. Version published to 10.1101/2020.05.03.20089151 on medRxiv