Association of SARS-CoV-2 Genomic Load with Outcomes in Patients with COVID-19

  1. Ioannis M. Zacharioudakis
  2. Prithiv J. Prasad
  3. Fainareti N. Zervou
  4. Atreyee Basu
  5. Kenneth Inglima
  6. Scott A. Weisenberg
  7. Maria E. Aguero-Rosenfeld

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Abstract

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  1. Version published to 10.1513/annalsats.202008-931rl
  2. ScreenIT

    SciScore for 10.1101/2020.07.02.20145151: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementConsent: This study was approved with a waiver of informed consent by the New York University Institutional Review Board.
    IRB: This study was approved with a waiver of informed consent by the New York University Institutional Review Board.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    All calculations were performed using the Stata v14.2 software package (Stata Corporation, College Station, TX).
    Stata
    suggested: (Stata, RRID:SCR_012763)

    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 this study should be acknowledged and arise primarily from its retrospective design. Information was obtained from chart review, and as such incomplete reporting of patients’ characteristics and history of present illness is a consideration. However, both the primary outcome and the genomic load are objective measures that would not be influenced by incomplete reporting. Second, this study relies on Ct values obtained through a single assay, and the generalizability of the outcomes across different RT-PCR methods should be examined. Next, variation in the technique of obtaining the nasopharyngeal swab or collection of the specimen at different phases of the respiratory cycle could potentially cause fluctuation in the genomic load detected by the assay. These fluctuations would not be expected to result in systematic error and would have favored the null hypothesis. Finally, only the results of PCR-assay collected within 24 hours of admission were used in our analysis. Future studies should examine if a change in viral load during hospitalization is associated with a measurable effect in clinical status. In summary, we showed that SARS-CoV-2 genomic load is an independent predictor of adverse outcomes in patients admitted to the hospital with COVID-19 pneumonia. Our findings suggest that antiviral therapy effective in reducing viral replication could potentially lead to improved outcomes. Importantly, we provide an independent predictor of adverse outcomes, that...

    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 10.1101/2020.07.02.20145151v1 on medRxiv