SARS-CoV-2 detection in different respiratory sites: A systematic review and meta-analysis

  1. Abbas Mohammadi
  2. Elmira Esmaeilzadeh
  3. Yijia Li
  4. Ronald J. Bosch
  5. Jonathan Z. Li

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Abstract

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  1. ScreenIT

    SciScore for 10.1101/2020.05.14.20102038: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    A computerized search was implemented in PubMed, MedRxiv and BioRxiv using a search term, “((COVID OR COVID-19 OR SARS) AND (throat OR nasal OR nasopharyngeal OR oropharyngeal OR oral OR saliva OR sputum OR PCR))”.
    PubMed
    suggested: (PubMed, RRID:SCR_004846)
    BioRxiv
    suggested: (bioRxiv, RRID:SCR_003933)
    Meta-analyses were performed using Stata 13.1 (StataCorp).
    StataCorp
    suggested: (Stata, RRID:SCR_012763)
    GraphPad 8.5 (Prism) was used to demonstrate sensitivities at different time points from different sites of respiratory tracts.
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)

    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:
    One limitation of this meta-analysis is that the majority of participants in these studies enrolled hospitalized patients and it is unclear how the results may differ for individuals with asymptomatic infection or only mild symptoms. However, there are reports that rates of nasopharyngeal, oropharyngeal, and sputum positivity may not be substantially altered in those with mild symptoms versus those with severe disease.12 A potential limitation with the use of sputum is that not all COVID-19 patients are able to expectorate sputum, which may be reflected by the lower number of tested sputum samples in the included studies compared to nasopharyngeal or oropharyngeal swabs. Thus, for those who are unable to produce sputum, nasopharyngeal testing may continue to play an important role in the diagnosis or monitoring of COVID-19 patients. A recent report also suggested that saliva samples had comparable diagnostic accuracy compared to nasopharyngeal swabs, although this will need to be confirmed with additional studies.23 Finally, there were differences between studies in the qPCR assay and patient selection (Supplemental Tables 1 and 2) that likely accounted for some of the heterogeneity, the results were generally consistent within most studies and we were able to dramatically reduce the detected heterogeneity of the studies by comparing results by timing of symptom onset. In summary, this systematic review and meta-analysis demonstrates that compared to nasopharyngeal swab sampl...

    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.

  2. Version published to 10.1016/j.ebiom.2020.102903
  3. Version published to 10.1101/2020.05.14.20102038v1 on medRxiv