Detection profile of SARS‐CoV‐2 using RT‐PCR in different types of clinical specimens: A systematic review and meta‐analysis

  1. George M. Bwire
  2. Mtebe V. Majigo
  3. Belinda J. Njiro
  4. Akili Mawazo

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Abstract

Testing is one of the commendable measures for curbing the spread of coronavirus disease (COVID‐19). But, it should be done using the most appropriate specimen and an accurate diagnostic test such as real‐time reverse transcription‐polymerase chain reaction (qRT‐PCR). Therefore, a systematic review was conducted to determine the positive detection rate of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) in different clinical specimens using qRT‐PCR. A total of 8136 pooled clinical specimens were analyzed to detect SARS‐CoV‐2, the majority were nasopharyngeal swabs (69.6%). A lower respiratory tract (LRT) specimens had a positive rate (PR) of 71.3% (95% confidence interval [CI]: 60.3%‐82.3%) while no virus was detected in the urinogenital specimens. Bronchoalveolar lavage fluid (BLF) specimen had the PR of 91.8% (95% CI: 79.9%‐103.7%), followed by rectal swabs; 87.8% (95% CI: 78.6%‐96.9%) then sputum; 68.1% (95% CI: 56.9%‐79.4%). A low PR was observed in oropharyngeal swabs; 7.6% (95% CI: 5.7%‐9.6%) and blood samples; 1.0% (95% CI: −0.1%‐2.1%) whereas no SARS‐CoV‐2 was detected in urine samples. Feces had a PR of 32.8% (95% CI:1 5.8%‐49.8%). Nasopharyngeal swab, a widely used specimen had a PR of 45.5% (95% CI: 31.2%‐59.7%). In this study, SARS‐CoV‐2 was highly detected in LRT specimens while no virus was detected in urinogenital specimens. BLF had the highest PR followed by rectal swab then sputum. Nasopharyngeal swab which is widely used had moderate PR. Low PR was recorded in oropharyngeal swab and blood samples while no virus was found in urine samples. Last, the virus was detected in feces, suggesting SARS‐CoV‐2 transmission by the fecal route.

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  1. Version published to 10.1002/jmv.26349
  2. ScreenIT

    SciScore for 10.1101/2020.06.11.20128389: (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
    Search strategy: A rigorous systematic search strategy was developed with the help from librarian using published guidelines of the Cochrane Collaboration (11).
    Cochrane Collaboration
    suggested: None
    A systematically search from PubMed/MEDLINE, Science Direct and Google scholar (12) was conducted.
    Google scholar
    suggested: (Google Scholar, RRID:SCR_008878)
    The strategy was primarily developed for PubMed using keywords (Additional file 1).
    PubMed
    suggested: (PubMed, RRID:SCR_004846)
    Data extraction: Study selection was managed using EndNote software version X7
    EndNote
    suggested: (EndNote, RRID:SCR_014001)

    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: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    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 10.1101/2020.06.11.20128389v1 on medRxiv