Evaluating the efficiency of specimen pooling for PCR‐based detection of COVID‐19

  1. Supaporn Wacharapluesadee
  2. Thongchai Kaewpom
  3. Weenassarin Ampoot
  4. Siriporn Ghai
  5. Worrawat Khamhang
  6. Kanthita Worachotsueptrakun
  7. Phanni Wanthong
  8. Chatchai Nopvichai
  9. Thirawat Supharatpariyakorn
  10. Opass Putcharoen
  11. Leilani Paitoonpong
  12. Gompol Suwanpimolkul
  13. Watsamon Jantarabenjakul
  14. Pasin Hemachudha
  15. Artit Krichphiphat
  16. Rome Buathong
  17. Tanarak Plipat
  18. Thiravat Hemachudha

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Abstract

In the age of a pandemic, such as the ongoing one caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), the world faces a limited supply of tests, personal protective equipment, and factories and supply chains are struggling to meet the growing demands. This study aimed to evaluate the efficacy of specimen pooling for testing of SARS‐CoV‐2 virus, to determine whether costs and resource savings could be achieved without impacting the sensitivity of the testing. Ten previously tested nasopharyngeal and throat swab specimens by real‐time polymerase chain reaction (PCR), were pooled for testing, containing either one or two known positive specimens of varying viral concentrations. Specimen pooling did not affect the sensitivity of detecting SARS‐CoV‐2 when the PCR cycle threshold (Ct) of original specimen was lower than 35. In specimens with low viral load (Ct > 35), 2 of 15 pools (13.3%) were false negative. Pooling specimens to test for Coronavirus Disease 2019 infection in low prevalence (≤1%) areas or in low risk populations can dramatically decrease the resource burden on laboratory operations by up to 80%. This paves the way for large‐scale population screening, allowing for assured policy decisions by governmental bodies to ease lockdown restrictions in areas with a low incidence of infection, or with lower‐risk populations.

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  1. Version published to 10.1002/jmv.26005
  2. ScreenIT

    SciScore for 10.1101/2020.05.02.20087221: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: This study is an evaluation of laboratory techniques using archived clinical specimens and was exempted from Chulalongkorn University Institutional Review Board (IRB) review.
    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:
    A limitation of this study is the maximum number of two positive specimens in the 10-specimen pool. In theory, more positive specimens in a pool could decrease the sensitivity of qPCR as it would result in too many viral copies, causing an insufficiency of PCR enzyme and other reagents in the mix to amplify all the viral copies. Practically, however, this does not affect the overall testing results, since positive pools would require individual testing in any case. Rapid identification of SARS-CoV-2 infection is crucial to curb the COVID-19 pandemic. The current gold standard for testing SARS-CoV-2 is real-time PCR, which requires resources that are currently limited, along with specialized equipment and technically skilled labor. Shortage of testing reagents and equipment in countries where there is no capability to produce their own tests may result in delays in testing and result in reduced effectiveness in containing the outbreak. Pooled specimen testing would enable substantial savings in reagent costs, technical burden and time to generate laboratory results.

    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 10.1101/2020.05.02.20087221v1 on medRxiv