Increased PCR screening capacity using a multi-replicate pooling scheme

  1. A. Viehweger
  2. F. Kühnl
  3. C. Brandt
  4. B. König
  5. A. C. Rodloff

Reviewed by

Read the full article

Listed in

Log in to save this article

Abstract

Effective public health response to viral outbreaks such as SARS-CoV-2 require reliable information about the spread of the infecting agent. Often real-time PCR screening of large populations is a feasible method to generate this information. Since test capacities are usually limited, pooling of test specimens is often necessary to increase screening capacity, provided that the test sensitivity is not significantly compromised. However, when a traditional pool is tested positive, all samples in the pool need individual retesting, which becomes ineffective at a higher proportion of positive samples. Here, we report a new pooling protocol that mitigates this problem by replicating samples across multiple pools. The resulting pool set allows the sample status to be resolved more often than with traditional pooling. At 2% prevalence and 20 samples per pool, our protocol increases screening capacity by factors of 5 and 2 compared to individual testing and traditional pooling, respectively. The corresponding software to layout and resolve samples is freely available under a BSD license ( https://github.com/phiweger/clonepool ).

Article activity feed

  1. ScreenIT

    SciScore for 10.1101/2020.04.16.20067603: (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

    No key resources detected.

    Results from OddPub: Thank you for sharing your code.

    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.

  2. Version published to 10.1101/2020.04.16.20067603 on medRxiv