Implementation and validation of a pooling strategy for a sustainable screening campaign for the presence of SARS-CoV-2

  1. Daniela Cesselli
  2. Michela Bulfoni
  3. Stefania Marzinotto
  4. Barbara Marcon
  5. Sara Cmet
  6. Anna Rosa Cussigh
  7. Angelica Migotti
  8. Romina Martinella
  9. Corrado Pipan
  10. Antonio Paolo Beltrami
  11. Francesco Curcio

Reviewed by

Read the full article

Listed in

Log in to save this article

Abstract

Mass screening aimed at detecting, in asymptomatic subjects, the presence of SARS-CoV-2 is considered a strategic measure for the control of the present pandemic. It allows virus carriers to be identified and quarantined, thus preventing local spread and protecting vulnerable individuals. Although the screening strategy should be determined by the epidemiological situation, the size of the population that can be screened is indeed limited by the availability of resources. Here we present the implementation of an 8-sample pool strategy that relies on protocols, reagents and equipment currently used in clinical diagnostics. The method permitted to identify, with 100% sensitivity, specificity and accuracy, samples with low viral load, being the limit of detection of 11 viral copies extracted from the equivalent of 133μl of nasopharyngeal sample-pool. When the protocol has been applied, as a proof of principle, in a real population of 3592 consecutive nasopharyngeal swabs collected by healthcare providers in asymptomatic subjects, 20 positive pools were detected and in 100% of cases the positive specimens identified. Considering these performances, the 8-sample pool will allow, in populations with an expected positive rate of less than 1%, reducing costs by at least 80%, being a suitable method for a sustainable mass screening strategy in a population of asymptomatic subjects.

Article activity feed

  1. ScreenIT

    SciScore for 10.1101/2020.08.28.20174946: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: Sample collection: Ethical approval was obtained from the Medical Research Ethics Committee of the Region Friuli Venezia Giulia, Italy (Consent CEUR-2020-0s- 033).
    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:
    Indeed, in USA Food and Drug Administration (FDA), under an Emergency Use Authorization (EUA) only, has authorized molecular test to detect SARS-CoV-2 in pools of, respectively, 5 and 4 upper or lower respiratory specimens7, 8 In any case, pooling testing procedures are affected by some limitations, that must be taken into account. First, the adequacy of each nasopharyngeal swab included in the pool is not verified before testing. Therefore, inadequate samples will result as negative. Moreover, the dilution in the pool of a specimen with a low viral load, could bring to false negative results. We have implemented a series of corrective measures to reduce this risk, which nevertheless remains.

    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 10.1101/2020.08.28.20174946v1 on medRxiv