The Application of Sample Pooling for Mass Screening of SARS-CoV-2 in an Outbreak of COVID-19 in Vietnam

  1. Ton That Thanh
  2. Nguyen Thi Thanh Nhan
  3. Huynh Kim Mai
  4. Nguyen Bao Trieu
  5. Le Xuan Huy
  6. Ho Thi Thanh Thuy
  7. Le Thanh Chung
  8. Nguyen Ngoc Anh
  9. Nguyen Thi Thu Hong
  10. Bui Thuc Thang
  11. Nguyen Thi Hoai Thu
  12. Le Thi Kim Chi
  13. Nguyen Thi Hanh
  14. Nguyen Huy Hoang
  15. Nguyen Van Vinh Chau
  16. Guy Thwaites
  17. Do Thai Hung
  18. Le Van Tan
  19. Ngo Thi Kim Yen

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Abstract

We sampled nasal–pharyngeal throat swabs from 96,123 asymptomatic individuals at risk of SARS-CoV-2 infection, and generated 22,290 pools at collection, each containing samples from two to seven individuals. We detected SARS-CoV-2 in 24 pools, and confirmed the infection in 32 individuals after resampling and testing of 104 samples from positive pools. We completed the testing within 14 days. We would have required 64 days to complete the screening for the same number of individuals if we had based our testing strategy on individual testing. There was no difference in cycle threshold (Ct) values of pooled and individual samples. Thus, compared with individual sample testing, our approach did not compromise PCR sensitivity, but saved 77% of the resources. The present strategy might be applicable in settings, where there are shortages of reagents and the disease prevalence is low, but the demand for testing is high.

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  1. Version published to 10.4269/ajtmh.20-1583
  2. ScreenIT

    SciScore for 10.1101/2020.09.11.20192484: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementConsent: Accordingly, obtaining inform consent from individuals was deemed unnecessary.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Statistical analysis: We used Wilcoxon signed-rank text available in GraphPad Prism version 5.04 (GraphPad Software, San Diego, California) to compare the Ct values obtained from the pooled samples and individual samples.
    GraphPad Prism
    suggested: (GraphPad Prism, RRID:SCR_002798)
    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: 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 10.1101/2020.09.11.20192484v1 on medRxiv