Evaluation of commercial qPCR kits for detection of SARS-CoV-2 in pooled samples

  1. Vlad Petrovan
  2. Virgil Vrajmasu
  3. Paula Dimon
  4. Mihaela Zaulet

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Abstract

Due to the current pandemic, global shortage of reagents has drawn interest in developing alternatives to increase the number coronavirus tests. One such alternative is sample pooling. Here we compared commercial kits that are used in COVID-19 diagnostics, in terms of sensitivity and feasibility for use in pooling. We showed that pooling of up to 60 samples did not affect the efficiency of the kits. Also, the RNA dependent RNA polymerase (RdRp) is a more suitable target in pooled samples than the Envelope (E) protein. This approach could provide an easy method of screening large number of samples and help adjust different government regulations.

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    SciScore for 10.1101/2020.05.28.120667: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementConsent: Ethical considerations: The study was conducted as part of surveillance program for COVID-19 implemented by the Romanian government, with no disclosure regarding name, physical, economic, cultural, social status of the patients, therefore did not require individual patient consent or ethical approval.
    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:
    However, there are several limitations that might arise using the pooled sample approach. One limitation of this approach is that it seems only the RdRp gene is suitable for detection of SARS-CoV-2 in pools larger than 30 samples, which might arise in false negative results due to equipment variation and sample handling. However, this could be easily circumvented by integrating additional SARS-CoV-2 specific targets. Moreover, the complexity of the disease can influence the sensitivity and specificity of the assay (15). Our results are showing that RdRp would be the ideal target for sample pooling, rather than E gene. This agrees with the initial development of molecular tests for SARS-CoV-2 detection, when RdRp gene assays 3.6 copies per reaction for the RdRp assay (4; 13). In this research, we showed that sample pooling for SARS-CoV-2 diagnostic is a feasible measure using commercial kits widely available.

    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.
    • No funding statement was detected.
    • No protocol registration statement was detected.

    About SciScore

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  2. Version published to 10.1101/2020.05.28.120667v1 on bioRxiv