Comparison of Primer-Probe Sets among Different Master Mixes for Laboratory Screening of Severe Acute Respiratory Syndrome Coronavirus 2 ( SARS-CoV-2 )

  1. Hoang Quoc Cuong
  2. Nguyen Duc Hai
  3. Hoang Thuy Linh
  4. Nguyen Hoang Anh
  5. Nguyen Trung Hieu
  6. Cao Minh Thang
  7. Nguyen Thi Thanh Thao
  8. Phan Trong Lan

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Abstract

Background . There is a shortage of chemical reagents for severe acute respiratory syndrome coronavirus 2 ( SARS-CoV-2 ) diagnosis and a surge of SARS-CoV-2 cases, especially in limited-resource settings. Therefore, the combination of an optimal assay kit is necessary. Methods . We compared the ability to screen SARS-CoV-2 among three primer-probe sets in two different master mixes, Invitrogen™ SuperScript™ III One-Step RT-PCR and LightCycler Multiplex RNA Virus Master. Results . The assay with TIB-Molbiol, IDT, and Phu Sa sets for LightCycler Multiplex RNA Virus Master or Invitrogen™ SuperScript™ III One-Step RT-PCR showed positive results from a single reaction of triplicate in the three days of 4.8 copies per reaction. R squared and amplification efficiency were 0.97 and ranged from 107 to 108%, respectively. Conclusions . Our findings indicated that TIB-Molbiol, IDT, and Phu Sa primer-probe sets could be beneficial for the laboratory screening of SARS-CoV-2 by RT-qPCR assay of E gene. There is a need to consider the combination of these reagent sets as a new strategy to increase the testing capacity of screening programs for COVID-19.

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  1. Version published to 10.1155/2020/7610678
  2. Version published to 10.1101/2020.06.20.20136242v3 on medRxiv
  3. Version published to 10.1101/2020.06.20.20136242v2 on medRxiv
  4. ScreenIT

    SciScore for 10.1101/2020.06.20.20136242: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: Ethical statement: The study protocol has been reviewed and ratified by the Pasteur Institute Ho Chi Minh City Institutional Review Board (reference number: 433/XN-PAS).
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    Vero E6 cell lines were infected with a clinical isolate SARS-CoV-2 [9].
    Vero E6
    suggested: RRID:CVCL_XD71)
    Software and Algorithms
    SentencesResources
    A cycle threshold value (Ct-value) of ≥40 was defined as a negative test [8]. 2.4. Analysis: In this study, Data were entered using Epi-Data version 3.1 (EpiData Association, Odense, Denmark, 2005), and all statistical analyses were performed using Stata version 13.0 (StataCorp, TX, 2013).
    StataCorp
    suggested: (Stata, RRID:SCR_012763)

    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

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  5. Version published to 10.1101/2020.06.20.20136242v1 on medRxiv