Analysis by real‐time PCR of five transport and conservation mediums of nasopharyngeal swab samples to COVID‐19 diagnosis in Santiago of Chile

  1. Carlos Barrera‐Avalos
  2. Roberto Luraschi
  3. Eva Vallejos‐Vidal
  4. Maximiliano Figueroa
  5. Esteban Arenillas
  6. Daniela Barría
  7. Felipe Hernández
  8. Carlos Mateluna
  9. Javier Mena
  10. Claudia Rioseco
  11. Claudia Torrent
  12. Claudio Vergara
  13. Gaby Gutiérrez
  14. Javiera Quiroz
  15. Javiera Alarcón
  16. Julio Cartagena
  17. Javiera Cayunao
  18. Andrea Mella‐Torres
  19. Álvaro Santibañez
  20. Sebastián Tapia
  21. Alejandro Undurraga
  22. Deborah Vargas
  23. Valentina Wong
  24. Ailen Inostroza‐Molina
  25. Daniel Valdés
  26. Mónica Imarai
  27. Claudio Acuña‐Castillo
  28. Felipe E. Reyes‐López
  29. Ana M. Sandino

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Abstract

Due to the COVID‐19 pandemic, many transport kits have been manufactured to preserve and transport nasopharyngeal swab samples (NPSs) from patients. However, there is no information on the performance of the different virus transport media (VTM) used in COVID‐19 diagnosis in the population of Santiago de Chile. We compared the RT‐qPCR amplification profile of five different viral transport kit mediums, including DNA/RNA Shield™, NAT, VTM‐N, Ezmedlab™, and phosphate‐buffered saline (PBS), for NPSs from Central Metropolitan Health Service, Santiago, Chile. The DNA/RNA Shield™ medium showed a better performance in terms of Cq and RFU values for the internal reference RNase P and viral ORF1ab probes. By contrast, the PBS transport medium registered higher Cq values for the viral and reference gene, compared to the other VTM. DNA/RNA Shield™ shows higher relative fluorescence units (RFUs) and lower Cq values for the reference gene. Collectively, our results suggest that the PBS medium could compromise the sample diagnosis because of its lower RT‐qPCR performance. The NAT, Ezmedlab and VTM‐N, and DNA/RNA Shield™ media show acceptable RT‐qPCR parameters and, consequently, seem suitable for use in COVID‐19 diagnosis.

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  1. Version published to 10.1002/jmv.27446
  2. ScreenIT

    SciScore for 10.1101/2021.07.13.21260473: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: 2.8 Ethical Considerations: All the experimental procedures included in this study was authorized by the Ethical Committee of the University of Santiago of Chile (No. 226/2021) and the Scientific Ethical Committee of the Central Metropolitan Health Service, Ministry of Health, Government of Chile (No. 370/2021), and following the Chilean law in force.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    All the RT-qPCR reactions were performed on the Agilent AriaMx Real-Time PCR System (Agilent Technologies, Part. Santa Clara, CA. No. G8830A).
    Agilent AriaMx
    suggested: (Agilent AriaMx Real-time PCR System, RRID:SCR_019469)
    All the RT-qPCR reactions were performed on the Agilent AriaMx Real-Time PCR System. 2.7 Data representation and statistical analysis: GraphPad Prism 8 statistical software was used to analyze and plot the data obtained.
    GraphPad Prism
    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.

    Results from scite Reference Check: We found no unreliable references.

    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 10.1101/2021.07.13.21260473 on medRxiv