Detection of SARS-CoV-2 by real-time PCR under challenging pre-analytical conditions reveals independence of swab media and cooling chain

  1. Sabrina Summer
  2. Ralf Schmidt
  3. Anna Nele Herdina
  4. Isabella Krickl
  5. Julia Madner
  6. Georg Greiner
  7. Florian J. Mayer
  8. Nicole Perkmann-Nagele
  9. Robert Strassl

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Abstract

With global demand for SARS-CoV-2 testing ever rising, shortages in commercially available viral transport media pose a serious problem for laboratories and health care providers. For reliable diagnosis of SARS-CoV-2 and other respiratory viruses, executed by Real-time PCR, the quality of respiratory specimens, predominantly determined by transport and storage conditions, is crucial. Therefore, our aim was to explore the reliability of minimal transport media, comprising saline or the CDC recommended Viral Transport Media (HBSS VTM), for the diagnosis of SARS-CoV-2 and other respiratory viruses (influenza A, respiratory syncytial virus, adenovirus, rhinovirus and human metapneumovirus) compared to commercial products, such as the Universal Transport Media (UTM). We question the assumptions, that the choice of medium and temperature for storage and transport affect the accuracy of viral detection by RT-PCR. Both alternatives to the commercial transport medium (UTM), HBSS VTM or saline, allow adequate detection of SARS-CoV-2 and other respiratory viruses, regardless of storage temperatures up to 28 °C and storage times up to 28 days. Our study revealed the high resilience of SARS-CoV-2 and other respiratory viruses, enabling proper detection in clinical specimens even after long-time storage at high temperatures, independent of the transport medium’s composition.

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  1. Version published to 10.1038/s41598-021-93028-8
  2. ScreenIT

    SciScore for 10.1101/2020.07.21.20158154: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Cq-values (cycle threshold values as calculated specifically by the Bio-Rad CFX Manager software) less than 45 cycles for both tested targets were interpreted as positive for SARS-CoV-2.
    Bio-Rad CFX Manager
    suggested: None
    CFX
    suggested: None
    The presence of other respiratory viruses used in this study, influenza virus A, adenovirus, respiratory syncytial virus, rhinovirus and human metapneumovirus, were confirmed by TaqMan-based RT-PCR using the LightCycler Multiplex RNA Virus Master (Roche Diagnostics, Rotkreuz, Switzerland) on a Bio-Rad CFX Connect Real-Time PCR Detection System (Bio-Rad Laboratories, Hercules, California, USA).
    Bio-Rad Laboratories
    suggested: (Bio-Rad Laboratories, RRID:SCR_008426)
    ΔCq-values were calculated in Microsoft Excel Version 2019 as the differences between the target Cq measured at the dedicated day and temperature and the target Cq of the initial measurement (T0).
    Microsoft Excel
    suggested: (Microsoft Excel, RRID:SCR_016137)
    Kolmogorov-Smirnov normality test was done in GraphPad Prism Version 5.0 (GraphPad).
    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 10.1101/2020.07.21.20158154 on medRxiv