Clinical Performance of Direct RT-PCR Testing of Raw Saliva for Detection of SARS-CoV-2 in Symptomatic and Asymptomatic Individuals

  1. Rosa Castillo-Bravo
  2. Noel Lucca
  3. Linyi Lai
  4. Killian Marlborough
  5. Galina Brychkova
  6. Charlie Lonergan
  7. Justin O’Grady
  8. Nabil-Fareed Alikhan
  9. Alexander J. Trotter
  10. Andrew J. Page
  11. Breda Smyth
  12. Peter C. McKeown
  13. Jelena D. M. Feenstra
  14. Camilla Ulekleiv
  15. Oceane Sorel
  16. Manoj Gandhi
  17. Charles Spillane

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Abstract

RT-qPCR tests based on RNA extraction from nasopharyngeal swab samples are promoted as the “gold standard” for SARS-CoV-2 detection. However, self-collected saliva samples offer a non-invasive alternative more suited to high-throughput testing. This study evaluated the performance of TaqPath COVID-19 Fast PCR Combo Kit 2.0 assay for detection of SARS-CoV-2 in raw saliva relative to a lab-developed direct RT-qPCR test (SalivaDirect-based PCR) and a RT-qPCR test based on RNA extraction from NPS samples. Both samples were collected from symptomatic and asymptomatic individuals (N=615). Saliva samples were tested for SARS-CoV-2 using the TaqPath COVID-19 Fast PCR Combo Kit 2.0 and the SalivaDirect-based PCR, while RNA extracts from NPS samples were tested by RT-qPCR according to the Irish national testing system. The TaqPath™ COVID-19 Fast PCR detected SARS-CoV-2 in 52 saliva samples, of which 51 were also positive with the SalivaDirect-based PCR. 49 samples displayed concordant results with the NPS extraction-based method, while three samples were positive on raw saliva. Among the negative samples, 10 discordant cases were found with the TaqPath COVID-19 Fast PCR (PPA–85.7%; NPA–99.5%), when compared to the RNA extraction-based NPS method, performing similarly to the SalivaDirect-based PCR (PPA-87.5%; NPA-99.5%). The direct RT-qPCR testing of saliva samples shows high concordance with NPS extraction-based method for SARS-CoV-2 detection, providing a cost-effective and highly-scalable system for high-throughput COVID-19 rapid-testing.

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  1. ScreenIT

    SciScore for 10.1101/2022.05.15.22275086: (What is this?)

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

    Table 1: Rigor

    EthicsConsent: All individuals provided a signed informed consent, and the study was approved by the NUI Galway Research Ethics
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    WGS was performed using the Illumina NextSeq 500 platform with one positive control and one negative control.
    WGS
    suggested: None
    The raw reads were demultiplexed using bcl2fastq (v2.20).
    bcl2fastq
    suggested: (bcl2fastq , RRID:SCR_015058)
    Briefly, the reads had adapters trimmed with TrimGalore17, and were aligned to the Wuhan Hu-1 reference genome (accession MN908947.3) using BWA-MEM (v0.7.17)18; the ARTIC amplicons were trimmed and a consensus built using iVAR (v.1.3.0)19.
    BWA-MEM
    suggested: (Sniffles, RRID:SCR_017619)

    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.

  2. Version published to 10.1101/2022.05.15.22275086v1 on medRxiv