A Community Study of SARS-CoV-2 Detection by RT-PCR in Saliva: A Reliable and Effective Method

  1. Filippo Fronza
  2. Nelli Groff
  3. Angela Martinelli
  4. Beatrice Zita Passerini
  5. Nicolò Rensi
  6. Irene Cortelletti
  7. Nicolò Vivori
  8. Valentina Adami
  9. Anna Helander
  10. Simone Bridi
  11. Michael Pancher
  12. Valentina Greco
  13. Sonia Iolanda Garritano
  14. Elena Piffer
  15. Lara Stefani
  16. Veronica De Sanctis
  17. Roberto Bertorelli
  18. Serena Pancheri
  19. Lucia Collini
  20. Erik Dassi
  21. Alessandro Quattrone
  22. Maria Rosaria Capobianchi
  23. Giancarlo Icardi
  24. Guido Poli
  25. Patrizio Caciagli
  26. Antonio Ferro
  27. Massimo Pizzato

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Abstract

Efficient, wide-scale testing for SARS-CoV-2 is crucial for monitoring the incidence of the infection in the community. The gold standard for COVID-19 diagnosis is the molecular analysis of epithelial secretions from the upper respiratory system captured by nasopharyngeal (NP) or oropharyngeal swabs. Given the ease of collection, saliva has been proposed as a possible substitute to support testing at the population level. Here, we used a novel saliva collection device designed to favour the safe and correct acquisition of the sample, as well as the processivity of the downstream molecular analysis. We tested 1003 nasopharyngeal swabs and paired saliva samples self-collected by individuals recruited at a public drive-through testing facility. An overall moderate concordance (68%) between the two tests was found, with evidence that neither system can diagnose the infection in 100% of the cases. While the two methods performed equally well in symptomatic individuals, their discordance was mainly restricted to samples from convalescent subjects. The saliva test was at least as effective as NP swabs in asymptomatic individuals recruited for contact tracing. Our study describes a testing strategy of self-collected saliva samples, which is reliable for wide-scale COVID-19 screening in the community and is particularly effective for contact tracing.

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  1. Version published to 10.3390/v14020313
  2. ScreenIT

    SciScore for 10.1101/2021.09.15.21263644: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: The study received prior approval by the Ethical Committee of the Azienda Provinciale per i Servizi Sanitari of the autonomous province of Trento.
    Consent: An informed consent was obtained from all participants undergoing testing.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Statistical analysis: Quantification of agreement (concordance) by kappa and the Pearson correlation coefficient were both calculated using the calculator from GraphPad (Prism).
    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.

    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 10.1101/2021.09.15.21263644v1 on medRxiv