Saliva for diagnosis of SARS‐CoV‐2: First report from India

  1. Debdutta Bhattacharya
  2. Debaprasad Parai
  3. Usha K. Rout
  4. Pujarini Dash
  5. Rashmi R. Nanda
  6. Girish C. Dash
  7. Srikanta Kanungo
  8. Subrata K. Palo
  9. Sidhartha Giri
  10. Hari R. Choudhary
  11. Jaya S. Kshatri
  12. Jyotirmayee Turuk
  13. Bijay K. Mishra
  14. Rajesh K. Lenka
  15. Saroj Dash
  16. Sanghamitra Pati

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Abstract

There are very few studies in search of an alternate and convenient diagnostic tool which can substitute nasopharyngeal swab (NPS) specimen for detection of SARS‐CoV‐2. In the study we analyzed, the comparison and agreement between the feasibility of using the saliva in comparison to NPS for diagnosis of SARS‐CoV‐2. A total number of 74 patients were enrolled for this study. We analyzed and compared the NPS and saliva specimen collected within 48 h after the symptom onset. We carried out real‐time quantitative polymerase chain reaction, gene sequencing for the detection and determination SARS‐CoV‐2 specific genes. Phylogenetic tree was constructed to establish the isolation of viral RNA from saliva. We used the Bland–Altman model to identify the agreement between two specimens. This study showed a lower cycle threshold ( C T ) mean value for the detection of SARS‐CoV‐2 ORF1 gene (mean, 27.07; 95% confidence interval [CI], 25.62 to 28.52) in saliva methods than that of NPS (mean 28.24; 95% CI, 26.62 to 29.85) specimen although the difference is statistically nonsignificant ( p  > .05). Bland–Altman analysis produced relatively smaller bias and high agreement between these two clinical specimens. Phylogenetic analysis with the RdRp and S gene confirmed the presence of SARS‐CoV‐2 in the saliva samples. Saliva represented a promising tool in COVID‐19 diagnosis and the collection method would reduce the exposure risk of frontline health workers which is one of the major concerns in primary healthcare settings.

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  1. ScreenIT

    SciScore for 10.1101/2020.09.11.20192591: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: The study was approved by Institutional Ethics Committee and written consent was obtained from the patients.
    Consent: The study was approved by Institutional Ethics Committee and written consent was obtained from the patients.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Gene sequence and phylogenetic tree analysis: The forward and reverse sequences of RdRp and S genes isolated from saliva were edited manually in the electro-pherograms by SeqScape v2.5 software (Applied Biosystem, USA).
    SeqScape
    suggested: (SeqScape Software, RRID:SCR_001604)
    Statistical analysis: Descriptive statistical analyses were performed using GraphPad Prism 7.04 for Windows (GraphPad Software, La Jolla, USA)
    GraphPad
    suggested: (GraphPad Prism, RRID:SCR_002798)

    Results from OddPub: Thank you for sharing your data.

    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.

  2. Version published to 10.1002/jmv.26719
  3. Version published to 10.1101/2020.09.11.20192591 on medRxiv