Sample collection and transport strategies to enhance yield, accessibility, and biosafety of COVID-19 RT-PCR testing

  1. Padmapriya Banada
  2. David Elson
  3. Naranjargal Daivaa
  4. Claire Park
  5. Samuel Desind
  6. Ibsen Montalvan
  7. Robert Kwiatkowski
  8. Soumitesh Chakravorty
  9. David Alland
  10. Yingda L. Xie

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Abstract

Introduction. Non-invasive sample collection and viral sterilizing buffers have independently enabled workflows for more widespread COVID-19 testing by reverse-transcriptase polymerase chain reaction (RT-PCR).

Gap statement. The combined use of sterilizing buffers across non-invasive sample types to optimize sensitive, accessible, and biosafe sampling methods has not been directly and systematically compared.

Aim. We aimed to evaluate diagnostic yield across different non-invasive samples with standard viral transport media (VTM) versus a sterilizing buffer eNAT- (Copan diagnostics Murrieta, CA) in a point-of-care diagnostic assay system.

Methods. We prospectively collected 84 sets of nasal swabs, oral swabs, and saliva, from 52 COVID-19 RT-PCR-confirmed patients, and nasopharyngeal (NP) swabs from 37 patients. Nasal swabs, oral swabs, and saliva were placed in either VTM or eNAT, prior to testing with the Xpert Xpress SARS-CoV-2 (Xpert). The sensitivity of each sampling strategy was compared using a composite positive standard.

Results. Swab specimens collected in eNAT showed an overall superior sensitivity compared to swabs in VTM (70 % vs 57 %, P =0.0022). Direct saliva 90.5 %, (95 % CI: 82 %, 95 %), followed by NP swabs in VTM and saliva in eNAT, was significantly more sensitive than nasal swabs in VTM (50 %, P <0.001) or eNAT (67.8 %, P =0.0012) and oral swabs in VTM (50 %, P <0.0001) or eNAT (58 %, P <0.0001). Saliva and use of eNAT buffer each increased detection of SARS-CoV-2 with the Xpert; however, no single sample matrix identified all positive cases.

Conclusion. Saliva and eNAT sterilizing buffer can enhance safe and sensitive detection of COVID-19 using point-of-care GeneXpert instruments.

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  1. Version published to 10.1099/jmm.0.001380 on Access Microbiology
  2. ScreenIT

    SciScore for 10.1101/2021.03.03.21251172: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: This study was approved by the Rutgers Institutional Review Board for human subject research (Rutgers IRB #
    Consent: Patients that could not or did not consent, were pregnant or breastfeeding, prisoners, or who were unable to provide any respiratory specimens were excluded.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Statistical analyses: Standard statistical analyses (average, standard deviation, and t-test) and proportion of positive tests by each sampling method were compared by Chi-square, t-test or z-test as appropriate, using Microsoft Excel 365 for Windows, GraphPad Prism version 8 or online software (
    Microsoft Excel
    suggested: (Microsoft Excel, RRID:SCR_016137)
    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: We detected the following sentences addressing limitations in the study:
    There were several limitations in this study. First, there were less contemporaneous NP swabs collected with saliva, thereby reducing the number of direct comparisons between these two sample types, although they were found to be comparable. An underlying reason for this – participants declining NP swab collection due to its discomfort – also demonstrates the real-world limitations that would be magnified with larger scale testing such as in schools or the workplace. Secondly, we added eNAT to saliva in the laboratory, whereas the benefit of eNAT would be to sterilize samples immediately after collection and before transport and test set up. However, this allowed us to evaluate the combination of eNAT and saliva under different conditions and inform optimal design of kits to add eNAT immediately to saliva upon collection. Finally, our participants were patients who had either been admitted to the hospital or seen in the emergency department. This population may not be generalizable to ambulatory individuals who would benefit the most from self-collection. However, we captured a diverse patient group in our cohort including those who were never admitted, as well as patients who were detected by universal screening but reported no COVID symptoms. Altogether, our findings support the use of saliva and eNAT sterilizing buffer to enhance effective, safe, and accessible COVID testing and screening in the many health care systems worldwide already using GeneXpert instruments.

    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 10.1101/2021.03.03.21251172v1 on medRxiv