A Sensitive and Rapid Wastewater Test for SARS-COV-2 and Its Use for the Early Detection of a Cluster of Cases in a Remote Community

  1. Jade Daigle
  2. Kathleen Racher
  3. Justin Hazenberg
  4. Allan Yeoman
  5. Heather Hannah
  6. Diep Duong
  7. Umar Mohammed
  8. Dave Spreitzer
  9. Branden S. J. Gregorchuk
  10. Breanne M. Head
  11. Adrienne F. A. Meyers
  12. Paul A. Sandstrom
  13. Anil Nichani
  14. James I. Brooks
  15. Michael R. Mulvey
  16. Chand S. Mangat
  17. Michael G. Becker

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Abstract

Wastewater-based surveillance is a powerful tool that provides an unbiased measure of COVID-19 prevalence in a community. This work describes a sensitive wastewater rapid test for SARS-CoV-2 based on a widely distributed technology, the GeneXpert.

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  1. Version published to 10.1128/aem.01740-21
  2. ScreenIT

    SciScore for 10.1101/2021.08.13.21262039: (What is this?)

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

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    Briefly, SARS-CoV-2 was cultured in Vero cells in minimum essential media, and cellular debris was removed via low-speed centrifugation.
    Vero
    suggested: CLS Cat# 605372/p622_VERO, RRID:CVCL_0059)

    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 are some limitations to the GeneXpert technology. Notably, the targets are determined by the manufacturer and the system itself is optimized for clinical testing. The system currently does not monitor for SARS-CoV-2 variant detection, nor include fecal indicators such as pepper mild mottle virus that may be useful for data normalization (D’Aoust et al., 2021b). As the cartridge uses an internal filter there is also a risk of clogging; however, this was only observed once in this study and the sample was successfully processed in a repeat test. The input volume of the GeneXpert SARS-CoV-2/Flu/RSV test is also quite low at 300 µL, which may introduce sampling biases when testing large volumes of heterogeneous wastewater. This sampling bias makes any quantitative data from the GeneXpert less reliable unless a concentration step is performed. Ideally, wastewater-specific test cartridges for the GeneXpert could be developed with optimized targets and larger input volumes; or a similar large-volume assay could be developed using a competing technology. The Xpert Xpress SARS-CoV-2/Flu/RSV assay used in this study is also used clinically for the detection of Influenza A, Influenza B, and Respiratory Syncytial Virus. Therefore, it is theoretically possible that this assay will be able to detect these other pathogens in wastewater in addition to SARS-CoV-2. In this study, we only observed one positive detection of Influenza A in a wastewater sample from a major Canadian city, and...

    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 10.1101/2021.08.13.21262039 on medRxiv