Nanotrap ® particles improve detection of SARS-CoV-2 for pooled sample methods, extraction-free saliva methods, and extraction-free transport medium methods

  1. RA Barclay
  2. I Akhrymuk
  3. A Patnaik
  4. V Callahan
  5. C Lehman
  6. P Andersen
  7. R Barbero
  8. S Barksdale
  9. R Dunlap
  10. D Goldfarb
  11. T Jones-Roe
  12. R Kelly
  13. B Kim
  14. S Miao
  15. A Munns
  16. D Munns
  17. S Patel
  18. E Porter
  19. R Ramsey
  20. S Sahoo
  21. O Swahn
  22. J Warsh
  23. K Kehn-Hall
  24. B Lepene

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Abstract

Here we present a rapid and versatile method for capturing and concentrating SARS-CoV-2 from transport medium and saliva using affinity-capture magnetic hydrogel particles. We demonstrate that the method concentrates virus prior to RNA extraction, thus significantly improving detection of the virus using a real-time RT-PCR assay across a range of viral titers, from 100 to 1,000,000 viral copies/mL; in particular, detection of virus in low viral load samples is enhanced when using the method coupled with the IDT 2019-nCoV CDC EUA Kit. This method is compatible with commercially available nucleic acid extraction kits, as well with a simple heat and detergent method. Using transport medium diagnostic remnant samples that previously had been tested for SARS-CoV-2 using either the Abbott RealTime SARS-CoV-2 EUA Test (n=14) or the Cepheid Xpert Xpress SARS-CoV-2 EUA Test (n=35), we demonstrate that our method not only correctly identifies all positive samples (n = 17) but also significantly improves detection of the virus in low viral load samples. The average improvement in cycle threshold (Ct) value as measured with the IDT 2019-nCoV CDC EUA Kit was 3.1; n = 10. Finally, to demonstrate that the method could potentially be used to enable pooled testing, we spiked infectious virus or a confirmed positive diagnostic remnant sample into 5 mL and 10 mL of negative transport medium and observed significant improvement in the detection of the virus from those larger sample volumes.

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  1. ScreenIT

    SciScore for 10.1101/2020.06.25.172510: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board Statementnot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.
    Cell Line Authenticationnot detected.

    Table 2: Resources

    Experimental Models: Cell Lines
    SentencesResources
    Cells, Viruses, and Reagents: Vero E6 cells were obtained from ATCC (CRL-1586) and were grown in DMEM complete medium, consisting of 10% FBS, 5% L-glutamine, and 5% penicillin/streptomycin, at 37°C and 5% CO2.
    Vero E6
    suggested: None

    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 several limitations to this study. First, we only had fourteen diagnostic remnant samples that had been previously tested on the Abbott RealTime SARS-CoV-2 EUA assay, and only five of those samples had previously tested negative for SARS-CoV-2. A larger set of samples would help us assess how our method compares to that assay. Second, for all of the diagnostic remnant samples that we used, the storage conditions were inconsistent. Some samples were unintentionally subjected to multiple freeze-thaw cycles, others were only subjected to one free-thaw cycle, and others were shipped and stored at 4°C and never frozen. Third, it is important to note that we used a different detection assay (from IDT) than had been used previously on the diagnostic remnant samples; therefore, we cannot make any direct conclusions regarding whether Nanotrap particles would improve the performance of those assays. Additionally, our saliva data is limited to contrived samples and it is therefore difficult to gauge how effective our method would be for saliva SARS-CoV-2 testing in a clinical setting. Despite these limitations, we are confident that the method described here can offer increased sensitivity for SARS-CoV-2 molecular testing from transport medium and saliva while enabling the use of faster and easier nucleic acid extraction methods, which will help address supply chain limitations. Also, as we have previously demonstrated that the Nanotrap particles used in this study can also ca...

    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 10.1101/2020.06.25.172510v2 on bioRxiv
  3. Version published to 10.1101/2020.06.25.172510v1 on bioRxiv