A scalable saliva-based, extraction-free rt-lamp protocol for sars-cov-2 diagnosis

  1. Paula Asprino
  2. Fabiana Bettoni
  3. Anamaria Camargo
  4. Diego Coelho
  5. Guilherme Coppini
  6. Igor Correa
  7. Erika Freitas
  8. Lilian Inoue
  9. João Paulo Kitajima
  10. Mayra Kuroki
  11. Cibele Masotti
  12. Tatiana Marques
  13. Alice Reis
  14. Luiz Fernando Reis
  15. Bibiana Santos
  16. Ernande dos Santos
  17. David Schlesinger
  18. Cecília Sena
  19. Talita Spadaccini
  20. Lucas Taniguti

Reviewed by

Read the full article See related articles

Listed in

Log in to save this article

Abstract

I.

Scalable, cost-effective screening methods are an essential tool to control SARS-CoV-2 spread. We have developed a straight saliva-based, RNA extraction-free, RT-LAMP test that is comparable to current nasopharyngeal swab RT-PCR tests in both sensitivity and specificity. Using a 2-step readout of fluorescence and melting-point curve analysis, the test is scalable to more than 30,000 tests per day with average turnaround time of less than 3 hours. The test was validated using samples from 244 symptomatic patients, and showed sensitivity of 78.9% (vs. 85.5% for nasopharyngeal swabs RT-PCR) and specificity of 100% (vs. 100% for nasopharyngeal swabs RT-PCR). Our method is therefore accurate, robust, time and cost effective and therefore can be used for screening of SARS-CoV-2.

Article activity feed

  1. ScreenIT

    SciScore for 10.1101/2020.10.27.20220541: (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.

    Table 2: Resources

    No key resources detected.

    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:
    The comparison of different techniques, RT-LAMP and RT-PCR, in different types of biological samples is a limitation of this work. This comparison may render incongruent results due to the presence of virus in only one of these biological samples, and not represent the real efficiency of the methods. The protocol described and validated here focuses on scalability and short turnaround times. Variations on this protocol, such as the addition of standard RNA extraction and concentration can be used to improve sensitivity in detriment of speed and cost. Alternatively, increase in the fluorescence detection cutoff, with removal of the dissociation curve, can be used to speed and decrease costs in detriment of sensitivity and specificity. Each variation can serve distinct purposes (screening or diagnosis), fit different geographic location socio-economic constraints, and moment of the pandemic. In conclusion, we contribute efforts to contain the pandemic by describing and validating a scalable, fast, and low cost SARS-CoV-2 test that can be easily collected. The ease of implementation should allow this to be implemented in both developed and developing countries.

    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 10.1101/2020.10.27.20220541v1 on medRxiv