Detection of SARS‐CoV‐2 in different human biofluids using the loop‐mediated isothermal amplification assay: A prospective diagnostic study in Fortaleza, Brazil

  1. Marco Clementino
  2. Karene F. Cavalcante
  3. Vania A. F. Viana
  4. Dayara de Oliveira Silva
  5. Caroline R. Damasceno
  6. Jessica Fernandes de Souza
  7. Rafhaella N. D. G. Gondim
  8. Daniel M. de Melo Jorge
  9. Lyvia M. V. C. Magalhães
  10. Érico A. G. de Arruda
  11. Roberto da J. P. Neto
  12. Melissa S. Medeiros
  13. Armênio A. dos Santos
  14. Pedro J. C. Magalhães
  15. Liana P. Mello
  16. Eurico Arruda
  17. Aldo Â. M. Lima
  18. Alexandre Havt

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Abstract

We adopted the reverse‐transcriptase‐loop‐mediated isothermal amplification (RT‐LAMP) to detect severe acute respiratory syndrome coronavirus 2 (SARS‐Cov‐2) in patient samples. Two primer sets for genes N and Orf1ab were designed to detect SARS‐CoV‐2, and one primer set was designed to detect the human gene Actin . We collected prospective 138 nasopharyngeal swabs, 70 oropharyngeal swabs, 69 salivae, and 68 mouth saline wash samples from patients suspected to have severe acute respiratory syndrome (SARS) caused by SARS‐CoV‐2 to test the RT‐LAMP in comparison with the gold standard technique reverse‐transcription quantitative polymerase chain reaction  (RT‐qPCR). The accuracy of diagnosis using both primers, N5 and Orf9, was evaluated. Sensitivity and specificity for diagnosis were 96% (95% confidence interval [CI]: 87–99) and 85% (95% CI: 76–91) in 138 samples, respectively. Accurate diagnosis results were obtained only in nasopharyngeal swabs processed via extraction kit. Accurate and rapid diagnosis could aid coronavirus disease 2019 (COVID‐19) pandemic management by identifying, isolating, and treating patients rapidly.

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  1. Version published to 10.1002/jmv.27842
  2. ScreenIT

    SciScore for 10.1101/2022.01.23.22269711: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: Ethical approval: This proposal was approved by the National Ethical Review Board on 06/10/2020 with the code CAAE 33460220.7.0000.5045.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    BlindingThen, 71 SARS suspected individuals’ nasopharyngeal swabs samples were collected and aliquoted blindly by our collaborators at LACEN-CE.
    Power AnalysisSample size and statistical analysis: Estimation of the required population size for this proposal was calculated with statistical power set to at least 80%, and confidence was set to be at least 95% [15, 16].

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Positive predictive values (PPV), positive negative values (PNV), sensitivity, and specificity were calculated using GraphPad Prism software (ver. 8.4.0) [18].
    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: 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.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

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  3. Version published to 10.1101/2022.01.23.22269711v1 on medRxiv