Diagnostic performance of attenuated total reflection Fourier-transform infrared spectroscopy for detecting COVID-19 from routine nasopharyngeal swab samples

  1. Helinä Heino
  2. Lassi Rieppo
  3. Tuija Männistö
  4. Mikko J. Sillanpää
  5. Vesa Mäntynen
  6. Simo Saarakkala

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Abstract

Attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy coupled with machine learning-based partial least squares discriminant analysis (PLS-DA) was applied to study if severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could be detected from nasopharyngeal swab samples originally collected for polymerase chain reaction (PCR) analysis. Our retrospective study included 558 positive and 558 negative samples collected from Northern Finland. Overall, we found moderate diagnostic performance for ATR-FTIR when PCR analysis was used as the gold standard: the average area under the receiver operating characteristics curve (AUROC) was 0.67–0.68 (min. 0.65, max. 0.69) with 20, 10 and 5 k-fold cross validations. Mean accuracy, sensitivity and specificity was 0.62–0.63 (min. 0.60, max. 0.65), 0.61 (min. 0.58, max. 0.65) and 0.64 (min. 0.59, max. 0.67) with 20, 10 and 5 k-fold cross validations. As a conclusion, our study with relatively large sample set clearly indicate that measured ATR-FTIR spectrum contains specific information for SARS-CoV-2 infection (P < 0.001 for AUROC in label permutation test). However, the diagnostic performance of ATR-FTIR remained only moderate, potentially due to low concentration of viral particles in the transport medium. Further studies are needed before ATR-FTIR can be recommended for fast screening of SARS-CoV-2 from nasopharyngeal swab samples.

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  1. Version published to 10.1038/s41598-022-24751-z
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    SciScore for 10.1101/2021.11.29.21266906: (What is this?)

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

    Table 1: Rigor

    EthicsIRB: The ethical permissions were obtained both locally from the Ethical Committee of North Ostrobothnia’s Hospital District as well as nationally from the Finnish Medicines Agency (www.fimea.fi).
    Sex as a biological variablenot detected.
    RandomizationEvery k-fold cross-validation was repeated 100 times with different random seed initializations to make sure that the results are not affected by the random seed choice used to divide data into training and validation sets.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Preprocessing steps were performed with Anaconda3 (Conda 4.8.3 package manager and Python version 3.8.3) using NumPy, scikit-learn and SciPy packages.
    Python
    suggested: (IPython, RRID:SCR_001658)
    NumPy
    suggested: (NumPy, RRID:SCR_008633)
    SciPy
    suggested: (SciPy, RRID:SCR_008058)
    Anaconda3 (Conda 4.8.3 package manager and Python version 3.8.3) and PLS Regression package of the scikit-learn library was used to create the PLS-DA model.
    scikit-learn
    suggested: (scikit-learn, RRID:SCR_002577)

    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 10.1101/2021.11.29.21266906v1 on medRxiv