Heino, H., Rieppo, L., Männistö, T. et al. Diagnostic performance of attenuated total reflection Fourier-transform infrared spectroscopy for detecting COVID-19 from routine nasopharyngeal swab samples. Sci Rep 12, 20358 (2022). https://doi.org/10.1038/s41598-022-24751-z
Diagnostic performance of attenuated total reflection Fourier-transform infrared spectroscopy for detecting COVID-19 from routine nasopharyngeal swab samples
|Author:||Heino, Helinä1; Rieppo, Lassi1; Männistö, Tuija2;|
1Research Unit of Medical Imaging, Physics and Technology, University of Oulu, Oulu, Finland
2Northern Finland Laboratory Centre NordLab, Oulu, Finland
3Research Unit of Mathematical Sciences, University of Oulu, Oulu, Finland
4Department of Diagnostic Radiology, Oulu University Hospital, Oulu, Finland
|Online Access:||PDF Full Text (PDF, 2.4 MB)|
|Persistent link:|| http://urn.fi/urn:nbn:fi-fe202301255788
|Publish Date:|| 2023-01-25
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.
|Type of Publication:||
A1 Journal article – refereed
|Field of Science:||
119 Other natural sciences
112 Statistics and probability
113 Computer and information sciences
Financial support for this research project was received from European Regional Development Fund (ERDF) (Funding Number A76179). All the figures have been produced by corresponding author as stated in author contributions.
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