Diagnostic performance of attenuated total reflection Fourier-transform infrared spectroscopy for detecting COVID-19 from routine nasopharyngeal swab samples
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...
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ftdoajarticles:oai:doaj.org/article:6e68ae891de04775b6b88533166de8b9 2023-05-15T17:42:37+02:00 Diagnostic performance of attenuated total reflection Fourier-transform infrared spectroscopy for detecting COVID-19 from routine nasopharyngeal swab samples Helinä Heino Lassi Rieppo Tuija Männistö Mikko J. Sillanpää Vesa Mäntynen Simo Saarakkala 2022-11-01T00:00:00Z https://doi.org/10.1038/s41598-022-24751-z https://doaj.org/article/6e68ae891de04775b6b88533166de8b9 EN eng Nature Portfolio https://doi.org/10.1038/s41598-022-24751-z https://doaj.org/toc/2045-2322 doi:10.1038/s41598-022-24751-z 2045-2322 https://doaj.org/article/6e68ae891de04775b6b88533166de8b9 Scientific Reports, Vol 12, Iss 1, Pp 1-9 (2022) Medicine R Science Q article 2022 ftdoajarticles https://doi.org/10.1038/s41598-022-24751-z 2022-12-30T19:42:25Z 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. Article in Journal/Newspaper Northern Finland Directory of Open Access Journals: DOAJ Articles Scientific Reports 12 1 |
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Medicine R Science Q Helinä Heino Lassi Rieppo Tuija Männistö Mikko J. Sillanpää Vesa Mäntynen Simo Saarakkala Diagnostic performance of attenuated total reflection Fourier-transform infrared spectroscopy for detecting COVID-19 from routine nasopharyngeal swab samples |
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Medicine R Science Q |
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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. |
format |
Article in Journal/Newspaper |
author |
Helinä Heino Lassi Rieppo Tuija Männistö Mikko J. Sillanpää Vesa Mäntynen Simo Saarakkala |
author_facet |
Helinä Heino Lassi Rieppo Tuija Männistö Mikko J. Sillanpää Vesa Mäntynen Simo Saarakkala |
author_sort |
Helinä Heino |
title |
Diagnostic performance of attenuated total reflection Fourier-transform infrared spectroscopy for detecting COVID-19 from routine nasopharyngeal swab samples |
title_short |
Diagnostic performance of attenuated total reflection Fourier-transform infrared spectroscopy for detecting COVID-19 from routine nasopharyngeal swab samples |
title_full |
Diagnostic performance of attenuated total reflection Fourier-transform infrared spectroscopy for detecting COVID-19 from routine nasopharyngeal swab samples |
title_fullStr |
Diagnostic performance of attenuated total reflection Fourier-transform infrared spectroscopy for detecting COVID-19 from routine nasopharyngeal swab samples |
title_full_unstemmed |
Diagnostic performance of attenuated total reflection Fourier-transform infrared spectroscopy for detecting COVID-19 from routine nasopharyngeal swab samples |
title_sort |
diagnostic performance of attenuated total reflection fourier-transform infrared spectroscopy for detecting covid-19 from routine nasopharyngeal swab samples |
publisher |
Nature Portfolio |
publishDate |
2022 |
url |
https://doi.org/10.1038/s41598-022-24751-z https://doaj.org/article/6e68ae891de04775b6b88533166de8b9 |
genre |
Northern Finland |
genre_facet |
Northern Finland |
op_source |
Scientific Reports, Vol 12, Iss 1, Pp 1-9 (2022) |
op_relation |
https://doi.org/10.1038/s41598-022-24751-z https://doaj.org/toc/2045-2322 doi:10.1038/s41598-022-24751-z 2045-2322 https://doaj.org/article/6e68ae891de04775b6b88533166de8b9 |
op_doi |
https://doi.org/10.1038/s41598-022-24751-z |
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Scientific Reports |
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