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

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing global COVID-19 pandemic since 2019 has led to increasing amount of research to study how to do fast screening and diagnosis to efficiently detect COVID-19 positive cases, and how to prevent spreading of the virus. Our research objective was to study whether SARS-CoV-2 could be detected from routine nasopharyngeal swab samples by using attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy coupled with partial least squares discriminant analysis (PLS-DA). The advantage of ATR-FTIR is that measurements can be conducted without any sample preparation and no reagents are needed. Our study included 558 positive and 558 negative samples collected from Northern Finland. Overall, we found moderate diagnostic performance for ATR-FTIR when polymerase chain reaction (PCR) 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 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 routine nasopharyngeal swab samples.