Rapid diagnosis of COVID-19 using FT-IR ATR spectroscopy and machine learning

Abstract

Early diagnosis of COVID-19 in suspected patients is essential for contagion control and damage reduction strategies. We investigated the applicability of attenuated total reflection (ATR) Fourier transform infrared (FTIR) spectroscopy associated with machine learning in oropharyngeal swab suspension fluid to predict COVID-19 positive samples. The study included samples of 243 patients from two Brazilian States. Samples were transported by using different viral transport mediums (liquid 1 or 2). Clinical COVID-19 diagnosis was performed by the RT-PCR. We built a classification model based on partial least squares (PLS) associated with cosine k-nearest neighbours (KNN). Our analysis led to 84% and 87% sensitivity, 66% and 64% specificity, and 76.9% and 78.4% accuracy for samples of liquids 1 and 2, respectively. Based on this proof-of-concept study, we believe this method could offer a simple, label-free, cost-effective solution for high-throughput screening of suspect patients for COVID-19 in health care centres and emergency departments.

Contributions of vibrational spectroscopy to virology: A review

“…A further study conducted by Nogueira et al sought to verify the use of ATR FTIR as a potential method for screening for SARS-CoV-2 infection. Utilising oropharyngeal swabs of 243 individuals coupled with PLS-DA, it was shown to have an 84–87% sensitivity and 64–66% specificity, when compared to the standard PCR method [178] , somewhat lower than the results reported by Barauna et al [177] . Wood et al followed an alternative route of optimising the sampling geometry for improved signal to noise ratio compared to ATR-IR, to demonstrate the potential of transflection based IR spectroscopy for rapid point-of-care detection of SARS-CoV-2 markers in saliva.…”

Towards the direct detection of viral materials at the surface of protective face masks via infrared spectroscopy

“…Overall, these publications clearly substantiate the claims of the present study to potentially utilize (FT)IR spectroscopy as a rapid and cost-effective, yet reliable diagnostic tool for deriving potential exposition to contagious viral material, and especially the corona virus. In contrast to the published literature, the present approach does not rely on sampling body fluids to distinguish between healthy and diseased patients 39 . Utilizing face masks as sampling objects to pre-concentrate any matter that individuals may have been exposed to is becoming increasingly relevant, yet, remains a neglected strategy especially for routine screening scenarios 40 .…”

Current trends in COVID-19 diagnosis and its new variants in physiological fluids: Surface antigens, antibodies, nucleic acids, and RNA sequencing

“…Rapid detection of viral infections using UV–Vis spectroscopy [ 83 ], Raman spectroscopy [ 95 ], and Attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) [ 96 , 97 ] have been reported for predicting SARS-CoV-2 in blood, sera, plasma, infected cells, among others [ 98 ]. Zhang and coworkers [ 98 ] used ATR-FTIR for a SARS-CoV-2 detection in a time of 2–3 min using only ∼3 μL of serum sample.…”