Noninvasive Diagnostic for COVID-19 from Saliva Biofluid via FTIR Spectroscopy and Multivariate Analysis

• Published in: Analytical chemistry (Washington) Vol. 94; no. 5; pp. 2425 - 2433
• Main Authors: Nascimento, Márcia H. C, Marcarini, Wena D, Folli, Gabriely S, da Silva Filho, Walter G, Barbosa, Leonardo L, Paulo, Ellisson Henrique de, Vassallo, Paula F, Mill, José G, Barauna, Valério G, Martin, Francis L, de Castro, Eustáquio V. R, Romão, Wanderson, Filgueiras, Paulo R
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 08.02.2022
• Subjects: Algorithms; analytical chemistry; Chemistry; Coronaviruses; Correlation coefficient; Correlation coefficients; COVID-19; COVID-19 infection; data collection; diagnostic techniques; Discriminant Analysis; Fourier transform infrared spectroscopy; Genetic algorithms; Global health; Humans; Least-Squares Analysis; Lipids; Multivariate Analysis; Nucleic acids; Particle swarm optimization; Polymerase chain reaction; Public health; reverse transcriptase polymerase chain reaction; Reverse transcription; Risk management; risk reduction; Saliva; SARS-CoV-2; Severe acute respiratory syndrome coronavirus 2; Spectra; Spectroscopy, Fourier Transform Infrared; Spectrum analysis
• ISSN: 0003-2700; 1520-6882; 1520-6882
• DOI: 10.1021/acs.analchem.1c04162

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the worst global health crisis in living memory. The reverse transcription polymerase chain reaction (RT-qPCR) is considered the gold standard diagnostic method, but it exhibits limitations in the face of enormous demands. We evaluated a mid-infrared (MIR) data set of 237 saliva samples obtained from symptomatic patients (138 COVID-19 infections diagnosed via RT-qPCR). MIR spectra were evaluated via unsupervised random forest (URF) and classification models. Linear discriminant analysis (LDA) was applied following the genetic algorithm (GA-LDA), successive projection algorithm (SPA-LDA), partial least squares (PLS-DA), and a combination of dimension reduction and variable selection methods by particle swarm optimization (PSO-PLS-DA). Additionally, a consensus class was used. URF models can identify structures even in highly complex data. Individual models performed well, but the consensus class improved the validation performance to 85% accuracy, 93% sensitivity, 83% specificity, and a Matthew’s correlation coefficient value of 0.69, with information at different spectral regions. Therefore, through this unsupervised and supervised framework methodology, it is possible to better highlight the spectral regions associated with positive samples, including lipid (∼1700 cm–1), protein (∼1400 cm–1), and nucleic acid (∼1200–950 cm–1) regions. This methodology presents an important tool for a fast, noninvasive diagnostic technique, reducing costs and allowing for risk reduction strategies.