tetano
Editor, Senior Moderator
Anal Chem
. 2022 Jan 25.
doi: 10.1021/acs.analchem.1c04162. Online ahead of print.
Noninvasive Diagnostic for COVID-19 from Saliva Biofluid via FTIR Spectroscopy and Multivariate Analysis
Márcia H C Nascimento[SUP] 1 [/SUP], Wena D Marcarini[SUP] 2 [/SUP], Gabriely S Folli[SUP] 1 [/SUP], Walter G da Silva Filho[SUP] 2 [/SUP], Leonardo L Barbosa[SUP] 2 [/SUP], Ellisson Henrique de Paulo[SUP] 1 [/SUP], Paula F Vassallo[SUP] 3 [/SUP], José G Mill[SUP] 2 [/SUP], Valério G Barauna[SUP] 2 [/SUP], Francis L Martin[SUP] 4 [/SUP], Eustáquio V R de Castro[SUP] 1 [/SUP], Wanderson Romão[SUP] 5 [/SUP], Paulo R Filgueiras[SUP] 1 [/SUP]
Affiliations
Abstract
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[SUP]-1[/SUP]), protein (∼1400 cm[SUP]-1[/SUP]), and nucleic acid (∼1200-950 cm[SUP]-1[/SUP]) regions. This methodology presents an important tool for a fast, noninvasive diagnostic technique, reducing costs and allowing for risk reduction strategies.
. 2022 Jan 25.
doi: 10.1021/acs.analchem.1c04162. Online ahead of print.
Noninvasive Diagnostic for COVID-19 from Saliva Biofluid via FTIR Spectroscopy and Multivariate Analysis
Márcia H C Nascimento[SUP] 1 [/SUP], Wena D Marcarini[SUP] 2 [/SUP], Gabriely S Folli[SUP] 1 [/SUP], Walter G da Silva Filho[SUP] 2 [/SUP], Leonardo L Barbosa[SUP] 2 [/SUP], Ellisson Henrique de Paulo[SUP] 1 [/SUP], Paula F Vassallo[SUP] 3 [/SUP], José G Mill[SUP] 2 [/SUP], Valério G Barauna[SUP] 2 [/SUP], Francis L Martin[SUP] 4 [/SUP], Eustáquio V R de Castro[SUP] 1 [/SUP], Wanderson Romão[SUP] 5 [/SUP], Paulo R Filgueiras[SUP] 1 [/SUP]
Affiliations
- PMID: 35076208
- DOI: 10.1021/acs.analchem.1c04162
Abstract
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[SUP]-1[/SUP]), protein (∼1400 cm[SUP]-1[/SUP]), and nucleic acid (∼1200-950 cm[SUP]-1[/SUP]) regions. This methodology presents an important tool for a fast, noninvasive diagnostic technique, reducing costs and allowing for risk reduction strategies.