Abstract
.Significance: The primary method of COVID-19 detection is reverse transcription polymerase chain reaction (RT-PCR) testing. PCR test sensitivity may decrease as more variants of concern arise and reagents may become less specific to the virus.Aim: We aimed to develop a reagent-free way to detect COVID-19 in a real-world setting with minimal constraints on sample acquisition. The machine learning (ML) models involved could be frequently updated to include spectral information about variants without needing to develop new reagents.Approach: We present a workflow for collecting, preparing, and imaging dried saliva supernatant droplets using a non-invasive, label-free technique—Raman spectroscopy—to detect changes in the molecular profile of saliva associated with COVID-19 infection.Results: We used an innovative multiple instance learning-based ML approach and droplet segmentation to analyze droplets. Amongst all confounding factors, we discriminated between COVID-positive and COVID-negative individuals yielding receiver operating coefficient curves with an area under curve (AUC) of 0.8 in both males (79% sensitivity and 75% specificity) and females (84% sensitivity and 64% specificity). Taking the sex of the saliva donor into account increased the AUC by 5%.Conclusion: These findings may pave the way for new rapid Raman spectroscopic screening tools for COVID-19 and other infectious diseases.
Highlights
1.1 Current State of the COVID-19 PandemicCOVID-19 has precipitated the deaths of 3.9 million people worldwide as of the end of June 2021 and is the world’s most costly health crisis to date
We developed a technique for obtaining Raman spectra from saliva supernatant in a way that minimized person-to-person variation (Fig. 1)
We have shown that Raman spectroscopy can be used to detect biomolecular changes between COVID-positive and COVID-negative saliva supernatant and that accounting for the sex of the saliva donor can increase the accuracy of predictive models
Summary
1.1 Current State of the COVID-19 PandemicCOVID-19 has precipitated the deaths of 3.9 million people worldwide as of the end of June 2021 and is the world’s most costly health crisis to date. The current gold standards for SARS-CoV-2 testing are nucleic acid amplification tests (NAATs) using saliva or oro-nasopharyngeal swabs in which viral ribonucleic acid (RNA) is amplified and detected using tools, such as reverse transcription polymerase chain reaction (RT-PCR).[6] This uses nucleic acid primers, enzymes, and cycles of heat to amplify a specific genomic sequence (from the SARS-CoV-2 genome in this case), enabling it to be detected more .[7] The sensitivity and specificity for saliva-based NAATs are ∼83% and 99%, respectively, and the sensitivity and specificity for nasopharyngeal swab-based NAATs are ∼84% and 99%, respectively.[6] Despite the fact that RT-PCR has successfully been used in testing for respiratory diseases, this method can show lower sensitivity for SARS-CoV-2 detection before presentation of symptoms.[8] Identifying asymptomatic patients early on can help prevent and control the spread of COVID-19, so RT-PCR may fall short as a tool for mass serial screening of asymptomatic populations.[7,9] this method of testing typically necessitates time-consuming transport of samples to clinical laboratories where complex tailored reagents are used.[10]
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