Pathophysiological Response to SARS-CoV-2 Infection Detected by Infrared Spectroscopy Enables Rapid and Robust Saliva Screening for COVID-19

Accuracy of COVID-19 diagnostic tests via infrared spectroscopy: A systematic review and meta-analysis

This study aims to synthesize the evidence on the accuracy parameters of COVID-19 diagnosis methods using infrared spectroscopy (FTIR). A systematic review with searches in PubMed and Embase was performed (September 2023). Studies reporting data on test specificity, sensitivity, true positive, true negative, false positive, and false negative using different human samples were included. Meta-analysis of accuracy estimates with 95 % confidence intervals and area under the ROC Curve (AUC) were conducted (Meta-Disc 1.4.7). Seventeen studies were included - all of them highlighted regions 650-1800 cm-1 and 2300-3900 cm-1 as most important for diagnosing COVID-19. The FTIR technique presented high sensitivity [0.912 (95 %CI, 0.878-0.939), especially in vaccinated [0.959 (CI95 %, 0.908-0.987)] compared to unvaccinated [0.625 (CI95 %, 0.584-0.664)] individuals for COVID-19. Overall specificity was also high [0.886 (95 %CI, 0.855-0.912), with increased rates in vaccinated [0.884 (CI95 %, 0.819-0.932)] than in unvaccinated [0.667 (CI95 %, 0.629-0.704)] patients. These findings reveal that FTIR is an accurate technique for detecting SARS-CoV-2 infection in different biological matrices with advantages including low cost, rapid and environmentally friendly with minimal preparation analyses. This could lead to an easy implementation of this technique in practice as a screening tool for patients with suspected COVID-19, especially in low-income countries.

Spectrochemical and explainable artificial intelligence approaches for molecular level identification of the status of critically ill patients with COVID-19

This study explores the molecular alterations and disease progression in COVID-19 patients using ATR-FTIR spectroscopy combined with spectrochemical and explainable artificial intelligence (XAI) approaches. Blood serum samples from intubated patients (IC), those receiving hospital services (SC), and recovered patients (PC) were analyzed to identify potential spectrochemical serum biomarkers. Spectrochemical parameters such as lipid, protein, nucleic acid concentrations, and IgG glycosylation were quantified, revealing significant alterations indicative of disease severity. Notably, increased lipid content, altered protein concentrations, and enhanced protein phosphorylation were observed in IC patients compared to SC and PC groups. The serum AGR (Albumin/Globulin Ratio) index demonstrated a distinct shift among patient groups, suggesting its potential as a rapid biochemical marker for COVID-19 severity. Additionally, alterations in IgG glycosylation and glucose concentrations were associated with disease severity. Spectral analysis highlighted specific bands indicative of nucleic acid concentrations, with notable changes observed in IC patients. XAI techniques further elucidated the importance of various spectral features in predicting disease severity across patient categories, emphasizing the heterogeneity of COVID-19's impact. Overall, this comprehensive approach provides insights into the molecular mechanisms underlying COVID-19 pathogenesis and offers a transparent and interpretable prediction algorithm to aid decision-making and patient management.

Laboratory studies on the infectivity of human respiratory viruses: Experimental conditions, detections, and resistance to the atmospheric environment

The environmental stability of infectious viruses in the laboratory setting is crucial to the transmission potential of human respiratory viruses. Different experimental techniques or conditions used in studies over the past decades have led to diverse understandings and predictions for the stability of viral infectivity in the atmospheric environment. In this paper, we review the current knowledge on the effect of simulated atmospheric conditions on the infectivity of respiratory viruses, mainly focusing on influenza viruses and coronaviruses, including severe acute respiratory syndrome coronavirus 2 and Middle East respiratory syndrome coronavirus. First, we summarize the impact of the experimental conditions on viral stability; these involve the methods of viral aerosol generation, storage during aging and collection, the virus types and strains, the suspension matrixes, the initial inoculum volumes and concentrations, and the drying process. Second, we summarize and discuss the detection methods of viral infectivity and their disadvantages. Finally, we integrate the results from the reviewed studies to obtain an overall understanding of the effects of atmospheric environmental conditions on the decay of infectious viruses, especially aerosolized viruses. Overall, this review highlights the knowledge gaps in predicting the ability of viruses to maintain infectivity during airborne transmission.

Perspectives of FTIR as Promising Tool for Pathogen Diagnosis, Sanitary and Welfare Monitoring in Animal Experimentation Models: A Review Based on Pertinent Literature

Currently, there is a wide application in the literature of the use of the Fourier Transform Infrared Spectroscopy (FTIR) technique. This basic tool has also proven to be efficient for detecting molecules associated with hosts and pathogens in infections, as well as other molecules present in humans and animals' biological samples. However, there is a crisis in science data reproducibility. This crisis can also be observed in data from experimental animal models (EAMs). When it comes to rodents, a major challenge is to carry out sanitary monitoring, which is currently expensive and requires a large volume of biological samples, generating ethical, legal, and psychological conflicts for professionals and researchers. We carried out a survey of data from the relevant literature on the use of this technique in different diagnostic protocols and combined the data with the aim of presenting the technique as a promising tool for use in EAM. Since FTIR can detect molecules associated with different diseases and has advantages such as the low volume of samples required, low cost, sustainability, and provides diagnostic tests with high specificity and sensitivity, we believe that the technique is highly promising for the sanitary and stress and the detection of molecules of interest of infectious or non-infectious origin.

Two-trace two-dimensional correlation spectra (2T2D-COS) analysis using FTIR spectra to monitor the immune response by COVID-19

There is a growing trend in using saliva for SARS-CoV-2 detection with reasonable accuracy. We have studied the responses of IgA, IgG, and IgM in human saliva by directly comparing disease with control analyzing two-trace two-dimensional correlation spectra (2T2D-COS) employing Fourier transform infrared (FTIR) spectra. It explores the molecular-level variation between control and COVID-19 saliva samples. The advantage of 2T2D spectra is that it helps in discriminating remarkably subtle features between two simple pairs of spectra. It gives spectral information from highly overlapped bands associated with different systems. The clinical findings from 2T2D show the decrease of IgG and IgM salivary antibodies in the 50, 60, 65, and 75-years COVID-19 samples. Among the various COVID-19 populations studied the female 30-years group reveals defense mechanisms exhibited by IgM and IgA. Lipids and fatty acids decrease, resulting in lipid oxidation due to the SARS-CoV-2 in the samples studied. Study shows salivary thiocyanate plays defense against SARS-CoV-2 in the male population in 25 and 35 age groups. The receiver operation characteristics statistical method shows a sensitivity of 98% and a specificity of 94% for the samples studied. The measure of accuracy computed as F score and G score has a high value, supporting our study's validation. Thus, 2T2D-COS analysis can potentially monitor the progression of immunoglobulin's response function to COVID-19 with reasonable accuracy, which could help diagnose clinical trials. KEY MESSAGES: The molecular profile of salivary antibodies is well resolved and identified from 2T2D-COS FTIR spectra. The IgG antibody plays a significant role in the defense mechanism against SARS-CoV-2 in 25-40 years. 2T2D-COS reveals the absence of salivary thiocyanate in the 40-75 years COVID-19 population. The receiver operation characteristic (ROC) analysis validates our study with high sensitivity and specificity.

A review on current diagnostic tools and potential optical absorption spectroscopy for HFMD detection

Hand, Foot, and Mouth Disease (HFMD) is an outbreak infectious disease that can easily spread among children under the age of five. The most common causative agents of HFMD are enterovirus 71 (EV71) and coxsackievirus A16 (CVA16), but infection caused by EV71 is more associated with fatalities due to severe neurological disorders. The present diagnosis methods rely on physical examinations by the doctors and further confirmation by laboratories detection methods such as viral culture and polymerase chain reaction. Clinical signs of HFMD infection and other childhood diseases such as chicken pox, and allergies are similar, yet the genetics and pathogenicity of the viruses are substantially different. Thus, there is an urgent need for an early screening of HFMD using an inexpensive and user-friendly device that can directly detect the causative agents of the disease. This paper reviews current HFMD diagnostic methods based on various target types, such as nucleic acid, protein, and whole virus. This was followed by a thorough discussion on the emerging sensing technologies for HFMD detection, including surface plasmon resonance, electrochemical sensor, and surface enhanced Raman spectroscopy. Lastly, optical absorption spectroscopic method was critically discussed and proposed as a promising technology for HFMD screening and detection.

Dynamic response antibodies SARS-CoV-2 human saliva studied using two-dimensional correlation (2DCOS) infrared spectral analysis coupled with receiver operation characteristics analysis

COVID-19 has affected the entire world due to the rapid spread of SARS-CoV-2, mainly through airborne particles from saliva, which, being easily obtained, help monitor the progression of the disease. Fourier transform infrared (FTIR) spectra combined with chemometric analysis could increase the diagnostic efficiency of the disease. However, two-dimensional correlation spectroscopy (2DCOS) is superior to conventional spectra as it helps to resolve the minute overlapped peaks. In this work, we aimed to use 2DCOS and receiver operating characteristic (ROC) analyses to compare the immune response in saliva associated with COVID-19, which could be important in biomedical diagnosis. FTIR spectra of human saliva samples from male (575) and female (366) patients ranging from 20 to 82 ± 2 years of age were used for the study. Age groups were segregated as G1 (25-40 ± 2 years), G2 (45-60 ± 2 years), and G3 (65-80 ± 2 years). The results of the 2DCOS analysis showed biomolecular changes in response to SARS-CoV-2. 2DCOS analyses of the male G1 + (1579,1644) and -(1531,1598) crossover peaks evidenced changes such as amide I > IgG. Female G1 crossover peaks -(1504,1645), (1504,1545) and -(1391,1645) resulted in amide I > IgG > IgM. The asynchronous spectra in 1300-900 cm-1 of the G2 male group showed that IgM is more important in diagnosing infections than IgA. Female G2 asynchronous spectra -(1027,1242) and + (1068,1176) showed that IgA > IgM is produced against SARS-CoV-2. The G3 male group evidenced antibody changes in IgG > IgM. The absence of IgM in the female G3 population diagnoses a specifically targeted immunoglobulin associated with sex. Moreover, ROC analysis showed sensitivity (85-89 % men; 81-88 % women) and specificity (90-93 % men; 78-92 % women) for the samples studied. The general classification performance (F1 score) of the studied samples is high for the male (88-91 %) and female (80-90 %) populations. This high PPV (positive predictive value) and NPV (negative predictive value) verify our segregation of COVID-19 positive and negative sample groups. Therefore, 2DCOS with ROC analysis using FTIR spectra have the potential for a non-invasive approach to monitoring COVID-19.

Unlocking the Diagnostic Potential of Saliva: A Comprehensive Review of Infrared Spectroscopy and Its Applications in Salivary Analysis

Infrared (IR) spectroscopy is a noninvasive and rapid analytical technique that provides information on the chemical composition, structure, and conformation of biomolecules in saliva. This technique has been widely used to analyze salivary biomolecules, owing to its label-free advantages. Saliva contains a complex mixture of biomolecules including water, electrolytes, lipids, carbohydrates, proteins, and nucleic acids which are potential biomarkers for several diseases. IR spectroscopy has shown great promise for the diagnosis and monitoring of diseases such as dental caries, periodontitis, infectious diseases, cancer, diabetes mellitus, and chronic kidney disease, as well as for drug monitoring. Recent advancements in IR spectroscopy, such as Fourier-transform infrared (FTIR) spectroscopy and attenuated total reflectance (ATR) spectroscopy, have further enhanced its utility in salivary analysis. FTIR spectroscopy enables the collection of a complete IR spectrum of the sample, whereas ATR spectroscopy enables the analysis of samples in their native form, without the need for sample preparation. With the development of standardized protocols for sample collection and analysis and further advancements in IR spectroscopy, the potential for salivary diagnostics using IR spectroscopy is vast.

Raman and fourier transform infrared spectroscopy techniques for detection of coronavirus (COVID-19): a mini review

Coronavirus pandemic has been a huge jeopardy to human health in various systems since it outbroke, early detection and prevention of further escalation has become a priority. The current popular approach is to collect samples using the nasopharyngeal swab method and then test for RNA using the real-time polymerase chain reaction, which suffers from false-positive results and a longer diagnostic time scale. Alternatively, various optical techniques, namely, optical sensing, spectroscopy, and imaging shows a great promise in virus detection. In this mini review, we briefly summarize the development progress of vibrational spectroscopy techniques and its applications in the detection of SARS-CoV family. Vibrational spectroscopy techniques such as Raman spectroscopy and infrared spectroscopy received increasing appreciation in bio-analysis for their speediness, accuracy and cost-effectiveness in detection of SARS-CoV. Further, an account of emerging photonics technologies of SARS-CoV-2 detection and future possibilities is also explained. The progress in the field of vibrational spectroscopy techniques for virus detection unambiguously show a great promise in the development of rapid photonics-based devices for COVID-19 detection.

The Role of the Preanalytical Step for Human Saliva Analysis via Vibrational Spectroscopy

Saliva is an easily sampled matrix containing a variety of biochemical information, which can be correlated with the individual health status. The fast, straightforward analysis of saliva by vibrational (ATR-FTIR and Raman) spectroscopy is a good premise for large-scale preclinical studies to aid translation into clinics. In this work, the effects of saliva collection (spitting/swab) and processing (two different deproteinization procedures) were explored by principal component analysis (PCA) of ATR-FTIR and Raman data and by investigating the effects on the main saliva metabolites by reversed-phase chromatography (RPC-HPLC-DAD). Our results show that, depending on the bioanalytical information needed, special care must be taken when saliva is collected with swabs because the polymeric material significantly interacts with some saliva components. Moreover, the analysis of saliva before and after deproteinization by FTIR and Raman spectroscopy allows to obtain complementary biological information.

ATR-FTIR spectrum analysis of plasma samples for rapid identification of recovered COVID-19 individuals

The development of fast, cheap and reliable methods to determine seroconversion against infectious agents is of great practical importance. In the context of the COVID-19 pandemic, an important issue is to study the rate of formation of the immune layer in the population of different regions, as well as the study of the formation of post-vaccination immunity in individuals after vaccination. Currently, the main method for this kind of research is enzyme immunoassay (ELISA, enzyme-linked immunosorbent assay). This technique is sufficiently sensitive and specific, but it requires significant time and material costs. We investigated the applicability of attenuated total reflection (ATR) Fourier transform infrared (FTIR) spectroscopy associated with machine learning in blood plasma to detect seroconversion against SARS-CoV-2. The study included samples of 60 patients. Clear spectral differences in plasma samples from recovered COVID-19 patients and conditionally healthy donors were identified using multivariate and statistical analysis. The results showed that ATR-FTIR spectroscopy, combined with principal components analysis (PCA) and linear discriminant analysis (LDA) or artificial neural network (ANN), made it possible to efficiently identify specimens from recovered COVID-19 patients. We built classification models based on PCA associated with LDA and ANN. Our analysis led to 87% accuracy for PCA-LDA model and 91% accuracy for ANN, respectively. Based on this proof-of-concept study, we believe this method could offer a simple, label-free, cost-effective tool for detecting seroconversion against SARS-CoV-2. This approach could be used as an alternative to ELISA.

SARS-CoV-2 severity classification from plasma sample using confocal Raman spectroscopy

The world is on the brink of facing coronavirus's (COVID-19) fourth wave as the mutant forms of viruses are escaping neutralizing antibodies in spite of being vaccinated. As we have already witnessed that it has encumbered our health system, with hospitals swamped with infected patients observed during the viral outbreak. Rapid triage of patients infected with SARS-CoV-2 is required during hospitalization to prioritize and provide the best point of care. Traditional diagnostics techniques such as RT-PCR and clinical parameters such as symptoms, comorbidities, sex and age are not enough to identify the severity of patients. Here, we investigated the potential of confocal Raman microspectroscopy as a powerful tool to generate an expeditious blood-based test for the classification of COVID-19 disease severity using 65 patients plasma samples from cohorts infected with SARS-CoV-2. We designed an easy manageable blood test where we used a small volume (8 μl) of inactivated whole plasma samples from infected patients without any extra solvent usage in plasma processing. Raman spectra of plasma samples were acquired and multivariate exploratory analysis PC-LDA (principal component based linear discriminant analysis) was used to build a model, which segregated the severe from the non-severe COVID-19 group with a sensitivity of 83.87%, specificity of 70.60% and classification efficiency of 76.92%. Among the bands expressed in both the cohorts, the study led to the identification of Raman fingerprint regions corresponding to lipids (1661, 1742), proteins amide I and amide III (1555, 1247), proteins (Phe) (1006, 1034), and nucleic acids (760) to be differentially expressed in severe COVID-19 patient's samples. In summary, the current study exhibits the potential of confocal Raman to generate simple, rapid, and less expensive blood tests to triage the severity of patients infected with SARS-CoV-2.

Contributions of vibrational spectroscopy to virology: A review

Vibrational spectroscopic techniques, both infrared absorption and Raman scattering, are high precision, label free analytical techniques which have found applications in fields as diverse as analytical chemistry, pharmacology, forensics and archeometrics and, in recent times, have attracted increasing attention for biomedical applications. As analytical techniques, they have been applied to the characterisation of viruses as early as the 1970 s, and, in the context of the coronavirus disease 2019 (COVID-19) pandemic, have been explored in response to the World Health Organisation as novel methodologies to aid in the global efforts to implement and improve rapid screening of viral infection. This review considers the history of the application of vibrational spectroscopic techniques to the characterisation of the morphology and chemical compositions of viruses, their attachment to, uptake by and replication in cells, and their potential for the detection of viruses in population screening, and in infection response monitoring applications. Particular consideration is devoted to recent efforts in the detection of severe acute respiratory syndrome coronavirus 2, and monitoring COVID-19.

DETERMINATION OF COVID-19 VIRUSES IN SALIVA USING FOURIER TRANSFORM INFRARED SPECTROSCOPY

The rapid spread of severe syndrome coronavirus 2 (SARS-CoV-2) has led to the coronavirus disease 2019 (COVID-19) worldwide pandemic. Scientists and researchers all over the world studied different methods in order to accelerate the testing results. In this review, we present some of the most important papers related to the determination of COVID – 19 in saliva using the Fourier Transform Infrared Spectroscopy technique.