Rapid and Low-Cost Detection of Human Corona Virus Using MEMS ATR-FTIR Spectroscopy

The conventional methods used for the diagnostics of viral infection are either expensive and time-consuming or not accurate enough and dependent on consumable reagents. In the presence of pandemics, a fast and reagent-free solution is needed for mass screening. Recently, the diagnosis of viral infections using infrared spectroscopy has been reported as a fast and low-cost method. In this work a fast and low-cost solution for corona viral detection using infrared spectroscopy based on a compact micro-electro-mechanical systems (MEMS) device and artificial intelligence (AI) suitable for mass deployment is presented. Among the different variants of the corona virus that can infect people, 229E is used in this study due to its low pathogeny. The MEMS ATR-FTIR device employs a 6 reflections ZnSe crystal interface working in the spectral range of 2200-7000 cm-1. The virus was propagated and maintained in a medium for long enough time then cell supernatant was collected and centrifuged. The supernatant was then transferred and titrated using plaque titration assay. Positive virus samples were prepared with a concentration of 105 PFU/mL. Positive and negative control samples were applied on the crystal surface, dried using a heating lamp and the spectrum was captured. Principal component analysis and logistic regression were used as simple AI techniques. A sensitivity of about 90 % and a specificity of about 80 % were obtained demonstrating the potential detection of the virus based on the MEMS FTIR device. © 2023 SPIE.

Anomalies of O3, CO, C2H2, H2CO, and C2H6 detected with multiple ground-based Fourier-transform infrared spectrometers and assessed with model simulation in 2020: COVID-19 lockdowns versus natural variability

Anomalies of tropospheric columns of ozone (O3), carbon monoxide (CO), acetylene (C2H2), formaldehyde (H2CO), and ethane (C2H6) are quantified during the 2020 stringent COVID-19 world-wide lockdown using multiple ground-based Fourier-transform infrared spectrometers covering urban and remote conditions. We applied an exponential smoothing forecasting approach to the data sets to estimate business-as-usual values for 2020, which are then contrasted with actual observations. The Community Atmosphere Model with chemistry (CAM-chem) is used to simulate the same gases using lockdown-adjusted and business-as-usual emissions. The role of meteorology, or natural variability, is assessed with additional CAM-chem simulations. The tropospheric column of O3 declined between March and May 2020 for most sites with a mean decrease of 9.2% ± 4.7%. Simulations reproduce these anomalies, especially under background conditions where natural variability explains up to 80% of the decline for sites in the Northern Hemisphere. While urban sites show a reduction between 1% and 12% in tropospheric CO, the remote sites do not show a significant change. Overall, CAM-chem simulations capture the magnitude of the anomalies and in many cases natural variability and lockdowns have opposite effects. We further used the long-term record of the Measurements of Pollution in the Troposphere (MOPITT) satellite instrument to capture global anomalies of CO. Reductions of CO vary highly across regions but North America and Europe registered lower values in March 2020.The absence of CO reduction in April and May, concomitant with reductions of anthropogenic emissions, is explained by a negative anomaly in the hydroxyl radical (OH) found with CAM-chem.The implications of these findings are discussed for methane (CH4), which shows a positive lifetime anomaly during the COVID-19 lockdown period. The fossil fuel combustion by-product tracer C2H2 shows a mean drop of 13.6% ± 8.3% in urban Northern Hemisphere sites due to the reduction in emissions and in some sites exacerbated by natural variability. For some sites with anthropogenic influence there is a decrease in C2H6.The simulations capture the anomalies but the main cause may be related to natural variability. H2CO declined during the stringent 2020 lockdown in all urban sites explained by reductions in emissions of precursors. Copyright: © 2023 The Author(s).

Evaluation of The Effect of Crude Extracts of Fenugreek on Resistant Isolates of Candida species (In vitro study)

Background: The recent emergence of fungal resistance strains has caused concern in medical settings. Medicinal plants continue to be viable sources of bioactive chemicals with therapeutic potential. These compounds can be extracted in different techniques using various solvents that give rise to a wide variety of extracted bioactive compounds that act as anti-fungal. The research aimed to evaluate the effect of fenugreek seed extracts on resistant isolates of Candida spp. isolated from sever COVID-19 patients.Methodology: The study was conducted from August 2021 to November 2022 at Al-Imam Al -Hussein Medical City and Al-Hayat Respiratory Diseases Units. Under a specialist's physician's supervision, severe COVID-19 cases were collected. The collected 455 sputum samples were examined directly and cultured on Sabouraud ' s Dextrose agar (SDA) media;growth colonies were distinguished and used Grams stain with the API system before the antifungal susceptibility test was performed in accordance with clinical and laboratory standards institute (CLSI 2020) by disc diffusion method to differentiate the resistance microorganism. The extraction process was conducted using the soxhlet technique (100 grams of seed powder and 800 milliliters of solvents (chloroform, methanol, and water) for eight hours. Electrical rotatory evaporators were used to evaporate the extract to get the concentrated crude extracts. FTIR and GC -MS instruments used to detection of bioactive compounds in crude fenugreek seed extracts(aqueous, methanol, and chloroform). Then, different concentrations of each extract (25, 50, 100, and 150 mg/ml) and their effect against the tested resistance study isolated were examined by well diffusion method and Minimum inhibitory concentration was measured.Results: A 455 were enrolled in this study. Patients' ages ranged from 20 to 91 years (mean 52.23, SD 15.009). This study indicated that more than half of the samples were males [(262) 57.6%] and [(193) 42.4%] were females. The FTIR and GC-MS showed the methanolic extract potent the most bioactive compounds, followed by the chloroform and water extracts. Evaluation of antimicrobial effects at 50 mg/ml, the methanolic extract showed the greatest effect, with a mean inhibition zone of 9.33 mm and a significant value of 0.01;at 100 mg/ml, the chloroform extract showed the next greatest effect, with a mean inhibition zone of 10.33 mm and a significant value of 0.005. At 150 mg/ml, the aqueous extracts showed the least effect, with a mean inhibition zone of 8.33 mm and a non-significant value of 0.024.Conclusions: Candida spp. were most frequent isolated yeast from sputum of patients with severe COVID-19. Methanol extract was the most effective anti-candida, followed by chloroform extract, and the aqueous extract was the least effective. The most effective anti-candida drug is ketoconazole.

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.

Experimental (FT-Raman, FT-IR and NMR) and theoretical (DFT) calculations, thermodynamic parameters, molecular docking and NLO (non-linear optical) properties of N-(2,6-dimethylphenyl)-1-piperazineacetamide

Theoretical and experimental studies are performed on the new organic-inorganic hybrid molecule N-(2,6-dimethylphenyl)-1-piperazineacetamide. The vibrational spectra of the molecule are characterized using FT-IR and FT-Raman in the range 4000-600 cm(-1) and 4000-100 cm(-1), respectively. Density functional theory with B3LYP/3-21G and B3LYP/cc-pVDZ basis sets is used to calculate energy, geometrical structure, and vibrational modes of stretching, bending, and torsion. The VEDA software Autodock Vina revealed a good binding is employed to calculate the detailed vibrational assignments. The theoretical and experimental vibrational data are compared to support the present study. Density functional theory is used to calculate thermodynamic parameters (heat capacity, entropy, and enthalpy) and nonlinear optical properties. The software Gaussian09W and Gaussview 6.0 are used for theoretical calculations. Molecular docking studies are carried out to investigate the effect of the titled molecule against various proteins such as SARS-CoV-2 that affect the immune system in humans. Chemical shifts are identified using carbon and proton NMR. Non-covalent interactions are studied using a reduced density gradient. The chemical reactivity and selectivity for a local reactivity site are analyzed with the help of Fukui functions.

DFT, molecular docking and ADME prediction of tenofovir drug as a promising therapeutic inhibitor of SARS-CoV-2 M-pro

In the present work, at first, DFT calculations were carried out to study the molecular structure of the tenofovir at B3LYP/MidiX level of theory and in the water as solvent. The HOMO/LUMO molecular orbitals, excitation energies and oscillator strengths of investigated drug were also calculated and presented. NBO analysis was performed to illustrate the intramolecular rehybridization and electron density delocalization. In the following, a molecular docking study was performed for screening of effective available tenofovir drug which may act as an efficient inhibitor for the SARS-CoV-2 M-pro. The binding energy value showed a good binding affinity between the tenofovir and SARS-CoV-2 Mpro with binding energy of-47.206 kcal/mol. Therefore, tenofovir can be used for possible application against the SARS-CoV-2 M-pro.

Abundance, spatial distribution, and chemical characterization of face masks on the beaches of SE Kanyakumari, India.

Personal Protective Equipment (PPE) is a new world of waste during the COVID-19 pandemic. In this baseline study, the occurrence of PPE faces masks were assessed on the eleven beaches of Kanyakumari, India concerning the abundance, spatial distribution, and chemical characterization (ATR-FTIR spectroscopy). A total of 1593 items/m2 of PPE face masks and their mean density of 0.16 PPE/m2, ranging from 0.02 to 0.54 PPE/m2 were determined in the study area. Kanyakumari beach (n = 430 items/m2) has the highest concentration of masks (26.99 %), with a mean density of 0.54 m2 due to recreational, sewage disposal, and tourism activities. This is perhaps the most important study describing the scientific data that focuses on the significant effects of communal activities and accessibility on COVID-19 PPE face mask pollution. It also highlights the need for sufficient management facilities to optimize PPE disposal.

Assessment of uncertainty estimation for measurement of ethanol concentration in COVID-19 hand sanitizer using FTIR spectroscopy

Analysis of uncertainty estimation for measurement of type and concentration of alcohol in hand sanitisers is a matter of urgency in the COVID-19 situation. FTIR spectroscopy was used to investigate hand sanitisers made in our laboratory and commercial products. An internal standard addition method was used to control the measurement quality. The absorption spectra of ethanol were found to be at 1086 and 1044 cm-1, corresponding to C-O stretching. The area under the C-O adsorptions is used to create a calibration curve, which is then used to calculate the ethanol percentage. Additional standard sample and quality control sample showed calibration curves with slopes of 0.1267 and 0.1285, respectively. The regression coefficients and residual variance of 0.0057 showed a 'best fit' with the predicted value. These parameters were used to estimate the uncertainty of six commercial products. The ethanol concentration of commercial products is measured between 71.38 and 81.54% v/v, with an estimated uncertainty of 1.14% v/v. The results showed that the ethanol content of all products differed from the label but could be used to kill bacteria and viruses. This entire process was established as a SOP for measuring alcohol concentration in hand sanitizer.

Preparation and FTIR-ATR combined with chemometrics analysis of self-emulsifying loaded sungkai extract from Peronema canecens

The use of immunomodulators is one strategy in maintaining the immune system during the Covid-19 pandemic. Sungkai leaf extract from Peronema canecens keeps the immune system in good shape. Therefore, in this study, we formulated a self-emulsifying loaded sungkai leaves extract (SE-SLE) with oleic acid and virgin coconut oil (VCO) oil phases, span 80 and tween 80 as surfactants and co-surfactants in the form of PEG-400 and PG. Chemometric analysis was conducted by observing the typical pattern in each FTIR-ATR spectra. The pattern is divided into several groups based on the wavenumber and analyzed using principal component analysis (PCA) to identify the compounds contained therein. Grouping based on chemical properties via IR spectra on SE-SLE resulted in two large groups. The results obtained are beneficial as initial information in developing and optimizing the self-nano emulsifying drug delivery system formula.Copyright © RJPT All right reserved.

Evaluation of The Effect of Crude Extracts of Fenugreek on Resistant Isolates of Candida species (In vitro study)

Background: The recent emergence of fungal resistance strains has caused concern in medical settings. Medicinal plants continue to be viable sources of bioactive chemicals with therapeutic potential. These compounds can be extracted in different techniques using various solvents that give rise to a wide variety of extracted bioactive compounds that act as anti-fungal. The research aimed to evaluate the effect of fenugreek seed extracts on resistant isolates of Candida spp. isolated from sever COVID-19 patients. Methodology: The study was conducted from August 2021 to November 2022 at Al-Imam Al-Hussein Medical City and Al-Hayat Respiratory Diseases Units. Under a specialist's physician's supervision, severe COVID-19 cases were collected. The collected 455 sputum samples were examined directly and cultured on Sabouraud's Dextrose agar (SDA) media;growth colonies were distinguished and used Grams stain with the API system before the antifungal susceptibility test was performed in accordance with clinical and laboratory standards institute (CLSI 2020) by disc diffusion method to differentiate the resistance microorganism. The extraction process was conducted using the soxhlet technique (100 grams of seed powder and 800 milliliters of solvents (chloroform, methanol, and water) for eight hours. Electrical rotatory evaporators were used to evaporate the extract to get the concentrated crude extracts. FTIR and GC-MS instruments used to detection of bioactive compounds in crude fenugreek seed extracts(aqueous, methanol, and chloroform). Then, different concentrations of each extract (25, 50, 100, and 150 mg/ml) and their effect against the tested resistance study isolated were examined by well diffusion method and Minimum inhibitory concentration was measured. Result(s): A 455 were enrolled in this study. Patients' ages ranged from 20 to 91 years (mean 52.23, SD 15.009). This study indicated that more than half of the samples were males [(262) 57.6%] and [(193) 42.4%] were females. The FTIR and GC-MS showed the methanolic extract potent the most bioactive compounds, followed by the chloroform and water extracts. Evaluation of antimicrobial effects at 50 mg/ml, the methanolic extract showed the greatest effect, with a mean inhibition zone of 9.33 mm and a significant value of 0.01;at 100 mg/ml, the chloroform extract showed the next greatest effect, with a mean inhibition zone of 10.33 mm and a significant value of 0.005. At 150 mg/ml, the aqueous extracts showed the least effect, with a mean inhibition zone of 8.33 mm and a non-significant value of 0.024. Conclusion(s): Candida spp. were most frequent isolated yeast from sputum of patients with severe COVID-19. Methanol extract was the most effective anti-candida, followed by chloroform extract, and the aqueous extract was the least effective. The most effective anti-candida drug is ketoconazole.Copyright © 2022.

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.

Development of thermosensitive hydrogel of Amphotericin-B and Lactoferrin combination-loaded PLGA-PEG-PEI nanoparticles for potential eradication of ocular fungal infections: In-vitro, ex-vivo and in-vivo studies.

The most prevalent conditions among ocular surgery and COVID-19 patients are fungal eye infections, which may cause inflammation and dry eye, and may cause ocular morbidity. Amphotericin-B eye drops are commonly used in the treatment of ocular fungal infections. Lactoferrin is an iron-binding glycoprotein with broad-spectrum antimicrobial activity and is used for the treatment of dry eye, conjunctivitis, and ocular inflammation. However, poor aqueous stability and excessive nasolacrimal duct draining impede these agens' efficiency. The aim of this study was to examine the effect of Amphotericin-B, as an antifungal against Candida albicans, Fusarium, and Aspergillus flavus, and Lactoferrin, as an anti-inflammatory and anti-dry eye, when co-loaded in triblock polymers PLGA-PEG-PEI nanoparticles embedded in P188-P407 ophthalmic thermosensitive gel. The nanoparticles were prepared by a double emulsion solvent evaporation method. The optimized formula showed particle size (177.0 ± 0.3 nm), poly-dispersity index (0.011 ± 0.01), zeta-potential (31.9 ± 0.3 mV), and entrapment% (90.9 ± 0.5) with improved ex-vivo pharmacokinetic parameters and ex-vivo trans-corneal penetrability, compared with drug solution. Confocal laser scanning revealed valuable penetration of fluoro-labeled nanoparticles. Irritation tests (Draize Test), Atomic force microscopy, cell culture and animal tests including histopathological analysis revealed superiority of the nanoparticles in reducing signs of inflammation and eradication of fungal infection in rabbits, without causing any damage to rabbit eyeballs. The nanoparticles exhibited favorable pharmacodynamic features with sustained release profile, and is neither cytotoxic nor irritating in-vitro or in-vivo. The developed formulation might provide a new and safe nanotechnology for treating eye problems, like inflammation and fungal infections.

Heat-Treated Lysozyme Hydrochloride: A Study on Its Structural Modifications and Anti-SARS-CoV-2 Activity.

Lysozyme (E.C. 3.2.1.17), an about 14 kDa protein and pI 11, widely spread in nature, is present in humans mainly in milk, saliva, and intestinal mucus as a part of innate defense mechanisms. It is endowed with antimicrobial activity due to its action as an N-acetylmuramidase, cleaving the 1-4ß glycosidic linkage in the peptidoglycan layer of Gram-positive bacteria. This antimicrobial activity is exerted only against a limited number of Gram-negative bacteria. Different action mechanisms are proposed to explain its activity against Gram-negative bacteria, viruses, and fungi. The antiviral activity prompted the study of a possible application of lysozyme in the treatment of SARS-CoV-2 infections. Among the different sources of lysozyme, the chicken egg albumen was chosen, being the richest source of this protein (c-type lysozyme, 129 amino acids). Interestingly, the activity of lysozyme hydrochloride against SARS-CoV-2 was related to the heating (to about 100 °C) of this molecule. A chemical-physical characterization was required to investigate the possible modifications of native lysozyme hydrochloride by heat treatment. The FTIR analysis of the two preparations of lysozyme hydrochloride showed appreciable differences in the secondary structure of the two protein chains. HPLC and NMR analyses, as well as the enzymatic activity determination, did not show significant modifications.

Studies towards investigation of Naphthoquinone-based scaffold with crystal structure as lead for SARS-CoV-19 management.

In this work, 1-(4-bromophenyl)-2a,8a-dihydrocyclobuta[b]naphthalene-3,8­dione (1-(4-BP)DHCBN-3,8-D) has been characterized by single crystal X-ray to get it's crystal structure with R(all data) - R1 = 0.0569, wR2 = 0.0824, 13C and 1HNMR, as well as UV-Vis and IR spectroscopy. Quantum chemical calculations via DFT were used to predict the compound structural, electronic, and vibrational properties. The molecular geometry of 1-(4-BP)DHCBN-3,8-Dwas optimized utilizing the B3LYP functional at the 6-311++G(d,p) level of theory. The Infrared spectrum has been recorded in the range of 4000-550 cm-1. The Potential Energy Distribution (PED) assignments of the vibrational modes were used to determine the geometrical dimensions, energies, and wavenumbers, and to assign basic vibrations. The UV-Vis spectra of the titled compound were recorded in the range of 200-800 nm in ACN and DMSO solvents. Additionally, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy gap and electronic transitions were determined using TD-DFT calculations, which also simulate the UV-Vis absorption spectrum. Natural Bond Orbital (NBO) analysis can be used to investigate electronic interactions and transfer reactions between donor and acceptor molecules. Temperature-dependent thermodynamic properties were also calculated. To identify the interactions in the crystal structure, Hirshfeld Surface Analysis was also assessed. The Molecular Electrostatic Potential (MEP) and Fukui functions were used to determine the nucleophilic and electrophilic sites. Additionally, the biological activities of 1-(4-BP)DHCBN-3,8-D were done using molecular docking. These results demonstrate a significant therapeutic potential for 1-(4-BP)DHCBN-3,8-D in the management of Covid-19 disorders. Molecular Dynamics Simulation was used to look at the stability of biomolecules.

COVID-19 antibody level analysis with feature selection approach.

The study presented here considers the analysis of a medical dataset for the identification of the stage of onset of COVID-19 coronavirus. These data, presented in previous work by the authors, have been subjected to extensive analysis and additional calculations. The data were obtained by analyzing blood samples of infected individuals at 1, 3, and 6 months after COVID-19 infection. Results were obtained from FTIR spectrometry experiments. The results indicate a very effective ability to identify the different states of infection, and between 1 and 6 months even perfect. Specific spectrometry wavelength ranges can also be distinguished as medical markers.

Study of the Long-Term Aging of Polypropylene-Made Disposable Surgical Masks and Filtering Facepiece Respirators.

The main purpose of this work is to contribute to understanding the mechanism of oxidation of the polymeric components of common disposable masks used during the COVID-19 pandemic to offer the chemical basis to understand their long-term behavior under typical environmental conditions. Artificial aging of representative mask layers under isothermal conditions (110 °C) or accelerated photoaging showed that all the PP-made components underwent a fast oxidation process, following the typical hydrocarbon oxidation mechanism. In particular, yellowing and the melting temperature drop are early indicators of their diffusion-limited oxidation. Morphology changes also induced a loss of mechanical properties, observable as embrittlement of the fabric fibers. Results were validated through preliminary outdoor aging of masks, which allows us to predict they will suffer fast and extensive oxidation only in the case of contemporary exposure to sunlight and relatively high environmental temperature, leading to their extensive breakdown in the form of microfiber fragments, i.e., microplastics.

Liquid biopsy on serum samples: Fourier-Transform Infrared Spectroscopy as fatality predictor for COVID-19

The fatality prediction in hyperinflammation diseases like COVID-19 is a challenge. We show here that FTIR could probe the degree of IgG glycosylation discriminating subpopulations of COVID-19 patients depending on their degree of severity. © Optica Publishing Group 2022 The Authors.

SARS-CoV-2 structures detection in artificial saliva using ATR-FTIR associated with Linear Discriminant Analysis

Here, we used ATR-FTIR platform supported by artificial intelligence algorithms to identify unique infrared vibrational modes of a pseudotyped human immunodeficiency virus type-1 (HIV-1) coupled to Spike (S) protein of SARS-CoV-2 (HIV/NanoLuc-SARS-CoV-2 pseudotype virus). © Optica Publishing Group 2022 The Authors.

SARS-CoV-2 structures detection in artificial saliva using ATR-FTIR associated with Linear Discriminant Analysis

Here, we used ATR-FTIR platform supported by artificial intelligence algorithms to identify unique infrared vibrational modes of a pseudotyped human immunodeficiency virus type-1 (HIV-1) coupled to Spike (S) protein of SARS-CoV-2 (HIV/NanoLuc-SARS-CoV-2 pseudotype virus). © Optica Publishing Group 2022 The Authors.

Liquid biopsy on serum samples: Fourier-Transform Infrared Spectroscopy as fatality predictor for COVID-19

The fatality prediction in hyperinflammation diseases like COVID-19 is a challenge. We show here that FTIR could probe the degree of IgG glycosylation discriminating subpopulations of COVID-19 patients depending on their degree of severity. © Optica Publishing Group 2022 The Authors.