1
|
Tokgoz G, Kirboga KK, Ozel F, Yucepur S, Ardahanli I, Gurbanov R. Spectrochemical and explainable artificial intelligence approaches for molecular level identification of the status of critically ill patients with COVID-19. Talanta 2024; 279:126652. [PMID: 39106646 DOI: 10.1016/j.talanta.2024.126652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 07/29/2024] [Accepted: 07/31/2024] [Indexed: 08/09/2024]
Abstract
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.
Collapse
Affiliation(s)
- Gorkem Tokgoz
- Department of Bioengineering, Faculty of Engineering, Bilecik Şeyh Edebali University, Bilecik, 11100, Turkey
| | - K Kubra Kirboga
- Department of Bioengineering, Faculty of Engineering, Bilecik Şeyh Edebali University, Bilecik, 11100, Turkey
| | - Faik Ozel
- Department of Internal Medicine, Faculty of Medicine, Bilecik Şeyh Edebali University Bilecik, 11100, Turkey
| | - Serkan Yucepur
- Department of Anesthesiology and Reanimation, Faculty of Medicine, Bilecik Şeyh Edebali University Bilecik, 11100, Turkey
| | - Isa Ardahanli
- Department of Cardiology, Faculty of Medicine, Bilecik Şeyh Edebali University Bilecik, 11100, Turkey
| | - Rafig Gurbanov
- Department of Bioengineering, Faculty of Engineering, Bilecik Şeyh Edebali University, Bilecik, 11100, Turkey; Central Research Laboratory, Bilecik Şeyh Edebali University, Bilecik, 11100, Turkey.
| |
Collapse
|
2
|
Araujo Gomes GJ, Beltrão FEDL, Fragoso WD, Lemos SG. Discrimination between Covid-19 positive and negative blood serum based on excitation-emission matrix fluorescence spectroscopy and chemometrics. Talanta 2024; 280:126788. [PMID: 39216418 DOI: 10.1016/j.talanta.2024.126788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 08/26/2024] [Accepted: 08/27/2024] [Indexed: 09/04/2024]
Abstract
The outbreak of the disease caused by the SARS-CoV-2 virus (Covid-19) has resulted in a global health emergency that has caused millions of deaths in recent years. The control of the pandemic was significantly impacted by the availability of inputs and qualified labor to correctly diagnose the population. The challenges faced by numerous countries in conducting this extensive diagnosis, utilizing methods such as RT-PCR, emphasize the necessity for alternative testing strategies that are less reliant on expensive raw materials and can be implemented on a larger scale. This paper proposes a methodology for classifying blood serum samples as either positive or negative for Covid-19 infection using excitation-emission matrix (EEM) fluorescence spectroscopy associated with multivariate analysis. The proposed methodology uses EEM spectra of samples diagnosed by the reference method (RT-PCR) to train and validate classification models. Two approaches were tested: the first using PARAFAC and the second by unfolding the excitation-emission matrices. The DD-SIMCA model performed best in the PARAFAC approach, with an error rate of 0.05, sensitivity of 0.98 and specificity of 0.96. The PLS-DA and PCA-DA models in the second approach effectively distinguished between classes. The PCA-DA model performed the best with an error rate of 0.06 and sensitivity and specificity of 0.94. Fluorescence spectroscopy was found to be effective in analyzing serum samples and obtaining discrimination models to determine if a patient is infected with SARS-CoV-2. The findings are encouraging and could aid in the development of an inexpensive and reliable auxiliary diagnostic method.
Collapse
Affiliation(s)
- Glaucio Jefferson Araujo Gomes
- Advanced Analytical Chemistry Research Group, Department of Chemistry, Federal University of Paraíba, C.P. 5093, 58051-970, João Pessoa, PB, Brazil
| | | | - Wallace Duarte Fragoso
- Advanced Analytical Chemistry Research Group, Department of Chemistry, Federal University of Paraíba, C.P. 5093, 58051-970, João Pessoa, PB, Brazil
| | - Sherlan Guimarães Lemos
- Advanced Analytical Chemistry Research Group, Department of Chemistry, Federal University of Paraíba, C.P. 5093, 58051-970, João Pessoa, PB, Brazil.
| |
Collapse
|
3
|
Morais CLM, Lima KMG, Dickinson AW, Saba T, Bongers T, Singh MN, Martin FL, Bury D. Non-invasive diagnostic test for lung cancer using biospectroscopy and variable selection techniques in saliva samples. Analyst 2024. [PMID: 39105622 DOI: 10.1039/d4an00726c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
Abstract
Lung cancer is one of the most commonly occurring malignant tumours worldwide. Although some reference methods such as X-ray, computed tomography or bronchoscope are widely used for clinical diagnosis of lung cancer, there is still a need to develop new methods for early detection of lung cancer. Especially needed are approaches that might be non-invasive and fast with high analytical precision and statistically reliable. Herein, we developed a swab "dip" test in saliva whereby swabs were analysed using attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy harnessed to principal component analysis-quadratic discriminant analysis (QDA) and variable selection techniques employing successive projections algorithm (SPA) and genetic algorithm (GA) for feature selection/extraction combined with QDA. A total of 1944 saliva samples (56 designated as lung-cancer positive and 1888 designed as controls) were obtained in a lung cancer-screening programme being undertaken in North-West England. GA-QDA models achieved, for the test set, sensitivity and specificity values of 100.0% and 99.1%, respectively. Three wavenumbers (1422 cm-1, 1546 cm-1 and 1578 cm-1) were identified using the GA-QDA model to distinguish between lung cancer and controls, including ring C-C stretching, CN adenine, Amide II [δ(NH), ν(CN)] and νs(COO-) (polysaccharides, pectin). These findings highlight the potential of using biospectroscopy associated with multivariate classification algorithms to discriminate between benign saliva samples and those with underlying lung cancer.
Collapse
Affiliation(s)
- Camilo L M Morais
- Biological Chemistry and Chemometrics, Institute of Chemistry, Federal University of Rio Grande do Norte, Natal 59072-970, Brazil
- Center for Education, Science and Technology of the Inhamuns Region, State University of Ceará, Tauá 63660-000, Brazil
| | - Kássio M G Lima
- Biological Chemistry and Chemometrics, Institute of Chemistry, Federal University of Rio Grande do Norte, Natal 59072-970, Brazil
| | - Andrew W Dickinson
- Department of Cellular Pathology, Blackpool Teaching Hospitals NHS Foundation Trust, Whinney Heys Road, Blackpool FY3 8NR, UK.
| | - Tarek Saba
- Department of Cellular Pathology, Blackpool Teaching Hospitals NHS Foundation Trust, Whinney Heys Road, Blackpool FY3 8NR, UK.
| | - Thomas Bongers
- Department of Cellular Pathology, Blackpool Teaching Hospitals NHS Foundation Trust, Whinney Heys Road, Blackpool FY3 8NR, UK.
| | - Maneesh N Singh
- Biocel UK Ltd, Hull HU10 6TS, UK
- Chesterfield Royal Hospital, Chesterfield Road, Calow, Chesterfield S44 5BL, UK
| | - Francis L Martin
- Department of Cellular Pathology, Blackpool Teaching Hospitals NHS Foundation Trust, Whinney Heys Road, Blackpool FY3 8NR, UK.
- Biocel UK Ltd, Hull HU10 6TS, UK
| | - Danielle Bury
- Department of Cellular Pathology, Blackpool Teaching Hospitals NHS Foundation Trust, Whinney Heys Road, Blackpool FY3 8NR, UK.
| |
Collapse
|
4
|
Thümmel L, Tintner-Olifiers J, Amendt J. A methodological approach to age estimation of the intra-puparial period of the forensically relevant blow fly Calliphora vicina via Fourier transform infrared spectroscopy. MEDICAL AND VETERINARY ENTOMOLOGY 2024. [PMID: 39093723 DOI: 10.1111/mve.12748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 07/19/2024] [Indexed: 08/04/2024]
Abstract
Estimating the age of immature blow flies is of great importance for forensic entomology. However, no gold-standard technique for an accurate determination of the intra-puparial age has yet been established. Fourier transform infrared (FTIR) spectroscopy is a method to (bio-)chemically characterise material based on the absorbance of electromagnetic energy by functional groups of molecules. In recent years, it also has become a powerful tool in forensic and life sciences, as it is a fast and cost-effective way to characterise all kinds of material and biological traces. This study is the first to collect developmental reference data on the changes in absorption spectra during the intra-puparial period of the forensically important blow fly Calliphora vicina Robineau-Desvoidy (Diptera: Calliphoridae). Calliphora vicina was reared at constant 20°C and 25°C and specimens were killed every other day throughout their intra-puparial development. In order to investigate which part yields the highest detectable differences in absorption spectra throughout the intra-puparial development, each specimen was divided into two different subsamples: the pupal body and the former cuticle of the third instar, that is, the puparium. Absorption spectra were collected with a FTIR spectrometer coupled to an attenuated total reflection (ATR) unit. Classification accuracies of different wavenumber regions with two machine learning models, i.e., random forests (RF) and support vector machines (SVMs), were tested. The best age predictions for both temperature settings and machine learning models were obtained by using the full spectral range from 3700 to 600 cm-1. While SVMs resulted in better accuracies for C. vicina reared at 20°C, RFs performed almost as good as SVMs for data obtained from 25°C. In terms of sample type, the pupal body gave smoother spectra and usually better classification accuracies than the puparia. This study shows that FTIR spectroscopy is a promising technique in forensic entomology to support the estimation of the minimum post-mortem interval (PMImin), by estimating the age of a given insect specimen.
Collapse
Affiliation(s)
- Luise Thümmel
- Goethe-University Frankfurt, University Hospital, Institute of Legal Medicine, Frankfurt am Main, Germany
- Department of Aquatic Ecotoxicology, Faculty of Biological Sciences, Goethe University, Frankfurt am Main, Germany
| | | | - Jens Amendt
- Goethe-University Frankfurt, University Hospital, Institute of Legal Medicine, Frankfurt am Main, Germany
| |
Collapse
|
5
|
Mishra S, Chakinala N, Sethia G, Chakinala AG, Surolia PK. Enhanced photocatalytic performance of Bi-doped TiO 2 under sunlight and UV light: mechanistic insights and comparative analysis. Photochem Photobiol Sci 2024; 23:1495-1507. [PMID: 39008233 DOI: 10.1007/s43630-024-00609-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 06/30/2024] [Indexed: 07/16/2024]
Abstract
Bismuth-doped metal oxides exhibit favourable photocatalytic features when exposed to both sunlight and UV light. In this approach, Bi0/TiO2 and Bi+3/TiO2 photocatalysts were prepared and their structural and optical properties are analysed using various characterization techniques. These developed photocatalysts were further tested for the photocatalytic elimination of Nitrobenzene in UV light and sunlight and compared with the performance of bare TiO2. The catalyst Bi+3/TiO2 performed better in UV light with 72.31% degradation, and 4.74 × 10-6 mol.litre-1.min-1 initial rate of reaction. However, when exposed to sunlight, Bi0/TiO2 outperformed with 73.85% degradation, and 4.63 × 10-6 mol.min-1 initial rate of reaction. This significant increase in photocatalytic activity of Bi0/TiO2 under sunlight could be accredited to increased light harvesting and enhanced efficiency in charge carrier separation, both of which were made possible by bismuth-induced surface plasmon resonance.
Collapse
Affiliation(s)
- Saurav Mishra
- Solar Energy Conversion and Nanomaterials Laboratory, Department of Chemistry, Manipal University Jaipur, Jaipur, Rajasthan, 303007, India
| | - Nandana Chakinala
- Chemical Reaction Engineering Laboratory, Department of Biotechnology and Chemical Engineering, Manipal University Jaipur, Jaipur, Rajasthan, 303007, India
| | - Govind Sethia
- Inorganic Material and Catalysis Division, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364002, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Anand G Chakinala
- Chemical Reaction Engineering Laboratory, Department of Biotechnology and Chemical Engineering, Manipal University Jaipur, Jaipur, Rajasthan, 303007, India.
| | - Praveen K Surolia
- Solar Energy Conversion and Nanomaterials Laboratory, Department of Chemistry, Manipal University Jaipur, Jaipur, Rajasthan, 303007, India.
| |
Collapse
|
6
|
Greco E, Gaetano AS, De Spirt A, Semeraro S, Piscitelli P, Miani A, Mecca S, Karaj S, Trombin R, Hodgton R, Barbieri P. AI-Enhanced Tools and Strategies for Airborne Disease Prevention in Cultural Heritage Sites. EPIDEMIOLOGIA 2024; 5:267-274. [PMID: 38920753 PMCID: PMC11203220 DOI: 10.3390/epidemiologia5020018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 05/29/2024] [Accepted: 06/03/2024] [Indexed: 06/27/2024] Open
Abstract
In the wake of the COVID-19 pandemic, the surveillance and safety measures of indoor Cultural Heritage sites have become a paramount concern due to the unique challenges posed by their enclosed environments and high visitor volumes. This communication explores the integration of Artificial Intelligence (AI) in enhancing epidemiological surveillance and health safety protocols in these culturally significant spaces. AI technologies, including machine learning algorithms and Internet of Things (IoT) sensors, have shown promising potential in monitoring air quality, detecting pathogens, and managing crowd dynamics to mitigate the spread of infectious diseases. We review various applications of AI that have been employed to address both direct health risks and indirect impacts such as visitor experience and preservation practices. Additionally, this paper discusses the challenges and limitations of AI deployment, such as ethical considerations, privacy issues, and financial constraints. By harnessing AI, Cultural Heritage sites can not only improve their resilience against future pandemics but also ensure the safety and well-being of visitors and staff, thus preserving these treasured sites for future generations. This exploration into AI's role in post-COVID surveillance at Cultural Heritage sites opens new frontiers in combining technology with traditional conservation and public health efforts, providing a blueprint for enhanced safety and operational efficiency in response to global health challenges.
Collapse
Affiliation(s)
- Enrico Greco
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy; (A.S.G.); (A.D.S.); (S.S.); (P.B.)
- Italian Society of Environmental Medicine (SIMA), Viale di Porta Vercellina, 9, 20123 Milan, Italy; (P.P.); (A.M.)
- National Interuniversity Consortium of Material Science and Technology (INSTM), Via G. Giusti, 9, 50121 Firenze, Italy
| | - Anastasia Serena Gaetano
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy; (A.S.G.); (A.D.S.); (S.S.); (P.B.)
| | - Alessia De Spirt
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy; (A.S.G.); (A.D.S.); (S.S.); (P.B.)
| | - Sabrina Semeraro
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy; (A.S.G.); (A.D.S.); (S.S.); (P.B.)
| | - Prisco Piscitelli
- Italian Society of Environmental Medicine (SIMA), Viale di Porta Vercellina, 9, 20123 Milan, Italy; (P.P.); (A.M.)
- Department of Experimental Medicine, University of Salento, Via Monteroni, 73100 Lecce, Italy
| | - Alessandro Miani
- Italian Society of Environmental Medicine (SIMA), Viale di Porta Vercellina, 9, 20123 Milan, Italy; (P.P.); (A.M.)
- Department of Environmental Science and Policy, University of Milan, Via Celoria 2, 20133 Milano, Italy
| | - Saverio Mecca
- Department of Architecture, University of Firenze, Via della Mattonaia 14, 50121 Firenze, Italy;
- Italian Academy of Biophilia (AIB), Lungadige Galtarossa 21, 37133 Verona, Italy;
| | - Stela Karaj
- Faculty of Social Sciences, European University of Tirana, Rruga Xhanfize Keko, 1000 Tirana, Albania;
| | - Rita Trombin
- Italian Academy of Biophilia (AIB), Lungadige Galtarossa 21, 37133 Verona, Italy;
| | - Rachel Hodgton
- International WELL Building Institute, New York, NY 10001, USA;
| | - Pierluigi Barbieri
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy; (A.S.G.); (A.D.S.); (S.S.); (P.B.)
- Italian Society of Environmental Medicine (SIMA), Viale di Porta Vercellina, 9, 20123 Milan, Italy; (P.P.); (A.M.)
| |
Collapse
|
7
|
Lee T, Mischler SE, Wolfe C. Classification of asbestos and their nonasbestiform analogues using FTIR and multivariate data analysis. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133874. [PMID: 38430588 DOI: 10.1016/j.jhazmat.2024.133874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 02/08/2024] [Accepted: 02/22/2024] [Indexed: 03/05/2024]
Abstract
This study presents a possible application of Fourier transform infrared (FTIR) spectrometry and multivariate data analysis, principal component analysis (PCA), and partial least squares-discriminant analysis (PLS-DA) for classifying asbestos and their nonasbestiform analogues. The objectives of the study are: 1) to classify six regulated asbestos types and 2) to classify between asbestos types and their nonasbestiform analogues. The respirable fraction of six regulated asbestos types and their nonasbestiform analogues were prepared in potassium bromide pellets and collected on polyvinyl chloride membrane filters for FTIR measurement. Both PCA and PLS-DA classified asbestos types and their nonasbestiform analogues on the score plots showed a very distinct clustering of samples between the serpentine (chrysotile) and amphibole groups. The PLS-DA model provided ∼95% correct prediction with a single asbestos type in the sample, although it did not provide all correct predictions for all the challenge samples due to their inherent complexity and the limited sample number. Further studies are necessary for a better prediction level in real samples and standardization of sampling and analysis procedures.
Collapse
Affiliation(s)
- Taekhee Lee
- Health Hazards Prevention Branch, Pittsburgh Mining Research Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Pittsburgh, PA 15236, USA.
| | - Steven E Mischler
- Health Hazards Prevention Branch, Pittsburgh Mining Research Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Pittsburgh, PA 15236, USA
| | - Cody Wolfe
- Health Hazards Prevention Branch, Pittsburgh Mining Research Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Pittsburgh, PA 15236, USA
| |
Collapse
|
8
|
Juchem CF, Corbellini VA, Horst A, Heidrich D. Infrared spectroscopy combined with chemometrics in transflectance mode: An alternative approach in the photodiagnosis of COVID-19 using saliva. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 312:124066. [PMID: 38428213 DOI: 10.1016/j.saa.2024.124066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 03/03/2024]
Abstract
The Coronavirus Disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has required the search for sensitive, rapid, specific, and lower-cost diagnostic methods to meet the high demand. The gold standard method of laboratory diagnosis is real-time reverse transcription polymerase chain reaction (RT-PCR). However, this method is costly and results can take time. In the literature, several studies have already described the potential of Fourier transform infrared spectroscopy (FTIR) as a tool in the biomedical field, including the diagnosis of viral infections, while being fast and inexpensive. In view of this, the objective of this study was to develop an FTIR model for the diagnosis of COVID-19. For this analysis, all private clients who had performed a face-to-face collection at the Univates Clinical Analysis Laboratory (LAC Univates) within a period of six months were invited to participate. Data from clients who agreed to participate in the study were collected, as well as nasopharyngeal secretions and a saliva sample. For the development of models, the RT-PCR result of nasopharyngeal secretions was used as a reference method. Absorptions with high discrimination (p < 0.001) between GI (28 patients, RT-PCR test positive to SARS-CoV-2 virus) and GII (173 patients who did not have the virus detected in the test) were most relevant at 3512 cm-1, 3385 cm-1 and 1321 cm-1 after 2nd derivative data transformation. To carry out the diagnostic modeling, chemometrics via FTIR and Discriminant Analysis of Orthogonal Partial Least Squares (OPLS-DA) by salivary transflectance mode with one latent variable and one orthogonal signal correction component were used. The model generated predictions with 100 % sensitivity, specificity and accuracy. With the proposed model, in a single application of an individual's saliva in the FTIR equipment, results related to the detection of SARS-CoV-2 can be obtained in a few minutes of spectral evaluation.
Collapse
Affiliation(s)
- Calebe Fernando Juchem
- Postgraduate Program in Medical Sciences, Universidade do Vale do Taquari - Univates, Lajeado, RS, Brazil
| | - Valeriano Antonio Corbellini
- Postgraduate Program in Health Promotion, Postgraduate Program in Environmental Technology, Universidade de Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil
| | - Andréa Horst
- Life Sciences Center, Universidade do Vale do Taquari - Univates, Lajeado, RS, Brazil
| | - Daiane Heidrich
- Postgraduate Program in Medical Sciences, Universidade do Vale do Taquari - Univates, Lajeado, RS, Brazil; Postgraduate Program in Biotechnology, Universidade do Vale do Taquari - Univates, Lajeado, RS, Brazil.
| |
Collapse
|
9
|
Cusack RP, Larracy R, Morrell CB, Ranjbar M, Le Roux J, Whetstone CE, Boudreau M, Poitras PF, Srinathan T, Cheng E, Howie K, Obminski C, O'Shea T, Kruisselbrink RJ, Ho T, Scheme E, Graham S, Beydaghyan G, Gavreau GM, Duong M. Machine learning enabled detection of COVID-19 pneumonia using exhaled breath analysis: a proof-of-concept study. J Breath Res 2024; 18:026009. [PMID: 38382095 DOI: 10.1088/1752-7163/ad2b6e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 02/21/2024] [Indexed: 02/23/2024]
Abstract
Detection of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) relies on real-time-reverse-transcriptase polymerase chain reaction (RT-PCR) on nasopharyngeal swabs. The false-negative rate of RT-PCR can be high when viral burden and infection is localized distally in the lower airways and lung parenchyma. An alternate safe, simple and accessible method for sampling the lower airways is needed to aid in the early and rapid diagnosis of COVID-19 pneumonia. In a prospective unblinded observational study, patients admitted with a positive RT-PCR and symptoms of SARS-CoV-2 infection were enrolled from three hospitals in Ontario, Canada. Healthy individuals or hospitalized patients with negative RT-PCR and without respiratory symptoms were enrolled into the control group. Breath samples were collected and analyzed by laser absorption spectroscopy (LAS) for volatile organic compounds (VOCs) and classified by machine learning (ML) approaches to identify unique LAS-spectra patterns (breathprints) for SARS-CoV-2. Of the 135 patients enrolled, 115 patients provided analyzable breath samples. Using LAS-breathprints to train ML classifier models resulted in an accuracy of 72.2%-81.7% in differentiating between SARS-CoV2 positive and negative groups. The performance was consistent across subgroups of different age, sex, body mass index, SARS-CoV-2 variants, time of disease onset and oxygen requirement. The overall performance was higher than compared to VOC-trained classifier model, which had an accuracy of 63%-74.7%. This study demonstrates that a ML-based breathprint model using LAS analysis of exhaled breath may be a valuable non-invasive method for studying the lower airways and detecting SARS-CoV-2 and other respiratory pathogens. The technology and the ML approach can be easily deployed in any setting with minimal training. This will greatly improve access and scalability to meet surge capacity; allow early and rapid detection to inform therapy; and offers great versatility in developing new classifier models quickly for future outbreaks.
Collapse
Affiliation(s)
- Ruth P Cusack
- Department of Respiratory Medicine, Galway University Hospital, Galway, Ireland
- School of Medicine, University of Galway, Galway, Ireland
| | - Robyn Larracy
- Institute of Biomedical Engineering, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Christian B Morrell
- Institute of Biomedical Engineering, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Maral Ranjbar
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Jennifer Le Roux
- Department of Medicine, Juravinski Hospital and Cancer Centre, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | | | | | | | - Thiviya Srinathan
- Firestone Institute for Respiratory Health, St. Joseph's Healthcare Hamilton, Hamilton, Ontario, L8N 4A6, Canada
| | - Eric Cheng
- Firestone Institute for Respiratory Health, St. Joseph's Healthcare Hamilton, Hamilton, Ontario, L8N 4A6, Canada
| | - Karen Howie
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Catie Obminski
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Tim O'Shea
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | | | - Terence Ho
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Erik Scheme
- Institute of Biomedical Engineering, University of New Brunswick, Fredericton, New Brunswick, Canada
| | | | | | - Gail M Gavreau
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - MyLinh Duong
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- Firestone Institute for Respiratory Health, St. Joseph's Healthcare Hamilton, Hamilton, Ontario, L8N 4A6, Canada
| |
Collapse
|
10
|
Hu D, Li Z, Wang R, Gao X, Mou M, Xiang N. Improved discrimination of COVID-19 based on data enhancement technology and an information balance feature selection (INB) method. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 308:123742. [PMID: 38113559 DOI: 10.1016/j.saa.2023.123742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 12/21/2023]
Abstract
The coronavirus disease (COVID-19) ravaged the world in late 2019 and posed a serious threat to human life and property destruction on a global scale. In this paper, the Wasserstein generative adversarial network with gradient penalty (WGAN-GP) method was selected for balancing the data sample, and an information balance feature selection (INB) method was first proposed to realize the accurate discrimination of COVID-19 saliva samples based on the attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy. The results of the experiment showed that the INB method obtained higher classification accuracy than the traditional feature selection methods in both the original spectrum and the second-order derivative spectrum, especially in the second-order derivative spectrum where all the indexes reached about 85 %. In addition, the combination of WGAN_GP data augmentation and the INB method resulted in an accuracy of 88.7 % for the original spectrum and even 90.6 % for the second-order derivative spectrum. According to these findings, classification research using the WGAN_GP data enhancement model may increase classification accuracy. Additionally, the ability to successfully separate COVID-19 indicates that the INB method to identify spectral data features is a workable method, which also offers a fresh viewpoint on feature selection.
Collapse
Affiliation(s)
- Dean Hu
- College of Information Science and Engineering, Northeastern University, Shenyang 110819, China; Hebei Key Laboratory of Micro-Nano Precision Optical Sensing and Measurement Technology, Qinhuangdao 066004, China
| | - Zhigang Li
- College of Information Science and Engineering, Northeastern University, Shenyang 110819, China; Hebei Key Laboratory of Micro-Nano Precision Optical Sensing and Measurement Technology, Qinhuangdao 066004, China.
| | - Ruixin Wang
- College of Information Science and Engineering, Northeastern University, Shenyang 110819, China; Hebei Key Laboratory of Micro-Nano Precision Optical Sensing and Measurement Technology, Qinhuangdao 066004, China
| | - Xuning Gao
- College of Medicine and Biological Information Engineering, Northeastern University, Shenyang 110819, China
| | - Mingkai Mou
- College of Information Science and Engineering, Northeastern University, Shenyang 110819, China; Hebei Key Laboratory of Micro-Nano Precision Optical Sensing and Measurement Technology, Qinhuangdao 066004, China
| | - Nan Xiang
- College of Information Science and Engineering, Northeastern University, Shenyang 110819, China; Hebei Key Laboratory of Micro-Nano Precision Optical Sensing and Measurement Technology, Qinhuangdao 066004, China
| |
Collapse
|
11
|
Brun BF, Nascimento MHC, Dias PAC, Marcarini WD, Singh MN, Filgueiras PR, Vassallo PF, Romão W, Mill JG, Martin FL, Barauna VG. Fast screening using attenuated total reflectance- fourier transform infrared (ATR-FTIR) spectroscopy of patients based on D-dimer threshold value. Talanta 2024; 269:125482. [PMID: 38042146 DOI: 10.1016/j.talanta.2023.125482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 12/04/2023]
Abstract
Attenuated Total Reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy is an emerging technology in the medical field. Blood D-dimer was initially studied as a marker of the activation of coagulation and fibrinolysis. It is mainly used as a potential diagnosis screening test for pulmonary embolism or deep vein thrombosis but was recently associated with COVID-19 severity. This study aimed to evaluate the use of ATR-FTIR spectroscopy with machine learning to classify plasma D-dimer concentrations. The plasma ATR-FTIR spectra from 100 patients were studied through principal component analysis (PCA) and two supervised approaches: genetic algorithm with linear discriminant analysis (GA-LDA) and partial least squares with linear discriminant (PLS-DA). The spectra were truncated to the fingerprint region (1800-1000 cm-1). The GA-LDA method effectively classified patients according to D-dimer cutoff (≤0.5 μg/mL and >0.5 μg/mL) with 87.5 % specificity and 100 % sensitivity on the training set, and 85.7 % specificity, and 95.6 % sensitivity on the test set. Thus, we demonstrate that ATR-FTIR spectroscopy might be an important additional tool for classifying patients according to D-dimer values. ATR-FTIR spectral analyses associated with clinical evidence can contribute to a faster and more accurate medical diagnosis, reduce patient morbidity, and save resources and demand for professionals.
Collapse
Affiliation(s)
- Bruna F Brun
- Department of Physiological Science, Federal University of Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Marcia H C Nascimento
- Exact Sciences Center, Federal University of Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Pedro A C Dias
- Department of Physiological Science, Federal University of Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Wena D Marcarini
- Department of Physiological Science, Federal University of Espírito Santo, Vitória, Espírito Santo, Brazil; Centro Universitário Vale do CRICARÉ, São Matheus, Espírito Santo, Brazil
| | - Maneesh N Singh
- Biocel UK Ltd, Hull, HU10 6TS, UK; Chesterfield Royal Hospital, Chesterfield Road, Calow, Chesterfield, S44 5BL, UK
| | - Paulo R Filgueiras
- Exact Sciences Center, Federal University of Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Paula F Vassallo
- Clinical Hospital, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Wanderson Romão
- Exact Sciences Center, Federal University of Espírito Santo, Vitória, Espírito Santo, Brazil; Federal Institute of Education Science and Technology of Espírito Santo, Vila Velha, Espírito Santo, Brazil
| | - José G Mill
- Department of Physiological Science, Federal University of Espírito Santo, Vitória, Espírito Santo, Brazil
| | - Francis L Martin
- Biocel UK Ltd, Hull, HU10 6TS, UK; Department of Cellular Pathology, Blackpool Teaching Hospitals NHS Foundation Trust, Whinney Heys Road, Blackpool, FY3 8NR, UK
| | - Valerio G Barauna
- Department of Physiological Science, Federal University of Espírito Santo, Vitória, Espírito Santo, Brazil.
| |
Collapse
|
12
|
Othman AM, Sabry YM, Khalil D, Bourouina T. Single Infrared Spectrum Enables Simultaneous Identification of (Bio)Chemical Nature and Particle Size of Microorganisms and Synthetic Microplastic Beads. Anal Chem 2023; 95:17826-17833. [PMID: 37982148 DOI: 10.1021/acs.analchem.3c03919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
Populations of nearly identical chemical and biological microparticles include the synthetic microbeads used in cosmetic, biomedical, agri-food, and pharmaceutical industries as well as the class of living microorganisms such as yeast, pollen, and biological cells. Herein, we identify simultaneously the size and chemical nature of spherical microparticle populations with diameters larger than 1 μm. Our analysis relies on the extraction of both physical and chemical signatures from the same optical spectrum recorded using attenuated total reflection (ATR)-Fourier transform infrared (FTIR) spectroscopy. These signatures are the spectral resonances caused by the microparticles, which depend on their size and the absorption peaks revealing their chemical nature. We validate the method first on separated and mixed groups of spherical microplastic particles of two different diameters, where the method is used to calculate the diameter of the microspherical particles. Then, we apply the method to correctly identify and measure the diameter of Saccharomyces cerevisiae yeast cells. Theoretical simulations to help in understanding the effect of size distribution and dispersion support our results.
Collapse
Affiliation(s)
- Ahmed M Othman
- Université Gustave Eiffel, ESYCOM CNRS UMR 9007, Noisy-le-Grand ESIEE Paris, Noisy-le-Grand 93162, France
- Si-Ware Systems, 3 Khalid Ibn Al-Waleed St., Heliopolis, Cairo 11361, Egypt
| | - Yasser M Sabry
- Si-Ware Systems, 3 Khalid Ibn Al-Waleed St., Heliopolis, Cairo 11361, Egypt
- Faculty of Engineering, Ain-Shams University, 1 Elsarayat St. Abbassia, Cairo 11535, Egypt
| | - Diaa Khalil
- Si-Ware Systems, 3 Khalid Ibn Al-Waleed St., Heliopolis, Cairo 11361, Egypt
- Faculty of Engineering, Ain-Shams University, 1 Elsarayat St. Abbassia, Cairo 11535, Egypt
| | - Tarik Bourouina
- Université Gustave Eiffel, ESYCOM CNRS UMR 9007, Noisy-le-Grand ESIEE Paris, Noisy-le-Grand 93162, France
- Si-Ware Systems, 3 Khalid Ibn Al-Waleed St., Heliopolis, Cairo 11361, Egypt
- CINTRA, IRL 3288 CNRS-NTU-THALES, Nanyang Technological University, 637553 Singapore
| |
Collapse
|
13
|
Condino F, Crocco MC, Pirritano D, Petrone A, Del Giudice F, Guzzi R. A Linear Predictor Based on FTIR Spectral Biomarkers Improves Disease Diagnosis Classification: An Application to Multiple Sclerosis. J Pers Med 2023; 13:1596. [PMID: 38003911 PMCID: PMC10672539 DOI: 10.3390/jpm13111596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/02/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Multiple sclerosis (MS) is a neurodegenerative disease of the central nervous system that can lead to long-term disability. The diagnosis of MS is not simple and requires many instrumental and clinical tests. Sampling easily collected biofluids using spectroscopic approaches is becoming of increasing interest in the medical field to integrate and improve diagnostic procedures. Here we present a statistical approach where we combine a number of spectral biomarkers derived from the ATR-FTIR spectra of blood plasma samples of healthy control subjects and MS patients, to obtain a linear predictor useful for discriminating between the two groups of individuals. This predictor provides a simple tool in which the contribution of different molecular components is summarized and, as a result, the sensitivity (80%) and specificity (93%) of the identification are significantly improved compared to those obtained with typical classification algorithms. The strategy proposed can be very helpful when applied to the diagnosis of diseases whose presence is reflected in a minimal way in the analyzed biofluids (blood and its derivatives), as it is for MS as well as for other neurological disorders.
Collapse
Affiliation(s)
- Francesca Condino
- Department of Economics, Statistics and Finance ”Giovanni Anania”, University of Calabria, 87036 Rende, Italy;
| | - Maria Caterina Crocco
- STAR Research Infrastructure, University of Calabria, 87036 Rende, Italy;
- Department of Physics, Molecular Biophysics Laboratory, University of Calabria, 87036 Rende, Italy
| | - Domenico Pirritano
- SOC Neurologia, Azienda Ospedaliero-Universitaria Renato Dulbecco, 88100 Catanzaro, Italy;
- UOC Neurologia, Azienda Ospedaliera dell’Annunziata, 87100 Cosenza, Italy; (A.P.); (F.D.G.)
| | - Alfredo Petrone
- UOC Neurologia, Azienda Ospedaliera dell’Annunziata, 87100 Cosenza, Italy; (A.P.); (F.D.G.)
| | - Francesco Del Giudice
- UOC Neurologia, Azienda Ospedaliera dell’Annunziata, 87100 Cosenza, Italy; (A.P.); (F.D.G.)
- SOC Neurologia, Ospedale Jazzolino, Azienda Ospedaliera Provinciale, 89900 Vibo Valentia, Italy
| | - Rita Guzzi
- STAR Research Infrastructure, University of Calabria, 87036 Rende, Italy;
- CNR-NANOTEC, Department of Physics, University of Calabria, 87036 Rende, Italy
| |
Collapse
|
14
|
Xing Y, Li J, Yang J, Li J, Pang W, Martin FL, Xu L. Application of spectrochemical analysis with chemometrics to profile biochemical alterations in nanoplastic-exposed HepG 2 cells. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 336:122309. [PMID: 37543068 DOI: 10.1016/j.envpol.2023.122309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/07/2023]
Abstract
Humans are routinely exposed to nanoplastics (NPs) in various ways, and this exposure presents a significant health risk. Nevertheless, there remain gaps in our knowledge, particularly in the mechanisms of toxicity of NPs with different surface charges at very low environmental concentrations. Herein, a spectrochemical approach was used to profile the cytotoxicity of NPs with different surface charges in HepG2 cells. It was found that all three NPs can cause some biomolecular alterations in cells, affecting cellular lipids, proteins, amino acids, and genetic material. Of these, PS and PS-COOH led to a non-linear dose-response, which may be related to a biphasic dose-response, whereas PS-NH2 led to a linear dose-response with a gradual increase in toxicity with increasing exposure concentration. In addition, the spectroscopic results showed that surface modifications led to cellular biochemical changes and caused adverse biological effects, with PS-NH2 exhibiting higher toxicity compared to PS or PS-COOH along with an inhibition of cell proliferation. Surprisingly PS-COOH, although considered the least toxic NP, appears to cause DNA damage. Overall, the toxic effects of different surface-modified NPs in cells were detected for the first time by applying spectrochemical techniques, and these findings provide important data towards understanding the emerging widespread environmental pollution of NPs and their effects on humans.
Collapse
Affiliation(s)
- Yu Xing
- Institute of Quality Standard and Testing Technology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Jing Li
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographical Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jingjing Yang
- Department of Biochemistry and Molecular Biology, School of Medicine & Holistic Integrative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Junyi Li
- National University of Singapore (Suzhou) Research Institute, Suzhou, 215128, China
| | - Weiyi Pang
- School of Public Health, Guilin Medical University, Guilin, 541199, China
| | - Francis L Martin
- Biocel Ltd, Hull, HU10 7TS, UK; Department of Cellular Pathology, Blackpool Teaching Hospitals NHS Foundation Trust, Whinney Heys Road, Blackpool, FY3 8NR, UK
| | - Li Xu
- Institute of Quality Standard and Testing Technology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| |
Collapse
|
15
|
Martin FL, Morais CLM, Dickinson AW, Saba T, Bongers T, Singh MN, Bury D. Point-of-Care Disease Screening in Primary Care Using Saliva: A Biospectroscopy Approach for Lung Cancer and Prostate Cancer. J Pers Med 2023; 13:1533. [PMID: 38003848 PMCID: PMC10672293 DOI: 10.3390/jpm13111533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 11/26/2023] Open
Abstract
Saliva is a largely unexplored liquid biopsy that can be readily obtained noninvasively. Not dissimilar to blood plasma or serum, it contains a vast array of bioconstituents that may be associated with the absence or presence of a disease condition. Given its ease of access, the use of saliva is potentially ideal in a point-of-care screening or diagnostic test. Herein, we developed a swab "dip" test in saliva obtained from consenting patients participating in a lung cancer-screening programme being undertaken in north-west England. A total of 998 saliva samples (31 designated as lung-cancer positive and 17 as prostate-cancer positive) were taken in the order in which they entered the clinic (i.e., there was no selection of participants) during the course of this prospective screening programme. Samples (sterile Copan blue rayon swabs dipped in saliva) were analysed using attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy. In addition to unsupervised classification on resultant infrared (IR) spectra using principal component analysis (PCA), a range of feature selection/extraction algorithms were tested. Following preprocessing, the data were split between training (70% of samples, 22 lung-cancer positive versus 664 other) and test (30% of samples, 9 lung-cancer positive versus 284 other) sets. The training set was used for model construction and the test set was used for validation. The best model was the PCA-quadratic discriminant analysis (QDA) algorithm. This PCA-QDA model was built using 8 PCs (90.4% of explained variance) and resulted in 93% accuracy for training and 91% for testing, with clinical sensitivity at 100% and specificity at 91%. Additionally, for prostate cancer patients amongst the male cohort (n = 585), following preprocessing, the data were split between training (70% of samples, 12 prostate-cancer positive versus 399 other) and test (30% of samples, 5 prostate-cancer positive versus 171 other) sets. A PCA-QDA model, again the best model, was built using 5 PCs (84.2% of explained variance) and resulted in 97% accuracy for training and 93% for testing, with clinical sensitivity at 100% and specificity at 92%. These results point to a powerful new approach towards the capability to screen large cohorts of individuals in primary care settings for underlying malignant disease.
Collapse
Affiliation(s)
- Francis L. Martin
- Biocel UK Ltd., Hull HU10 6TS, UK;
- Department of Cellular Pathology, Blackpool Teaching Hospitals NHS Foundation Trust, Whinney Heys Road, Blackpool FY3 8NR, UK; (A.W.D.); (T.S.); (T.B.)
| | - Camilo L. M. Morais
- Center for Education, Science and Technology of the Inhamuns Region, State University of Ceará, Tauá 63660-000, Brazil;
| | - Andrew W. Dickinson
- Department of Cellular Pathology, Blackpool Teaching Hospitals NHS Foundation Trust, Whinney Heys Road, Blackpool FY3 8NR, UK; (A.W.D.); (T.S.); (T.B.)
| | - Tarek Saba
- Department of Cellular Pathology, Blackpool Teaching Hospitals NHS Foundation Trust, Whinney Heys Road, Blackpool FY3 8NR, UK; (A.W.D.); (T.S.); (T.B.)
| | - Thomas Bongers
- Department of Cellular Pathology, Blackpool Teaching Hospitals NHS Foundation Trust, Whinney Heys Road, Blackpool FY3 8NR, UK; (A.W.D.); (T.S.); (T.B.)
| | - Maneesh N. Singh
- Biocel UK Ltd., Hull HU10 6TS, UK;
- Chesterfield Royal Hospital, Chesterfield Road, Calow, Chesterfield S44 5BL, UK
| | | |
Collapse
|
16
|
Martin FL. Translating Biospectroscopy Techniques to Clinical Settings: A New Paradigm in Point-of-Care Screening and/or Diagnostics. J Pers Med 2023; 13:1511. [PMID: 37888122 PMCID: PMC10608143 DOI: 10.3390/jpm13101511] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/11/2023] [Accepted: 10/18/2023] [Indexed: 10/28/2023] Open
Abstract
As healthcare tools increasingly move towards a more digital and computational format, there is an increasing need for sensor-based technologies that allow for rapid screening and/or diagnostics [...].
Collapse
Affiliation(s)
- Francis L Martin
- Department of Cellular Pathology, Blackpool Teaching Hospitals NHS Foundation Trust, Whinney Heys Road, Blackpool FY3 8NR, UK
| |
Collapse
|
17
|
Hackshaw KV, Yao S, Bao H, de Lamo Castellvi S, Aziz R, Nuguri SM, Yu L, Osuna-Diaz MM, Brode WM, Sebastian KR, Giusti MM, Rodriguez-Saona L. Metabolic Fingerprinting for the Diagnosis of Clinically Similar Long COVID and Fibromyalgia Using a Portable FT-MIR Spectroscopic Combined with Chemometrics. Biomedicines 2023; 11:2704. [PMID: 37893078 PMCID: PMC10604557 DOI: 10.3390/biomedicines11102704] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/01/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
Post Acute Sequelae of SARS-CoV-2 infection (PASC or Long COVID) is characterized by lingering symptomatology post-initial COVID-19 illness that is often debilitating. It is seen in up to 30-40% of individuals post-infection. Patients with Long COVID (LC) suffer from dysautonomia, malaise, fatigue, and pain, amongst a multitude of other symptoms. Fibromyalgia (FM) is a chronic musculoskeletal pain disorder that often leads to functional disability and severe impairment of quality of life. LC and FM share several clinical features, including pain that often makes them indistinguishable. The aim of this study is to develop a metabolic fingerprinting approach using portable Fourier-transform mid-infrared (FT-MIR) spectroscopic techniques to diagnose clinically similar LC and FM. Blood samples were obtained from LC (n = 50) and FM (n = 50) patients and stored on conventional bloodspot protein saver cards. A semi-permeable membrane filtration approach was used to extract the blood samples, and spectral data were collected using a portable FT-MIR spectrometer. Through the deconvolution analysis of the spectral data, a distinct spectral marker at 1565 cm-1 was identified based on a statistically significant analysis, only present in FM patients. This IR band has been linked to the presence of side chains of glutamate. An OPLS-DA algorithm created using the spectral region 1500 to 1700 cm-1 enabled the classification of the spectra into their corresponding classes (Rcv > 0.96) with 100% accuracy and specificity. This high-throughput approach allows unique metabolic signatures associated with LC and FM to be identified, allowing these conditions to be distinguished and implemented for in-clinic diagnostics, which is crucial to guide future therapeutic approaches.
Collapse
Affiliation(s)
- Kevin V. Hackshaw
- Department of Internal Medicine, Division of Rheumatology, Dell Medical School, The University of Texas, 1601 Trinity St., Austin, TX 78712, USA
| | - Siyu Yao
- Department of Food Science and Technology, The Ohio State University, Columbus, OH 43210, USA; (S.Y.); (H.B.); (S.d.L.C.); (S.M.N.); (M.M.G.); (L.R.-S.)
| | - Haona Bao
- Department of Food Science and Technology, The Ohio State University, Columbus, OH 43210, USA; (S.Y.); (H.B.); (S.d.L.C.); (S.M.N.); (M.M.G.); (L.R.-S.)
| | - Silvia de Lamo Castellvi
- Department of Food Science and Technology, The Ohio State University, Columbus, OH 43210, USA; (S.Y.); (H.B.); (S.d.L.C.); (S.M.N.); (M.M.G.); (L.R.-S.)
- Campus Sescelades, Departament d’Enginyeria Química, Universitat Rovira i Virgili, Av. Països Catalans 26, 43007 Tarragona, Spain
| | - Rija Aziz
- Department of Internal Medicine, Dell Medical School, The University of Texas, 1601 Trinity St., Austin, TX 78712, USA; (R.A.); (M.M.O.-D.); (W.M.B.); (K.R.S.)
| | - Shreya Madhav Nuguri
- Department of Food Science and Technology, The Ohio State University, Columbus, OH 43210, USA; (S.Y.); (H.B.); (S.d.L.C.); (S.M.N.); (M.M.G.); (L.R.-S.)
| | - Lianbo Yu
- Center of Biostatistics and Bioinformatics, The Ohio State University, Columbus, OH 43210, USA;
| | - Michelle M. Osuna-Diaz
- Department of Internal Medicine, Dell Medical School, The University of Texas, 1601 Trinity St., Austin, TX 78712, USA; (R.A.); (M.M.O.-D.); (W.M.B.); (K.R.S.)
| | - W. Michael Brode
- Department of Internal Medicine, Dell Medical School, The University of Texas, 1601 Trinity St., Austin, TX 78712, USA; (R.A.); (M.M.O.-D.); (W.M.B.); (K.R.S.)
| | - Katherine R. Sebastian
- Department of Internal Medicine, Dell Medical School, The University of Texas, 1601 Trinity St., Austin, TX 78712, USA; (R.A.); (M.M.O.-D.); (W.M.B.); (K.R.S.)
| | - M. Monica Giusti
- Department of Food Science and Technology, The Ohio State University, Columbus, OH 43210, USA; (S.Y.); (H.B.); (S.d.L.C.); (S.M.N.); (M.M.G.); (L.R.-S.)
| | - Luis Rodriguez-Saona
- Department of Food Science and Technology, The Ohio State University, Columbus, OH 43210, USA; (S.Y.); (H.B.); (S.d.L.C.); (S.M.N.); (M.M.G.); (L.R.-S.)
| |
Collapse
|
18
|
Goulart ACC, Zângaro RA, Carvalho HC, Lednev IK, Silveira L. Diagnosing COVID-19 in nasopharyngeal secretion through Raman spectroscopy: a feasibility study. Lasers Med Sci 2023; 38:210. [PMID: 37698685 DOI: 10.1007/s10103-023-03871-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 08/29/2023] [Indexed: 09/13/2023]
Abstract
Since the beginning of the COVID-19 pandemic, the scientific community has sought to develop fast and accurate techniques for detecting the SARS-CoV-2 virus. Raman spectroscopy is a promising technique for diagnosing COVID-19 through serum samples. In the present study, the diagnosis of COVID-19 through nasopharyngeal secretion has been proposed. Raman spectra from nasopharyngeal secretion samples (15 Control, negative and 12 COVID-19, positive, assayed by immunofluorescence antigen test) were obtained in triplicate in a dispersive Raman spectrometer (830 nm, 350 mW), accounting for a total of 80 spectra. Using principal component analysis (PCA) the main spectral differences between the Control and COVID-19 samples were attributed to N and S proteins from the virus in the COVID-19 group. Features assigned to mucin (serine, threonine and proline amino acids) were observed in the Control group. A binary model based on partial least squares discriminant analysis (PLS-DA) differentiated COVID-19 versus Control samples with accuracy of 91%, sensitivity of 80% and specificity of 100%. Raman spectroscopy has a great potential for becoming a technique of choice for rapid and label-free evaluation of nasopharyngeal secretion for COVID-19 diagnosis.
Collapse
Affiliation(s)
| | - Renato Amaro Zângaro
- Universidade Anhembi Morumbi - UAM, R. Casa do Ator, 275, São Paulo, SP, 04546-001, Brazil
- Center for Innovation, Technology and Education - CITÉ, Parque Tecnológico de São José dos Campos, Estr. Dr. Altino Bondensan, 500, São José dos Campos, SP, 12247-016, Brazil
| | - Henrique Cunha Carvalho
- Center for Innovation, Technology and Education - CITÉ, Parque Tecnológico de São José dos Campos, Estr. Dr. Altino Bondensan, 500, São José dos Campos, SP, 12247-016, Brazil
- Federal University of Technology - Paraná - UTFPR, Via Marginal Rosalina Maria dos Santos, 1233, Bl. B, Campo Mourão, PR, 87301-899, Brazil
| | - Igor K Lednev
- Department of Chemistry, University at Albany - SUNY, 1400 Washington Av., Albany, NY, 12222, USA
| | - Landulfo Silveira
- Universidade Anhembi Morumbi - UAM, R. Casa do Ator, 275, São Paulo, SP, 04546-001, Brazil.
- Center for Innovation, Technology and Education - CITÉ, Parque Tecnológico de São José dos Campos, Estr. Dr. Altino Bondensan, 500, São José dos Campos, SP, 12247-016, Brazil.
| |
Collapse
|
19
|
Ryu SR, Suh J, Kim H, Shin K. The surface and internal features of pubic hair: A comparative study with those of scalp hair. Exp Dermatol 2023; 32:1509-1520. [PMID: 37317710 DOI: 10.1111/exd.14855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 05/14/2023] [Accepted: 05/20/2023] [Indexed: 06/16/2023]
Abstract
Although pubic hair has been a subject of public interest, little is known about its structure or characteristics beyond its curly and coarse appearance. In this study, we investigated the surface and internal features of pubic hair from Korean males and compared them to those of scalp hair from the same donors. Our findings indicate that the cuticle layer of pubic hair has a greater number of scales than that of scalp hair, resulting in a thicker cuticle layer overall. Fourier-transform infrared (FT-IR) spectroscopy analysis showed that the protein in the cortex layer of pubic hair was less affected by exposure to urine or ammonia than the protein in the cortex layer of scalp hair. This suggests that the cuticle layer of pubic hair, which is thicker and composed of more scales, acts as a physical barrier that protects the hair's internal structure. Furthermore, we observed that the secondary and tertiary structures of keratin in the pubic hair cuticle layer are essentially different from those in scalp hair. Based on these findings, we hypothesize that the thickened cuticle layer in pubic hair may have evolved as a defence mechanism against chemical damage from urine, urea and ammonia.
Collapse
Affiliation(s)
- Soo Ryeon Ryu
- Department of Chemistry, Institute of Biological Interfaces, Sogang University, Seoul, Republic of Korea
| | - Jungwoo Suh
- Department of Chemistry, Institute of Biological Interfaces, Sogang University, Seoul, Republic of Korea
| | - Hyeyoung Kim
- Department of Chemistry, Institute of Biological Interfaces, Sogang University, Seoul, Republic of Korea
| | - Kwanwoo Shin
- Department of Chemistry, Institute of Biological Interfaces, Sogang University, Seoul, Republic of Korea
| |
Collapse
|
20
|
John P, Vasa NJ, Zam A. Optical Biosensors for the Diagnosis of COVID-19 and Other Viruses-A Review. Diagnostics (Basel) 2023; 13:2418. [PMID: 37510162 PMCID: PMC10378272 DOI: 10.3390/diagnostics13142418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 07/12/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
The sudden outbreak of the COVID-19 pandemic led to a huge concern globally because of the astounding increase in mortality rates worldwide. The medical imaging computed tomography technique, whole-genome sequencing, and electron microscopy are the methods generally used for the screening and identification of the SARS-CoV-2 virus. The main aim of this review is to emphasize the capabilities of various optical techniques to facilitate not only the timely and effective diagnosis of the virus but also to apply its potential toward therapy in the field of virology. This review paper categorizes the potential optical biosensors into the three main categories, spectroscopic-, nanomaterial-, and interferometry-based approaches, used for detecting various types of viruses, including SARS-CoV-2. Various classifications of spectroscopic techniques such as Raman spectroscopy, near-infrared spectroscopy, and fluorescence spectroscopy are discussed in the first part. The second aspect highlights advances related to nanomaterial-based optical biosensors, while the third part describes various optical interferometric biosensors used for the detection of viruses. The tremendous progress made by lab-on-a-chip technology in conjunction with smartphones for improving the point-of-care and portability features of the optical biosensors is also discussed. Finally, the review discusses the emergence of artificial intelligence and its applications in the field of bio-photonics and medical imaging for the diagnosis of COVID-19. The review concludes by providing insights into the future perspectives of optical techniques in the effective diagnosis of viruses.
Collapse
Affiliation(s)
- Pauline John
- Division of Engineering, New York University Abu Dhabi (NYUAD), Abu Dhabi 129188, United Arab Emirates
| | - Nilesh J Vasa
- Department of Engineering Design, Indian Institute of Technology Madras, Chennai 600036, India
| | - Azhar Zam
- Division of Engineering, New York University Abu Dhabi (NYUAD), Abu Dhabi 129188, United Arab Emirates
- Tandon School of Engineering, New York University, Brooklyn, NY 11201, USA
| |
Collapse
|
21
|
Martin FL, Dickinson AW, Saba T, Bongers T, Singh MN, Bury D. ATR-FTIR Spectroscopy with Chemometrics for Analysis of Saliva Samples Obtained in a Lung-Cancer-Screening Programme: Application of Swabs as a Paradigm for High Throughput in a Clinical Setting. J Pers Med 2023; 13:1039. [PMID: 37511652 PMCID: PMC10381591 DOI: 10.3390/jpm13071039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/18/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
There is an increasing need for inexpensive and rapid screening tests in point-of-care clinical oncology settings. Herein, we develop a swab "dip" test in saliva obtained from consenting patients participating in a lung-cancer-screening programme being undertaken in North West England. In a pilot study, a total of 211 saliva samples (n = 170 benign, 41 designated cancer-positive) were randomly taken during the course of this prospective lung-cancer-screening programme. The samples (sterile Copan blue rayon swabs dipped in saliva) were analysed using attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy. An exploratory analysis using principal component analysis (PCA,) with or without linear discriminant analysis (LDA), was then undertaken. Three pairwise comparisons were undertaken including: (1) benign vs. cancer following swab analysis; (2) benign vs. cancer following swab analysis with the subtraction of dry swab spectra; and (3) benign vs. cancer following swab analysis with the subtraction of wet swab spectra. Consistent and remarkably similar patterns of clustering for the benign control vs. cancer categories, irrespective of whether the swab plus saliva sample was analysed or whether there was a subtraction of wet or dry swab spectra, was observed. In each case, MANOVA demonstrated that this segregation of categories is highly significant. A k-NN (using three nearest neighbours) machine-learning algorithm also showed that the specificity (90%) and sensitivity (75%) are consistent for each pairwise comparison. In detailed analyses, the swab as a substrate did not alter the level of spectral discrimination between benign control vs. cancer saliva samples. These results demonstrate a novel swab "dip" test using saliva as a biofluid that is highly applicable to be rolled out into a larger lung-cancer-screening programme.
Collapse
Affiliation(s)
- Francis L Martin
- Biocel UK Ltd., Hull HU10 6TS, UK
- Department of Cellular Pathology, Blackpool Teaching Hospitals NHS Foundation Trust, Whinney Heys Road, Blackpool FY3 8NR, UK
| | - Andrew W Dickinson
- Department of Cellular Pathology, Blackpool Teaching Hospitals NHS Foundation Trust, Whinney Heys Road, Blackpool FY3 8NR, UK
| | - Tarek Saba
- Department of Cellular Pathology, Blackpool Teaching Hospitals NHS Foundation Trust, Whinney Heys Road, Blackpool FY3 8NR, UK
| | - Thomas Bongers
- Department of Cellular Pathology, Blackpool Teaching Hospitals NHS Foundation Trust, Whinney Heys Road, Blackpool FY3 8NR, UK
| | - Maneesh N Singh
- Biocel UK Ltd., Hull HU10 6TS, UK
- Chesterfield Royal Hospital, Chesterfield Road, Calow, Chesterfield S44 5BL, UK
| | | |
Collapse
|
22
|
Shen Q, Hossain F, Fang C, Shu T, Zhang X, Law JLM, Logan M, Houghton M, Tyrrell DL, Joyce MA, Serpe MJ. Bovine Serum Albumin-Protected Gold Nanoclusters for Sensing of SARS-CoV-2 Antibodies and Virus. ACS APPLIED MATERIALS & INTERFACES 2023. [PMID: 37314985 DOI: 10.1021/acsami.3c03705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
An approach to assess severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (and past infection) was developed. For virus detection, the SARS-CoV-2 virus nucleocapsid protein (NP) was targeted. To detect the NP, antibodies were immobilized on magnetic beads to capture the NPs, which were subsequently detected using rabbit anti-SARS-CoV-2 nucleocapsid antibodies and alkaline phosphatase (AP)-conjugated anti-rabbit antibodies. A similar approach was used to assess SARS-CoV-2-neutralizing antibody levels by capturing spike receptor-binding domain (RBD)-specific antibodies utilizing RBD protein-modified magnetic beads and detecting them using AP-conjugated anti-human IgG antibodies. The sensing mechanism for both assays is based on cysteamine etching-induced fluorescence quenching of bovine serum albumin-protected gold nanoclusters where cysteamine is generated in proportion to the amount of either SARS-CoV-2 virus or anti-SARS-CoV-2 receptor-binding domain-specific immunoglobulin antibodies (anti-RBD IgG antibodies). High sensitivity can be achieved in 5 h 15 min for the anti-RBD IgG antibody detection and 6 h 15 min for virus detection, although the assay can be run in "rapid" mode, which takes 1 h 45 min for the anti-RBD IgG antibody detection and 3 h 15 min for the virus. By spiking the anti-RBD IgG antibodies and virus in serum and saliva, we demonstrate that the assay can detect the anti-RBD IgG antibodies with a limit of detection (LOD) of 4.0 and 2.0 ng/mL in serum and saliva, respectively. For the virus, we can achieve an LOD of 8.5 × 105 RNA copies/mL and 8.8 × 105 RNA copies/mL in serum and saliva, respectively. Interestingly, this assay can be easily modified to detect myriad analytes of interest.
Collapse
Affiliation(s)
- Qiming Shen
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Faisal Hossain
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
- Department of Chemistry, Faculty of Science, University of Chittagong, Chattogram 4331, Bangladesh
| | - Changhao Fang
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Tong Shu
- Guangdong Laboratory of Artificial Intelligence and Digital Economy (SZ), Shenzhen Key Laboratory for Nano-Biosensing Technology, Research Center for Biosensor and Nanotheranostic, International Health Science Innovation Center, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, Guangdong 518060, P. R. China
| | - Xueji Zhang
- Guangdong Laboratory of Artificial Intelligence and Digital Economy (SZ), Shenzhen Key Laboratory for Nano-Biosensing Technology, Research Center for Biosensor and Nanotheranostic, International Health Science Innovation Center, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, Guangdong 518060, P. R. China
| | - John Lok Man Law
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
- Li Ka Shing Institute of Virology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Michael Logan
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
- Li Ka Shing Institute of Virology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Michael Houghton
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
- Li Ka Shing Institute of Virology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - D Lorne Tyrrell
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
- Li Ka Shing Institute of Virology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Michael A Joyce
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
- Li Ka Shing Institute of Virology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Michael J Serpe
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| |
Collapse
|
23
|
Delrue C, De Bruyne S, Speeckaert MM. Unlocking the Diagnostic Potential of Saliva: A Comprehensive Review of Infrared Spectroscopy and Its Applications in Salivary Analysis. J Pers Med 2023; 13:907. [PMID: 37373896 DOI: 10.3390/jpm13060907] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/20/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
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.
Collapse
Affiliation(s)
- Charlotte Delrue
- Department of Nephrology, Ghent University Hospital, 9000 Ghent, Belgium
| | - Sander De Bruyne
- Department of Clinical Biology, Ghent University Hospital, 9000 Ghent, Belgium
| | - Marijn M Speeckaert
- Department of Nephrology, Ghent University Hospital, 9000 Ghent, Belgium
- Research Foundation-Flanders (FWO), 1000 Brussels, Belgium
| |
Collapse
|
24
|
Alkhuder K. Fourier-transform infrared spectroscopy: a universal optical sensing technique with auspicious application prospects in the diagnosis and management of autoimmune diseases. Photodiagnosis Photodyn Ther 2023; 42:103606. [PMID: 37187270 DOI: 10.1016/j.pdpdt.2023.103606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/27/2023] [Accepted: 05/09/2023] [Indexed: 05/17/2023]
Abstract
Autoimmune diseases (AIDs) are poorly understood clinical syndromes due to breakdown of immune tolerance towards specific types of self-antigens. They are generally associated with an inflammatory response mediated by lymphocytes T, autoantibodies or both. Ultimately, chronic inflammation culminates in tissue damages and clinical manifestations. AIDs affect 5% of the world population, and they represent the main cause of fatality in young to middle-aged females. In addition, the chronic nature of AIDs has a devastating impact on the patient's quality of life. It also places a heavy burden on the health care system. Establishing a rapid and accurate diagnosis is considered vital for an ideal medical management of these autoimmune disorders. However, for some AIDs, this task might be challenging. Vibrational spectroscopies, and more particularly Fourier-transform infrared (FTIR) spectroscopy, have emerged as universal analytical techniques with promising applications in the diagnosis of various types of malignancies and metabolic and infectious diseases. The high sensitivity of these optical sensing techniques and their minimal requirements for test reagents qualify them to be ideal analytical techniques. The aim of the current review is to explore the potential applications of FTIR spectroscopy in the diagnosis and management of most common AIDs. It also aims to demonstrate how this technique has contributed to deciphering the biochemical and physiopathological aspects of these chronic inflammatory diseases. The advantages that can be offered by this optical sensing technique over the traditional and gold standard methods used in the diagnosis of these autoimmune disorders have also been extensively discussed.
Collapse
|
25
|
Shang Y, Yang F, Ngando FJ, Zhang X, Feng Y, Ren L, Guo Y. Development of Forensically Important Sarcophaga peregrina (Diptera: Sarcophagidae) and Intra-Puparial Age Estimation Utilizing Multiple Methods at Constant and Fluctuating Temperatures. Animals (Basel) 2023; 13:ani13101607. [PMID: 37238037 DOI: 10.3390/ani13101607] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/29/2023] [Accepted: 05/02/2023] [Indexed: 05/28/2023] Open
Abstract
Sarcophaga peregrina (Robineau-Desvoidy, 1830) has the potential to estimate the minimum postmortem interval (PMImin). Development data and intra-puparial age estimation are significant for PMImin estimation. Previous research has focused on constant temperatures, although fluctuating temperatures are a more real scenario at a crime scene. The current study examined the growth patterns of S. peregrina under constant (25.75 °C) and fluctuating temperatures (18-36 °C; 22-30 °C). Furthermore, differentially expressed genes, attenuated total reflectance Fourier-transform infrared spectroscopy, and cuticular hydrocarbons of S. peregrina during the intra-puparial period were used to estimate age. The results indicated that S. peregrina at fluctuating temperatures took longer to develop and had a lower pupariation rate, eclosion rate, and pupal weight than the group at constant temperatures did. Moreover, we found that six DEG expression profiles and ATR-FTIR technology, CHCs detection methods, and chemometrics can potentially estimate the intra-puparial age of S. peregrina at both constant and fluctuating temperatures. The findings of the study support the use of S. peregrina for PMImin estimation and encourage the use of entomological evidence in forensic practice.
Collapse
Affiliation(s)
- Yanjie Shang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha 410013, China
| | - Fengqin Yang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha 410013, China
| | - Fernand Jocelin Ngando
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha 410013, China
| | - Xiangyan Zhang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha 410013, China
| | - Yakai Feng
- Department of Forensic Medicine, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi 830017, China
| | - Lipin Ren
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha 410013, China
| | - Yadong Guo
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha 410013, China
| |
Collapse
|
26
|
Oliveira SW, Cardoso-Sousa L, Georjutti RP, Shimizu JF, Silva S, Caixeta DC, Guevara-Vega M, Cunha TM, Carneiro MG, Goulart LR, Jardim ACG, Sabino-Silva R. Salivary Detection of Zika Virus Infection Using ATR-FTIR Spectroscopy Coupled with Machine Learning Algorithms and Univariate Analysis: A Proof-of-Concept Animal Study. Diagnostics (Basel) 2023; 13:diagnostics13081443. [PMID: 37189545 DOI: 10.3390/diagnostics13081443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/08/2023] [Accepted: 03/11/2023] [Indexed: 05/17/2023] Open
Abstract
Zika virus (ZIKV) diagnosis is currently performed through an invasive, painful, and costly procedure using molecular biology. Consequently, the search for a non-invasive, more cost-effective, reagent-free, and sustainable method for ZIKV diagnosis is of great relevance. It is critical to prepare a global strategy for the next ZIKV outbreak given its devastating consequences, particularly in pregnant women. Attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy has been used to discriminate systemic diseases using saliva; however, the salivary diagnostic application in viral diseases is unknown. To test this hypothesis, we intradermally challenged interferon-gamma gene knockout C57/BL6 mice with ZIKV (50 µL,105 FFU, n = 7) or vehicle (50 µL, n = 8). Saliva samples were collected on day three (due to the peak of viremia) and the spleen was also harvested. Changes in the salivary spectral profile were analyzed by Student's t test (p < 0.05), multivariate analysis, and the diagnostic capacity by ROC curve. ZIKV infection was confirmed by real-time PCR of the spleen sample. The infrared spectroscopy coupled with univariate analysis suggested the vibrational mode at 1547 cm-1 as a potential candidate to discriminate ZIKV and control salivary samples. Three PCs explained 93.2% of the cumulative variance in PCA analysis and the spectrochemical analysis with LDA achieved an accuracy of 93.3%, with a specificity of 87.5% and sensitivity of 100%. The LDA-SVM analysis showed 100% discrimination between both classes. Our results suggest that ATR-FTIR applied to saliva might have high accuracy in ZIKV diagnosis with potential as a non-invasive and cost-effective diagnostic tool.
Collapse
Affiliation(s)
- Stephanie Wutke Oliveira
- Innovation Center in Salivary Diagnostic and Nanobiotechnology, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia 38408-100, Brazil
| | - Leia Cardoso-Sousa
- Innovation Center in Salivary Diagnostic and Nanobiotechnology, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia 38408-100, Brazil
| | - Renata Pereira Georjutti
- Innovation Center in Salivary Diagnostic and Nanobiotechnology, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia 38408-100, Brazil
- College of Dentistry, University Center of Triangle (UNITRI), Uberlandia 38411-869, Brazil
| | - Jacqueline Farinha Shimizu
- Laboratory of Antiviral Research, Institute of Biomedical Science, Federal University of Uberlandia, Uberlandia 38408-100, Brazil
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University, São José do Rio Preto 15054-000, Brazil
| | - Suely Silva
- Laboratory of Antiviral Research, Institute of Biomedical Science, Federal University of Uberlandia, Uberlandia 38408-100, Brazil
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University, São José do Rio Preto 15054-000, Brazil
| | - Douglas Carvalho Caixeta
- Innovation Center in Salivary Diagnostic and Nanobiotechnology, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia 38408-100, Brazil
| | - Marco Guevara-Vega
- Innovation Center in Salivary Diagnostic and Nanobiotechnology, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia 38408-100, Brazil
| | - Thúlio Marquez Cunha
- School of Medicine, Federal University of Uberlandia (UFU), Uberlandia 38408-100, Brazil
| | | | - Luiz Ricardo Goulart
- Institute of Biotechnology, Federal University of Uberlandia, Uberlandia 38408-100, Brazil
| | - Ana Carolina Gomes Jardim
- Laboratory of Antiviral Research, Institute of Biomedical Science, Federal University of Uberlandia, Uberlandia 38408-100, Brazil
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University, São José do Rio Preto 15054-000, Brazil
| | - Robinson Sabino-Silva
- Innovation Center in Salivary Diagnostic and Nanobiotechnology, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia 38408-100, Brazil
| |
Collapse
|
27
|
Liang Q, Chan YC, Toscano J, Bjorkman KK, Leinwand LA, Parker R, Nozik ES, Nesbitt DJ, Ye J. Breath analysis by ultra-sensitive broadband laser spectroscopy detects SARS-CoV-2 infection. J Breath Res 2023; 17:10.1088/1752-7163/acc6e4. [PMID: 37016829 PMCID: PMC10930087 DOI: 10.1088/1752-7163/acc6e4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 03/23/2023] [Indexed: 04/06/2023]
Abstract
Rapid testing is essential to fighting pandemics such as coronavirus disease 2019 (COVID-19), the disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Exhaled human breath contains multiple volatile molecules providing powerful potential for non-invasive diagnosis of diverse medical conditions. We investigated breath detection of SARS-CoV-2 infection using cavity-enhanced direct frequency comb spectroscopy (CE-DFCS), a state-of-the-art laser spectroscopic technique capable of a real-time massive collection of broadband molecular absorption features at ro-vibrational quantum state resolution and at parts-per-trillion volume detection sensitivity. Using a total of 170 individual breath samples (83 positive and 87 negative with SARS-CoV-2 based on reverse transcription polymerase chain reaction tests), we report excellent discrimination capability for SARS-CoV-2 infection with an area under the receiver-operating-characteristics curve of 0.849(4). Our results support the development of CE-DFCS as an alternative, rapid, non-invasive test for COVID-19 and highlight its remarkable potential for optical diagnoses of diverse biological conditions and disease states.
Collapse
Affiliation(s)
- Qizhong Liang
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, United States of America
- Department of Physics, University of Colorado, Boulder, CO 80309, United States of America
| | - Ya-Chu Chan
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, United States of America
- Department of Chemistry, University of Colorado, Boulder, CO 80309, United States of America
| | - Jutta Toscano
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, United States of America
- Department of Physics, University of Colorado, Boulder, CO 80309, United States of America
- Present address: Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Kristen K Bjorkman
- BioFrontiers Institute, University of Colorado, Boulder, CO 80303, United States of America
| | - Leslie A Leinwand
- BioFrontiers Institute, University of Colorado, Boulder, CO 80303, United States of America
- Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder, CO 80303, United States of America
| | - Roy Parker
- BioFrontiers Institute, University of Colorado, Boulder, CO 80303, United States of America
- Department of Biochemistry and HHMI, University of Colorado, Boulder, CO 80303, United States of America
| | - Eva S Nozik
- Cardiovascular Pulmonary Research Laboratories, Departments of Pediatrics and Medicine, and Division of Pediatric Critical Care Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States of America
| | - David J Nesbitt
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, United States of America
- Department of Physics, University of Colorado, Boulder, CO 80309, United States of America
- Department of Chemistry, University of Colorado, Boulder, CO 80309, United States of America
| | - Jun Ye
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, United States of America
- Department of Physics, University of Colorado, Boulder, CO 80309, United States of America
| |
Collapse
|
28
|
Bian Y, Li Y, Liu K, He H, Feng Y, Yu X. Dendric nanostructures for SARS-CoV-2 proteins detection based on surface enhanced infrared absorption spectroscopy. JOURNAL OF BIOPHOTONICS 2023; 16:e202200277. [PMID: 36419375 DOI: 10.1002/jbio.202200277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/10/2022] [Accepted: 11/21/2022] [Indexed: 06/16/2023]
Abstract
Infrared spectroscopy is a non-destructive and rapid characterization tool that can distinguish different viral proteins by spectral details. However, traditional infrared spectroscopy has insufficient absorption signal intensity contrast when measuring low-concentration samples. In this work, surface enhanced infrared absorption (SEIRA) spectroscopy is proposed by deploying a novel nanostructure array as SEIRA substrates. An array of gold dendric nanostructures are designed and fabricated with a precision resonance control to achieve surface enhancement covering a broadband molecular "finger-print" region. The spectral positions of the multiple resonances accurately correspond to the characteristic absorption peaks of the SARS-CoV-2 proteins. An approach for SARS-CoV-2 protein detection based on SEIRA spectroscopy is then proposed. A low concentration detection of 40 μg/ml diluted SARS-CoV-2 nucleocapsid protein is experimentally demonstrated and the enhancement factor (EF) achieved is in good agreement with simulation results. The SEIRA methodology based on broadband resonance nanostructure design provides a systematic approach for sensitive, non-destructive and rapid protein molecular detection, which could be extended to various kind of molecular characterization and biomedical diagnostics.
Collapse
Affiliation(s)
- Yupei Bian
- School of Instrumentation and Optoelectronic Engineering, Beihang University, Beijing, China
| | - Yang Li
- School of Instrumentation and Optoelectronic Engineering, Beihang University, Beijing, China
| | - Kang Liu
- School of Instrumentation and Optoelectronic Engineering, Beihang University, Beijing, China
| | - Houshu He
- School of Instrumentation and Optoelectronic Engineering, Beihang University, Beijing, China
| | - Yingmei Feng
- Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Xia Yu
- School of Instrumentation and Optoelectronic Engineering, Beihang University, Beijing, China
| |
Collapse
|
29
|
Campanella B, Legnaioli S, Onor M, Benedetti E, Bramanti E. The Role of the Preanalytical Step for Human Saliva Analysis via Vibrational Spectroscopy. Metabolites 2023; 13:metabo13030393. [PMID: 36984834 PMCID: PMC10055013 DOI: 10.3390/metabo13030393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 02/27/2023] [Accepted: 03/06/2023] [Indexed: 03/10/2023] Open
Abstract
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.
Collapse
Affiliation(s)
- Beatrice Campanella
- Institute of Chemistry of Organometallic Compounds (ICCOM), Consiglio Nazionale delle Ricerche(CNR), 56124 Pisa, Italy
| | - Stefano Legnaioli
- Institute of Chemistry of Organometallic Compounds (ICCOM), Consiglio Nazionale delle Ricerche(CNR), 56124 Pisa, Italy
| | - Massimo Onor
- Institute of Chemistry of Organometallic Compounds (ICCOM), Consiglio Nazionale delle Ricerche(CNR), 56124 Pisa, Italy
| | - Edoardo Benedetti
- Hematology Unit of Azienda Ospedaliero Universitaria Pisana (AOUP), 56100 Pisa, Italy
| | - Emilia Bramanti
- Institute of Chemistry of Organometallic Compounds (ICCOM), Consiglio Nazionale delle Ricerche(CNR), 56124 Pisa, Italy
- Correspondence: ; Tel.: +39-050-315-2293
| |
Collapse
|
30
|
Karas BY, Sitnikova VE, Nosenko TN, Dedkov VG, Arsentieva NA, Gavrilenko NV, Moiseev IS, Totolian AA, Kajava AV, Uspenskaya MV. ATR-FTIR spectrum analysis of plasma samples for rapid identification of recovered COVID-19 individuals. JOURNAL OF BIOPHOTONICS 2023:e202200166. [PMID: 36869427 DOI: 10.1002/jbio.202200166] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 01/08/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
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.
Collapse
Affiliation(s)
- Boris Y Karas
- Institute BioEngineering, ITMO University, St. Petersburg, Russia
| | - Vera E Sitnikova
- Institute BioEngineering, ITMO University, St. Petersburg, Russia
| | | | - Vladimir G Dedkov
- Saint-Petersburg Pasteur Institute, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, St. Petersburg, Russia
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Natalia A Arsentieva
- Saint-Petersburg Pasteur Institute, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, St. Petersburg, Russia
| | - Natalia V Gavrilenko
- Raisa Gorbacheva memorial Research Institute for Pediatric Oncology, Hematology and Transplantation, Pavlov First Saint Petersburg State Medical University, St. Petersburg, Russia
| | - Ivan S Moiseev
- Raisa Gorbacheva memorial Research Institute for Pediatric Oncology, Hematology and Transplantation, Pavlov First Saint Petersburg State Medical University, St. Petersburg, Russia
| | - Areg A Totolian
- Saint-Petersburg Pasteur Institute, Federal Service on Consumers' Rights Protection and Human Well-Being Surveillance, St. Petersburg, Russia
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier, Université Montpellier, Montpellier, France
| | | |
Collapse
|
31
|
Ceccon DM, Amaral PHR, Andrade LM, da Silva MIN, Andrade LAF, Moraes TFS, Bagno FF, Rocha RP, de Almeida Marques DP, Ferreira GM, Lourenço AA, Ribeiro ÁL, Coelho-dos-Reis JGA, da Fonseca FG, Gonzalez JC. New, fast, and precise method of COVID-19 detection in nasopharyngeal and tracheal aspirate samples combining optical spectroscopy and machine learning. Braz J Microbiol 2023:10.1007/s42770-023-00923-5. [PMID: 36854899 PMCID: PMC9974055 DOI: 10.1007/s42770-023-00923-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 02/07/2023] [Indexed: 03/02/2023] Open
Abstract
Fast, precise, and low-cost diagnostic testing to identify persons infected with SARS-CoV-2 virus is pivotal to control the global pandemic of COVID-19 that began in late 2019. The gold standard method of diagnostic recommended is the RT-qPCR test. However, this method is not universally available, and is time-consuming and requires specialized personnel, as well as sophisticated laboratories. Currently, machine learning is a useful predictive tool for biomedical applications, being able to classify data from diverse nature. Relying on the artificial intelligence learning process, spectroscopic data from nasopharyngeal swab and tracheal aspirate samples can be used to leverage characteristic patterns and nuances in healthy and infected body fluids, which allows to identify infection regardless of symptoms or any other clinical or laboratorial tests. Hence, when new measurements are performed on samples of unknown status and the corresponding data is submitted to such an algorithm, it will be possible to predict whether the source individual is infected or not. This work presents a new methodology for rapid and precise label-free diagnosing of SARS-CoV-2 infection in clinical samples, which combines spectroscopic data acquisition and analysis via artificial intelligence algorithms. Our results show an accuracy of 85% for detection of SARS-CoV-2 in nasopharyngeal swab samples collected from asymptomatic patients or with mild symptoms, as well as an accuracy of 97% in tracheal aspirate samples collected from critically ill COVID-19 patients under mechanical ventilation. Moreover, the acquisition and processing of the information is fast, simple, and cheaper than traditional approaches, suggesting this methodology as a promising tool for biomedical diagnosis vis-à-vis the emerging and re-emerging viral SARS-CoV-2 variant threats in the future.
Collapse
Affiliation(s)
- Denny M. Ceccon
- Departamento de Física, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, Campus Pampulha 31270-901, Belo Horizonte, Minas Gerais 6627 Brazil
| | - Paulo Henrique R. Amaral
- Departamento de Física, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, Campus Pampulha 31270-901, Belo Horizonte, Minas Gerais 6627 Brazil
| | - Lídia M. Andrade
- Departamento de Física, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, Campus Pampulha 31270-901, Belo Horizonte, Minas Gerais 6627 Brazil
| | - Maria I. N. da Silva
- Departamento de Física, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, Campus Pampulha 31270-901, Belo Horizonte, Minas Gerais 6627 Brazil
| | - Luis A. F. Andrade
- Centro de Tecnologia Em Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Thais F. S. Moraes
- Laboratório de Virologia Básica E Aplicada, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Flavia F. Bagno
- Centro de Tecnologia Em Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Raissa P. Rocha
- Centro de Tecnologia Em Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Geovane Marques Ferreira
- Laboratório de Virologia Básica E Aplicada, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Alice Aparecida Lourenço
- Laboratório de Virologia Básica E Aplicada, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ágata Lopes Ribeiro
- Laboratório de Virologia Básica E Aplicada, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Jordana G. A. Coelho-dos-Reis
- Laboratório de Virologia Básica E Aplicada, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Flavio G. da Fonseca
- Centro de Tecnologia Em Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil ,Laboratório de Virologia Básica E Aplicada, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - J. C. Gonzalez
- Departamento de Física, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, Campus Pampulha 31270-901, Belo Horizonte, Minas Gerais 6627 Brazil
| |
Collapse
|
32
|
Yan HH, Huang M, Zhu F, Cheng R, Wen S, Li LT, Liu H, Zhao XH, Luo FK, Huang CZ, Wang J. Two-Dimensional Analysis Method for Highly Sensitive Detection of Dual MicroRNAs in Breast Cancer Cells. Anal Chem 2023; 95:3968-3975. [PMID: 36792543 DOI: 10.1021/acs.analchem.2c03479] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Multiple biomarker detection is crucial for early clinical diagnosis, and it is significant to achieve the simultaneous detection of multiple biomarkers with the same nanomaterial. In this work, the hairpin DNA strands were selectively modified on the surface of gold nanorods (AuNRs) to construct two kinds of nanoprobes by rational design. When in the presence of dual microRNAs, AuNRs were assembled to form end-to-end (ETE) and side-by-side (SBS) dimers. Compared with a single AuNR, the dark-field scattering intensity and red color percentage variation of dimers were extremely distinguished, which could be developed for dual microRNA detection by combining the red color percentage and scattering intensity with the data processing method of principal component analysis to construct a two-dimensional analysis method. Especially, the fraction of AuNR dimers presented a linear relationship with the amount of microRNAs. Based on this, microRNA-21 and microRNA Let-7a in breast cancer cells were detected with the detection limits of 1.72 and 0.53 fM, respectively. This method not only achieved the sensitive detection of dual microRNAs in human serum but also realized the high-resolution intracellular imaging, which developed a new way for the oriented assembly of nanomaterials and biological detection in living cells.
Collapse
Affiliation(s)
- Hui Hong Yan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Chongqing Science and Technology Bureau, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Min Huang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Chongqing Science and Technology Bureau, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Fu Zhu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Chongqing Science and Technology Bureau, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Ru Cheng
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Chongqing Science and Technology Bureau, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | | | - Liang Tong Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Chongqing Science and Technology Bureau, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Hui Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Chongqing Science and Technology Bureau, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Xiao Hui Zhao
- The Ninth People's Hospital of Chongqing, No. 69 Jialing Village, Beibei District, Chongqing 400700, China
| | - Fu Kang Luo
- The Ninth People's Hospital of Chongqing, No. 69 Jialing Village, Beibei District, Chongqing 400700, China
| | - Cheng Zhi Huang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Chongqing Science and Technology Bureau, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| | - Jian Wang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Chongqing Science and Technology Bureau, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, P. R. China
| |
Collapse
|
33
|
Abbasian MH, Mahmanzar M, Rahimian K, Mahdavi B, Tokhanbigli S, Moradi B, Sisakht MM, Deng Y. Global landscape of SARS-CoV-2 mutations and conserved regions. J Transl Med 2023; 21:152. [PMID: 36841805 PMCID: PMC9958328 DOI: 10.1186/s12967-023-03996-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/15/2023] [Indexed: 02/27/2023] Open
Abstract
BACKGROUND At the end of December 2019, a novel strain of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) disease (COVID-19) has been identified in Wuhan, a central city in China, and then spread to every corner of the globe. As of October 8, 2022, the total number of COVID-19 cases had reached over 621 million worldwide, with more than 6.56 million confirmed deaths. Since SARS-CoV-2 genome sequences change due to mutation and recombination, it is pivotal to surveil emerging variants and monitor changes for improving pandemic management. METHODS 10,287,271 SARS-CoV-2 genome sequence samples were downloaded in FASTA format from the GISAID databases from February 24, 2020, to April 2022. Python programming language (version 3.8.0) software was utilized to process FASTA files to identify variants and sequence conservation. The NCBI RefSeq SARS-CoV-2 genome (accession no. NC_045512.2) was considered as the reference sequence. RESULTS Six mutations had more than 50% frequency in global SARS-CoV-2. These mutations include the P323L (99.3%) in NSP12, D614G (97.6) in S, the T492I (70.4) in NSP4, R203M (62.8%) in N, T60A (61.4%) in Orf9b, and P1228L (50.0%) in NSP3. In the SARS-CoV-2 genome, no mutation was observed in more than 90% of nsp11, nsp7, nsp10, nsp9, nsp8, and nsp16 regions. On the other hand, N, nsp3, S, nsp4, nsp12, and M had the maximum rate of mutations. In the S protein, the highest mutation frequency was observed in aa 508-635(0.77%) and aa 381-508 (0.43%). The highest frequency of mutation was observed in aa 66-88 (2.19%), aa 7-14, and aa 164-246 (2.92%) in M, E, and N proteins, respectively. CONCLUSION Therefore, monitoring SARS-CoV-2 proteomic changes and detecting hot spots mutations and conserved regions could be applied to improve the SARS-CoV-2 diagnostic efficiency and design safe and effective vaccines against emerging variants.
Collapse
Affiliation(s)
- Mohammad Hadi Abbasian
- Department of Medical Genetics, National Institute for Genetic Engineering and Biotechnology, Tehran, Iran
| | - Mohammadamin Mahmanzar
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, 96813, USA
| | - Karim Rahimian
- Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Bahar Mahdavi
- Department of Computer Science, Tarbiat Modares University, Tehran, Iran
| | - Samaneh Tokhanbigli
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, Australia
| | - Bahman Moradi
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Mahsa Mollapour Sisakht
- Department of Biochemistry, Erasmus University Medical Center, 2040, 3000 CA, Rotterdam, The Netherlands
| | - Youping Deng
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI, 96813, USA.
| |
Collapse
|
34
|
Weerasuriya DRK, Hiniduma K, Bhakta S, Nigro LM, Posada LF, Tan H, Suib SL, Kremer R, Rusling JF. COVID-19 Detection Using a 3D-Printed Micropipette Tip and a Smartphone. ACS Sens 2023; 8:848-857. [PMID: 36689276 PMCID: PMC9888406 DOI: 10.1021/acssensors.2c02516] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/27/2022] [Indexed: 01/24/2023]
Abstract
The COVID-19 pandemic has caused over 7 million deaths worldwide and over 1 million deaths in the US as of October 15, 2022. Virus testing lags behind the level or availability necessary for pandemic events like COVID-19, especially in resource-limited settings. Here, we report a low cost, mix-and-read COVID-19 assay using a synthetic SARS-CoV-2 sensor, imaged and processed using a smartphone. The assay was optimized for saliva and employs 3D-printed micropipette tips with a layer of monoclonal anti-SARS-CoV-2 inside the tip. A polymeric sensor for SARS-CoV-2 spike (S) protein (COVRs) synthesized as a thin film on silica nanoparticles provides 3,3',5-5'-tetramethylbenzidine responsive color detection using streptavidin-poly-horseradish peroxidase (ST-poly-HRP) with 400 HRP labels per molecule. COVRs were engineered with an NHS-PEG4-biotin coating to reduce nonspecific binding and provide affinity for ST-poly-HRP labels. COVRs binds to S-proteins with binding strengths and capacities much larger than salivary proteins in 10% artificial saliva-0.01%-Triton X-100 (as virus deactivator). A limit of detection (LOD) of 200 TCID50/mL (TCID50 = tissue culture infectious dose 50%) in artificial saliva was obtained using the Color Grab smartphone app and verified using ImageJ. Viral load values obtained in 10% pooled human saliva spiked with inactivated SARS-COV-2 virus gave excellent correlation with viral loads obtained from qPCR (p = 0.0003, r = 0.99).
Collapse
Affiliation(s)
- D. Randil K. Weerasuriya
- Department of Chemistry, University of
Connecticut, Storrs, Connecticut06269-3060, United
States
| | - Keshani Hiniduma
- Department of Chemistry, University of
Connecticut, Storrs, Connecticut06269-3060, United
States
| | - Snehasis Bhakta
- Department of Chemistry, Cooch Behar
College, Cooch Behar, WB736101, India
| | - Lisa M. Nigro
- Microbial Analysis, Resources and Services, Center for
Open Research Resources and Equipment, University of
Connecticut, Storrs, Connecticut06269-3032, United
States
- Institute for Systems Genomics,
University of Connecticut, Storrs, Connecticut06269-3003,
United States
| | - Luisa F. Posada
- Department of Chemistry, University of
Connecticut, Storrs, Connecticut06269-3060, United
States
| | - Haiyan Tan
- Innovation Partnership Building at UConn Tech Park,
University of Connecticut, Storrs, Connecticut06269,
United States
| | - Steven L. Suib
- Department of Chemistry, University of
Connecticut, Storrs, Connecticut06269-3060, United
States
- Institute of Materials Science,
University of Connecticut, Storrs, Connecticut06269-3136,
United States
| | - Richard Kremer
- Department of Medicine, McGill University Health
Centre, 1001 Decarie Blvd., Montreal, QCH4A,
Canada
| | - James F. Rusling
- Department of Chemistry, University of
Connecticut, Storrs, Connecticut06269-3060, United
States
- Institute of Materials Science,
University of Connecticut, Storrs, Connecticut06269-3136,
United States
- Department of Surgery and Neag Cancer Center,
Uconn Health, Farmington, Connecticut06030, United
States
- School of Chemistry, National University
of Ireland at Galway, GalwayH91 TK33, Ireland
| |
Collapse
|
35
|
Tessaro L, Mutz YDS, Andrade JCD, Aquino A, Belem NKR, Silva FGS, Conte-Junior CA. ATR-FTIR spectroscopy and chemometrics as a quick and simple alternative for discrimination of SARS-CoV-2 infected food of animal origin. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 285:121883. [PMID: 36126622 PMCID: PMC9473138 DOI: 10.1016/j.saa.2022.121883] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/29/2022] [Accepted: 09/10/2022] [Indexed: 06/15/2023]
Abstract
Alternative routes such as virus transmission or cross-contamination by food have been suggested, due to reported cases of SARS-CoV-2 in frozen chicken wings and fish or seafood. Delay in routine testing due to the dependence on the PCR technique as the standard method leads to greater virus dissemination. Therefore, alternative detection methods such as FTIR spectroscopy emerge as an option. Here, we demonstrate a fast (3 min), simple and reagent-free methodology using attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy for discrimination of food (chicken, beef and fish) contaminated with the SARS-CoV-2 virus. From the IR spectra of the samples, the "bio-fingerprint" (800 - 1900 cm-1) was selected to investigate the distinctions caused by the virus contamination. Exploratory analysis of the spectra, using Principal Component of Analysis (PCA), indicated the differentiation in the data due to the presence of single bands, marked as contamination from nucleic acids including viral RNA. Furthermore, the partial least squares discriminant analysis (PLS-DA) classification model allowed for discrimination of each matrix in its pure form and its contaminated counterpart with sensitivity, specificity and accuracy of 100 %. Therefore, this study indicates that the use of ATR-FTIR can offer a fast and low cost and not require chemical reagents and with minimal sample preparation to detect the SARS-CoV-2 virus in food matrices, ensuring food safety and non-dissemination by consumers.
Collapse
Affiliation(s)
- Leticia Tessaro
- Analytical and Molecular Laboratorial Center (CLAn), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ 21941-909, Brazil; COVID-19 Research Group, Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Cidade Universitária, Rio de Janeiro, RJ 21941-598, Brazil; Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), University City, Rio de Janeiro, RJ, Brazil; Nanotechnology Network, Carlos Chagas Filho Research Support Foundation of the State of Rio de Janeiro (FAPERJ), Rio de Janeiro, RJ, Brazil; Post-Graduation Program of Chemistry (PGQu), Institute of chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), University City, Rio de Janeiro, RJ, Brazil.
| | - Yhan da Silva Mutz
- Analytical and Molecular Laboratorial Center (CLAn), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ 21941-909, Brazil; COVID-19 Research Group, Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Cidade Universitária, Rio de Janeiro, RJ 21941-598, Brazil; Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), University City, Rio de Janeiro, RJ, Brazil; Nanotechnology Network, Carlos Chagas Filho Research Support Foundation of the State of Rio de Janeiro (FAPERJ), Rio de Janeiro, RJ, Brazil
| | - Jelmir Craveiro de Andrade
- Analytical and Molecular Laboratorial Center (CLAn), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ 21941-909, Brazil; COVID-19 Research Group, Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Cidade Universitária, Rio de Janeiro, RJ 21941-598, Brazil; Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), University City, Rio de Janeiro, RJ, Brazil; Nanotechnology Network, Carlos Chagas Filho Research Support Foundation of the State of Rio de Janeiro (FAPERJ), Rio de Janeiro, RJ, Brazil; Post-Graduation Program of Chemistry (PGQu), Institute of chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), University City, Rio de Janeiro, RJ, Brazil
| | - Adriano Aquino
- Analytical and Molecular Laboratorial Center (CLAn), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ 21941-909, Brazil; COVID-19 Research Group, Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Cidade Universitária, Rio de Janeiro, RJ 21941-598, Brazil; Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), University City, Rio de Janeiro, RJ, Brazil; Nanotechnology Network, Carlos Chagas Filho Research Support Foundation of the State of Rio de Janeiro (FAPERJ), Rio de Janeiro, RJ, Brazil
| | - Natasha Kilsy Rocha Belem
- Laboratory of Immunogenetics and Molecular Biology of the General Hospital and Maternity Hospital of Cuiabá, Brazil
| | | | - Carlos Adam Conte-Junior
- Analytical and Molecular Laboratorial Center (CLAn), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ 21941-909, Brazil; COVID-19 Research Group, Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Cidade Universitária, Rio de Janeiro, RJ 21941-598, Brazil; Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), University City, Rio de Janeiro, RJ, Brazil; Nanotechnology Network, Carlos Chagas Filho Research Support Foundation of the State of Rio de Janeiro (FAPERJ), Rio de Janeiro, RJ, Brazil; Post-Graduation Program of Chemistry (PGQu), Institute of chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), University City, Rio de Janeiro, RJ, Brazil.
| |
Collapse
|
36
|
Banerjee A, Halder A, Jadhav P, Sarkar A, Hole A, Shastri JS, Agrawal S, Chilakapati MK, Srivastava S. SARS-CoV-2 severity classification from plasma sample using confocal Raman spectroscopy. JOURNAL OF RAMAN SPECTROSCOPY : JRS 2023; 54:124-132. [PMID: 36713977 PMCID: PMC9874663 DOI: 10.1002/jrs.6461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 10/05/2022] [Accepted: 10/10/2022] [Indexed: 06/18/2023]
Abstract
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.
Collapse
Affiliation(s)
- Arghya Banerjee
- Department of Biosciences and BioengineeringIndian Institute of Technology BombayMumbaiIndia
| | - Ankit Halder
- Department of Biosciences and BioengineeringIndian Institute of Technology BombayMumbaiIndia
| | - Priyanka Jadhav
- Advanced Centre for Treatment Research and Education in Cancer (ACTREC)Tata Memorial Centre (TMC)Navi MumbaiIndia
- Homi Bhabha National InstituteTraining School Complex, Anushakti NagarMumbaiIndia
| | - Anushka Sarkar
- Department of Life SciencesPresidency University (Main Campus)KolkataIndia
| | - Arti Hole
- Advanced Centre for Treatment Research and Education in Cancer (ACTREC)Tata Memorial Centre (TMC)Navi MumbaiIndia
| | | | | | - Murali Krishna Chilakapati
- Advanced Centre for Treatment Research and Education in Cancer (ACTREC)Tata Memorial Centre (TMC)Navi MumbaiIndia
| | - Sanjeeva Srivastava
- Department of Biosciences and BioengineeringIndian Institute of Technology BombayMumbaiIndia
| |
Collapse
|
37
|
Pushpa S, Sukumaran RK, Savithri S. Robustness of FTIR-Based Ultrarapid COVID-19 Diagnosis Using PLS-DA. ACS OMEGA 2022; 7:47357-47371. [PMID: 36570187 PMCID: PMC9773962 DOI: 10.1021/acsomega.2c06786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
The World Health Organization (WHO) declared the Omicron variant (B.1.1.529) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogen responsible for the Coronavirus disease 2019 (COVID-19) pandemic, as a variant of concern on 26 November 2021. By this time, 42% of the world's population had received at least one dose of the vaccine against COVID-19. As on 1 October 2022, only 68% of the world population got the first dose of the vaccine. Although the vaccination is incredibly protective against severe complications of the disease and death, the highly contagious Omicron variant, compared to the Delta variant (B.1.617.2), has led the whole world into more chaotic situations. Furthermore, the virus has a high mutation rate, and hence, the possibility of a new variant of concern in the future cannot be ruled out. To face such a challenging situation, paramount importance should be given to rapid diagnosis and isolation of the infected patient. Current diagnosis methods, including reverse transcription-polymerase chain reaction and rapid antigen tests, face significant burdens during a COVID-19 wave. However, studies reported ultrarapid, reagent-free, cost-efficient, and non-destructive diagnosis methods based on chemometrics for COVID-19 and COVID-19 severity diagnosis. These studies used a smaller sample cohort to construct the diagnosis model and failed to discuss the robustness of the model. The current study systematically evaluated the robustness of the diagnosis models trained using smaller (real and augmented spectra) and larger (augmented spectra) datasets. The Monte Carlo cross-validation and permutation test results suggest that diagnosis using models trained by larger datasets was accurate and statistically significant (Q 2 > 99% and AUROC = 100%).
Collapse
Affiliation(s)
- Sreejith
Remanan Pushpa
- Material
Science and Technology Division, CSIR-National
Institute for Interdisciplinary Science and Technology, Industrial Estate P.O., Thiruvananthapuram695019, Kerala, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad201002, India
| | - Rajeev Kumar Sukumaran
- Microbial
Processes and Technology Division, CSIR-National
Institute for Interdisciplinary Science and Technology, Industrial Estate P.O., Thiruvananthapuram695019, Kerala, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad201002, India
| | - Sivaraman Savithri
- Material
Science and Technology Division, CSIR-National
Institute for Interdisciplinary Science and Technology, Industrial Estate P.O., Thiruvananthapuram695019, Kerala, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad201002, India
| |
Collapse
|
38
|
Rapid Detection of Recurrent Non-Muscle Invasive Bladder Cancer in Urine Using ATR-FTIR Technology. Molecules 2022; 27:molecules27248890. [PMID: 36558023 PMCID: PMC9785428 DOI: 10.3390/molecules27248890] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/17/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Non-muscle Invasive Bladder Cancer (NMIBC) accounts for 80% of all bladder cancers. Although it is mostly low-grade tumors, its high recurrence rate necessitates three-times-monthly follow-ups and cystoscopy examinations to detect and prevent its progression. A rapid liquid biopsy-based assay is needed to improve detection and reduce complications from invasive cystoscopy. Here, we present a rapid spectroscopic method to detect the recurrence of NMIBC in urine. Urine samples from previously-diagnosed NMIBC patients (n = 62) were collected during their follow-up visits before cystoscopy examination. Cystoscopy results were recorded (41 cancer-free and 21 recurrence) and attenuated total refraction Fourier transform infrared (ATR-FTIR) spectra were acquired from urine samples using direct application. Spectral processing and normalization were optimized using parameter grid searching. We assessed their technical variability through multivariate analysis and principal component analysis (PCA). We assessed 35 machine learning models on a training set (70%), and the performance was evaluated on a held-out test set (30%). A Regularized Random Forests (RRF) model achieved a 0.92 area under the receiver operating characteristic (AUROC) with 86% sensitivity and 77% specificity. In conclusion, our spectroscopic liquid biopsy approach provides a promising technique for the early identification of NMIBC with a less invasive examination.
Collapse
|
39
|
Tessaro L, da Silva Mutz Y, Lelis CA, Andrade JCD, Aquino A, Panzenhagen P, Ochioni AC, Sousa Vieira IR, Conte-Junior CA. Combination of RT-LAMP and fluorescence spectroscopy using chemometric techniques for an ultra-sensitive and rapid alternative for the detection of SARS-CoV-2. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:4922-4930. [PMID: 36426753 DOI: 10.1039/d2ay01502a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The increased spread of COVID-19 caused by SARS-CoV-2 has made it necessary to develop more efficient, fast, accurate, specific, sensitive and easy-to-use detection platforms to overcome the disadvantages of gold standard methods (RT-qPCR). Here an approach was developed for the detection of the SARS-CoV-2 virus using the loop-mediated isothermal amplification (LAMP) technique for SARS-CoV-2 RNA target amplification in samples of nasopharyngeal swabs. The discrimination between positive and negative SARS-CoV-2 samples was achieved by using fluorescence spectra generated by the excitation of the LAMP's DNA intercalator dye at λ497 nm in a fluorescence spectrophotometer and chemometric tools. Exploratory analysis of the 83 sample spectra using principal component analysis (PCA) indicated a trend in differentiation between positive and negative samples resulting from the peak emission of the fluorescent dye. The classification was performed by partial least squares discriminant analysis (PLS-DA) achieving a sensitivity, a specificity and an accuracy of 100%, 95% and 89%, respectively for the discrimination between negative and positive samples from 1.58 to 0.25 ng L-1 after LAMP amplification. Therefore, this study indicates that the use of the LAMP technique in fluorescence spectroscopy may offer a fast (<1 hour), sensitive and low-cost method.
Collapse
Affiliation(s)
- Leticia Tessaro
- Analytical and Molecular Laboratorial Center (CLAn), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), University City, Rio de Janeiro RJ, 21941-909, Brazil
- COVID-19 Research Group, Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), University City, Rio de Janeiro RJ, 21941-598, Brazil
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), University City, Rio de Janeiro RJ, Brazil
- Nanotechnology Network, Carlos Chagas Filho Research Support Foundation of the State of Rio de Janeiro (FAPERJ), Rio de Janeiro, RJ, Brazil
- Post-Graduation Program of Chemistry (PGQu), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), University City, Rio de Janeiro, RJ, Brazil
| | - Yhan da Silva Mutz
- Analytical and Molecular Laboratorial Center (CLAn), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), University City, Rio de Janeiro RJ, 21941-909, Brazil
- COVID-19 Research Group, Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), University City, Rio de Janeiro RJ, 21941-598, Brazil
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), University City, Rio de Janeiro RJ, Brazil
- Nanotechnology Network, Carlos Chagas Filho Research Support Foundation of the State of Rio de Janeiro (FAPERJ), Rio de Janeiro, RJ, Brazil
| | - Carini Aparecida Lelis
- Analytical and Molecular Laboratorial Center (CLAn), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), University City, Rio de Janeiro RJ, 21941-909, Brazil
- COVID-19 Research Group, Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), University City, Rio de Janeiro RJ, 21941-598, Brazil
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), University City, Rio de Janeiro RJ, Brazil
- Nanotechnology Network, Carlos Chagas Filho Research Support Foundation of the State of Rio de Janeiro (FAPERJ), Rio de Janeiro, RJ, Brazil
| | - Jelmir Craveiro de Andrade
- Analytical and Molecular Laboratorial Center (CLAn), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), University City, Rio de Janeiro RJ, 21941-909, Brazil
- COVID-19 Research Group, Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), University City, Rio de Janeiro RJ, 21941-598, Brazil
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), University City, Rio de Janeiro RJ, Brazil
- Nanotechnology Network, Carlos Chagas Filho Research Support Foundation of the State of Rio de Janeiro (FAPERJ), Rio de Janeiro, RJ, Brazil
- Post-Graduation Program of Chemistry (PGQu), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), University City, Rio de Janeiro, RJ, Brazil
| | - Adriano Aquino
- Analytical and Molecular Laboratorial Center (CLAn), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), University City, Rio de Janeiro RJ, 21941-909, Brazil
- COVID-19 Research Group, Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), University City, Rio de Janeiro RJ, 21941-598, Brazil
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), University City, Rio de Janeiro RJ, Brazil
- Nanotechnology Network, Carlos Chagas Filho Research Support Foundation of the State of Rio de Janeiro (FAPERJ), Rio de Janeiro, RJ, Brazil
- Post-Graduation Program of Chemistry (PGQu), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), University City, Rio de Janeiro, RJ, Brazil
| | - Pedro Panzenhagen
- Analytical and Molecular Laboratorial Center (CLAn), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), University City, Rio de Janeiro RJ, 21941-909, Brazil
- COVID-19 Research Group, Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), University City, Rio de Janeiro RJ, 21941-598, Brazil
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), University City, Rio de Janeiro RJ, Brazil
- Nanotechnology Network, Carlos Chagas Filho Research Support Foundation of the State of Rio de Janeiro (FAPERJ), Rio de Janeiro, RJ, Brazil
| | - Alan Clavelland Ochioni
- Analytical and Molecular Laboratorial Center (CLAn), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), University City, Rio de Janeiro RJ, 21941-909, Brazil
- COVID-19 Research Group, Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), University City, Rio de Janeiro RJ, 21941-598, Brazil
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), University City, Rio de Janeiro RJ, Brazil
- Nanotechnology Network, Carlos Chagas Filho Research Support Foundation of the State of Rio de Janeiro (FAPERJ), Rio de Janeiro, RJ, Brazil
| | - Italo Rennan Sousa Vieira
- Analytical and Molecular Laboratorial Center (CLAn), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), University City, Rio de Janeiro RJ, 21941-909, Brazil
- COVID-19 Research Group, Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), University City, Rio de Janeiro RJ, 21941-598, Brazil
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), University City, Rio de Janeiro RJ, Brazil
- Nanotechnology Network, Carlos Chagas Filho Research Support Foundation of the State of Rio de Janeiro (FAPERJ), Rio de Janeiro, RJ, Brazil
| | - Carlos Adam Conte-Junior
- Analytical and Molecular Laboratorial Center (CLAn), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), University City, Rio de Janeiro RJ, 21941-909, Brazil
- COVID-19 Research Group, Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), University City, Rio de Janeiro RJ, 21941-598, Brazil
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), University City, Rio de Janeiro RJ, Brazil
- Nanotechnology Network, Carlos Chagas Filho Research Support Foundation of the State of Rio de Janeiro (FAPERJ), Rio de Janeiro, RJ, Brazil
- Post-Graduation Program of Chemistry (PGQu), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), University City, Rio de Janeiro, RJ, Brazil
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, 21941-901, Brazil
| |
Collapse
|
40
|
Contributions of vibrational spectroscopy to virology: A review. CLINICAL SPECTROSCOPY 2022; 4:100022. [PMCID: PMC9093054 DOI: 10.1016/j.clispe.2022.100022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/30/2022] [Accepted: 05/04/2022] [Indexed: 06/17/2023]
Abstract
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.
Collapse
|
41
|
Diagnostic performance of attenuated total reflection Fourier-transform infrared spectroscopy for detecting COVID-19 from routine nasopharyngeal swab samples. Sci Rep 2022; 12:20358. [PMID: 36437268 PMCID: PMC9701801 DOI: 10.1038/s41598-022-24751-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 11/21/2022] [Indexed: 11/28/2022] Open
Abstract
Attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy coupled with machine learning-based partial least squares discriminant analysis (PLS-DA) was applied to study if severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could be detected from nasopharyngeal swab samples originally collected for polymerase chain reaction (PCR) analysis. Our retrospective study included 558 positive and 558 negative samples collected from Northern Finland. Overall, we found moderate diagnostic performance for ATR-FTIR when PCR analysis was used as the gold standard: the average area under the receiver operating characteristics curve (AUROC) was 0.67-0.68 (min. 0.65, max. 0.69) with 20, 10 and 5 k-fold cross validations. Mean accuracy, sensitivity and specificity was 0.62-0.63 (min. 0.60, max. 0.65), 0.61 (min. 0.58, max. 0.65) and 0.64 (min. 0.59, max. 0.67) with 20, 10 and 5 k-fold cross validations. As a conclusion, our study with relatively large sample set clearly indicate that measured ATR-FTIR spectrum contains specific information for SARS-CoV-2 infection (P < 0.001 for AUROC in label permutation test). However, the diagnostic performance of ATR-FTIR remained only moderate, potentially due to low concentration of viral particles in the transport medium. Further studies are needed before ATR-FTIR can be recommended for fast screening of SARS-CoV-2 from nasopharyngeal swab samples.
Collapse
|
42
|
Mandal A, Mallik S, Mondal S, Subhadarshini S, Sadhukhan R, Ghoshal T, Mitra S, Manna M, Mandal S, Goswami DK. Diffusion-Induced Ingress of Angiotensin-Converting Enzyme 2 into the Charge Conducting Path of a Pentacene Channel for Efficient Detection of SARS-CoV-2 in Saliva Samples. ACS Sens 2022; 7:3006-3013. [PMID: 36129125 PMCID: PMC9514329 DOI: 10.1021/acssensors.2c01287] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 09/09/2022] [Indexed: 01/31/2023]
Abstract
Rapid and accurate identification of a pathogen is crucial for disease control and prevention of the epidemic of emerging infectious like SARS-CoV-2. However, no foolproof gold standard assay exists to date. Nucleic acid-based molecular diagnostic tests have been established for identifying COVID-19. However, viral RNAs are highly unstable in handling with poor laboratory procedures, leading to a false negative that accelerates the spread of the disease. Detection of the spike protein (S1) of the SARS-CoV-2 virus through a proper receptor, commonly used in antigen-based rapid testing kits, also suffers from false-negative predictions due to decreasing viral titers in clinical specimens. Organic field-effect transistor (OFET)-based sensors can be highly sensitive upon properly integrating receptors in the conducting channel. This work demonstrates how angiotensin-converting enzyme 2 (ACE2) molecules can be used as receptor molecules of the SARS-CoV-2 virus in the OFET platform. Integration of ACE2 molecules into pentacene grain boundaries has been studied through the statistical analysis of rough surfaces in terms of lateral correlation length and interface width. The uniform coating of ACE2 molecules has been confirmed through growth studies to achieve better ingress of the receptors into the conducting channel at the semiconductor/dielectric interface of OFETs. We have observed less than a minute detection time with 94% sensitivity, which is the highest reported value. The sensor works with a saliva sample, requiring no sample preparation or virus transfer medium. A prototype module developed for remote monitoring confirms the suitability for point-of-care (POC) application at large-scale testing in more crowded areas like airports, railway stations, shopping malls, etc.
Collapse
Affiliation(s)
- Ajoy Mandal
- Organic Electronics Laboratory, Department of Physics,
Indian Institute of Technology Kharagpur, Kharagpur721302,
India
| | - Samik Mallik
- School of Nanoscience and Technology,
Indian Institute of Technology Kharagpur, Kharagpur721302,
India
| | - Sovanlal Mondal
- School of Nanoscience and Technology,
Indian Institute of Technology Kharagpur, Kharagpur721302,
India
| | - Suvani Subhadarshini
- School of Nanoscience and Technology,
Indian Institute of Technology Kharagpur, Kharagpur721302,
India
| | - Riya Sadhukhan
- Organic Electronics Laboratory, Department of Physics,
Indian Institute of Technology Kharagpur, Kharagpur721302,
India
| | - Tanmay Ghoshal
- Department of Electronics and Electrical Communication
Engineering, Indian Institute of Technology Kharagpur,
Kharagpur721302, India
| | - Suman Mitra
- School of Nanoscience and Technology,
Indian Institute of Technology Kharagpur, Kharagpur721302,
India
| | - Mousam Manna
- B C Roy Technology Hospital, Indian
Institute of Technology Kharagpur, Kharagpur721302,
India
| | - Suman Mandal
- Organic Electronics Laboratory, Department of Physics,
Indian Institute of Technology Kharagpur, Kharagpur721302,
India
| | - Dipak K. Goswami
- Organic Electronics Laboratory, Department of Physics,
Indian Institute of Technology Kharagpur, Kharagpur721302,
India
- School of Nanoscience and Technology,
Indian Institute of Technology Kharagpur, Kharagpur721302,
India
| |
Collapse
|
43
|
Zhang D, Guo Y, Zhang L, Wang Y, Peng S, Duan S, Geng L, Zhang X, Wang W, Yang M, Wu G, Chen J, Feng Z, Wang X, Wu Y, Jiang H, Zhang Q, Sun J, Li S, He Y, Xiao M, Xu Y, Wang H, Liu P, Zhou Q, Luo H. Integrated System for On-Site Rapid and Safe Screening of COVID-19. Anal Chem 2022; 94:13810-13819. [PMID: 36184789 PMCID: PMC9578365 DOI: 10.1021/acs.analchem.2c02337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/22/2022] [Indexed: 12/04/2022]
Abstract
Since the outbreak of coronavirus disease 2019 (COVID-19), the epidemic has been spreading around the world for more than 2 years. Rapid, safe, and on-site detection methods of COVID-19 are in urgent demand for the control of the epidemic. Here, we established an integrated system, which incorporates a machine-learning-based Fourier transform infrared spectroscopy technique for rapid COVID-19 screening and air-plasma-based disinfection modules to prevent potential secondary infections. A partial least-squares discrimination analysis and a convolutional neural network model were built using the collected infrared spectral dataset containing 857 training serum samples. Furthermore, the sensitivity, specificity, and prediction accuracy could all reach over 94% from the results of the field test regarding 968 blind testing samples. Additionally, the disinfection modules achieved an inactivation efficiency of 99.9% for surface and airborne tested bacteria. The proposed system is conducive and promising for point-of-care and on-site COVID-19 screening in the mass population.
Collapse
Affiliation(s)
- Dongheyu Zhang
- Department
of Electrical Engineering, Tsinghua University, Beijing100084, China
| | - Yuntao Guo
- Department
of Electrical Engineering, Tsinghua University, Beijing100084, China
| | - Liyang Zhang
- Department
of Electrical Engineering, Tsinghua University, Beijing100084, China
| | - Yao Wang
- Department
of Clinical Laboratory, Peking Union Medical
College Hospital, Chinese Academy of Medical Sciences, Beijing100730, China
| | - Siqi Peng
- Department
of Electrical Engineering, Tsinghua University, Beijing100084, China
| | - Simeng Duan
- Department
of Clinical Laboratory, Peking Union Medical
College Hospital, Chinese Academy of Medical Sciences, Beijing100730, China
| | - Lin Geng
- JINSP
Co., Ltd., Beijing100083, China
| | | | - Wei Wang
- Shanghai
Customs Port Clinic, Shanghai International
Travel Healthcare Center, Shanghai200335, China
| | - Mengjie Yang
- Chinese
Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing102206, China
| | - Guizhen Wu
- Chinese
Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing102206, China
| | - Jiayi Chen
- Department
of Electrical Engineering, Tsinghua University, Beijing100084, China
| | - Zihao Feng
- Department
of Electrical Engineering, Tsinghua University, Beijing100084, China
| | - Xinyuan Wang
- Holy-shine
Technology Co., Ltd., Beijing100045, China
| | - Yue Wu
- Holy-shine
Technology Co., Ltd., Beijing100045, China
| | - Haotian Jiang
- Department
of Electrical Engineering, Tsinghua University, Beijing100084, China
| | - Qikang Zhang
- Department
of Electrical Engineering, Tsinghua University, Beijing100084, China
| | - Jingjun Sun
- Department
of Electrical Engineering, Tsinghua University, Beijing100084, China
| | - Shenwei Li
- Shanghai
Customs Port Clinic, Shanghai International
Travel Healthcare Center, Shanghai200335, China
| | - Yuping He
- Shanghai
Customs Port Clinic, Shanghai International
Travel Healthcare Center, Shanghai200335, China
| | - Meng Xiao
- Department
of Clinical Laboratory, Peking Union Medical
College Hospital, Chinese Academy of Medical Sciences, Beijing100730, China
| | - Yingchun Xu
- Department
of Clinical Laboratory, Peking Union Medical
College Hospital, Chinese Academy of Medical Sciences, Beijing100730, China
| | | | - Peipei Liu
- Chinese
Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing102206, China
| | - Qun Zhou
- Department
of Chemistry, Tsinghua University, Beijing100084, China
| | - Haiyun Luo
- Department
of Electrical Engineering, Tsinghua University, Beijing100084, China
| |
Collapse
|
44
|
Wu Y, Liu B, Liu Z, Zhang P, Mu X, Tong Z. Construction, Characterization, and Application of a Nonpathogenic Virus-like Model for SARS-CoV-2 Nucleocapsid Protein by Phage Display. Toxins (Basel) 2022; 14:toxins14100683. [PMID: 36287952 PMCID: PMC9607219 DOI: 10.3390/toxins14100683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/07/2022] Open
Abstract
With the outbreak and spread of COVID-19, a deep investigation of SARS-CoV-2 is urgent. Direct usage of this virus for scientific research could provide reliable results and authenticity. However, it is strictly constrained and unrealistic due to its high pathogenicity and infectiousness. Considering its biosafety, different systems and technologies have been employed in immunology and biomedical studies. In this study, phage display technology was used to construct a nonpathogenic model for COVID-19 research. The nucleocapsid protein of SARS-CoV-2 was fused with the M13 phage capsid p3 protein and expressed on the M13 phages. After validation of its successful expression, its potential as the standard for qPCR quantification and affinity with antibodies were confirmed, which may show the possibility of using this nonpathogenic bacteriophage to replace the pathogenic virus in scientific research concerning SARS-CoV-2. In addition, the model was used to develop a system for the classification and identification of different samples using ATR–FTIR, which may provide an idea for the development and evaluation of virus monitoring equipment in the future.
Collapse
|
45
|
Spectroscopic methods for COVID-19 detection and early diagnosis. Virol J 2022; 19:152. [PMID: 36138463 PMCID: PMC9502632 DOI: 10.1186/s12985-022-01867-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 08/16/2022] [Indexed: 11/10/2022] Open
Abstract
The coronavirus pandemic is a worldwide hazard that poses a threat to millions of individuals throughout the world. This pandemic is caused by the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), which was initially identified in Wuhan, China's Hubei provincial capital, and has since spread throughout the world. According to the World Health Organization's Weekly Epidemiological Update, there were more than 250 million documented cases of coronavirus infections globally, with five million fatalities. Early detection of coronavirus does not only reduce the spread of the virus, but it also increases the chance of curing the infection. Spectroscopic techniques have been widely used in the early detection and diagnosis of COVID-19 using Raman, Infrared, mass spectrometry and fluorescence spectroscopy. In this review, the reported spectroscopic methods for COVID-19 detection were discussed with emphasis on the practical aspects, limitations and applications.
Collapse
|
46
|
Calvo-Gomez O, Calvo H, Cedillo-Barrón L, Vivanco-Cid H, Alvarado-Orozco JM, Fernandez-Benavides DA, Arriaga-Pizano L, Ferat-Osorio E, Anda-Garay JC, López-Macias C, López MG. Potential of ATR-FTIR-Chemometrics in Covid-19: Disease Recognition. ACS OMEGA 2022; 7:30756-30767. [PMID: 36092630 PMCID: PMC9453986 DOI: 10.1021/acsomega.2c01374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The COVID-19 pandemic has caused major disturbances to human health and economy on a global scale. Although vaccination campaigns and important advances in treatments have been developed, an early diagnosis is still crucial. While PCR is the golden standard for diagnosing SARS-CoV-2 infection, rapid and low-cost techniques such as ATR-FTIR followed by multivariate analyses, where dimensions are reduced for obtaining valuable information from highly complex data sets, have been investigated. Most dimensionality reduction techniques attempt to discriminate and create new combinations of attributes prior to the classification stage; thus, the user needs to optimize a wealth of parameters before reaching reliable and valid outcomes. In this work, we developed a method for evaluating SARS-CoV-2 infection and COVID-19 disease severity on infrared spectra of sera, based on a rather simple feature selection technique (correlation-based feature subset selection). Dengue infection was also evaluated for assessing whether selectivity toward a different virus was possible with the same algorithm, although independent models were built for both viruses. High sensitivity (94.55%) and high specificity (98.44%) were obtained for assessing SARS-CoV-2 infection with our model; for severe COVID-19 disease classification, sensitivity is 70.97% and specificity is 94.95%; for mild disease classification, sensitivity is 33.33% and specificity is 94.64%; and for dengue infection assessment, sensitivity is 84.27% and specificity is 94.64%.
Collapse
Affiliation(s)
- Octavio Calvo-Gomez
- Centro
de Investigación y de Estudios Avanzados del IPN, Km. 9.6 Libramiento Norte Carretera
Irapuato León, 36824 Irapuato, Guanajuato, Mexico
| | - Hiram Calvo
- Center
for Computing Research, Instituto Politécnico
Nacional, 07738 Mexico City, Mexico
| | - Leticia Cedillo-Barrón
- Centro
de Investigación y de Estudios Avanzados del IPN. Avenida IPN #2508, Col. San Pedro
Zacatenco, CP 07360 Mexico, Distrito Federal, Mexico
| | - Héctor Vivanco-Cid
- Laboratorio
Multidisciplinario en Ciencias Biomédicas, Instituto de Investigaciones
Médico-Biológicas, Universidad
Veracruzana, 91000Veracruz, Mexico
| | - Juan Manuel Alvarado-Orozco
- Centro
de Ingeniería y Desarrollo Industrial, Avenida Playa Pie de la Cuesta No.
702, Desarrollo San Pablo, 76125 Santiago de Querétaro, Mexico
| | - David Andrés Fernandez-Benavides
- Centro
de Ingeniería y Desarrollo Industrial, Avenida Playa Pie de la Cuesta No.
702, Desarrollo San Pablo, 76125 Santiago de Querétaro, Mexico
| | - Lourdes Arriaga-Pizano
- Unidad
de
Investigación Médica en Inmunoquímica, UMAE,
Hospital de Especialidades del Centro Médico Nacional Siglo
XXI. Instituto Mexicano del Seguro Social
(IMSS), 06600 Mexico City, Mexico
| | - Eduardo Ferat-Osorio
- Unidad
de
Investigación Médica en Inmunoquímica, UMAE,
Hospital de Especialidades del Centro Médico Nacional Siglo
XXI. Instituto Mexicano del Seguro Social
(IMSS), 06600 Mexico City, Mexico
| | - Juan Carlos Anda-Garay
- Unidad
de
Investigación Médica en Inmunoquímica, UMAE,
Hospital de Especialidades del Centro Médico Nacional Siglo
XXI. Instituto Mexicano del Seguro Social
(IMSS), 06600 Mexico City, Mexico
| | - Constantino López-Macias
- Unidad
de
Investigación Médica en Inmunoquímica, UMAE,
Hospital de Especialidades del Centro Médico Nacional Siglo
XXI. Instituto Mexicano del Seguro Social
(IMSS), 06600 Mexico City, Mexico
| | - Mercedes G. López
- Centro
de Investigación y de Estudios Avanzados del IPN, Km. 9.6 Libramiento Norte Carretera
Irapuato León, 36824 Irapuato, Guanajuato, Mexico
| |
Collapse
|
47
|
Rumaling MI, Chee FP, Bade A, Hasbi NH, Daim S, Juhim F, Duinong M, Rasmidi R. Methods of optical spectroscopy in detection of virus in infected samples: A review. Heliyon 2022; 8:e10472. [PMID: 36060463 PMCID: PMC9422564 DOI: 10.1016/j.heliyon.2022.e10472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/05/2022] [Accepted: 08/23/2022] [Indexed: 01/08/2023] Open
Affiliation(s)
- Muhammad Izzuddin Rumaling
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia
| | - Fuei Pien Chee
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia
- Corresponding author.
| | - Abdullah Bade
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia
| | - Nur Hasshima Hasbi
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia
| | - Sylvia Daim
- Faculty of Medicine and Health Science, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia
| | - Floressy Juhim
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia
| | - Mivolil Duinong
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia
| | - Rosfayanti Rasmidi
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Sabah, Malaysia
- Faculty of Applied Sciences, Universiti Teknologi MARA Sabah Branch, Kota Kinabalu Campus, 88997 Kota Kinabalu, Sabah, Malaysia
| |
Collapse
|
48
|
Bunaciu AA, Aboul-Enein HY. DETERMINATION OF COVID-19 VIRUSES IN SALIVA USING FOURIER TRANSFORM INFRARED SPECTROSCOPY. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2022. [PMCID: PMC9519369 DOI: 10.1016/j.cjac.2022.100178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
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.
Collapse
|
49
|
de Almeida C, Motta LC, Folli GS, Marcarini WD, Costa CA, Vilela ACS, Barauna VG, Martin FL, Singh MN, Campos LCG, Costa NL, Vassallo PF, Chaves AR, Endringer DC, Mill JG, Filgueiras PR, Romão W. MALDI(+) FT-ICR Mass Spectrometry (MS) Combined with Machine Learning toward Saliva-Based Diagnostic Screening for COVID-19. J Proteome Res 2022; 21:1868-1875. [PMID: 35880262 PMCID: PMC9344790 DOI: 10.1021/acs.jproteome.2c00148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Indexed: 11/28/2022]
Abstract
Rapid identification of existing respiratory viruses in biological samples is of utmost importance in strategies to combat pandemics. Inputting MALDI FT-ICR MS (matrix-assisted laser desorption/ionization Fourier-transform ion cyclotron resonance mass spectrometry) data output into machine learning algorithms could hold promise in classifying positive samples for SARS-CoV-2. This study aimed to develop a fast and effective methodology to perform saliva-based screening of patients with suspected COVID-19, using the MALDI FT-ICR MS technique with a support vector machine (SVM). In the method optimization, the best sample preparation was obtained with the digestion of saliva in 10 μL of trypsin for 2 h and the MALDI analysis, which presented a satisfactory resolution for the analysis with 1 M. SVM models were created with data from the analysis of 97 samples that were designated as SARS-CoV-2 positives versus 52 negatives, confirmed by RT-PCR tests. SVM1 and SVM2 models showed the best results. The calibration group obtained 100% accuracy, and the test group 95.6% (SVM1) and 86.7% (SVM2). SVM1 selected 780 variables and has a false negative rate (FNR) of 0%, while SVM2 selected only two variables with a FNR of 3%. The proposed methodology suggests a promising tool to aid screening for COVID-19.
Collapse
Affiliation(s)
- Camila
M. de Almeida
- Chemistry
Department, Federal University of Espírito
Santo, Vitória, ES 29040-090, Brazil
| | - Larissa C. Motta
- Chemistry
Department, Federal University of Espírito
Santo, Vitória, ES 29040-090, Brazil
| | - Gabriely S. Folli
- Chemistry
Department, Federal University of Espírito
Santo, Vitória, ES 29040-090, Brazil
| | - Wena D. Marcarini
- Department
of Physiological Sciences, Federal University
of Espírito Santo, Vitória, ES 29040-090, Brazil
| | - Camila A. Costa
- School
of Dentistry, Department of Stomatology (Oral Pathology), Federal University of Goiás, Goiânia, GO 74000-000, Brazil
| | - Ana C. S. Vilela
- School
of Dentistry, Department of Stomatology (Oral Pathology), Federal University of Goiás, Goiânia, GO 74000-000, Brazil
| | - Valério G. Barauna
- Department
of Physiological Sciences, Federal University
of Espírito Santo, Vitória, ES 29040-090, Brazil
| | | | - Maneesh N. Singh
- Biocel
UK Ltd., 15 Riplingham
Road, West Ella, Hull HU10
6TS, U.K.
| | - Luciene C. G. Campos
- Department
of Biological Science, Santa Cruz State
University, Ilhéus, BA 45662-900, Brazil
| | - Nádia L. Costa
- School
of Dentistry, Department of Stomatology (Oral Pathology), Federal University of Goiás, Goiânia, GO 74000-000, Brazil
| | - Paula F. Vassallo
- Clinical
Hospital, Federal University of Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Andrea R. Chaves
- Chromatography
and Mass Spectrometry Laboratory, Institute of Chemistry, Federal University of Goiás, Goiânia, GO 74690-900, Brazil
| | - Denise C. Endringer
- Pharmaceutical
Science Graduate Program, Universidade Vila
Velha, Vila Velha, ES 29106-010, Brazil
| | - José G. Mill
- Department
of Physiological Sciences, Federal University
of Espírito Santo, Vitória, ES 29040-090, Brazil
| | - Paulo R. Filgueiras
- Chemistry
Department, Federal University of Espírito
Santo, Vitória, ES 29040-090, Brazil
| | - Wanderson Romão
- Chemistry
Department, Federal University of Espírito
Santo, Vitória, ES 29040-090, Brazil
- Science
Department, Federal Institute of Education,
Science, and Technology of Espírito Santo, Vila Velha, ES 29106-010, Brazil
| |
Collapse
|
50
|
Madurani KA, Suprapto, Yudha Syahputra M, Puspita I, Furqoni AH, Puspasari L, Rosyidah H, Hatta AM, Juniastuti, Lusida MI, Tominaga M, Kurniawan F. Fluorescence spectrophotometry for COVID-19 determination in clinical swab samples. ARAB J CHEM 2022; 15:104020. [PMID: 35664893 PMCID: PMC9150911 DOI: 10.1016/j.arabjc.2022.104020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/25/2022] [Indexed: 11/29/2022] Open
Abstract
Considering the limitations of the assays currently available for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its emerging variants, a simple and rapid method using fluorescence spectrophotometry was developed to detect coronavirus disease 2019 (COVID-19). Forty clinical swab samples were collected from the nasopharyngeal and oropharyngeal cavities of COVID-19-positive and -negative. Each sample was divided into two parts. The first part of the samples was analyzed using reverse transcription-polymerase chain reaction (RT-qPCR) as the control method to identify COVID-19-positive and -negative samples. The second part of the samples was analyzed using fluorescence spectrophotometry. Fluorescence measurements were performed at excitation and emission wavelengths ranging from 200 to 800 nm. Twenty COVID-19-positive samples and twenty COVID-19-negative samples were detected based on RT-qPCR results. The fluorescence spectrum data indicated that the COVID-19-positive and -negative samples had significantly different characteristics. All positive samples could be distinguished from negative samples by fluorescence spectrophotometry. Principal component analysis showed that COVID-19-positive samples were clustered separately from COVID-19-negative samples. The specificity and accuracy of this experiment reached 100%. Limit of detection (LOD) obtained 42.20 copies/ml (Ct value of 33.65 cycles) for E gene and 63.60 copies/ml (Ct value of 31.36 cycles) for ORF1ab gene. This identification process only required 4 min. Thus, this technique offers an efficient and accurate method to identify an individual with active SARS-CoV-2 infection and can be easily adapted for the early investigation of COVID-19, in general.
Collapse
Affiliation(s)
- Kartika A Madurani
- Laboratory of Instrumentation and Analytical Science, Chemistry Department, Faculty of Science and Data Analytics, Institut Teknologi Sepuluh Nopember, Surabaya 60111, Indonesia
| | - Suprapto
- Laboratory of Instrumentation and Analytical Science, Chemistry Department, Faculty of Science and Data Analytics, Institut Teknologi Sepuluh Nopember, Surabaya 60111, Indonesia
| | - Muhammad Yudha Syahputra
- Laboratory of Instrumentation and Analytical Science, Chemistry Department, Faculty of Science and Data Analytics, Institut Teknologi Sepuluh Nopember, Surabaya 60111, Indonesia
| | - Ika Puspita
- Photonics Engineering Laboratory, Department of Engineering Physics, Faculty of Industrial Technology and Systems Engineering, Institut Teknologi Sepuluh Nopember, Surabaya 60111, Indonesia
| | - Abdul Hadi Furqoni
- Human Genetic Laboratory, Institute of Tropical Disease, Airlangga University, Surabaya 60115, Indonesia
| | - Listya Puspasari
- Laboratory of Instrumentation and Analytical Science, Chemistry Department, Faculty of Science and Data Analytics, Institut Teknologi Sepuluh Nopember, Surabaya 60111, Indonesia
| | - Hafildatur Rosyidah
- Laboratory of Instrumentation and Analytical Science, Chemistry Department, Faculty of Science and Data Analytics, Institut Teknologi Sepuluh Nopember, Surabaya 60111, Indonesia
| | - Agus Muhamad Hatta
- Photonics Engineering Laboratory, Department of Engineering Physics, Faculty of Industrial Technology and Systems Engineering, Institut Teknologi Sepuluh Nopember, Surabaya 60111, Indonesia
| | - Juniastuti
- Faculty of Medicine, Airlangga University, Surabaya 60131, Indonesia.,Institute of Tropical Disease, Airlangga University, Surabaya 60115, Indonesia
| | - Maria Inge Lusida
- Faculty of Medicine, Airlangga University, Surabaya 60131, Indonesia.,Institute of Tropical Disease, Airlangga University, Surabaya 60115, Indonesia
| | - Masato Tominaga
- Department of Chemistry and Applied Chemistry, Graduate School of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Fredy Kurniawan
- Laboratory of Instrumentation and Analytical Science, Chemistry Department, Faculty of Science and Data Analytics, Institut Teknologi Sepuluh Nopember, Surabaya 60111, Indonesia
| |
Collapse
|