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1.
Analyst ; 145(12): 4173-4180, 2020 Jun 21.
Article in English | MEDLINE | ID: covidwho-1721601

ABSTRACT

Studies have shown that microRNAs, which are small noncoding RNAs, hold tremendous promise as next-generation circulating biomarkers for early cancer detection via liquid biopsies. A novel, solid-state nanoplasmonic sensor capable of assaying circulating microRNAs through a combined surface-enhanced Raman scattering (SERS) and plasmon-enhanced fluorescence (PEF) approach has been developed. Here, the unique localized surface plasmon resonance properties of chemically-synthesized gold triangular nanoprisms (Au TNPs) are utilized to create large SERS and PEF enhancements. With careful modification to the surface of Au TNPs, this sensing approach is capable of quantifying circulating microRNAs at femtogram/microliter concentrations. Uniquely, the multimodal analytical methods mitigate both false positive and false negative responses and demonstrate the high stability of our sensors within bodily fluids. As a proof of concept, microRNA-10b and microRNA-96 were directly assayed from the plasma of six bladder cancer patients. Results show potential for a highly specific liquid biopsy method that could be used in point-of-care clinical diagnostics to increase early cancer detection or any other diseases including SARS-CoV-2 in which RNAs can be used as biomarkers.


Subject(s)
Circulating MicroRNA/blood , Fluorescent Dyes/chemistry , Spectrum Analysis, Raman , Urinary Bladder Neoplasms/diagnosis , Betacoronavirus/isolation & purification , Biomarkers, Tumor/blood , COVID-19 , Coronavirus Infections/diagnosis , Coronavirus Infections/pathology , Coronavirus Infections/virology , Gold/chemistry , Humans , Limit of Detection , Microscopy, Confocal , Nanostructures/chemistry , Pandemics , Pneumonia, Viral/diagnosis , Pneumonia, Viral/pathology , Pneumonia, Viral/virology , Point-of-Care Systems , SARS-CoV-2 , Urinary Bladder Neoplasms/genetics , Urinary Bladder Neoplasms/pathology
2.
Analyst ; 147(6): 1213-1221, 2022 Mar 14.
Article in English | MEDLINE | ID: covidwho-1713220

ABSTRACT

COVID-19 has caused millions of cases and deaths all over the world since late 2019. Rapid detection of the virus is crucial for controlling its spread through a population. COVID-19 is currently detected by nucleic acid-based tests and serological tests. However, these methods have limitations such as the requirement of high-cost reagents, false negative results and being time consuming. Surface-enhanced Raman scattering (SERS), which is a powerful technique that enhances the Raman signals of molecules using plasmonic nanostructures, can overcome these disadvantages. In this study, we developed a virus-infected cell model and analyzed this model by SERS combined with Principal Component Analysis (PCA). HEK293 cells were transfected with plasmids encoding the nucleocapsid (N), membrane (M) and envelope (E) proteins of SARS-CoV-2 via polyethyleneimine (PEI). Non-plasmid transfected HEK293 cells were used as the control group. Cellular uptake was optimized with green fluorescence protein (GFP) plasmids and evaluated by fluorescence microscopy and flow cytometry. The transfection efficiency was found to be around 60%. The expression of M, N, and E proteins was demonstrated by western blotting. The SERS spectra of the total proteins of transfected cells were obtained using a gold nanoparticle-based SERS substrate. Proteins of the transfected cells have peak positions at 646, 680, 713, 768, 780, 953, 1014, 1046, 1213, 1243, 1424, 2102, and 2124 cm-1. To reveal spectral differences between plasmid transfected cells and non-transfected control cells, PCA was applied to the spectra. The results demonstrated that SERS coupled with PCA might be a favorable and reliable way to develop a rapid, low-cost, and promising technique for the detection of COVID-19.


Subject(s)
COVID-19 , Metal Nanoparticles , Animals , COVID-19/diagnosis , Gold/chemistry , HEK293 Cells , Humans , Metal Nanoparticles/chemistry , Multivariate Analysis , SARS-CoV-2/genetics , Spectrum Analysis, Raman/methods
3.
Biosens Bioelectron ; 202: 114008, 2022 Apr 15.
Article in English | MEDLINE | ID: covidwho-1693899

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected humans worldwide for over a year now. Although various tests have been developed for the detection of SARS-CoV-2, advanced sensing methods are required for the diagnosis, screening, and surveillance of coronavirus disease 2019 (COVID-19). Here, we report a surface-enhanced Raman scattering (SERS)-based immunoassay involving an antibody pair, SERS-active hollow Au nanoparticles (NPs), and magnetic beads for the detection of SARS-CoV-2. The selected antibody pair against the SARS-CoV-2 antigen, along with the magnetic beads, facilitates the accurate direct detection of the virus. The hollow Au NPs exhibit strong, reproducible SERS signals, allowing sensitive quantitative detection of SARS-CoV-2. This assay had detection limits of 2.56 fg/mL for the SARS-CoV-2 antigen and 3.4 plaque-forming units/mL for the SARS-CoV-2 lysates. Furthermore, it facilitated the identification of SARS-CoV-2 in human nasopharyngeal aspirates and diagnosis of COVID-19 within 30 min using a portable Raman device. Thus, this assay can be potentially used for the diagnosis and prevention of COVID-19.


Subject(s)
Biosensing Techniques , COVID-19 , Metal Nanoparticles , Biosensing Techniques/methods , Gold , Humans , Immunoassay/methods , SARS-CoV-2 , Spectrum Analysis, Raman
4.
J Biomed Opt ; 27(2)2022 02.
Article in English | MEDLINE | ID: covidwho-1677373

ABSTRACT

SIGNIFICANCE: The primary method of COVID-19 detection is reverse transcription polymerase chain reaction (RT-PCR) testing. PCR test sensitivity may decrease as more variants of concern arise and reagents may become less specific to the virus. AIM: We aimed to develop a reagent-free way to detect COVID-19 in a real-world setting with minimal constraints on sample acquisition. The machine learning (ML) models involved could be frequently updated to include spectral information about variants without needing to develop new reagents. APPROACH: We present a workflow for collecting, preparing, and imaging dried saliva supernatant droplets using a non-invasive, label-free technique-Raman spectroscopy-to detect changes in the molecular profile of saliva associated with COVID-19 infection. RESULTS: We used an innovative multiple instance learning-based ML approach and droplet segmentation to analyze droplets. Amongst all confounding factors, we discriminated between COVID-positive and COVID-negative individuals yielding receiver operating coefficient curves with an area under curve (AUC) of 0.8 in both males (79% sensitivity and 75% specificity) and females (84% sensitivity and 64% specificity). Taking the sex of the saliva donor into account increased the AUC by 5%. CONCLUSION: These findings may pave the way for new rapid Raman spectroscopic screening tools for COVID-19 and other infectious diseases.


Subject(s)
COVID-19 , Saliva , Female , Humans , Indicators and Reagents , Machine Learning , Male , SARS-CoV-2 , Sensitivity and Specificity , Spectrum Analysis, Raman
5.
Anal Bioanal Chem ; 414(1): 85-93, 2022 Jan.
Article in English | MEDLINE | ID: covidwho-1669767

ABSTRACT

The analysis of glycosaminoglycans (GAGs) is a challenging task due to their high structural heterogeneity, which results in diverse GAG chains with similar chemical properties. Simultaneously, it is of high importance to understand their role and behavior in biological systems. It has been known for decades now that GAGs can interact with lipid molecules and thus contribute to the onset of atherosclerosis, but their interactions at and with biological interfaces, such as the cell membrane, are yet to be revealed. Here, analytical approaches that could yield important knowledge on the GAG-cell membrane interactions as well as the synthetic and analytical advances that make their study possible are discussed. Due to recent developments in laser technology, we particularly focus on nonlinear spectroscopic methods, especially vibrational sum-frequency generation spectroscopy, which has the potential to unravel the structural complexity of heterogeneous biological interfaces in contact with GAGs, in situ and in real time.


Subject(s)
Glycosaminoglycans/chemistry , Lipids/chemistry , Cell Membrane/chemistry , Molecular Structure , Spectrum Analysis, Raman/methods
6.
Biosens Bioelectron ; 204: 114079, 2022 May 15.
Article in English | MEDLINE | ID: covidwho-1670218

ABSTRACT

We introduce a label-free surface-enhanced Raman scattering (SERS) biosensing platform equipped with metallic nanostructures that can identify the efficacy of Oxford-AstraZeneca (AZD1222) vaccine in vaccinated individuals using non-invasive tear samples. We confirmed the hypothesis that the tears of people who receive the AZD1222 vaccine may be similar to those of adenovirus epidemic keratoconjunctivitis patients since the Oxford-AstraZeneca vaccine is derived from a replication-deficient ChAdOx1 vector of chimpanzee adenovirus. Additionally, we confirmed the potential of the three markers for estimating the vaccination status via analyzing the signals emanating from antibodies or immunoglobulin G by-product using our label-free, SERS biosensing technique with a high reproducibility (<3% relative standard deviation), femtomole-scale limit of detection (1 × 10-14 M), and high SERS response of >108. Therefore, our label-free SERS biosensing nanoplatforms with long-term storage and robust stability will enable rapid and robust monitoring of the vaccine presence in vaccinated individuals.


Subject(s)
Biosensing Techniques , COVID-19 , Adenoviridae/genetics , Biosensing Techniques/methods , COVID-19/prevention & control , COVID-19 Vaccines , Humans , Reproducibility of Results , SARS-CoV-2 , Spectrum Analysis, Raman/methods , Vaccination
7.
ACS Appl Mater Interfaces ; 14(3): 4714-4724, 2022 Jan 26.
Article in English | MEDLINE | ID: covidwho-1655444

ABSTRACT

Surface-enhanced Raman scattering (SERS)-based biosensors are promising tools for virus nucleic acid detection. However, it remains challenging for SERS-based biosensors using a sandwiching strategy to detect long-chain nucleic acids such as nucleocapsid (N) gene of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) because the extension of the coupling distance (CD) between the two tethered metallic nanostructures weakens electric field and SERS signals. Herein, we report a magnetic-responsive substrate consisting of heteoronanostructures that controls the CD for ultrasensitive and highly selective detection of the N gene of SARS-CoV-2. Significantly, our findings show that this platform reversibly shortens the CD and enhances SERS signals with a 10-fold increase in the detection limit from 1 fM to 100 aM, compared to those without magnetic modulation. The optical simulation that emulates the CD shortening process confirms the CD-dependent electric field strength and further supports the experimental results. Our study provides new insights into designing a stimuli-responsive SERS-based platform with tunable hot spots for long-chain nucleic acid detection.


Subject(s)
Biosensing Techniques/methods , COVID-19/diagnosis , Nucleic Acids/isolation & purification , SARS-CoV-2/isolation & purification , COVID-19/genetics , COVID-19/virology , Gold/chemistry , Humans , Limit of Detection , Metal Nanoparticles/chemistry , Nucleic Acids/chemistry , SARS-CoV-2/chemistry , SARS-CoV-2/genetics , Silver/chemistry , Spectrum Analysis, Raman/methods
8.
ACS Nano ; 16(2): 2629-2639, 2022 02 22.
Article in English | MEDLINE | ID: covidwho-1634583

ABSTRACT

Population-wide surveillance of COVID-19 requires tests to be quick and accurate to minimize community transmissions. The detection of breath volatile organic compounds presents a promising option for COVID-19 surveillance but is currently limited by bulky instrumentation and inflexible analysis protocol. Here, we design a hand-held surface-enhanced Raman scattering-based breathalyzer to identify COVID-19 infected individuals in under 5 min, achieving >95% sensitivity and specificity across 501 participants regardless of their displayed symptoms. Our SERS-based breathalyzer harnesses key variations in vibrational fingerprints arising from interactions between breath metabolites and multiple molecular receptors to establish a robust partial least-squares discriminant analysis model for high throughput classifications. Crucially, spectral regions influencing classification show strong corroboration with reported potential COVID-19 breath biomarkers, both through experiment and in silico. Our strategy strives to spur the development of next-generation, noninvasive human breath diagnostic toolkits tailored for mass screening purposes.


Subject(s)
COVID-19 , Humans , Mass Screening , Point-of-Care Systems , SARS-CoV-2 , Spectrum Analysis, Raman/methods
9.
Anal Chim Acta ; 1193: 339406, 2022 Feb 08.
Article in English | MEDLINE | ID: covidwho-1623286

ABSTRACT

The COVID-19 pandemic negatively affected the economy and health security on a global scale, causing a drastic change on lifestyle, calling a need to mitigate further transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. Surface-enhanced Raman spectroscopy (SERS) has shown great potential in the sensitive and rapid detection of various molecules including viruses, through the identification of characteristic peaks of their outer membrane proteins. Accurate detection can be developed through the synergistic integration effect among SERS-active substrate, the appropriate laser wavelength, and the target analyte. In this study, gold nanocavities (Au NC) and Au nanoparticles upon ZrO2 nano-bowls (Au NPs/pZrO2) were tested and used as SERS-active substrates in detecting SARS-CoV-2 pseudovirus containing S protein as a surface capsid glycoprotein (SARS-CoV-2 S pseudovirus) and vesicular stomatitis virus G (VSV-G) pseudo-type lentivirus (VSV-G pseudovirus) to demonstrate their virus detection capability. The optimized Au NCs and Au NPs/pZrO2 substrates were then verified by examining the repetition of measurement, reproducibility, and detection limit. Due to the difference in geometry and composition of the substrates, the characteristic peak-positions of live SARS-CoV-2 S and VSV-G pseudoviruses in the obtained Raman spectra vary, which were also compared with those of inactivated ones. Based on the experimental results, SERS mechanism of each substrate to detect virus is proposed. The formation of hot spots brought by the synergistic integration effect among substrate, analyte, and laser induction may result differences in the obtained SERS spectra.


Subject(s)
COVID-19 , Metal Nanoparticles , Gold , Humans , Pandemics , Reproducibility of Results , SARS-CoV-2 , Spectrum Analysis, Raman
10.
Biosensors (Basel) ; 11(12)2021 Nov 30.
Article in English | MEDLINE | ID: covidwho-1596793

ABSTRACT

Surface-Enhanced Raman Spectroscopy (SERS)-based biomolecule detection has been a challenge due to large variations in signal intensity, spectral profile, and nonlinearity. Recent advances in machine learning offer great opportunities to address these issues. However, well-documented procedures for model development and evaluation, as well as benchmark datasets, are lacking. Towards this end, we provide the SERS spectral benchmark dataset of Rhodamine 6G (R6G) for a molecule detection task and evaluate the classification performance of several machine learning models. We also perform a comparative study to find the best combination between the preprocessing methods and the machine learning models. Our best model, coined as the SERSNet, robustly identifies R6G molecule with excellent independent test performance. In particular, SERSNet shows 95.9% balanced accuracy for the cross-batch testing task.


Subject(s)
Neural Networks, Computer , Spectrum Analysis, Raman , Machine Learning
11.
Spectrochim Acta A Mol Biomol Spectrosc ; 269: 120725, 2022 Mar 15.
Article in English | MEDLINE | ID: covidwho-1591497

ABSTRACT

The task of assembling and calculating spectrally significant lines of Vitamin D2 and D3 is related to a wider goal of establishing if it is possible to develop non-invasive optical sensors for these substances present at concentrations on the order of tens of nmol/L. Such a non-invasive in vivo sensor would be helpful for medical considerations, among others, related to multiple sclerosis prevention, reduced risk of mortality in D3-treated acute in-patients admitted with COVID 19, systemic infection, acute respiratory tract infections, including epidemic influenza, community-acquired pneumonia at concentrations <50nmol/L(<20ng/mL), dental health (90-100nmol/L) of 25(OH) D, general health and others. Currently, to determine the concentration of these substances, it is necessary to draw a sample from a vein in ambulatory settings and analyse the sample with the gold standard of mass spectroscopy or immunoassay. In this article Vitamin D optical properties are studied by density functional theory calculations, compared to reported data, and the new calculated and measured D2 and D3 optical absorption lines are presented, as well as the calculations compared with spectral measurements of optical transmission, FTIR ATR and Raman spectra.


Subject(s)
COVID-19 , Cholecalciferol , Ergocalciferols , Humans , SARS-CoV-2 , Spectrum Analysis, Raman , Vitamin D
12.
ACS Appl Mater Interfaces ; 14(1): 138-149, 2022 Jan 12.
Article in English | MEDLINE | ID: covidwho-1574636

ABSTRACT

Highly sensitive, reliable assays with strong multiplexing capability for detecting nucleic acid targets are significantly important for diagnosing various diseases, particularly severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The nanomaterial-based assay platforms suffer from several critical issues such as non-specific binding and highly false-positive results. In this paper, to overcome such limitations, we reported sensitive and remarkably reproducible magnetic microparticles (MMPs) and a surface-enhanced Raman scattering (SERS)-based assay using stable silver nanoparticle clusters for detecting viral nucleic acids. The MMP-SERS-based assay exhibited a sensitivity of 1.0 fM, which is superior to the MMP-fluorescence-based assay. In addition, in the presence of anisotropic Ag nanostructures (nanostars and triangular nanoplates), the assay exhibited greatly enhanced sensitivity (10 aM) and excellent signal reproducibility. This assay platform intrinsically eliminated the non-specific binding that occurs in the target detection step, and the controlled formation of stable silver nanoparticle clusters in solution enabled the remarkable reproducibility of the results. These findings indicate that this assay can be employed for future practical bioanalytical applications.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/diagnosis , Magnetite Nanoparticles/chemistry , COVID-19/virology , Coronavirus Envelope Proteins/genetics , Humans , Limit of Detection , Metal Nanoparticles/chemistry , RNA, Viral/analysis , RNA, Viral/chemistry , RNA-Dependent RNA Polymerase/genetics , Reproducibility of Results , SARS-CoV-2/isolation & purification , SARS-CoV-2/metabolism , Silver/chemistry , Spectrum Analysis, Raman
13.
Biosensors (Basel) ; 11(12)2021 Dec 10.
Article in English | MEDLINE | ID: covidwho-1572366

ABSTRACT

The current COVID-19 pandemic has increased the demand for pathogen detection methods that combine low detection limits with rapid results. Despite the significant progress in methods and devices for nucleic acid amplification, immunochemical methods are still preferred for mass testing without specialized laboratories and highly qualified personnel. The most widely used immunoassays are microplate enzyme-linked immunosorbent assay (ELISA) with photometric detection and lateral flow immunoassay (LFIA) with visual results assessment. However, the disadvantage of ELISA is its considerable duration, and that of LFIA is its low sensitivity. In this study, the modified LFIA of a specific antigen of the causative agent of COVID-19, spike receptor-binding domain, was developed and characterized. This modified LFIA includes the use of gold nanoparticles with immobilized antibodies and 4-mercaptobenzoic acid as surface-enhanced Raman scattering (SERS) nanotag and registration of the nanotag binding by SERS spectrometry. To enhance the sensitivity of LFIA-SERS analysis, we determined the optimal compositions of SERS nanotags and membranes used in LFIA. For benchmark comparison, ELISA and conventional colorimetric LFIA were used with the same immune reagents. The proposed method combines a low detection limit of 0.1 ng/mL (at 0.4 ng/mL for ELISA and 1 ng/mL for qualitative LFIA) with a short assay time equal to 20 min (at 3.5 h for ELISA and 15 min for LFIA). The results obtained demonstrate the promise of using the SERS effects in membrane immuno-analytical systems.


Subject(s)
COVID-19 Testing/methods , COVID-19 , Immunoassay , Metal Nanoparticles , Spectrum Analysis, Raman , Antigens, Viral/isolation & purification , COVID-19/diagnosis , Gold , Humans , SARS-CoV-2
14.
Chem Soc Rev ; 51(1): 329-375, 2022 Jan 04.
Article in English | MEDLINE | ID: covidwho-1569286

ABSTRACT

This review article deals with the concepts, principles and applications of visible-light and near-infrared (NIR) fluorescence and surface-enhanced Raman scattering (SERS) in in vitro point-of-care testing (POCT) and in vivo bio-imaging. It has discussed how to utilize the biological transparency windows to improve the penetration depth and signal-to-noise ratio, and how to use surface plasmon resonance (SPR) to amplify fluorescence and SERS signals. This article has highlighted some plasmonic fluorescence and SERS probes. It has also reviewed the design strategies of fluorescent and SERS sensors in the detection of metal ions, small molecules, proteins and nucleic acids. Particularly, it has provided perspectives on the integration of fluorescent and SERS sensors into microfluidic chips as lab-on-chips to realize point-of-care testing. It has also discussed the design of active microfluidic devices and non-paper- or paper-based lateral flow assays for in vitro diagnostics. In addition, this article has discussed the strategies to design in vivo NIR fluorescence and SERS bio-imaging platforms for monitoring physiological processes and disease progression in live cells and tissues. Moreover, it has highlighted the applications of POCT and bio-imaging in testing toxins, heavy metals, illicit drugs, cancers, traumatic brain injuries, and infectious diseases such as COVID-19, influenza, HIV and sepsis.


Subject(s)
COVID-19 , Nucleic Acids , Humans , Point-of-Care Systems , SARS-CoV-2 , Spectrum Analysis, Raman
15.
Adv Sci (Weinh) ; 9(3): e2103287, 2022 01.
Article in English | MEDLINE | ID: covidwho-1557802

ABSTRACT

The multiple mutations of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus have created variants with structural differences in both their spike and nucleocapsid proteins. While the functional relevance of these mutations is under continuous scrutiny, current findings have documented their detrimental impact in terms of affinity with host receptors, antibody resistance, and diagnostic sensitivity. Raman spectra collected on two British variant sub-types found in Japan (QK002 and QHN001) are compared with that of the original Japanese isolate (JPN/TY/WK-521), and found bold vibrational differences. These included: i) fractions of sulfur-containing amino acid rotamers, ii) hydrophobic interactions of tyrosine phenol ring, iii) apparent fractions of RNA purines and pyrimidines, and iv) protein secondary structures. Building upon molecular scale results and their statistical validations, the authors propose to represent virus variants with a barcode specially tailored on Raman spectrum. Raman spectroscopy enables fast identification of virus variants, while the Raman barcode facilitates electronic recordkeeping and translates molecular characteristics into information rapidly accessible by users.


Subject(s)
COVID-19 Testing , COVID-19/diagnosis , Nucleocapsid Proteins/chemistry , SARS-CoV-2/chemistry , Spectrum Analysis, Raman , Spike Glycoprotein, Coronavirus/chemistry , Humans , Nucleocapsid Proteins/genetics , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics , United Kingdom
16.
ACS Appl Mater Interfaces ; 13(40): 47996-48008, 2021 Oct 13.
Article in English | MEDLINE | ID: covidwho-1440455

ABSTRACT

Use of masks is a primary tool to prevent the spread of the novel COVID-19 virus resulting from unintentional close contact with infected individuals. However, detailed characterization of the chemical properties and physical structure of common mask materials is lacking in the current literature. In this study, a series of commercial masks and potential mask materials, including 3M Particulate Respirator 8210 N95, a material provided by Oak Ridge National Laboratory Carbon Fiber Technology Facility (ORNL/CFTF), and a Filti Face Mask Material, were characterized by a suite of techniques, including scanning electron microscopy, X-ray diffraction, Raman spectroscopy, and X-ray photoelectron spectroscopy. Wetting properties of the mask materials were quantified by measurements of contact angle with a saliva substitute. Mask pass-through experiments were performed using a dispersed metal oxide nanoparticle suspension to model the SARS-CoV-2 virus, with quantification via spatially resolved X-ray fluorescence mapping. Notably, all mask materials tested provided a strong barrier against respiratory droplet breakthrough. The comparisons and characterizations provided in this study provide useful information when evaluating mask materials for respiratory protection.


Subject(s)
Filtration , Masks , Materials Testing/methods , N95 Respirators , COVID-19/prevention & control , Metal Nanoparticles/chemistry , Microscopy, Electron, Scanning , Photoelectron Spectroscopy , Polyesters/chemistry , Polypropylenes/chemistry , Porosity , SARS-CoV-2 , Spectrum Analysis, Raman , Wettability , X-Ray Diffraction
17.
Sci Rep ; 11(1): 18444, 2021 09 16.
Article in English | MEDLINE | ID: covidwho-1415956

ABSTRACT

Over the past year, the world's attention has focused on combating COVID-19 disease, but the other threat waiting at the door-antimicrobial resistance should not be forgotten. Although making the diagnosis rapidly and accurately is crucial in preventing antibiotic resistance development, bacterial identification techniques include some challenging processes. To address this challenge, we proposed a deep neural network (DNN) that can discriminate antibiotic-resistant bacteria using surface-enhanced Raman spectroscopy (SERS). Stacked autoencoder (SAE)-based DNN was used for the rapid identification of methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-sensitive S. aureus (MSSA) bacteria using a label-free SERS technique. The performance of the DNN was compared with traditional classifiers. Since the SERS technique provides high signal-to-noise ratio (SNR) data, some subtle differences were found between MRSA and MSSA in relative band intensities. SAE-based DNN can learn features from raw data and classify them with an accuracy of 97.66%. Moreover, the model discriminates bacteria with an area under curve (AUC) of 0.99. Compared to traditional classifiers, SAE-based DNN was found superior in accuracy and AUC values. The obtained results are also supported by statistical analysis. These results demonstrate that deep learning has great potential to characterize and detect antibiotic-resistant bacteria by using SERS spectral data.


Subject(s)
Methicillin Resistance , Staphylococcus aureus/classification , Staphylococcus aureus/growth & development , Deep Learning , Discriminant Analysis , Humans , Metal Nanoparticles/chemistry , Microbial Sensitivity Tests , Neural Networks, Computer , Signal-To-Noise Ratio , Silver/chemistry , Spectrum Analysis, Raman , Staphylococcus aureus/drug effects , Support Vector Machine
18.
J Nanobiotechnology ; 19(1): 273, 2021 Sep 08.
Article in English | MEDLINE | ID: covidwho-1403239

ABSTRACT

The control of contagious or refractory diseases requires early, rapid diagnostic assays that are simple, fast, and easy-to-use. Here, easy-to-implement CRISPR/Cas12a-based diagnostic platform through Raman transducer generated by Raman enhancement effect, term as SERS-CRISPR (S-CRISPR), are described. The S-CRISPR uses high-activity noble metallic nanoscopic materials to increase the sensitivity in the detection of nucleic acids, without amplification. This amplification-free platform, which can be performed within 30-40 min of incubation time, is then used for detection of SARS-CoV-2 derived nucleic acids in RNA extracts obtained from nasopharyngeal swab specimens (n = 112). Compared with the quantitative reverse transcription polymerase chain reaction (RT-qPCR), the sensitivity and specificity of S-CRISPR reaches 87.50% and 100%, respectively. In general, the S-CRISPR can rapidly identify the RNA of SARS-CoV-2 RNA without amplification and is a potential strategy for nucleic acid point of care test (POCT).


Subject(s)
CRISPR-Cas Systems/genetics , Nucleic Acid Amplification Techniques , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Spectrum Analysis, Raman , COVID-19/diagnosis , COVID-19/virology , Gene Expression Regulation, Fungal , Genes, Viral , Humans , RNA, Viral/analysis , Sensitivity and Specificity
19.
ACS Sens ; 6(9): 3436-3444, 2021 09 24.
Article in English | MEDLINE | ID: covidwho-1397836

ABSTRACT

COVID-19 remains an ongoing issue across the globe, highlighting the need for a rapid, selective, and accurate sensor for SARS-CoV-2 and its emerging variants. The chemical specificity and signal amplification of surface-enhanced Raman spectroscopy (SERS) could be advantageous for developing a quantitative assay for SARS-CoV-2 with improved speed and accuracy over current testing methods. Here, we have tackled the challenges associated with SERS detection of viruses. As viruses are large, multicomponent species, they can yield different SERS signals, but also other abundant biomolecules present in the sample can generate undesired signals. To improve selectivity in complex biological environments, we have employed peptides as capture probes for viral proteins and developed an angiotensin-converting enzyme 2 (ACE2) mimetic peptide-based SERS sensor for SARS-CoV-2. The unique vibrational signature of the spike protein bound to the peptide-modified surface is identified and used to construct a multivariate calibration model for quantification. The sensor demonstrates a 300 nM limit of detection and high selectivity in the presence of excess bovine serum albumin. This work provides the basis for designing a SERS-based assay for the detection of SARS-CoV-2 as well as engineering SERS biosensors for other viruses in the future.


Subject(s)
Biosensing Techniques , COVID-19 , Humans , Peptides , SARS-CoV-2 , Spectrum Analysis, Raman
20.
Spectrochim Acta A Mol Biomol Spectrosc ; 264: 120269, 2022 Jan 05.
Article in English | MEDLINE | ID: covidwho-1351828

ABSTRACT

In the present work the temperature response of the constitutive S1 segment of the SARS-CoV-2 Spike Glycoprotein (GPS) has been studied. The intensity of the Raman bands remained almost constant before reaching a temperature of 133 °C. At this temperature a significant reduction of peak intensities was observed. Above 144 °C the spectra ceased to show any recognizable feature as that of the GPS S1, indicating that it had transformed after the denaturation process that it was subjected. The GPS S1 change is irreversible. Hence, Raman Spectroscopy (RS) provides a precision method to determine the denaturation temperature (TD) of dry powder GPS S1. The ability of RS was calibrated through the reproduction of TD of other well studied proteins as well as those of the decomposition temperature of some amino acids (AA). Through this study we established a TD of 139 ± 3 °C for powder GPS S1 of SARS-CoV-2.


Subject(s)
COVID-19 , Spike Glycoprotein, Coronavirus , Humans , SARS-CoV-2 , Spectrum Analysis, Raman , Temperature
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