1
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Wang R, Lu S, Deng F, Wu L, Yang G, Chong S, Liu Y. Enhancing the understanding of SARS-CoV-2 protein with structure and detection methods: An integrative review. Int J Biol Macromol 2024; 270:132237. [PMID: 38734351 DOI: 10.1016/j.ijbiomac.2024.132237] [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: 04/15/2024] [Accepted: 05/07/2024] [Indexed: 05/13/2024]
Abstract
As the rapid and accurate screening of infectious diseases can provide meaningful information for outbreak prevention and control, as well as owing to the existing limitations of the polymerase chain reaction (PCR), it is imperative to have new and validated detection techniques for SARS-CoV-2. Therefore, the rationale for outlining the techniques used to detect SARS-CoV-2 proteins and performing a comprehensive comparison to serve as a practical benchmark for future identification of similar viral proteins is clear. This review highlights the urgent need to strengthen pandemic preparedness by emphasizing the importance of integrated measures. These include improved tools for pathogen characterization, optimized societal precautions, the establishment of early warning systems, and the deployment of highly sensitive diagnostics for effective surveillance, triage, and resource management. Additionally, with an improved understanding of the virus' protein structure, considerable advances in targeted detection, treatment, and prevention strategies are expected to greatly improve our ability to respond to future outbreaks.
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Affiliation(s)
- Ruiqi Wang
- Shenyang University of Chemical Technology, Shenyang 110142, China; National Institute of Metrology, Beijing 100029, China
| | - Song Lu
- National Institute of Metrology, Beijing 100029, China
| | - Fanyu Deng
- National Institute of Metrology, Beijing 100029, China; North University of China, Taiyuan 030051, China
| | - Liqing Wu
- National Institute of Metrology, Beijing 100029, China
| | - Guowu Yang
- Shenzhen Academy of Metrology and Quality Inspection, Shenzhen 518055, China
| | - Siying Chong
- Shenyang University of Chemical Technology, Shenyang 110142, China
| | - Yahui Liu
- National Institute of Metrology, Beijing 100029, China.
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2
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Sagdat K, Batyrkhan A, Kanayeva D. Exploring monkeypox virus proteins and rapid detection techniques. Front Cell Infect Microbiol 2024; 14:1414224. [PMID: 38863833 PMCID: PMC11165096 DOI: 10.3389/fcimb.2024.1414224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 05/03/2024] [Indexed: 06/13/2024] Open
Abstract
Monkeypox (mpox) is an infectious disease caused by the mpox virus and can potentially lead to fatal outcomes. It resembles infections caused by viruses from other families, challenging identification. The pathogenesis, transmission, and clinical manifestations of mpox and other Orthopoxvirus species are similar due to their closely related genetic material. This review provides a comprehensive discussion of the roles of various proteins, including extracellular enveloped virus (EEV), intracellular mature virus (IMV), and profilin-like proteins of mpox. It also highlights recent diagnostic techniques based on these proteins to detect this infection rapidly.
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Affiliation(s)
| | | | - Damira Kanayeva
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
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3
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Haseeb MW, Toutounji M. Vibration assisted electron tunnelling in COVID-19 infection using quantum state diffusion. Sci Rep 2024; 14:12152. [PMID: 38802472 PMCID: PMC11130241 DOI: 10.1038/s41598-024-62670-3] [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: 11/01/2023] [Accepted: 05/20/2024] [Indexed: 05/29/2024] Open
Abstract
The spread of the COVID-19 virus has become a global health crisis, and finding effective treatments and preventions is a top priority. The field of quantum biology primarily focuses on energy or charge transfer, with a particular emphasis on photosynthesis. However, there is evidence to suggest that cellular receptors such as olfactory or neural receptors may also use vibration-assisted electron tunnelling to enhance their functions. Quantum tunnelling has also been observed in enzyme activity, which is relevant to the invasion of host cells by the SARS-CoV-2 virus. Additionally, COVID-19 appears to disrupt receptors such as olfactory receptors. These findings suggest that quantum effects could provide new insights into the mechanisms of biological systems and disease, including potential treatments for COVID-19. We have applied the open quantum system approach using Quantum State Diffusion to solve the non-linear stochastic Schrödinger equation (SSE) for COVID-19 virus infection. Our model includes the mechanism when the spike protein of the virus binds with an ACE2 receptor is considered as dimer. These two entities form a system and then coupled with the cell membrane, which is modelled as a set of harmonic oscillators (bath). By simulating the SSE, we find that there is vibration-assisted electron tunnelling happening in certain biological parameters and coupling regimes. Furthermore, our model contributes to the ongoing research to understand the fundamental nature of virus dynamics. It proposes that vibration-assisted electron tunneling could be a molecular phenomenon that augments the lock-and-key process for olfaction. This insight may enhance our understanding of the underlying mechanisms governing virus-receptor interactions and could potentially lead to the development of novel therapeutic strategies.
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Affiliation(s)
| | - Mohamad Toutounji
- Department of Chemistry, United Arab Emirates University, Al-Ain, UAE.
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4
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Lu XY, Wu HP, Ma H, Li H, Li J, Liu YT, Pan ZY, Xie Y, Wang L, Ren B, Liu GK. Deep Learning-Assisted Spectrum-Structure Correlation: State-of-the-Art and Perspectives. Anal Chem 2024; 96:7959-7975. [PMID: 38662943 DOI: 10.1021/acs.analchem.4c01639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Spectrum-structure correlation is playing an increasingly crucial role in spectral analysis and has undergone significant development in recent decades. With the advancement of spectrometers, the high-throughput detection triggers the explosive growth of spectral data, and the research extension from small molecules to biomolecules accompanies massive chemical space. Facing the evolving landscape of spectrum-structure correlation, conventional chemometrics becomes ill-equipped, and deep learning assisted chemometrics rapidly emerges as a flourishing approach with superior ability of extracting latent features and making precise predictions. In this review, the molecular and spectral representations and fundamental knowledge of deep learning are first introduced. We then summarize the development of how deep learning assist to establish the correlation between spectrum and molecular structure in the recent 5 years, by empowering spectral prediction (i.e., forward structure-spectrum correlation) and further enabling library matching and de novo molecular generation (i.e., inverse spectrum-structure correlation). Finally, we highlight the most important open issues persisted with corresponding potential solutions. With the fast development of deep learning, it is expected to see ultimate solution of establishing spectrum-structure correlation soon, which would trigger substantial development of various disciplines.
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Affiliation(s)
- Xin-Yu Lu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
- Tan Kah Kee Innovation Laboratory, Xiamen 361005, P. R. China
| | - Hao-Ping Wu
- State Key Laboratory of Marine Environmental Science, Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Center for Marine Environmental Chemistry & Toxicology, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, P. R. China
| | - Hao Ma
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
- Tan Kah Kee Innovation Laboratory, Xiamen 361005, P. R. China
| | - Hui Li
- Key Laboratory of Multimedia Trusted Perception and Efficient Computing, Ministry of Education of China, Xiamen University, Xiamen 361005, P. R. China
| | - Jia Li
- Institute of Artificial Intelligence, Xiamen University, Xiamen 361005, P. R. China
| | - Yan-Ti Liu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
- Tan Kah Kee Innovation Laboratory, Xiamen 361005, P. R. China
| | - Zheng-Yan Pan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Yi Xie
- School of Informatics, Xiamen University, Xiamen 361005, P. R. China
| | - Lei Wang
- Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen 361005, P. R. China
| | - Bin Ren
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
- Tan Kah Kee Innovation Laboratory, Xiamen 361005, P. R. China
| | - Guo-Kun Liu
- State Key Laboratory of Marine Environmental Science, Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Center for Marine Environmental Chemistry & Toxicology, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, P. R. China
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5
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Nandipati M, Fatoki O, Desai S. Bridging Nanomanufacturing and Artificial Intelligence-A Comprehensive Review. MATERIALS (BASEL, SWITZERLAND) 2024; 17:1621. [PMID: 38612135 PMCID: PMC11012965 DOI: 10.3390/ma17071621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/05/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024]
Abstract
Nanomanufacturing and digital manufacturing (DM) are defining the forefront of the fourth industrial revolution-Industry 4.0-as enabling technologies for the processing of materials spanning several length scales. This review delineates the evolution of nanomaterials and nanomanufacturing in the digital age for applications in medicine, robotics, sensory technology, semiconductors, and consumer electronics. The incorporation of artificial intelligence (AI) tools to explore nanomaterial synthesis, optimize nanomanufacturing processes, and aid high-fidelity nanoscale characterization is discussed. This paper elaborates on different machine-learning and deep-learning algorithms for analyzing nanoscale images, designing nanomaterials, and nano quality assurance. The challenges associated with the application of machine- and deep-learning models to achieve robust and accurate predictions are outlined. The prospects of incorporating sophisticated AI algorithms such as reinforced learning, explainable artificial intelligence (XAI), big data analytics for material synthesis, manufacturing process innovation, and nanosystem integration are discussed.
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Affiliation(s)
- Mutha Nandipati
- Department of Industrial and Systems Engineering, North Carolina Agricultural and Technical State University, Greensboro, NC 27411, USA; (M.N.); (O.F.)
| | - Olukayode Fatoki
- Department of Industrial and Systems Engineering, North Carolina Agricultural and Technical State University, Greensboro, NC 27411, USA; (M.N.); (O.F.)
| | - Salil Desai
- Department of Industrial and Systems Engineering, North Carolina Agricultural and Technical State University, Greensboro, NC 27411, USA; (M.N.); (O.F.)
- Center of Excellence in Product Design and Advanced Manufacturing, North Carolina Agricultural and Technical State University, Greensboro, NC 27411, USA
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6
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Lu XY, Wang CY, Tang H, Qin YF, Cui L, Wang X, Liu GK, Ren B. Patch-Based Convolutional Encoder: A Deep Learning Algorithm for Spectral Classification Balancing the Local and Global Information. Anal Chem 2024. [PMID: 38324760 DOI: 10.1021/acs.analchem.3c03889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Molecular vibrational spectroscopies, including infrared absorption and Raman scattering, provide molecular fingerprint information and are powerful tools for qualitative and quantitative analysis. They benefit from the recent development of deep-learning-based algorithms to improve the spectral, spatial, and temporal resolutions. Although a variety of deep-learning-based algorithms, including those to simultaneously extract the global and local spectral features, have been developed for spectral classification, the classification accuracy is still far from satisfactory when the difference becomes very subtle. Here, we developed a lightweight algorithm named patch-based convolutional encoder (PACE), which effectively improved the accuracy of spectral classification by extracting spectral features while balancing local and global information. The local information was captured well by segmenting the spectrum into patches with an appropriate patch size. The global information was extracted by constructing the correlation between different patches with depthwise separable convolutions. In the five open-source spectral data sets, PACE achieved a state-of-the-art performance. The more difficult the classification, the better the performance of PACE, compared with that of residual neural network (ResNet), vision transformer (ViT), and other commonly used deep learning algorithms. PACE helped improve the accuracy to 92.1% in Raman identification of pathogen-derived extracellular vesicles at different physiological states, which is much better than those of ResNet (85.1%) and ViT (86.0%). In general, the precise recognition and extraction of subtle differences offered by PACE are expected to facilitate vibrational spectroscopy to be a powerful tool toward revealing the relevant chemical reaction mechanisms in surface science or realizing the early diagnosis in life science.
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Affiliation(s)
- Xin-Yu Lu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Chen-Yue Wang
- Institute of Artificial Intelligence, Xiamen University, Xiamen 361005, China
| | - Hui Tang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yi-Fei Qin
- Xiamen Key Laboratory of Indoor Air and Health, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Cui
- Xiamen Key Laboratory of Indoor Air and Health, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiang Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Tan Kah Kee Innovation Laboratory, Xiamen 361005, China
| | - Guo-Kun Liu
- State Key Laboratory of Marine Environmental Science, Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Center for Marine Environmental Chemistry & Toxicology, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Bin Ren
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Institute of Artificial Intelligence, Xiamen University, Xiamen 361005, China
- Tan Kah Kee Innovation Laboratory, Xiamen 361005, China
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7
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Chen L, Guo H, Wang C, Chen B, Sassa F, Hayashi K. Two-Dimensional SERS Sensor Array for Identifying and Visualizing the Gas Spatial Distributions of Two Distinct Odor Sources. SENSORS (BASEL, SWITZERLAND) 2024; 24:790. [PMID: 38339509 PMCID: PMC10857130 DOI: 10.3390/s24030790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024]
Abstract
The spatial distribution of gas emitted from an odor source provides valuable information regarding the composition, size, and localization of the odor source. Surface-enhanced Raman scattering (SERS) gas sensors exhibit ultra-high sensitivity, molecular specificity, rapid response, and large-area detection. In this paper, a SERS gas sensor array was developed for visualizing the spatial distribution of gas evaporated from benzaldehyde and 4-ethylbenzaldehyde odor sources. The SERS spectra of the gas were collected by scanning the sensor array using an automatic detection system. The non-negative matrix factorization algorithm was employed to extract feature and concentration information at each spot on the sensor array. A heatmap image was generated for visualizing the gas spatial distribution using concentration information. Gaussian fitting was applied to process the image for localizing the odor source. The size of the odor source was estimated using the processed image. Moreover, the spectra of benzaldehyde, 4-ethylbenzaldehyde, and their gas mixture were simultaneously detected using one SERS sensor array. The feature information was recognized using a convolutional neural network with an accuracy of 98.21%. As a result, the benzaldehyde and 4-ethylbenzaldehyde odor sources were identified and visualized. Our research findings have various potential applications, including odor source localization, environmental monitoring, and healthcare.
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Affiliation(s)
- Lin Chen
- Department of Information Science, Joint Graduate School of Mathematics for Innovation, Kyushu University, Fukuoka 819-0395, Japan
| | - Hao Guo
- Department of Electronics, Graduate School of Information Science and Electrical Engineering, Kyushu University, Fukuoka 819-0395, Japan; (H.G.); (C.W.); (F.S.)
| | - Cong Wang
- Department of Electronics, Graduate School of Information Science and Electrical Engineering, Kyushu University, Fukuoka 819-0395, Japan; (H.G.); (C.W.); (F.S.)
| | - Bin Chen
- Chongqing Key Laboratory of Non-Linear Circuit and Intelligent Information Processing, College of Electronic and Information Engineering, Southwest University, Chongqing 400715, China;
| | - Fumihiro Sassa
- Department of Electronics, Graduate School of Information Science and Electrical Engineering, Kyushu University, Fukuoka 819-0395, Japan; (H.G.); (C.W.); (F.S.)
| | - Kenshi Hayashi
- Department of Electronics, Graduate School of Information Science and Electrical Engineering, Kyushu University, Fukuoka 819-0395, Japan; (H.G.); (C.W.); (F.S.)
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8
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Qin J, Tian X, Liu S, Yang Z, Shi D, Xu S, Zhang Y. Rapid classification of SARS-CoV-2 variant strains using machine learning-based label-free SERS strategy. Talanta 2024; 267:125080. [PMID: 37678002 DOI: 10.1016/j.talanta.2023.125080] [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: 03/03/2023] [Revised: 08/05/2023] [Accepted: 08/13/2023] [Indexed: 09/09/2023]
Abstract
The spread of COVID-19 over the past three years is largely due to the continuous mutation of the virus, which has significantly impeded global efforts to prevent and control this epidemic. Specifically, mutations in the amino acid sequence of the surface spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have directly impacted its biological functions, leading to enhanced transmission and triggering an immune escape effect. Therefore, prompt identification of these mutations is crucial for formulating targeted treatment plans and implementing precise prevention and control measures. In this study, the label-free surface-enhanced Raman scattering (SERS) technology combined with machine learning (ML) algorithms provide a potential solution for accurate identification of SARS-CoV-2 variants. We establish a SERS spectral database of SARS-CoV-2 variants and demonstrate that a diagnostic classifier using a logistic regression (LR) algorithm can provide accurate results within 10 min. Our classifier achieves 100% accuracy for Beta (B.1.351/501Y.V2), Delta (B.1.617), Wuhan (COVID-19) and Omicron (BA.1) variants. In addition, our method achieves 100% accuracy in blind tests of positive and negative human nasal swabs based on the LR model. This method enables detection and classification of variants in complex biological samples. Therefore, ML-based SERS technology is expected to accurately discriminate various SARS-CoV-2 variants and may be used for rapid diagnosis and therapeutic decision-making.
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Affiliation(s)
- Jingwang Qin
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, PR China; Department of Translational Medicine, Xiamen Institute of Rare Earth Materials, Haixi Institute, Chinese Academy of Sciences, Xiamen, 361021, PR China
| | - Xiangdong Tian
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, PR China; Department of Translational Medicine, Xiamen Institute of Rare Earth Materials, Haixi Institute, Chinese Academy of Sciences, Xiamen, 361021, PR China
| | - Siying Liu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, PR China; Department of Translational Medicine, Xiamen Institute of Rare Earth Materials, Haixi Institute, Chinese Academy of Sciences, Xiamen, 361021, PR China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhengxia Yang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, PR China; Department of Translational Medicine, Xiamen Institute of Rare Earth Materials, Haixi Institute, Chinese Academy of Sciences, Xiamen, 361021, PR China; University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Dawei Shi
- National Institutes for Food and Drug Control, Beijing, 100050, China.
| | - Sihong Xu
- National Institutes for Food and Drug Control, Beijing, 100050, China.
| | - Yun Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, PR China; Department of Translational Medicine, Xiamen Institute of Rare Earth Materials, Haixi Institute, Chinese Academy of Sciences, Xiamen, 361021, PR China; University of the Chinese Academy of Sciences, Beijing, 100049, China.
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9
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Akdeniz M, Al-Shaebi Z, Altunbek M, Bayraktar C, Kayabolen A, Bagci-Onder T, Aydin O. Characterization and discrimination of spike protein in SARS-CoV-2 virus-like particles via surface-enhanced Raman spectroscopy. Biotechnol J 2024; 19:e2300191. [PMID: 37750467 DOI: 10.1002/biot.202300191] [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: 04/30/2023] [Revised: 09/11/2023] [Accepted: 09/22/2023] [Indexed: 09/27/2023]
Abstract
Non-infectious virus-like particles (VLPs) are excellent structures for development of many biomedical applications such as drug delivery systems, vaccine production platforms, and detection techniques for infectious diseases including SARS-CoV-2 VLPs. The characterization of biochemical and biophysical properties of purified VLPs is crucial for development of detection methods and therapeutics. The presence of spike (S) protein in their structure is especially important since S protein induces immunological response. In this study, development of a rapid, low-cost, and easy-to-use technique for both characterization and detection of S protein in the two VLPs, which are SARS-CoV-2 VLPs and HIV-based VLPs was achieved using surface-enhanced Raman spectroscopy (SERS). To analyze and classify datasets of SERS spectra obtained from the VLP groups, machine learning classification techniques including support vector machine (SVM), k-nearest neighbors (kNN), and random forest (RF) were utilized. Among them, the SVM classification algorithm demonstrated the best classification performance for SARS-CoV-2 VLPs and HIV-based VLPs groups with 87.5% and 92.5% accuracy, respectively. This study could be valuable for the rapid characterization of VLPs for the development of novel therapeutics or detection of structural proteins of viruses leading to a variety of infectious diseases.
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Affiliation(s)
- Munevver Akdeniz
- Department of Biomedical Engineering, Erciyes University, Kayseri, Turkey
- Nanothera Lab, Drug Application and Research Center (ERFARMA), Erciyes University, Kayseri, Turkey
| | - Zakarya Al-Shaebi
- Department of Biomedical Engineering, Erciyes University, Kayseri, Turkey
- Nanothera Lab, Drug Application and Research Center (ERFARMA), Erciyes University, Kayseri, Turkey
| | - Mine Altunbek
- Department of Chemical Engineering, University of Massachusetts, Lowell, Massachusetts, USA
| | - Canan Bayraktar
- Koç University Research Center for Translational Medicine (KUTTAM), Koç University, Istanbul, Turkey
| | - Alisan Kayabolen
- Koç University Research Center for Translational Medicine (KUTTAM), Koç University, Istanbul, Turkey
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Tugba Bagci-Onder
- Koç University Research Center for Translational Medicine (KUTTAM), Koç University, Istanbul, Turkey
| | - Omer Aydin
- Department of Biomedical Engineering, Erciyes University, Kayseri, Turkey
- Nanothera Lab, Drug Application and Research Center (ERFARMA), Erciyes University, Kayseri, Turkey
- Clinical Engineering Research and Implementation Center (ERKAM), Erciyes University, Kayseri, Turkey
- Nanotechnology Research and Application Center (ERNAM), Erciyes University, Kayseri, Turkey
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10
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Haapakoski M, Emelianov A, Reshamwala D, Laajala M, Tienaho J, Kilpeläinen P, Liimatainen J, Jyske T, Pettersson M, Marjomäki V. Antiviral functionalization of cellulose using tannic acid and tannin-rich extracts. Front Microbiol 2023; 14:1287167. [PMID: 38125579 PMCID: PMC10731304 DOI: 10.3389/fmicb.2023.1287167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/13/2023] [Indexed: 12/23/2023] Open
Abstract
Due to seasonally appearing viruses and several outbreaks and present pandemic, we are surrounded by viruses in our everyday life. In order to reduce viral transmission, functionalized surfaces that inactivate viruses are in large demand. Here the endeavor was to functionalize cellulose-based materials with tannic acid (TA) and tannin-rich extracts by using different binding polymers to prevent viral infectivity of both non-enveloped coxsackievirus B3 (CVB3) and enveloped human coronavirus OC43 (HCoV-OC43). Direct antiviral efficacy of TA and spruce bark extract in solution was measured: EC50 for CVB3 was 0.12 and 8.41 μg/ml and for HCoV-OC43, 78.16 and 95.49 μg/ml, respectively. TA also led to an excellent 5.8- to 7-log reduction of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus infectivity. TA functionalized materials reduced infectivity already after 5-min treatment at room temperature. All the tested methods to bind TA showed efficacy on paperboard with 0.1 to 1% (w/v) TA concentrations against CVB3 whereas material hydrophobicity decreased activities. Specific signatures for TA and HCoV-OC43 were discovered by Raman spectroscopy and showed clear co-localization on the material. qPCR study suggested efficient binding of CVB3 to the TA functionalized cellulose whereas HCoV-OC43 was flushed out from the surfaces more readily. In conclusion, the produced TA-materials showed efficient and broadly acting antiviral efficacy. Additionally, the co-localization of TA and HCoV-OC43 and strong binding of CVB3 to the functionalized cellulose demonstrates an interaction with the surfaces. The produced antiviral surfaces thus show promise for future use to increase biosafety and biosecurity by reducing pathogen persistence.
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Affiliation(s)
- Marjo Haapakoski
- Department of Biological and Environmental Sciences/Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Aleksei Emelianov
- Department of Chemistry/Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Dhanik Reshamwala
- Department of Biological and Environmental Sciences/Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Mira Laajala
- Department of Biological and Environmental Sciences/Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Jenni Tienaho
- Production Systems Unit, Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Petri Kilpeläinen
- Production Systems Unit, Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Jaana Liimatainen
- Production Systems Unit, Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Tuula Jyske
- Production Systems Unit, Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Mika Pettersson
- Department of Chemistry/Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Varpu Marjomäki
- Department of Biological and Environmental Sciences/Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
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11
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Chen Y, Feng L, Han Y, Zhao Z, Diao Z, Huang T, Ma Y, Feng W, Li J, Li Z, Liu C, Chang L, Li J, Zhang R. Performance evaluation of SARS-CoV-2 antigen detection in the post-pandemic era: multi-laboratory assessment. Clin Chem Lab Med 2023; 61:2237-2247. [PMID: 37377068 DOI: 10.1515/cclm-2023-0597] [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: 04/22/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023]
Abstract
OBJECTIVES Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antigen detection is an indispensable tool for epidemic surveillance in the post-pandemic era. Faced with irregular performance, a comprehensive external quality assessment (EQA) scheme was conducted by the National Center for Clinical Laboratories (NCCL) to evaluate the analytical performance and status of SARS-CoV-2 antigen tests. METHODS The EQA panel included ten lyophilized samples containing serial 5-fold dilutions of inactivated SARS-CoV-2-positive supernatants of the Omicron BA.1 and BA.5 strains and negative samples, which were classified into "validating" samples and "educational" samples. Data were analyzed according to qualitative results for each sample. RESULTS A total of 339 laboratories in China participated in this EQA scheme, and 378 effective results were collected. All validating samples were correctly reported by 90.56 % (307/339) of the participants and 90.21 % (341/378) of the datasets. The positive percent agreement (PPA) was >99 % for samples with concentrations of 2 × 107 copies/mL but was 92.20 % (697/756) for 4 × 106 copies/mL and 25.26 % (382/1,512) for 8 × 105 copies/mL samples. Colloidal gold was the most frequently used (84.66 %, 320/378) but showed the lowest PPAs (57.11 %, 1,462/2,560) for positive samples compared with fluorescence immunochromatography (90 %, 36/40) and latex chromatography (79.01 %, 335/424). Among 11 assays used in more than 10 clinical laboratories, ACON showed a higher sensitivity than other assays. CONCLUSIONS The EQA study can help to validate whether it's necessary to update antigen detection assays for manufacturers and provide participants with information about the performance of assays to take the first step toward routine post-market surveillance.
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Affiliation(s)
- Yuqing Chen
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P.R. China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Lei Feng
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P.R. China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Yanxi Han
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Zihong Zhao
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
- Peking University Fifth School of Clinical Medicine, Beijing, P.R. China
| | - Zhenli Diao
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P.R. China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Tao Huang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P.R. China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Yu Ma
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P.R. China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Wanyu Feng
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P.R. China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Jing Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P.R. China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Ziqiang Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P.R. China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Cong Liu
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P.R. China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Lu Chang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P.R. China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P.R. China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, P.R. China
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P.R. China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P.R. China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P.R. China
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, P.R. China
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12
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Tian Y, Cao Y, Zha G, Chen KE, Khan MI, Ren J, Liu W, Wang Y, Zhang Q, Cao C. Marker-Free Isoelectric Focusing Patterns for Identification of Meat Samples via Deep Learning. Anal Chem 2023; 95:13941-13948. [PMID: 37653711 DOI: 10.1021/acs.analchem.3c02461] [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: 09/02/2023]
Abstract
Isoelectric focusing (IEF) is a powerful tool for resolving complex protein samples, which generates IEF patterns consisting of multiplex analyte bands. However, the interpretation of IEF patterns requires the careful selection of isoelectric point (pI) markers for profiling the pH gradient and a trivial process of pI labeling, resulting in low IEF efficiency. Here, we for the first time proposed a marker-free IEF method for the efficient and accurate classification of IEF patterns by using a convolutional neural network (CNN) model. To verify our method, we identified 21 meat samples whose IEF patterns comprised different bands of meat hemoglobin, myoglobin, and their oxygen-binding variants but no pI marker. Thanks to the high throughput and short assay time of the microstrip IEF, we efficiently collected 1449 IEF patterns to construct the data set for model training. Despite the absence of pI markers, we experimentally introduced the severe pH gradient drift into 189 IEF patterns in the data set, thereby omitting the need for profiling the pH gradient. To enhance the model robustness, we further employed data augmentation during the model training to mimic pH gradient drift. With the advantages of simple preprocessing, a rapid inference of 50 ms, and a high accuracy of 97.1%, the CNN model outperformed the traditional algorithm for simultaneously identifying meat species and cuts of meat of 105 IEF patterns, suggesting its great potential of being combined with microstrip IEF for large-scale IEF analyses of complicated protein samples.
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Affiliation(s)
- Youli Tian
- School of Life Sciences and Biotechnology, State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Sensing Science and Engineering, School of Electronic Information & Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yiren Cao
- School of Sensing Science and Engineering, School of Electronic Information & Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Genhan Zha
- School of Sensing Science and Engineering, School of Electronic Information & Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ke-Er Chen
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 200240, China
| | - Muhammad Idrees Khan
- School of Sensing Science and Engineering, School of Electronic Information & Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jicun Ren
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Weiwen Liu
- School of Sensing Science and Engineering, School of Electronic Information & Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuxing Wang
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiang Zhang
- School of Sensing Science and Engineering, School of Electronic Information & Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chengxi Cao
- School of Life Sciences and Biotechnology, State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Sensing Science and Engineering, School of Electronic Information & Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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13
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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.
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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.
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14
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Andrzejewska W, Peplińska B, Litowczenko J, Obstarczyk P, Olesiak-Bańska J, Jurga S, Lewandowski M. SARS-CoV-2 Virus-like Particles with Plasmonic Au Cores and S1-Spike Protein Coronas. ACS Synth Biol 2023; 12:2320-2328. [PMID: 37449651 PMCID: PMC10443039 DOI: 10.1021/acssynbio.3c00133] [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: 03/03/2023] [Indexed: 07/18/2023]
Abstract
The COVID-19 pandemic has stimulated the scientific world to intensify virus-related studies aimed at the development of quick and safe ways of detecting viruses in the human body, studying the virus-antibody and virus-cell interactions, and designing nanocarriers for targeted antiviral therapies. However, research on dangerous viruses can only be performed in certified laboratories that follow strict safety procedures. Thus, developing deactivated virus constructs or safe-to-use virus-like objects, which imitate real viruses and allow performing virus-related studies in any research laboratory, constitutes an important scientific challenge. Such species, called virus-like particles (VLPs), contain instead of capsids with viral DNA/RNA empty or synthetic cores with real virus proteins attached to them. We have developed a method for the preparation of VLPs imitating the virus responsible for the COVID-19 disease: the SARS-CoV-2. The particles have Au cores surrounded by "coronas" of S1 domains of the virus's spike protein. Importantly, they are safe to use and specifically interact with SARS-CoV-2 antibodies. Moreover, Au cores exhibit localized surface plasmon resonance (LSPR), which makes the synthesized VLPs suitable for biosensing applications. During the studies, the effect allowed us to visualize the interaction between the VLPs and the antibodies and identify the characteristic vibrational signals. What is more, additional functionalization of the particles with a fluorescent label revealed their potential in studying specific virus-related interactions. Notably, the universal character of the developed synthesis method makes it potentially applicable for fabricating VLPs imitating other life-threatening viruses.
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Affiliation(s)
- Weronika Andrzejewska
- NanoBioMedical
Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznań, Poland
| | - Barbara Peplińska
- NanoBioMedical
Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznań, Poland
| | - Jagoda Litowczenko
- NanoBioMedical
Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznań, Poland
| | - Patryk Obstarczyk
- Institute
of Advanced Materials, Wroclaw University
of Science and Technology, Wybrzeże Wyspiańskiego 2, 50-370 Wrocław, Poland
| | - Joanna Olesiak-Bańska
- Institute
of Advanced Materials, Wroclaw University
of Science and Technology, Wybrzeże Wyspiańskiego 2, 50-370 Wrocław, Poland
| | - Stefan Jurga
- NanoBioMedical
Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznań, Poland
| | - Mikołaj Lewandowski
- NanoBioMedical
Centre, Adam Mickiewicz University, Wszechnicy Piastowskiej 3, 61-614 Poznań, Poland
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15
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Wetzel C, Jansen-Olliges L, Stadler M, Surup F, Zeilinger C, Roth B. Analysis of SARS-CoV-2 spike RBD binding to ACE2 and its inhibition by fungal cohaerin C using surface enhanced Raman spectroscopy. BIOMEDICAL OPTICS EXPRESS 2023; 14:4097-4111. [PMID: 37799683 PMCID: PMC10549735 DOI: 10.1364/boe.495685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/14/2023] [Accepted: 06/26/2023] [Indexed: 10/07/2023]
Abstract
The structure of the SARS-CoV-2 spike RBD and human ACE2 as well as changes in the structure due to binding activities were analysed using surface enhanced Raman spectroscopy. The inhibitor cohaerin C was applied to inhibit the binding between spike RBD and ACE2. Differences and changes in the Raman spectra were determined using deconvolution of the amide bands and principal component analysis. We thus demonstrate a fast and label-free analysis of the protein structures and the differentiation between bound and unbound states. The approach is suitable for sensing and screening and might be relevant to investigate other protein systems as well.
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Affiliation(s)
- Christoph Wetzel
- Leibniz University Hannover, Hannover Centre for Optical Technologies, Nienburger Str. 17, 30167 Hannover, Germany
| | - Linda Jansen-Olliges
- Leibniz University Hannover, Centre of Biomolecular Drug Research, Schneiderberg 38, 30167 Hannover, Germany
| | - Marc Stadler
- Helmholtz Centre for Infection Research GmbH, Department Microbial Drugs, Inhoffenstraße 7, 38124 Braunschweig, Germany
- Technische Universität Braunschweig, Institute of Microbiology, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Frank Surup
- Helmholtz Centre for Infection Research GmbH, Department Microbial Drugs, Inhoffenstraße 7, 38124 Braunschweig, Germany
- Technische Universität Braunschweig, Institute of Microbiology, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Carsten Zeilinger
- Leibniz University Hannover, Centre of Biomolecular Drug Research, Schneiderberg 38, 30167 Hannover, Germany
| | - Bernhard Roth
- Leibniz University Hannover, Hannover Centre for Optical Technologies, Nienburger Str. 17, 30167 Hannover, Germany
- Leibniz University Hannover, Cluster of Excellence PhoenixD, Welfenplatz 1, 30167 Hannover, Germany
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16
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Zhang Z, Jiang H, Jiang S, Dong T, Wang X, Wang Y, Li Y. Rapid Detection of the Monkeypox Virus Genome and Antigen Proteins Based on Surface-Enhanced Raman Spectroscopy. ACS APPLIED MATERIALS & INTERFACES 2023; 15:34419-34426. [PMID: 37436060 DOI: 10.1021/acsami.3c04285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
The conventional detection methods cannot satisfy the need for early and rapid detection of monkeypox virus (MPXV) infection. This is due to complicated pretreatment, time consumption, and complex operation of the diagnostic tests. Based on surface-enhanced Raman spectroscopy (SERS), this study attempted to capture the characteristic fingerprints of the MPXV genome and multiple antigenic proteins without the need to design specific probes. The minimum detection limit of this method is 100 copies/mL, with good reproducibility and signal-to-noise ratio. Therefore, the relationship between characteristic peak intensity and the protein and nucleic acid concentration can be used to construct a concentration-dependent spectral line with a good linear relationship. Additionally, principal component analysis (PCA) could identify the SERS spectra of four different MPXV proteins in serum. Therefore, this rapid detection method in the current outbreak of monkeypox control and the future response to possible new outbreaks has broad application prospects.
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Affiliation(s)
- Zhe Zhang
- State Key Laboratory of Frigid Zone Cardiovascular Diseases (SKLFZCD), College of Pharmacy, Harbin Medical University, Baojian Road No. 157, Harbin 150081, Heilongjiang, China
| | - Heng Jiang
- College of Public Health, Harbin Medical University, Baojian Road No. 157, Harbin 150081, Heilongjiang, China
| | - Shen Jiang
- State Key Laboratory of Frigid Zone Cardiovascular Diseases (SKLFZCD), College of Pharmacy, Harbin Medical University, Baojian Road No. 157, Harbin 150081, Heilongjiang, China
| | - Tuo Dong
- College of Public Health, Harbin Medical University, Baojian Road No. 157, Harbin 150081, Heilongjiang, China
| | - Xiaotong Wang
- State Key Laboratory of Frigid Zone Cardiovascular Diseases (SKLFZCD), College of Pharmacy, Harbin Medical University, Baojian Road No. 157, Harbin 150081, Heilongjiang, China
| | - Yunpeng Wang
- State Key Laboratory of Frigid Zone Cardiovascular Diseases (SKLFZCD), College of Pharmacy, Harbin Medical University, Baojian Road No. 157, Harbin 150081, Heilongjiang, China
| | - Yang Li
- State Key Laboratory of Frigid Zone Cardiovascular Diseases (SKLFZCD), College of Pharmacy, Harbin Medical University, Baojian Road No. 157, Harbin 150081, Heilongjiang, China
- Research Unit of Health Sciences and Technology (HST), Faculty of Medicine, University of Oulu, Oulu 90220, Finland
- Genomics Research Center (Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province), College of Pharmacy, Harbin Medical University, Harbin 150081, China
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17
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Gong L, Martinez O, Mesquita P, Kurtz K, Xu Y, Lin Y. A microfluidic approach for label-free identification of small-sized microplastics in seawater. Sci Rep 2023; 13:11011. [PMID: 37419935 PMCID: PMC10329028 DOI: 10.1038/s41598-023-37900-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/29/2023] [Indexed: 07/09/2023] Open
Abstract
Marine microplastics are emerging as a growing environmental concern due to their potential harm to marine biota. The substantial variations in their physical and chemical properties pose a significant challenge when it comes to sampling and characterizing small-sized microplastics. In this study, we introduce a novel microfluidic approach that simplifies the trapping and identification process of microplastics in surface seawater, eliminating the need for labeling. We examine various models, including support vector machine, random forest, convolutional neural network (CNN), and residual neural network (ResNet34), to assess their performance in identifying 11 common plastics. Our findings reveal that the CNN method outperforms the other models, achieving an impressive accuracy of 93% and a mean area under the curve of 98 ± 0.02%. Furthermore, we demonstrate that miniaturized devices can effectively trap and identify microplastics smaller than 50 µm. Overall, this proposed approach facilitates efficient sampling and identification of small-sized microplastics, potentially contributing to crucial long-term monitoring and treatment efforts.
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Affiliation(s)
- Liyuan Gong
- Department of Mechanical, Industrial and Systems Engineering, University of Rhode Island, Kingston, RI, USA
| | - Omar Martinez
- Department of Mechanical, Industrial and Systems Engineering, University of Rhode Island, Kingston, RI, USA
| | - Pedro Mesquita
- Department of Mechanical, Industrial and Systems Engineering, University of Rhode Island, Kingston, RI, USA
| | - Kayla Kurtz
- Department of Civil and Environmental Engineering, University of Rhode Island, Kingston, RI, USA
| | - Yang Xu
- Department of Computer Science, San Diego State University, San Diego, CA, USA
| | - Yang Lin
- Department of Mechanical, Industrial and Systems Engineering, University of Rhode Island, Kingston, RI, USA.
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18
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Dong T, Wang M, Liu J, Ma P, Pang S, Liu W, Liu A. Diagnostics and analysis of SARS-CoV-2: current status, recent advances, challenges and perspectives. Chem Sci 2023; 14:6149-6206. [PMID: 37325147 PMCID: PMC10266450 DOI: 10.1039/d2sc06665c] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/03/2023] [Indexed: 06/17/2023] Open
Abstract
The disastrous spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has induced severe public healthcare issues and weakened the global economy significantly. Although SARS-CoV-2 infection is not as fatal as the initial outbreak, many infected victims suffer from long COVID. Therefore, rapid and large-scale testing is critical in managing patients and alleviating its transmission. Herein, we review the recent advances in techniques to detect SARS-CoV-2. The sensing principles are detailed together with their application domains and analytical performances. In addition, the advantages and limits of each method are discussed and analyzed. Besides molecular diagnostics and antigen and antibody tests, we also review neutralizing antibodies and emerging SARS-CoV-2 variants. Further, the characteristics of the mutational locations in the different variants with epidemiological features are summarized. Finally, the challenges and possible strategies are prospected to develop new assays to meet different diagnostic needs. Thus, this comprehensive and systematic review of SARS-CoV-2 detection technologies may provide insightful guidance and direction for developing tools for the diagnosis and analysis of SARS-CoV-2 to support public healthcare and effective long-term pandemic management and control.
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Affiliation(s)
- Tao Dong
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
- School of Pharmacy, Medical College, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Mingyang Wang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Junchong Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Pengxin Ma
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Shuang Pang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Wanjian Liu
- Qingdao Hightop Biotech Co., Ltd 369 Hedong Road, Hi-tech Industrial Development Zone Qingdao 266112 China
| | - Aihua Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
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19
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Liu Y, Qin Z, Zhou J, Jia X, Li H, Wang X, Chen Y, Sun Z, He X, Li H, Wang G, Chang H. Nano-biosensor for SARS-CoV-2/COVID-19 detection: methods, mechanism and interface design. RSC Adv 2023; 13:17883-17906. [PMID: 37323463 PMCID: PMC10262965 DOI: 10.1039/d3ra02560h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 05/26/2023] [Indexed: 06/17/2023] Open
Abstract
The epidemic of coronavirus disease 2019 (COVID-19) was a huge disaster to human society. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which led to COVID-19, has resulted in a large number of deaths. Even though the reverse transcription-polymerase chain reaction (RT-PCR) is the most efficient method for the detection of SARS-CoV-2, the disadvantages (such as long detection time, professional operators, expensive instruments, and laboratory equipment) limit its application. In this review, the different kinds of nano-biosensors based on surface-enhanced Raman scattering (SERS), surface plasmon resonance (SPR), field-effect transistor (FET), fluorescence methods, and electrochemical methods are summarized, starting with a concise description of their sensing mechanism. The different bioprobes (such as ACE2, S protein-antibody, IgG antibody, IgM antibody, and SARS-CoV-2 DNA probes) with different bio-principles are introduced. The key structural components of the biosensors are briefly introduced to give readers an understanding of the principles behind the testing methods. In particular, SARS-CoV-2-related RNA mutation detection and its challenges are also briefly described. We hope that this review will encourage readers with different research backgrounds to design SARS-CoV-2 nano-biosensors with high selectivity and sensitivity.
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Affiliation(s)
- Yansheng Liu
- School of Electronic Engineering, Guangxi University of Science and Technology Liuzhou 545616 Guangxi China
- Quantum-Nano Matter and Device Lab, State Key Laboratory of Material Processing and Die and Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology Wuhan 430074 Hubei China
| | - Zhenle Qin
- School of Electronic Engineering, Guangxi University of Science and Technology Liuzhou 545616 Guangxi China
| | - Jin Zhou
- School of Electronic Engineering, Guangxi University of Science and Technology Liuzhou 545616 Guangxi China
| | - Xiaobo Jia
- School of Electronic Engineering, Guangxi University of Science and Technology Liuzhou 545616 Guangxi China
| | - Hongli Li
- School of Electronic Engineering, Guangxi University of Science and Technology Liuzhou 545616 Guangxi China
| | - Xiaohong Wang
- School of Electronic Engineering, Guangxi University of Science and Technology Liuzhou 545616 Guangxi China
| | - Yating Chen
- School of Electronic Engineering, Guangxi University of Science and Technology Liuzhou 545616 Guangxi China
| | - Zijun Sun
- School of Electronic Engineering, Guangxi University of Science and Technology Liuzhou 545616 Guangxi China
| | - Xiong He
- School of Electronic Engineering, Guangxi University of Science and Technology Liuzhou 545616 Guangxi China
| | - Hongda Li
- School of Electronic Engineering, Guangxi University of Science and Technology Liuzhou 545616 Guangxi China
- Quantum-Nano Matter and Device Lab, State Key Laboratory of Material Processing and Die and Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology Wuhan 430074 Hubei China
| | - Guofu Wang
- School of Electronic Engineering, Guangxi University of Science and Technology Liuzhou 545616 Guangxi China
| | - Haixin Chang
- Quantum-Nano Matter and Device Lab, State Key Laboratory of Material Processing and Die and Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology Wuhan 430074 Hubei China
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20
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Detection of live SARS-CoV-2 virus and its variants by specially designed SERS-active substrates and spectroscopic analyses. Anal Chim Acta 2023; 1256:341151. [PMID: 37037632 PMCID: PMC10060322 DOI: 10.1016/j.aca.2023.341151] [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: 12/30/2022] [Revised: 03/07/2023] [Accepted: 03/26/2023] [Indexed: 04/05/2023]
Abstract
A method using label-free surface enhanced Raman spectroscopy (SERS) based on substrate design is provided for an early detection and differentiation of spike glycoprotein mutation sites in live SARS-CoV-2 variants. Two SERS-active substrates, Au nanocavities (Au NCs) and Au NPs on porous ZrO2 (Au NPs/pZrO2), were used to identify specific peaks of A.3, Alpha, and Delta variants at different concentrations and demonstrated the ability to provide their SERS spectra with detection limits of 0.1–1.0% (or 104−5 copies/mL). Variant identification can be achieved by cross-examining reference spectra and analyzing the substrate-analyte relationship between the suitability of the analyte upon the hotspot(s) formed at high concentrations and the effective detection distance at low concentrations. Mutation sites on the S1 chain of the spike glycoprotein for each variant may be related and distinguishable. This method does not require sample preprocessing and therefore allows for fast screening, which is of high value for more comprehensive and specific studies to distinguish upcoming variants.
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21
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Lin C, Li Y, Peng Y, Zhao S, Xu M, Zhang L, Huang Z, Shi J, Yang Y. Recent development of surface-enhanced Raman scattering for biosensing. J Nanobiotechnology 2023; 21:149. [PMID: 37149605 PMCID: PMC10163864 DOI: 10.1186/s12951-023-01890-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 04/10/2023] [Indexed: 05/08/2023] Open
Abstract
Surface-Enhanced Raman Scattering (SERS) technology, as a powerful tool to identify molecular species by collecting molecular spectral signals at the single-molecule level, has achieved substantial progresses in the fields of environmental science, medical diagnosis, food safety, and biological analysis. As deepening research is delved into SERS sensing, more and more high-performance or multifunctional SERS substrate materials emerge, which are expected to push Raman sensing into more application fields. Especially in the field of biological analysis, intrinsic and extrinsic SERS sensing schemes have been widely used and explored due to their fast, sensitive and reliable advantages. Herein, recent developments of SERS substrates and their applications in biomolecular detection (SARS-CoV-2 virus, tumor etc.), biological imaging and pesticide detection are summarized. The SERS concepts (including its basic theory and sensing mechanism) and the important strategies (extending from nanomaterials with tunable shapes and nanostructures to surface bio-functionalization by modifying affinity groups or specific biomolecules) for improving SERS biosensing performance are comprehensively discussed. For data analysis and identification, the applications of machine learning methods and software acquisition sources in SERS biosensing and diagnosing are discussed in detail. In conclusion, the challenges and perspectives of SERS biosensing in the future are presented.
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Affiliation(s)
- Chenglong Lin
- State Key Laboratory of High-Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 1295 Dingxi Road, Shanghai, 200050, People's Republic of China
- Graduate School of the Chinese Academy of Sciences, No.19(A) Yuquan Road, Beijing, 100049, People's Republic of China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yanyan Li
- State Key Laboratory of High-Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 1295 Dingxi Road, Shanghai, 200050, People's Republic of China
- Graduate School of the Chinese Academy of Sciences, No.19(A) Yuquan Road, Beijing, 100049, People's Republic of China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yusi Peng
- State Key Laboratory of High-Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 1295 Dingxi Road, Shanghai, 200050, People's Republic of China
- Graduate School of the Chinese Academy of Sciences, No.19(A) Yuquan Road, Beijing, 100049, People's Republic of China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Shuai Zhao
- State Key Laboratory of High-Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 1295 Dingxi Road, Shanghai, 200050, People's Republic of China
- Graduate School of the Chinese Academy of Sciences, No.19(A) Yuquan Road, Beijing, 100049, People's Republic of China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Meimei Xu
- State Key Laboratory of High-Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 1295 Dingxi Road, Shanghai, 200050, People's Republic of China
- Graduate School of the Chinese Academy of Sciences, No.19(A) Yuquan Road, Beijing, 100049, People's Republic of China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Lingxia Zhang
- State Key Laboratory of High-Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 1295 Dingxi Road, Shanghai, 200050, People's Republic of China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Zhengren Huang
- State Key Laboratory of High-Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 1295 Dingxi Road, Shanghai, 200050, People's Republic of China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
| | - Jianlin Shi
- State Key Laboratory of High-Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 1295 Dingxi Road, Shanghai, 200050, People's Republic of China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yong Yang
- State Key Laboratory of High-Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 1295 Dingxi Road, Shanghai, 200050, People's Republic of China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
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22
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Lukose J, Barik AK, George SD, Murukeshan VM, Chidangil S. Raman spectroscopy for viral diagnostics. Biophys Rev 2023; 15:199-221. [PMID: 37113565 PMCID: PMC10088700 DOI: 10.1007/s12551-023-01059-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 03/24/2023] [Indexed: 04/29/2023] Open
Abstract
Raman spectroscopy offers the potential for fingerprinting biological molecules at ultra-low concentration and therefore has potential for the detection of viruses. Here we review various Raman techniques employed for the investigation of viruses. Different Raman techniques are discussed including conventional Raman spectroscopy, surface-enhanced Raman spectroscopy, Raman tweezer, tip-enhanced Raman Spectroscopy, and coherent anti-Stokes Raman scattering. Surface-enhanced Raman scattering can play an essential role in viral detection by multiplexing nanotechnology, microfluidics, and machine learning for ensuring spectral reproducibility and efficient workflow in sample processing and detection. The application of these techniques to diagnose the SARS-CoV-2 virus is also reviewed. Graphical abstract Supplementary Information The online version contains supplementary material available at 10.1007/s12551-023-01059-4.
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Affiliation(s)
- Jijo Lukose
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, 576104 Manipal, India
| | - Ajaya Kumar Barik
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, 576104 Manipal, India
| | - Sajan D. George
- Centre for Applied Nanosciences, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, 576104 Manipal, India
| | - V. M. Murukeshan
- Centre for Optical and Laser Engineering, School of Mechanical and Aerospace Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798 Singapore, Singapore
| | - Santhosh Chidangil
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, 576104 Manipal, India
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23
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Ganesh S, Dhinakaran AK, Premnath P, Venkatakrishnan K, Tan B. Label-Free Saliva Test for Rapid Detection of Coronavirus Using Nanosensor-Enabled SERS. Bioengineering (Basel) 2023; 10:bioengineering10030391. [PMID: 36978782 PMCID: PMC10045265 DOI: 10.3390/bioengineering10030391] [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: 02/07/2023] [Revised: 03/14/2023] [Accepted: 03/19/2023] [Indexed: 03/30/2023] Open
Abstract
The recent COVID-19 pandemic has highlighted the inadequacies of existing diagnostic techniques and the need for rapid and accurate diagnostic systems. Although molecular tests such as RT-PCR are the gold standard, they cannot be employed as point-of-care testing systems. Hence, a rapid, noninvasive diagnostic technique such as Surface-enhanced Raman scattering (SERS) is a promising analytical technique for rapid molecular or viral diagnosis. Here, we have designed a SERS- based test to rapidly diagnose SARS-CoV-2 from saliva. Physical methods synthesized the nanostructured sensor. It significantly increased the detection specificity and sensitivity by ~ten copies/mL of viral RNA (~femtomolar concentration of nucleic acids). Our technique combines the multiplexing capability of SERS with the sensitivity of novel nanostructures to detect whole virus particles and infection-associated antibodies. We have demonstrated the feasibility of the test with saliva samples from individuals who tested positive for SARS-CoV-2 with a specificity of 95%. The SERS-based test provides a promising breakthrough in detecting potential mutations that may come up with time while also preparing the world to deal with other pandemics in the future with rapid response and very accurate results.
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Affiliation(s)
- Swarna Ganesh
- Keenan Research Center for Biomedical Science, Unity Health Toronto, Toronto, ON M5B 1W8, Canada
- Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership between Toronto Metropolitan University and St. Michael's Hospital, Toronto, ON M5B 1W8, Canada
- Ultrashort Laser Nanomanufacturing Research Facility, Department of Mechanical and Industrial Engineering, Toronto Metropolitan University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada
| | - Ashok Kumar Dhinakaran
- Keenan Research Center for Biomedical Science, Unity Health Toronto, Toronto, ON M5B 1W8, Canada
- Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership between Toronto Metropolitan University and St. Michael's Hospital, Toronto, ON M5B 1W8, Canada
- Ultrashort Laser Nanomanufacturing Research Facility, Department of Mechanical and Industrial Engineering, Toronto Metropolitan University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada
| | - Priyatha Premnath
- Department of biomedical engineering, College of Engineering and Applied Sciences, University of Wisconsin, Milwaukee, WI 53211, USA
| | - Krishnan Venkatakrishnan
- Keenan Research Center for Biomedical Science, Unity Health Toronto, Toronto, ON M5B 1W8, Canada
- Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership between Toronto Metropolitan University and St. Michael's Hospital, Toronto, ON M5B 1W8, Canada
- Ultrashort Laser Nanomanufacturing Research Facility, Department of Mechanical and Industrial Engineering, Toronto Metropolitan University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada
| | - Bo Tan
- Keenan Research Center for Biomedical Science, Unity Health Toronto, Toronto, ON M5B 1W8, Canada
- Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership between Toronto Metropolitan University and St. Michael's Hospital, Toronto, ON M5B 1W8, Canada
- Nanocharacterization Laboratory, Department of Aerospace Engineering, Toronto Metropolitan University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada
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24
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Jin X, Xue L, Ye S, Cheng W, Hou JJ, Hou L, Marsh JH, Sun M, Liu X, Xiong J, Ni B. Asymmetric parameter enhancement in the split-ring cavity array for virus-like particle sensing. BIOMEDICAL OPTICS EXPRESS 2023; 14:1216-1227. [PMID: 36950230 PMCID: PMC10026587 DOI: 10.1364/boe.483831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/28/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Quantitative detection of virus-like particles under a low concentration is of vital importance for early infection diagnosis and water pollution analysis. In this paper, a novel virus detection method is proposed using indirect polarization parametric imaging method combined with a plasmonic split-ring nanocavity array coated with an Au film and a quantitative algorithm is implemented based on the extended Laplace operator. The attachment of viruses to the split-ring cavity breaks the structural symmetry, and such asymmetry can be enhanced by depositing a thin gold film on the sample, which allows an asymmetrical plasmon mode with a large shift of resonance peak generated under transverse polarization. Correspondingly, the far-field scattering state distribution encoded by the attached virus exhibits a specific asymmetric pattern that is highly correlated to the structural feature of the virus. By utilizing the parametric image sinδ to collect information on the spatial photon state distribution and far-field asymmetry with a sub-wavelength resolution, the appearance of viruses can be detected. To further reduce the background noise and enhance the asymmetric signals, an extended Laplace operator method which divides the detection area into topological units and then calculates the asymmetric parameter is applied, enabling easier determination of virus appearance. Experimental results show that the developed method can provide a detection limit as low as 56 vp/150µL on a large scale, which has great potential in early virus screening and other applications.
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Affiliation(s)
- Xiao Jin
- School of Electronic and Optical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
- Co-first authors
| | - Lu Xue
- School of Electronic and Optical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
- Co-first authors
| | - Shengwei Ye
- James Watt School of Engineering, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Weiqing Cheng
- James Watt School of Engineering, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Jamie Jiangmin Hou
- Department of Medicine, University of Cambridge, Hills Road, Cambridge, CB2 0QQ, UK
| | - Lianping Hou
- James Watt School of Engineering, University of Glasgow, Glasgow, G12 8QQ, UK
| | - John H. Marsh
- James Watt School of Engineering, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Ming Sun
- School of Electronic and Optical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Xuefeng Liu
- School of Electronic and Optical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Jichuan Xiong
- School of Electronic and Optical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
- Co-last authors
| | - Bin Ni
- School of Electronic and Optical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
- Co-last authors
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25
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Beeram R, Vepa KR, Soma VR. Recent Trends in SERS-Based Plasmonic Sensors for Disease Diagnostics, Biomolecules Detection, and Machine Learning Techniques. BIOSENSORS 2023; 13:328. [PMID: 36979540 PMCID: PMC10046859 DOI: 10.3390/bios13030328] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/20/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
Surface-enhanced Raman spectroscopy/scattering (SERS) has evolved into a popular tool for applications in biology and medicine owing to its ease-of-use, non-destructive, and label-free approach. Advances in plasmonics and instrumentation have enabled the realization of SERS's full potential for the trace detection of biomolecules, disease diagnostics, and monitoring. We provide a brief review on the recent developments in the SERS technique for biosensing applications, with a particular focus on machine learning techniques used for the same. Initially, the article discusses the need for plasmonic sensors in biology and the advantage of SERS over existing techniques. In the later sections, the applications are organized as SERS-based biosensing for disease diagnosis focusing on cancer identification and respiratory diseases, including the recent SARS-CoV-2 detection. We then discuss progress in sensing microorganisms, such as bacteria, with a particular focus on plasmonic sensors for detecting biohazardous materials in view of homeland security. At the end of the article, we focus on machine learning techniques for the (a) identification, (b) classification, and (c) quantification in SERS for biology applications. The review covers the work from 2010 onwards, and the language is simplified to suit the needs of the interdisciplinary audience.
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26
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Mo W, Ke Q, Zhou M, Xie G, Huang J, Gao F, Ni S, Yang X, Qi D, Wang A, Wen J, Yang Y, Jing M, Du K, Wang X, Du X, Zhao Z. Combined Morphological and Spectroscopic Diagnostic of HER2 Expression in Breast Cancer Tissues Based on Label-Free Surface-Enhanced Raman Scattering. Anal Chem 2023; 95:3019-3027. [PMID: 36706440 DOI: 10.1021/acs.analchem.2c05067] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Breast cancer is the most commonly diagnosed cancer type worldwide. Overexpression of human epidermal growth factor receptor 2 (HER2) is an important subtype of breast cancer and results in an increased risk of recurrence and metastasis in patients. At present, immunohistochemistry (IHC) is used to detect the expression of HER2 in breast cancer tissues as the golden standard. However, IHC has some shortcomings, such as large subjective impact, long time consumption, expensive reagents, etc. In this paper, a combined morphological and spectroscopic diagnostic method based on label-free surface-enhanced Raman scattering (SERS) for HER2 expression in breast cancer is proposed. It can not only quantitively detect HER2 expression in breast cancer tissues by spectroscopic measurements but also give morphological images reflecting the distribution of HER2 in tissues. The results show that the consistency between this method and IHC is 95% and achieves the annotation of tumor regions on tissue sections. This method is time-consuming, quantifiable, intuitive, scalable, and easy to understand. Combined with deep learning approaches, it is expected to promote the development of clinical detection and diagnosis technology for breast cancer and other cancers.
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Affiliation(s)
- Wenbo Mo
- China Academy of Engineering Physics, Laser Fusion Research Center, 621900 Mianyang, China.,Department of Engineering Physics, Tsinghua University, 100084 Beijing, China
| | - Qi Ke
- Mianyang Central Hospital, 621000 Mianyang, China
| | - Minjie Zhou
- China Academy of Engineering Physics, Laser Fusion Research Center, 621900 Mianyang, China
| | - Gang Xie
- Mianyang Central Hospital, 621000 Mianyang, China
| | - Jinglin Huang
- China Academy of Engineering Physics, Laser Fusion Research Center, 621900 Mianyang, China
| | - Feng Gao
- Mianyang Central Hospital, 621000 Mianyang, China
| | - Shuang Ni
- China Academy of Engineering Physics, Laser Fusion Research Center, 621900 Mianyang, China
| | - Xiyue Yang
- Mianyang Central Hospital, 621000 Mianyang, China
| | - Daojian Qi
- China Academy of Engineering Physics, Laser Fusion Research Center, 621900 Mianyang, China
| | - Anqun Wang
- Mianyang Central Hospital, 621000 Mianyang, China
| | - Jiaxing Wen
- China Academy of Engineering Physics, Laser Fusion Research Center, 621900 Mianyang, China
| | - Yue Yang
- China Academy of Engineering Physics, Laser Fusion Research Center, 621900 Mianyang, China
| | - Meng Jing
- Mianyang Central Hospital, 621000 Mianyang, China
| | - Kai Du
- China Academy of Engineering Physics, Laser Fusion Research Center, 621900 Mianyang, China
| | - Xuewu Wang
- Department of Engineering Physics, Tsinghua University, 100084 Beijing, China
| | - Xiaobo Du
- Mianyang Central Hospital, 621000 Mianyang, China
| | - Zongqing Zhao
- China Academy of Engineering Physics, Laser Fusion Research Center, 621900 Mianyang, China
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27
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Mo W, Wen J, Huang J, Yang Y, Zhou M, Ni S, Le W, Wei L, Qi D, Wang S, Su J, Wu Y, Zhou W, Du K, Wang X, Zhao Z. Classification of Coronavirus Spike Proteins by Deep-Learning-Based Raman Spectroscopy and its Interpretative Analysis. JOURNAL OF APPLIED SPECTROSCOPY 2023; 89:1203-1211. [PMID: 36718373 PMCID: PMC9876753 DOI: 10.1007/s10812-023-01487-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The outbreak of COVID-19 has spread worldwide, causing great damage to the global economy. Raman spectroscopy is expected to become a rapid and accurate method for the detection of coronavirus. A classification method of coronavirus spike proteins by Raman spectroscopy based on deep learning was implemented. A Raman spectra dataset of the spike proteins of five coronaviruses (including MERS-CoV, SARS-CoV, SARS-CoV-2, HCoVHKU1, and HCoV-OC43) was generated to establish the neural network model for classification. Even for rapidly acquired spectra with a low signal-to-noise ratio, the average accuracy exceeded 97%. An interpretive analysis of the classification results of the neural network was performed, which indicated that the differences in spectral characteristics captured by the neural network were consistent with the experimental analysis. The interpretative analysis method provided a valuable reference for identifying complex Raman spectra using deep-learning techniques. Our approach exhibited the potential to be applied in clinical practice to identify COVID-19 and other coronaviruses, and it can also be applied to other identification problems such as the identification of viruses or chemical agents, as well as in industrial areas such as oil and gas exploration.
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Affiliation(s)
- Wenbo Mo
- Laser Fusion Research Center at China Academy of Engineering Physics, Mianyang, China
- Department of Engineering Physics, Tsinghua University, Beijing, China
| | - Jiaxing Wen
- Laser Fusion Research Center at China Academy of Engineering Physics, Mianyang, China
- Department of Engineering Physics, Tsinghua University, Beijing, China
| | - Jinglin Huang
- Laser Fusion Research Center at China Academy of Engineering Physics, Mianyang, China
| | - Yue Yang
- Laser Fusion Research Center at China Academy of Engineering Physics, Mianyang, China
| | - Minjie Zhou
- Laser Fusion Research Center at China Academy of Engineering Physics, Mianyang, China
| | - Shuang Ni
- Laser Fusion Research Center at China Academy of Engineering Physics, Mianyang, China
| | - Wei Le
- Laser Fusion Research Center at China Academy of Engineering Physics, Mianyang, China
| | - Lai Wei
- Laser Fusion Research Center at China Academy of Engineering Physics, Mianyang, China
| | - Daojian Qi
- Laser Fusion Research Center at China Academy of Engineering Physics, Mianyang, China
| | - Shaoyi Wang
- Laser Fusion Research Center at China Academy of Engineering Physics, Mianyang, China
| | - Jingqin Su
- Laser Fusion Research Center at China Academy of Engineering Physics, Mianyang, China
| | - Yuchi Wu
- Laser Fusion Research Center at China Academy of Engineering Physics, Mianyang, China
| | - Weimin Zhou
- Laser Fusion Research Center at China Academy of Engineering Physics, Mianyang, China
| | - Kai Du
- Laser Fusion Research Center at China Academy of Engineering Physics, Mianyang, China
| | - Xuewu Wang
- Department of Engineering Physics, Tsinghua University, Beijing, China
| | - Zongqing Zhao
- Laser Fusion Research Center at China Academy of Engineering Physics, Mianyang, China
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28
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Luo Z, Cheng Y, He L, Feng Y, Tian Y, Chen Z, Feng Y, Li Y, Xie W, Huang W, Meng J, Li Y, He F, Wang X, Duan Y. T-Shaped Aptamer-Based LSPR Biosensor Using Ω-Shaped Fiber Optic for Rapid Detection of SARS-CoV-2. Anal Chem 2023; 95:1599-1607. [PMID: 36580626 PMCID: PMC9843628 DOI: 10.1021/acs.analchem.2c04709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/19/2022] [Indexed: 12/31/2022]
Abstract
SARS-CoV-2, especially the variant strains, is rapidly spreading around the world. Rapid detection methods for the virus are crucial for controlling the COVID-19 epidemic. Herein, a localized surface plasmonic resonance (LSPR) biosensor based on Ω-shaped fiber optic (Ω-FO) was developed for dual assays of SARS-CoV-2 monitoring. Due to its strong ability to control the orientation and density, a new T-shaped aptamer exhibits enhanced binding affinity toward N proteins. After being combined on the fiber optic surface, the T-shaped aptamer sensitively captured N proteins of SARS-CoV-2 for a direct assay. Further, core-shell structured gold/silver nanoparticles functionalized with a T-shaped aptamer (apt-Ag@AuNPs) can amplify the signal of N protein detection for a sandwich assay. The real-time analytical feature of the dual assays endows time-dependent sensitivity enhancement behavior, which provides a guideline to save analytical time. With those characteristics, the LSPR biosensor has been successfully used to rapidly identify 39 healthy volunteers and 39 COVID-19 patients infected with the ancestral or variant SARS-CoV-2. With the help of simple pretreatment, we obtain a true negative rate of 100% and a true positive rate of 92.3% with a short analysis time of 45 min using the direct assay. Further, the LSPR biosensor could also broaden the detection application range to the surface of cold-chain foods using a sandwich assay. Thus, the LSPR biosensor based on Ω-FO was demonstrated to have broad application potential to detect SARS-CoV-2 rapidly.
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Affiliation(s)
- Zewei Luo
- Research
Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, Chengdu 610065, China
- Research
Center of Analytical Instrumentation, College of Chemistry & Materials
Science, Northwest University, Xi’an 710069, China
| | - Yue Cheng
- Chengdu
Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Chengdu, Sichuan 610041, China
- Chengdu
Center for Disease Control and Prevention, Chengdu 610041, China
| | - Lu He
- Research
Center of Analytical Instrumentation, College of Chemistry & Materials
Science, Northwest University, Xi’an 710069, China
| | - Yanting Feng
- Research
Center of Analytical Instrumentation, College of Chemistry & Materials
Science, Northwest University, Xi’an 710069, China
| | - Yonghui Tian
- Research
Center of Analytical Instrumentation, College of Chemistry & Materials
Science, Northwest University, Xi’an 710069, China
| | - Zhenhua Chen
- Chengdu
Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Chengdu, Sichuan 610041, China
- Chengdu
Center for Disease Control and Prevention, Chengdu 610041, China
| | - Yaqiang Feng
- Research
Center of Analytical Instrumentation, College of Chemistry & Materials
Science, Northwest University, Xi’an 710069, China
| | - Yongxin Li
- West
China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610041, China
| | - Wenjun Xie
- Chengdu
Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Chengdu, Sichuan 610041, China
- Chengdu
Center for Disease Control and Prevention, Chengdu 610041, China
| | - Weiwei Huang
- Chengdu
Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Chengdu, Sichuan 610041, China
- Chengdu
Center for Disease Control and Prevention, Chengdu 610041, China
| | - Jiantong Meng
- Chengdu
Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences, Chengdu, Sichuan 610041, China
- Chengdu
Center for Disease Control and Prevention, Chengdu 610041, China
| | - Yu Li
- Research
Center of Analytical Instrumentation, Key Laboratory of Bio-resource
and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu 610065, China
| | - Fan He
- School
of Physics, Northwest University, Xi’an 710069, China
| | - Xu Wang
- Research
Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, Chengdu 610065, China
| | - Yixiang Duan
- Research
Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, Chengdu 610065, China
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29
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Luo X, Yue W, Zhang S, Liu H, Chen Z, Qiao L, Wu C, Li P, He Y. SARS-CoV-2 proteins monitored by long-range surface plasmon field-enhanced Raman scattering with hybrid bowtie nanoaperture arrays and nanocavities. LAB ON A CHIP 2023; 23:388-399. [PMID: 36621932 DOI: 10.1039/d2lc01006b] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The identification of biomacromolecules by using surface-enhanced Raman scattering (SERS) remains a challenge because of the near-field effect of traditional substrates. Long-range surface plasmon resonance (LRSPR) is a special type of surface optical phenomenon that provides higher electromagnetic field enhancement and longer penetration depth than conventional surface plasmon resonance. To break the limit of SERS detection distance and obtain a SERS substrate with increased enhancement ability, a bowtie nanoaperture array was sandwiched between two symmetric dielectric environments. Then, an Au mirror was inserted to form a metal-insulator-metal configuration. Finite-difference time-domain simulations revealed that numerous hybrid modes can be provided by this novel configuration (denoted as long-range SERS [LR-SERS] substrate). In particular, the LRSPR mode can be excited and reach the maximum value through the regulation of the polarizations of the incident light and the geometrical parameters of the LR-SERS substrate. The optimized LR-SERS substrate was then applied to detect SARS-CoV-2 spike (S) and nucleocapsid (N) proteins. This substrate displayed ultralow detection limits of ∼9.2 and ∼11.3 pg mL-1 for the S and N proteins, respectively. Moreover, with the help of principal component analysis and receiver operating characteristic methods, our fabricated sensors exhibited excellent selectivity and hold great potential for the diagnosis of SARS-CoV-2 proteins in real samples.
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Affiliation(s)
- Xiaojun Luo
- School of Science, Xihua University, Chengdu 610039, P. R. China.
| | - Weiling Yue
- School of Science, Xihua University, Chengdu 610039, P. R. China.
| | - Shutong Zhang
- School of Science, Xihua University, Chengdu 610039, P. R. China.
| | - Haopeng Liu
- School of Science, Xihua University, Chengdu 610039, P. R. China.
| | - Zhinan Chen
- School of Science, Xihua University, Chengdu 610039, P. R. China.
| | - Ling Qiao
- Division of Chemistry and Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Caijun Wu
- School of Science, Xihua University, Chengdu 610039, P. R. China.
| | - Panjie Li
- School of Chemistry and Chemical Engineering, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
| | - Yi He
- School of Science, Xihua University, Chengdu 610039, P. R. China.
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30
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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.
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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
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31
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Yuan K, Jurado-Sánchez B, Escarpa A. Nanomaterials meet surface-enhanced Raman scattering towards enhanced clinical diagnosis: a review. J Nanobiotechnology 2022; 20:537. [PMID: 36544151 PMCID: PMC9771791 DOI: 10.1186/s12951-022-01711-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022] Open
Abstract
Surface-enhanced Raman scattering (SERS) is a very promising tool for the direct detection of biomarkers for the diagnosis of i.e., cancer and pathogens. Yet, current SERS strategies are hampered by non-specific interactions with co-existing substances in the biological matrices and the difficulties of obtaining molecular fingerprint information from the complex vibrational spectrum. Raman signal enhancement is necessary, along with convenient surface modification and machine-based learning to address the former issues. This review aims to describe recent advances and prospects in SERS-based approaches for cancer and pathogens diagnosis. First, direct SERS strategies for key biomarker sensing, including the use of substrates such as plasmonic, semiconductor structures, and 3D order nanostructures for signal enhancement will be discussed. Secondly, we will illustrate recent advances for indirect diagnosis using active nanomaterials, Raman reporters, and specific capture elements as SERS tags. Thirdly, critical challenges for translating the potential of the SERS sensing techniques into clinical applications via machine learning and portable instrumentation will be described. The unique nature and integrated sensing capabilities of SERS provide great promise for early cancer diagnosis or fast pathogens detection, reducing sanitary costs but most importantly allowing disease prevention and decreasing mortality rates.
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Affiliation(s)
- Kaisong Yuan
- Bio-Analytical Laboratory, Shantou University Medical College, No. 22, Xinling Road, Shantou, 515041, China
- Department of Analytical Chemistry, Physical Chemistry, and Chemical Engineering, University of Alcala, Alcala de Henares, 28802, Madrid, Spain
| | - Beatriz Jurado-Sánchez
- Department of Analytical Chemistry, Physical Chemistry, and Chemical Engineering, University of Alcala, Alcala de Henares, 28802, Madrid, Spain
- Chemical Research Institute "Andrés M. del Río", University of Alcala, Alcala de Henares, 28802, Madrid, Spain
| | - Alberto Escarpa
- Department of Analytical Chemistry, Physical Chemistry, and Chemical Engineering, University of Alcala, Alcala de Henares, 28802, Madrid, Spain
- Chemical Research Institute "Andrés M. del Río", University of Alcala, Alcala de Henares, 28802, Madrid, Spain
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32
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Novikov A, Sayfutdinova A, Botchkova E, Kopitsyn D, Fakhrullin R. Antibiotic Susceptibility Testing with Raman Biosensing. Antibiotics (Basel) 2022; 11:antibiotics11121812. [PMID: 36551469 PMCID: PMC9774239 DOI: 10.3390/antibiotics11121812] [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: 10/20/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 12/15/2022] Open
Abstract
Antibiotics guard us against bacterial infections and are among the most commonly used medicines. The immediate consequence of their large-scale production and prescription is the development of antibiotic resistance. Therefore, rapid detection of antibiotic susceptibility is required for efficient antimicrobial therapy. One of the promising methods for rapid antibiotic susceptibility testing is Raman spectroscopy. Raman spectroscopy combines fast and contactless acquisition of spectra with good selectivity towards bacterial cells. The antibiotic-induced changes in bacterial cell physiology are detected as distinct features in Raman spectra and can be associated with antibiotic susceptibility. Therefore, the Raman-based approach may be beneficial in designing therapy against multidrug-resistant infections. The surface-enhanced Raman spectroscopy (SERS) and resonance Raman spectroscopy (RRS) additionally provide excellent sensitivity. In this review, we present an analysis of the Raman spectroscopy-based optical biosensing approaches aimed at antibiotic susceptibility testing.
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Affiliation(s)
- Andrei Novikov
- Department of Physical and Colloid Chemistry, Gubkin University, 65/1 Leninsky Prospect, 119991 Moscow, Russia
- Correspondence: (A.N.); (R.F.)
| | - Adeliya Sayfutdinova
- Department of Physical and Colloid Chemistry, Gubkin University, 65/1 Leninsky Prospect, 119991 Moscow, Russia
| | - Ekaterina Botchkova
- Department of Physical and Colloid Chemistry, Gubkin University, 65/1 Leninsky Prospect, 119991 Moscow, Russia
| | - Dmitry Kopitsyn
- Department of Physical and Colloid Chemistry, Gubkin University, 65/1 Leninsky Prospect, 119991 Moscow, Russia
| | - Rawil Fakhrullin
- Department of Physical and Colloid Chemistry, Gubkin University, 65/1 Leninsky Prospect, 119991 Moscow, Russia
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Republic of Tatarstan, Russia
- Correspondence: (A.N.); (R.F.)
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33
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Tabarov A, Vitkin V, Andreeva O, Shemanaeva A, Popov E, Dobroslavin A, Kurikova V, Kuznetsova O, Grigorenko K, Tzibizov I, Kovalev A, Savchenko V, Zheltuhina A, Gorshkov A, Danilenko D. Detection of A and B Influenza Viruses by Surface-Enhanced Raman Scattering Spectroscopy and Machine Learning. BIOSENSORS 2022; 12:bios12121065. [PMID: 36551032 PMCID: PMC9775719 DOI: 10.3390/bios12121065] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/11/2022] [Accepted: 11/20/2022] [Indexed: 05/28/2023]
Abstract
We demonstrate the possibility of applying surface-enhanced Raman spectroscopy (SERS) combined with machine learning technology to detect and differentiate influenza type A and B viruses in a buffer environment. The SERS spectra of the influenza viruses do not possess specific peaks that allow for their straight classification and detection. Machine learning technologies (particularly, the support vector machine method) enabled the differentiation of samples containing influenza A and B viruses using SERS with an accuracy of 93% at a concentration of 200 μg/mL. The minimum detectable concentration of the virus in the sample using the proposed approach was ~0.05 μg/mL of protein (according to the Lowry protein assay), and the detection accuracy of a sample with this pathogen concentration was 84%.
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Affiliation(s)
- Artem Tabarov
- Institute of Advanced Data Transfer Systems, ITMO University, Birzhevaya Liniya 14, 199034 Saint Petersburg, Russia
| | - Vladimir Vitkin
- Institute of Advanced Data Transfer Systems, ITMO University, Birzhevaya Liniya 14, 199034 Saint Petersburg, Russia
| | - Olga Andreeva
- Institute of Advanced Data Transfer Systems, ITMO University, Birzhevaya Liniya 14, 199034 Saint Petersburg, Russia
| | - Arina Shemanaeva
- Institute of Advanced Data Transfer Systems, ITMO University, Birzhevaya Liniya 14, 199034 Saint Petersburg, Russia
| | - Evgeniy Popov
- Institute of Advanced Data Transfer Systems, ITMO University, Birzhevaya Liniya 14, 199034 Saint Petersburg, Russia
| | - Alexander Dobroslavin
- Institute of Advanced Data Transfer Systems, ITMO University, Birzhevaya Liniya 14, 199034 Saint Petersburg, Russia
| | - Valeria Kurikova
- Institute of Advanced Data Transfer Systems, ITMO University, Birzhevaya Liniya 14, 199034 Saint Petersburg, Russia
| | - Olga Kuznetsova
- Institute of Advanced Data Transfer Systems, ITMO University, Birzhevaya Liniya 14, 199034 Saint Petersburg, Russia
| | - Konstantin Grigorenko
- Institute of Advanced Data Transfer Systems, ITMO University, Birzhevaya Liniya 14, 199034 Saint Petersburg, Russia
| | - Ivan Tzibizov
- Institute of Advanced Data Transfer Systems, ITMO University, Birzhevaya Liniya 14, 199034 Saint Petersburg, Russia
| | - Anton Kovalev
- Institute of Advanced Data Transfer Systems, ITMO University, Birzhevaya Liniya 14, 199034 Saint Petersburg, Russia
| | - Vitaliy Savchenko
- National Research Center “Kurchatov Institute”, Akademika Kurchatova Sq. 1, 123182 Moscow, Russia
| | - Alyona Zheltuhina
- Smorodintsev Research Institute of Influenza, Prof. Popova Str. 15/17, 197376 Saint Petersburg, Russia
| | - Andrey Gorshkov
- Smorodintsev Research Institute of Influenza, Prof. Popova Str. 15/17, 197376 Saint Petersburg, Russia
| | - Daria Danilenko
- Smorodintsev Research Institute of Influenza, Prof. Popova Str. 15/17, 197376 Saint Petersburg, Russia
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34
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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.
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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
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35
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Quantum tunnelling in the context of SARS-CoV-2 infection. Sci Rep 2022; 12:16929. [PMID: 36209224 PMCID: PMC9547378 DOI: 10.1038/s41598-022-21321-1] [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: 02/04/2022] [Accepted: 09/26/2022] [Indexed: 12/29/2022] Open
Abstract
The SARS-CoV-2 pandemic has added new urgency to the study of viral mechanisms of infection. But while vaccines offer a measure of protection against this specific outbreak, a new era of pandemics has been predicted. In addition to this, COVID-19 has drawn attention to post-viral syndromes and the healthcare burden they entail. It seems integral that knowledge of viral mechanisms is increased through as wide a research field as possible. To this end we propose that quantum biology might offer essential new insights into the problem, especially with regards to the important first step of virus-host invasion. Research in quantum biology often centres around energy or charge transfer. While this is predominantly in the context of photosynthesis there has also been some suggestion that cellular receptors such as olfactory or neural receptors might employ vibration assisted electron tunnelling to augment the lock-and-key mechanism. Quantum tunnelling has also been observed in enzyme function. Enzymes are implicated in the invasion of host cells by the SARS-CoV-2 virus. Receptors such as olfactory receptors also appear to be disrupted by COVID-19. Building on these observations we investigate the evidence that quantum tunnelling might be important in the context of infection with SARS-CoV-2. We illustrate this with a simple model relating the vibronic mode of, for example, a viral spike protein to the likelihood of charge transfer in an idealised receptor. Our results show a distinct parameter regime in which the vibronic mode of the spike protein enhances electron transfer. With this in mind, novel therapeutics to prevent SARS-CoV-2 transmission could potentially be identified by their vibrational spectra.
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36
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Kistenev YV, Das A, Mazumder N, Cherkasova OP, Knyazkova AI, Shkurinov AP, Tuchin VV, Lednev IK. Label-free laser spectroscopy for respiratory virus detection: A review. JOURNAL OF BIOPHOTONICS 2022; 15:e202200100. [PMID: 35866572 DOI: 10.1002/jbio.202200100] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/20/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
Infectious diseases are among the most severe threats to modern society. Current methods of virus infection detection based on genome tests need reagents and specialized laboratories. The desired characteristics of new virus detection methods are noninvasiveness, simplicity of implementation, real-time, low cost and label-free detection. There are two groups of methods for molecular biomarkers' detection and analysis: (i) a sample physical separation into individual molecular components and their identification, and (ii) sample content analysis by laser spectroscopy. Variations in the spectral data are typically minor. It requires the use of sophisticated analytical methods like machine learning. This review examines the current technological level of laser spectroscopy and machine learning methods in applications for virus infection detection.
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Affiliation(s)
- Yury V Kistenev
- Laboratory of Laser Molecular Imaging and Machine Learning, Tomsk State University, Tomsk, Russia
| | - Anubhab Das
- Department of Microbiology, Ramakrishna Mission Vivekananda Centenary College, Kolkata, India
| | - Nirmal Mazumder
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Olga P Cherkasova
- Laboratory of Laser Molecular Imaging and Machine Learning, Tomsk State University, Tomsk, Russia
- Institute of Laser Physics, Siberian Branch of the RAS, Novosibirsk, Russia
| | - Anastasia I Knyazkova
- Laboratory of Laser Molecular Imaging and Machine Learning, Tomsk State University, Tomsk, Russia
| | - Alexander P Shkurinov
- Laboratory of Laser Molecular Imaging and Machine Learning, Tomsk State University, Tomsk, Russia
- Institute on Laser and Information Technologies, Branch of the Federal Scientific Research Centre "Crystallography and Photonics" of RAS, Shatura, Russia
- Faculty of Physics, Lomonosov Moscow State University, Moscow, Russia
| | - Valery V Tuchin
- Laboratory of Laser Molecular Imaging and Machine Learning, Tomsk State University, Tomsk, Russia
- Science Medical Center, Saratov State University, Saratov, Russia
- Laboratory of Laser Diagnostics of Technical and Living Systems, Institute of Precision Mechanics and Control of the RAS, Saratov, Russia
| | - Igor K Lednev
- Laboratory of Laser Molecular Imaging and Machine Learning, Tomsk State University, Tomsk, Russia
- Department of Chemistry, University at Albany, SUNY, Albany, NY, USA
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37
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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.
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38
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Zhang K, Wang Z, Liu H, Perea-López N, Ranasinghe JC, Bepete G, Minns AM, Rossi RM, Lindner SE, Huang SX, Terrones M, Huang S. Understanding the Excitation Wavelength Dependence and Thermal Stability of the SARS-CoV-2 Receptor-Binding Domain Using Surface-Enhanced Raman Scattering and Machine Learning. ACS PHOTONICS 2022; 9:2963-2972. [PMID: 37552735 PMCID: PMC9438456 DOI: 10.1021/acsphotonics.2c00456] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Indexed: 05/28/2023]
Abstract
COVID-19 has cost millions of lives worldwide. The constant mutation of SARS-CoV-2 calls for thorough research to facilitate the development of variant surveillance. In this work, we studied the fundamental properties related to the optical identification of the receptor-binding domain (RBD) of SARS-CoV-2 spike protein, a key component of viral infection. The Raman modes of the SARS-CoV-2 RBD were captured by surface-enhanced Raman spectroscopy (SERS) using gold nanoparticles (AuNPs). The observed Raman enhancement strongly depends on the excitation wavelength as a result of the aggregation of AuNPs. The characteristic Raman spectra of RBDs from SARS-CoV-2 and MERS-CoV were analyzed by principal component analysis that reveals the role of secondary structures in the SERS process, which is corroborated with the thermal stability under laser heating. We can easily distinguish the Raman spectra of two RBDs using machine learning algorithms with accuracy, precision, recall, and F1 scores all over 95%. Our work provides an in-depth understanding of the SARS-CoV-2 RBD and paves the way toward rapid analysis and discrimination of complex proteins of infectious viruses and other biomolecules.
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Affiliation(s)
- Kunyan Zhang
- Department of Electrical Engineering, The
Pennsylvania State University, University Park, Pennsylvania16802,
United States
| | - Ziyang Wang
- Department of Electrical Engineering, The
Pennsylvania State University, University Park, Pennsylvania16802,
United States
- Department of Electrical and Computer Engineering,
Rice University, Houston, Texas77005, United
States
| | - He Liu
- Department of Chemistry, The Pennsylvania
State University, University Park, Pennsylvania16802, United
States
| | - Néstor Perea-López
- Department of Physics, The Pennsylvania
State University, University Park, Pennsylvania16802, United
States
- Center for 2-Dimensional and Layered Materials,
The Pennsylvania State University, University Park,
Pennsylvania16802, United States
| | - Jeewan C. Ranasinghe
- Department of Electrical Engineering, The
Pennsylvania State University, University Park, Pennsylvania16802,
United States
- Department of Electrical and Computer Engineering,
Rice University, Houston, Texas77005, United
States
| | - George Bepete
- Department of Chemistry, The Pennsylvania
State University, University Park, Pennsylvania16802, United
States
- Department of Physics, The Pennsylvania
State University, University Park, Pennsylvania16802, United
States
- Center for 2-Dimensional and Layered Materials,
The Pennsylvania State University, University Park,
Pennsylvania16802, United States
| | - Allen M. Minns
- Department of Biochemistry and Molecular Biology, Center for
Infectious Disease Dynamics, The Pennsylvania State University,
University Park, Pennsylvania16802, United States
- Huck Institutes of the Life Sciences, The
Pennsylvania State University, University Park, Pennsylvania16802,
United States
| | - Randall M. Rossi
- Huck Institutes of the Life Sciences, The
Pennsylvania State University, University Park, Pennsylvania16802,
United States
| | - Scott E. Lindner
- Department of Biochemistry and Molecular Biology, Center for
Infectious Disease Dynamics, The Pennsylvania State University,
University Park, Pennsylvania16802, United States
- Huck Institutes of the Life Sciences, The
Pennsylvania State University, University Park, Pennsylvania16802,
United States
| | - Sharon X. Huang
- College of Information Sciences and Technology,
The Pennsylvania State University, University Park,
Pennsylvania16802, United States
| | - Mauricio Terrones
- Department of Chemistry, The Pennsylvania
State University, University Park, Pennsylvania16802, United
States
- Department of Physics, The Pennsylvania
State University, University Park, Pennsylvania16802, United
States
- Center for 2-Dimensional and Layered Materials,
The Pennsylvania State University, University Park,
Pennsylvania16802, United States
- Department of Materials Science and Engineering,
The Pennsylvania State University, University Park,
Pennsylvania16802, United States
- Research Initiative for Supra Materials,
Shinshu University, 4-17-1 Wakasato, Nagano380-8553,
Japan
| | - Shengxi Huang
- Department of Electrical Engineering, The
Pennsylvania State University, University Park, Pennsylvania16802,
United States
- Department of Electrical and Computer Engineering,
Rice University, Houston, Texas77005, United
States
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39
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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
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40
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Li Y, Lin C, Peng Y, He J, Yang Y. High-sensitivity and point-of-care detection of SARS-CoV-2 from nasal and throat swabs by magnetic SERS biosensor. SENSORS AND ACTUATORS. B, CHEMICAL 2022; 365:131974. [PMID: 35505925 PMCID: PMC9047405 DOI: 10.1016/j.snb.2022.131974] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 04/13/2022] [Accepted: 04/26/2022] [Indexed: 05/20/2023]
Abstract
The outbreak of COVID-19 caused by SARS-CoV-2 urges the development of rapidly and accurately diagnostic methods. Here, one high-sensitivity and point-of-care detection method based on magnetic SERS biosensor composed of Fe3O4-Au nanocomposite and Au nanoneedles array was developed to detect SARS-CoV-2 directly. Among, the magnetic Fe3O4-Au nanocomposite is applied to capture and separate virus from nasal and throat swabs and enhance the Raman signals of SARS-CoV-2. The magnetic SERS biosensor possessed high sensitivity by optimizing the Fe3O4-Au nanocomposite. More significantly, the on-site detection of inactivated SARS-CoV-2 virus was achieved based on the magnetic SERS biosensor with ultra-low limit of detection of 100 copies/mL during 15 mins. Furthermore, the contaminated nasal and throat swabs samples were identified by support vector machine, and the diagnostic accuracy of 100% was obtained. The magnetic SERS biosensor combined with support vector machine provides giant potential as the point-of-care detection tool for SARS-CoV-2.
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Affiliation(s)
- Yanyan Li
- State Key Laboratory of High-Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 1295 Dingxi Road, Shanghai 200050, People's Republic of China
- Graduate School of the Chinese Academy of Sciences, No.19(A) Yuquan Road, Beijing 100049, People's Republic of China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenglong Lin
- State Key Laboratory of High-Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 1295 Dingxi Road, Shanghai 200050, People's Republic of China
- Graduate School of the Chinese Academy of Sciences, No.19(A) Yuquan Road, Beijing 100049, People's Republic of China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yusi Peng
- State Key Laboratory of High-Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 1295 Dingxi Road, Shanghai 200050, People's Republic of China
- Graduate School of the Chinese Academy of Sciences, No.19(A) Yuquan Road, Beijing 100049, People's Republic of China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun He
- Anhui Provincial Center for Disease Control and Prevention, Hefei 12560, Anhui, People's Republic of China
- Public Health Research Institute of Anhui Province, Hefei 12560, Anhui, People's Republic of China
| | - Yong Yang
- State Key Laboratory of High-Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 1295 Dingxi Road, Shanghai 200050, People's Republic of China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
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41
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Ni S, Yang Q, Huang J, Zhou M, Wei L, Yang Y, Wen J, Mo W, Le W, Qi D, Jin L, Li B, Zhao Z, Du K. Constructing high-accuracy theoretical Raman spectra of SARS-CoV-2 spike proteins based on a large fragment method. Chem Phys Lett 2022; 800:139663. [PMID: 35529782 PMCID: PMC9055380 DOI: 10.1016/j.cplett.2022.139663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/27/2022] [Accepted: 04/26/2022] [Indexed: 01/17/2023]
Abstract
In order to control COVID-19, rapid and accurate detection of the pathogenic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is an urgent task. The target spike proteins of SARS-CoV-2 have been detected experimentally via Raman spectroscopy. However, there lacks high-accuracy theoretical Raman spectra of the spike proteins to as a standard reference for the clinic diagnostic purpose. In this paper, we propose a large fragment method to construct the high-precision Raman spectra for the spike proteins. The large fragment method not only reduces the calculation error but also improves the accuracy of the protein Raman spectra by completely calculating the interactions within the large fragment. The Pearson correlation coefficient of theoretical Raman spectra is greater than 0.929 or more. Compared with the experimental spectra, the characteristic patterns are easily visible. This work provides a detection standard for the spike proteins which shall bring a step closer to the fast recognition of SARS-CoV-2 via Raman spectroscopy method.
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Affiliation(s)
- Shuang Ni
- Laser Fusion Research Center, China Academy of Engineering Physics, 621900 Mianyang, China
| | - Qiang Yang
- China Academy of Engineering Physics, 621900 Mianyang, China
| | - Jinling Huang
- Laser Fusion Research Center, China Academy of Engineering Physics, 621900 Mianyang, China
| | - Minjie Zhou
- Laser Fusion Research Center, China Academy of Engineering Physics, 621900 Mianyang, China,Corresponding author
| | - Lai Wei
- Laser Fusion Research Center, China Academy of Engineering Physics, 621900 Mianyang, China
| | - Yue Yang
- Laser Fusion Research Center, China Academy of Engineering Physics, 621900 Mianyang, China
| | - Jiaxin Wen
- Laser Fusion Research Center, China Academy of Engineering Physics, 621900 Mianyang, China,Department of Engineering Physics, Tsinghua University, 100084 Beijing, China
| | - Wenbo Mo
- Laser Fusion Research Center, China Academy of Engineering Physics, 621900 Mianyang, China,Department of Engineering Physics, Tsinghua University, 100084 Beijing, China
| | - Wei Le
- Laser Fusion Research Center, China Academy of Engineering Physics, 621900 Mianyang, China
| | - Daojian Qi
- Laser Fusion Research Center, China Academy of Engineering Physics, 621900 Mianyang, China
| | - Lei Jin
- Laser Fusion Research Center, China Academy of Engineering Physics, 621900 Mianyang, China
| | - Bo Li
- Laser Fusion Research Center, China Academy of Engineering Physics, 621900 Mianyang, China
| | - Zongqin Zhao
- Laser Fusion Research Center, China Academy of Engineering Physics, 621900 Mianyang, China
| | - Kai Du
- Laser Fusion Research Center, China Academy of Engineering Physics, 621900 Mianyang, China
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42
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Moitra P, Chaichi A, Abid Hasan SM, Dighe K, Alafeef M, Prasad A, Gartia MR, Pan D. Probing the mutation independent interaction of DNA probes with SARS-CoV-2 variants through a combination of surface-enhanced Raman scattering and machine learning. Biosens Bioelectron 2022; 208:114200. [PMID: 35367703 PMCID: PMC8938299 DOI: 10.1016/j.bios.2022.114200] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/06/2022] [Accepted: 03/17/2022] [Indexed: 12/01/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution has been characterized by the emergence of sets of mutations impacting the virus characteristics, such as transmissibility and antigenicity, presumably in response to the changing immune profile of the human population. The presence of mutations in the SARS-CoV-2 virus can potentially impact therapeutic and diagnostic test performances. We design and develop here a unique set of DNA probes i.e., antisense oligonucleotides (ASOs) which can interact with genetic sequences of the virus irrespective of its ongoing mutations. The probes, developed herein, target a specific segment of the nucleocapsid phosphoprotein (N) gene of SARS-CoV-2 with high binding efficiency which do not mutate among the known variants. Further probing into the interaction profile of the ASOs reveals that the ASO-RNA hybridization remains unaltered even for a hypothetical single point mutation at the target RNA site and diminished only in case of the hypothetical double or triple point mutations. The mechanism of interaction among the ASOs and SARS-CoV-2 RNA is then explored with a combination of surface-enhanced Raman scattering (SERS) and machine learning techniques. It has been observed that the technique, described herein, could efficiently discriminate between clinically positive and negative samples with ∼100% sensitivity and ∼90% specificity up to 63 copies/mL of SARS-CoV-2 RNA concentration. Thus, this study establishes N gene targeted ASOs as the fundamental machinery to efficiently detect all the current SARS-CoV-2 variants regardless of their mutations.
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Affiliation(s)
- Parikshit Moitra
- Department of Pediatrics, Center for Blood Oxygen Transport and Hemostasis, University of Maryland Baltimore School of Medicine, Baltimore, MD, 21201, United States
| | - Ardalan Chaichi
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, LA, 70803, United States
| | - Syed Mohammad Abid Hasan
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, LA, 70803, United States
| | - Ketan Dighe
- Department of Pediatrics, Center for Blood Oxygen Transport and Hemostasis, University of Maryland Baltimore School of Medicine, Baltimore, MD, 21201, United States; Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, 21250, United States
| | - Maha Alafeef
- Department of Pediatrics, Center for Blood Oxygen Transport and Hemostasis, University of Maryland Baltimore School of Medicine, Baltimore, MD, 21201, United States; Bioengineering Department, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States; Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, 21250, United States; Biomedical Engineering Department, Jordan University of Science and Technology, Irbid, 22110, Jordan
| | - Alisha Prasad
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, LA, 70803, United States
| | - Manas Ranjan Gartia
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, LA, 70803, United States.
| | - Dipanjan Pan
- Department of Pediatrics, Center for Blood Oxygen Transport and Hemostasis, University of Maryland Baltimore School of Medicine, Baltimore, MD, 21201, United States; Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland Baltimore School of Medicine, Baltimore, MD, 21201, United States; Bioengineering Department, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States; Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, 21250, United States.
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43
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Tapari A, Braliou GG, Papaefthimiou M, Mavriki H, Kontou PI, Nikolopoulos GK, Bagos PG. Performance of Antigen Detection Tests for SARS-CoV-2: A Systematic Review and Meta-Analysis. Diagnostics (Basel) 2022; 12:1388. [PMID: 35741198 PMCID: PMC9221910 DOI: 10.3390/diagnostics12061388] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 11/16/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) initiated global health care challenges such as the necessity for new diagnostic tests. Diagnosis by real-time PCR remains the gold-standard method, yet economical and technical issues prohibit its use in points of care (POC) or for repetitive tests in populations. A lot of effort has been exerted in developing, using, and validating antigen-based tests (ATs). Since individual studies focus on few methodological aspects of ATs, a comparison of different tests is needed. Herein, we perform a systematic review and meta-analysis of data from articles in PubMed, medRxiv and bioRxiv. The bivariate method for meta-analysis of diagnostic tests pooling sensitivities and specificities was used. Most of the AT types for SARS-CoV-2 were lateral flow immunoassays (LFIA), fluorescence immunoassays (FIA), and chemiluminescence enzyme immunoassays (CLEIA). We identified 235 articles containing data from 220,049 individuals. All ATs using nasopharyngeal samples show better performance than those with throat saliva (72% compared to 40%). Moreover, the rapid methods LFIA and FIA show about 10% lower sensitivity compared to the laboratory-based CLEIA method (72% compared to 82%). In addition, rapid ATs show higher sensitivity in symptomatic patients compared to asymptomatic patients, suggesting that viral load is a crucial parameter for ATs performed in POCs. Finally, all methods perform with very high specificity, reaching around 99%. LFIA tests, though with moderate sensitivity, appear as the most attractive method for use in POCs and for performing seroprevalence studies.
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Affiliation(s)
- Anastasia Tapari
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece; (A.T.); (G.G.B.); (M.P.); (H.M.); (P.I.K.)
| | - Georgia G. Braliou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece; (A.T.); (G.G.B.); (M.P.); (H.M.); (P.I.K.)
| | - Maria Papaefthimiou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece; (A.T.); (G.G.B.); (M.P.); (H.M.); (P.I.K.)
| | - Helen Mavriki
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece; (A.T.); (G.G.B.); (M.P.); (H.M.); (P.I.K.)
| | - Panagiota I. Kontou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece; (A.T.); (G.G.B.); (M.P.); (H.M.); (P.I.K.)
| | | | - Pantelis G. Bagos
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece; (A.T.); (G.G.B.); (M.P.); (H.M.); (P.I.K.)
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44
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Xue W, Chen B, Hong D, Yu J, Liu G. Research on the Comprehensive Evaluation Method for the Automatic Recognition of Raman Spectrum under Multidimensional Constraint. Anal Chem 2022; 94:7628-7636. [PMID: 35584207 DOI: 10.1021/acs.analchem.2c00852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Raman spectrum contains abundant substance information with fingerprint characteristics. However, due to the huge variety of substances and their complex characteristic information, it is difficult to recognize the Raman spectrum accurately. Starting from dimensions like the Raman shift, the relative peak intensity, and the overall hit ratio of characteristic peaks, we extracted and recognized the characteristics in the Raman spectrum and analyzed these characteristics from local and global perspectives and then proposed a comprehensive evaluation method for the recognition of Raman spectrum on the basis of the data fusion of the recognition results under multidimensional constraint. Based on the common spectrum database of the normal Raman and surface-enhanced Raman of thousands of substances, we analyzed the performance of the evaluation method. It shows that even for the identification of spectra from instruments of low technical specifications, the automatic recognition rate of the sample can reach 98% and above, a great improvement compared with that of the common identification algorithms, which proves the effectiveness of the comprehensive evaluation method under multidimensional constraint.
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Affiliation(s)
- Wendong Xue
- Department of Instrumental and Electrical Engineering, Xiamen University, Xiamen 361005, Fujian, China
| | - Benneng Chen
- Department of Instrumental and Electrical Engineering, Xiamen University, Xiamen 361005, Fujian, China
| | - Deming Hong
- Department of Instrumental and Electrical Engineering, Xiamen University, Xiamen 361005, Fujian, China
| | - Jiahan Yu
- Department of Instrumental and Electrical Engineering, Xiamen University, Xiamen 361005, Fujian, China
| | - Guokun Liu
- College of the Environment and Ecology, Xiamen University, Xiamen 361005, Fujian, China
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45
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Paria D, Kwok KS, Raj P, Zheng P, Gracias DH, Barman I. Label-Free Spectroscopic SARS-CoV-2 Detection on Versatile Nanoimprinted Substrates. NANO LETTERS 2022; 22:3620-3627. [PMID: 35348344 PMCID: PMC8982738 DOI: 10.1021/acs.nanolett.1c04722] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 03/17/2022] [Indexed: 05/08/2023]
Abstract
Widespread testing and isolation of infected patients is a cornerstone of viral outbreak management, as underscored during the ongoing COVID-19 pandemic. Here, we report a large-area and label-free testing platform that combines surface-enhanced Raman spectroscopy and machine learning for the rapid and accurate detection of SARS-CoV-2. Spectroscopic signatures acquired from virus samples on metal-insulator-metal nanostructures, fabricated using nanoimprint lithography and transfer printing, can provide test results within 25 min. Not only can our technique accurately distinguish between different respiratory and nonrespiratory viruses, but it can also detect virus signatures in physiologically relevant matrices such as human saliva without any additional sample preparation. Furthermore, our large area nanopatterning approach allows sensors to be fabricated on flexible surfaces allowing them to be mounted on any surface or used as wearables. We envision that our versatile and portable label-free spectroscopic platform will offer an important tool for virus detection and future outbreak preparedness.
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Affiliation(s)
- Debadrita Paria
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore 21218, MD, USA
| | - Kam Sang Kwok
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore 21218, MD, USA
| | - Piyush Raj
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore 21218, MD, USA
| | - Peng Zheng
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore 21218, MD, USA
| | - David H. Gracias
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore 21218, MD, USA
- Department of Materials Science and Engineering, Johns Hopkins University 21218, Baltimore, MD, USA
- Department of Chemistry, Johns Hopkins University, Baltimore 21218, MD, USA
- Laboratory for Computational Sensing and Robotics (LCSR). Johns Hopkins University, Baltimore 21218, MD, USA
- Sidney Kimmel Comprehensive Cancer Center (SKCCC), Johns Hopkins University School of Medicine, Baltimore 21287, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore 21287, MD, USA
| | - Ishan Barman
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore 21218, MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore 21287, MD, USA
- Department of Radiology & Radiological Science, Johns Hopkins University School of Medicine, Baltimore 21205, MD, USA
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Cha H, Kim H, Joung Y, Kang H, Moon J, Jang H, Park S, Kwon HJ, Lee IC, Kim S, Yong D, Yoon SW, Park SG, Guk K, Lim EK, Park HG, Choo J, Jung J, Kang T. Surface-enhanced Raman scattering-based immunoassay for severe acute respiratory syndrome coronavirus 2. Biosens Bioelectron 2022; 202:114008. [PMID: 35086030 PMCID: PMC8770391 DOI: 10.1016/j.bios.2022.114008] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 02/07/2023]
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.
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Affiliation(s)
- Hyunjung Cha
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Hyeran Kim
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Younju Joung
- Department of Chemistry, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Hyunju Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Jeong Moon
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Hyowon Jang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Sohyun Park
- Department of Chemistry, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Hyung-Jun Kwon
- Functional Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56212, Republic of Korea
| | - In-Chul Lee
- Functional Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56212, Republic of Korea
| | - Sunjoo Kim
- Department of Laboratory Medicine, Gyeongsang National University College of Medicine, Jinju, 52828, Republic of Korea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Sun-Woo Yoon
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Sung-Gyu Park
- Nano-Bio Convergence Department, Korea Institute of Materials Science (KIMS), Changwon, 51508, Republic of Korea
| | - Kyeonghye Guk
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Eun-Kyung Lim
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea; Department of Nanobiotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Jaebum Choo
- Department of Chemistry, Chung-Ang University, Seoul, 06974, Republic of Korea.
| | - Juyeon Jung
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
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47
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Flores-Contreras EA, González-González RB, Rodríguez-Sánchez IP, Yee-de León JF, Iqbal HMN, González-González E. Microfluidics-Based Biosensing Platforms: Emerging Frontiers in Point-of-Care Testing SARS-CoV-2 and Seroprevalence. BIOSENSORS 2022; 12:bios12030179. [PMID: 35323449 PMCID: PMC8946853 DOI: 10.3390/bios12030179] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 03/13/2022] [Accepted: 03/15/2022] [Indexed: 02/05/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the ongoing COVID-19 (coronavirus disease-2019) outbreak and has unprecedentedly impacted the public health and economic sector. The pandemic has forced researchers to focus on the accurate and early detection of SARS-CoV-2, developing novel diagnostic tests. Among these, microfluidic-based tests stand out for their multiple benefits, such as their portability, low cost, and minimal reagents used. This review discusses the different microfluidic platforms applied in detecting SARS-CoV-2 and seroprevalence, classified into three sections according to the molecules to be detected, i.e., (1) nucleic acid, (2) antigens, and (3) anti-SARS-CoV-2 antibodies. Moreover, commercially available alternatives based on microfluidic platforms are described. Timely and accurate results allow healthcare professionals to perform efficient treatments and make appropriate decisions for infection control; therefore, novel developments that integrate microfluidic technology may provide solutions in the form of massive diagnostics to control the spread of infectious diseases.
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Affiliation(s)
- Elda A. Flores-Contreras
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Nuevo León, Mexico; (E.A.F.-C.); (R.B.G.-G.)
| | | | - Iram P. Rodríguez-Sánchez
- Laboratorio de Fisiología Molecular y Estructural, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66455, Nuevo León, Mexico;
| | | | - Hafiz M. N. Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Nuevo León, Mexico; (E.A.F.-C.); (R.B.G.-G.)
- Correspondence: (H.M.N.I.); (E.G.-G.)
| | - Everardo González-González
- Laboratorio de Fisiología Molecular y Estructural, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66455, Nuevo León, Mexico;
- Correspondence: (H.M.N.I.); (E.G.-G.)
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Akdeniz M, Uysal Ciloglu F, Tunc CU, Yilmaz U, Kanarya D, Atalay P, Aydin O. Investigation of mammalian cells expressing SARS-CoV-2 proteins by surface-enhanced Raman scattering and multivariate analysis. Analyst 2022; 147:1213-1221. [PMID: 35212693 DOI: 10.1039/d1an01989a] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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.
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Affiliation(s)
- Munevver Akdeniz
- Department of Biomedical Engineering, Erciyes University, Kayseri 38039, Turkey. .,NanoThera Lab, ERFARMA-Drug Application and Research Center, Erciyes University, 38039, Kayseri, Turkey.,ERNAM-Nanotechnology Research and Application Center, Erciyes University, Kayseri 38039, Turkey
| | - Fatma Uysal Ciloglu
- Department of Biomedical Engineering, Erciyes University, Kayseri 38039, Turkey. .,NanoThera Lab, ERFARMA-Drug Application and Research Center, Erciyes University, 38039, Kayseri, Turkey
| | - Cansu Umran Tunc
- Department of Biomedical Engineering, Erciyes University, Kayseri 38039, Turkey. .,NanoThera Lab, ERFARMA-Drug Application and Research Center, Erciyes University, 38039, Kayseri, Turkey
| | - Ummugulsum Yilmaz
- Department of Biomedical Engineering, Erciyes University, Kayseri 38039, Turkey. .,NanoThera Lab, ERFARMA-Drug Application and Research Center, Erciyes University, 38039, Kayseri, Turkey
| | - Dilek Kanarya
- Department of Biomedical Engineering, Erciyes University, Kayseri 38039, Turkey. .,NanoThera Lab, ERFARMA-Drug Application and Research Center, Erciyes University, 38039, Kayseri, Turkey.,ERNAM-Nanotechnology Research and Application Center, Erciyes University, Kayseri 38039, Turkey
| | - Pinar Atalay
- NanoThera Lab, ERFARMA-Drug Application and Research Center, Erciyes University, 38039, Kayseri, Turkey.,Department of Basic Sciences, Faculty of Pharmacy, Erciyes University, Kayseri 38040, Turkey
| | - Omer Aydin
- Department of Biomedical Engineering, Erciyes University, Kayseri 38039, Turkey. .,NanoThera Lab, ERFARMA-Drug Application and Research Center, Erciyes University, 38039, Kayseri, Turkey.,ERNAM-Nanotechnology Research and Application Center, Erciyes University, Kayseri 38039, Turkey.,ERKAM-Clinical Engineering Research and Implementation Center, Erciyes University, Kayseri 38030, Turkey
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Lyu D, Wang P, Zhang S, Liu G, Ren B. Revealing protein binding affinity on metal surfaces: an electrochemical approach. Chem Commun (Camb) 2022; 58:3537-3540. [PMID: 35195625 DOI: 10.1039/d1cc07098c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Revealing the binding affinity between viruses and surfaces of environmental matrices is crucial to evaluate the bioactivity of an immobilized virus and accompanying indirect virus-related infection pathways. The understanding for SARS-CoV-2 remaining infective for even days on stainless steel but only hours on copper is still unclear. Electrochemical chronoamperometry, ultrasensitive to interfacial capacitance on surface species, was used to investigate the binding affinity of SARS-CoV-2 on metal surfaces. SRBD, the surrogate of SARS-CoV-2, shows the highest adsorption capacity on a gold surface, followed by Cu, but lowest on a stainless steel surface. The strong binding of SRBD on copper is a result of the naturally grown Cu2O under ambient conditions. Measurement of electrochemical capacitance provides a simple strategy to explore and evaluate the potential risk of an indirect virus-related infection pathway through conductive environmental matrices.
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Affiliation(s)
- Danya Lyu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Pingshi Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Shuo Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
| | - Guokun Liu
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University, Xiamen 361005, China. .,Fujian Provincial Key Laboratory for Coastal Ecology and Environmental Studies, Center for Marine Environmental Chemistry & Toxicology, Xiamen University, Xiamen 361102, China
| | - Bin Ren
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.
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Pramanik A, Gao Y, Patibandla S, Gates K, Ray PC. Bioconjugated Nanomaterial for Targeted Diagnosis of SARS-CoV-2. ACCOUNTS OF MATERIALS RESEARCH 2022; 3:134-148. [PMID: 37556282 PMCID: PMC8791035 DOI: 10.1021/accountsmr.1c00177] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 01/03/2022] [Indexed: 05/26/2023]
Abstract
Infectious diseases by pathogenic microorganisms are one of the leading causes of mortality worldwide. Healthcare and socio-economic development have been seriously affected for different civilizations because of bacterial and viral infections. According to the Centers for Disease Control and Prevention (CDC), pandemic in 1918 by the Influenza A virus of the H1N1 subtype was responsible for 50 to 100 million deaths worldwide. Similarly, the Asian flu pandemic in 1957, Hong Kong flu in 1968, and H1N1pdm09 flu pandemic in 2009 were responsible for more than 1 million deaths across the globe each time. As per the World Health Organization (WHO), the current pandemic by coronavirus disease 2019 (COVID-19) due to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus is responsible for more than 4.8 M death worldwide until now. Since the gold standard polymerase chain reaction (PCR) test is more time-consuming, the health care system cannot test all symptomatic and asymptomatic Covid patients every day, which is extremely important to tackle the outbreak. One of the significant challenges during the current pandemic is developing mass testing tools, which is critical to control the virus spread in the community. Therefore, it is highly desirable to develop advanced material-based approaches that can provide a rapid and accurate diagnosis of COVID-19, which will have the capability to save millions of human lives. Aiming for the targeted diagnosis of deadly virus, researchers have developed nanomaterials with various sizes, shapes, and dimensions. These nanomaterials have been used to identify biomolecules via unique optical, electrical, magnetic, structural, and functional properties, which are lacking in other materials. Despite significant progress, nanomaterial-based diagnosis of biomolecules is still facing several obstacles due to low targeting efficiency and nonspecific interactions. To overcome these problems, the bioconjugated nanoparticle has been designed via surface coating with polyethylene glycol (PEG) and then conjugated with antibodies, DNA, RNA, or peptide aptamers. Therefore, the current Account summarizes an overview of the recent advances in the design of bioconjugated nanomaterial-based approached as effective diagnosis of the SARS-CoV-2 virus and the SARS-CoV-2 viral RNA, antigen, or antibody, with a particular focus on our work and other's work related to this subject. First, we present how to tailor the surface functionalities of nanomaterials to achieve bioconjugated material for targeted diagnosis of the virus. Then we review the very recent advances in the design of antibody/aptamer/peptide conjugated nanostructure, which represent a powerful platform for naked-eye colorimetric detection via plasmonic nanoparticles. We then discuss nanomaterial-based surface-enhanced Raman scattering (SERS) spectroscopy, which has the capability for very low-level fingerprint identification of virus, antigen, and antibody via graphene, plasmonic nanoparticle, and heterostructure material. After that, we summarized about fluorescence and nanoparticle surface energy transfer (NSET)-based on specific identification of SARS-CoV-2 infections via CNT, quantum dots (QDs), and plasmonic nanoparticles. Finally, we highlight the merit and significant challenges of nanostructure-based tools in infectious diseases diagnosis. For the researchers who want to engage in the new development of bioconjugated material for our survival from the current and future pandemics, we hope that this Account will be helpful for generating ideas that are scientifically stimulating and practically challenging.
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Affiliation(s)
- Avijit Pramanik
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, Mississippi 39217, United States
| | - Ye Gao
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, Mississippi 39217, United States
| | - Shamily Patibandla
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, Mississippi 39217, United States
| | - Kalein Gates
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, Mississippi 39217, United States
| | - Paresh Chandra Ray
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, Mississippi 39217, United States
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