SARS-CoV-2 Receptor Binding Domain as a Stable-Potential Target for SARS-CoV-2 Detection by Surface-Enhanced Raman Spectroscopy

Rapid Detection of SARS-CoV-2 Variants Using an Angiotensin-Converting Enzyme 2-Based Surface-Enhanced Raman Spectroscopy Sensor Enhanced by CoVari Deep Learning Algorithms

An integrated approach combining surface-enhanced Raman spectroscopy (SERS) with a specialized deep learning algorithm to rapidly and accurately detect and quantify SARS-CoV-2 variants is developed based on an angiotensin-converting enzyme 2 (ACE2)-functionalized AgNR@SiO2 array SERS sensor. SERS spectra with concentrations of different variants were collected using a portable Raman system. After appropriate spectral preprocessing, a deep learning algorithm, CoVari, is developed to predict both the viral variant species and concentrations. Using a 10-fold cross-validation strategy, the model achieves an average accuracy of 99.9% in discriminating between different virus variants and R2 values larger than 0.98 for quantifying viral concentrations of the three viruses, demonstrating the high quality of the detection. The limit of detection of the ACE2 SERS sensor is determined to be 10.472, 11.882, and 21.591 PFU/mL for SARS-CoV-2, SARS-CoV-2 B1, and CoV-NL63, respectively. The feature importance of virus classification and concentration regression in the CoVari algorithm are calculated based on a permutation algorithm, which showed a clear correlation to the biochemical origins of the spectra or spectral changes. In an unknown specimen test, classification accuracy can achieve >90% for concentrations larger than 781 PFU/mL, and the predicted concentrations consistently align with actual values, highlighting the robustness of the proposed algorithm. Based on the CoVari architecture and the output vector, this algorithm can be generalized to predict both viral variant species and concentrations simultaneously for a broader range of viruses. These results demonstrate that the SERS + CoVari strategy has the potential for rapid and quantitative detection of virus variants and potentially point-of-care diagnostic platforms.

Investigating on sensing mechanism of MoS2-FET biosensors in response to proteins

Field-effect transistor (FET) biosensors based on two-dimensional materials have gained extensive attention due to their high sensitivity, label-free detection capability, and fast response. Molybdenum disulfide (MoS2), with tunable bandgap, high surface-to-volume ratio, and smooth surface without dangling bonds, is a promising material for FET biosensors. Previous reports have demonstrated the fabrication of MoS2-FET biosensors and their high sensitivity detection of proteins. However, most prior research has focused on the realization of MoS2-FETs for detecting different kinds of proteins or molecules, while comprehensive analysis of the sensing mechanism and dominant device factors of MoS2-FETs in response to proteins is yet to investigate. In this study, we first fabricated MoS2-FET biosensor and detected different types of proteins (immunoglobulin G (IgG),β-actin, and prostate-specific antigen (PSA)). Secondly, we built the model of the device and analyzed the sensing mechanism of MoS2-FETs in response to proteins. Experimental and modeling results showed that the induced doping effect and gating effect caused by the target protein binding to the device surface were the major influential factors. Specifically, the channel doping concentration and gate voltage (Vg) offset exhibited monotonic change as the concentration of the protein solution increases. For example, the channel doping concentration increased up to ∼37.9% and theVgoffset was ∼-1.3 V with 10-7μgμl-1IgG. The change was less affected by the device size. We also investigated the effects of proteins with opposite acid-base properties (β-actin and PSA) to IgG on the device sensing mechanism.β-actin and PSA exhibited behavior opposite to that of IgG. Additionally, we studied the response behavior of MoS2-FETs with different dimensions and dielectric materials (channel length, MoS2thickness, dielectric layer thickness, dielectric layer material) to proteins. The underlying mechanisms were discussed in details. This study provides valuable guidelines for the design and application of MoS2-FET biosensors.

Diagnostics and analysis of SARS-CoV-2: current status, recent advances, challenges and perspectives

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.

Magnetic biosensors for identification of SARS-CoV-2, Influenza, HIV, and Ebola viruses: a review

Infectious diseases such as novel coronavirus (SARS-CoV-2), Influenza, HIV, Ebola, etc kill many people around the world every year (SARS-CoV-2 in 2019, Ebola in 2013, HIV in 1980, Influenza in 1918). For example, SARS-CoV-2 has plagued higher than 317 000 000 people around the world from December 2019 to January 13, 2022. Some infectious diseases do not yet have not a proper vaccine, drug, therapeutic, and/or detection method, which makes rapid identification and definitive treatments the main challenges. Different device techniques have been used to detect infectious diseases. However, in recent years, magnetic materials have emerged as active sensors/biosensors for detecting viral, bacterial, and plasmids agents. In this review, the recent applications of magnetic materials in biosensors for infectious viruses detection have been discussed. Also, this work addresses the future trends and perspectives of magnetic biosensors.

Raman spectroscopy for viral diagnostics

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.

SERS-based immunosensor for E. coli contaminants detection in milk using silver-coated nanoporous silicon substrates

The dairy sector is frequently affected by contagious and environmental factors that spread between animals by numerous means and induce the inflammatory disease of bovine mastitis (BM). Herein, silver decorated porous silicon (Ag-pSi) SERS platform was designed for rapid and reliable Escherichia coli (predominant BM pathogen) detection in various milk origins. The inherent surface void and pore morphology were physically optimized to augment the SERS effect using 4-aminothiphenol (4ATP) while achieving an enhancement factor >4.6 × 10⁷. An indirect immunoassay evaluated the residual unreacted antibodies using an optimized 4ATP/Ag-pSi SERS platform modified with secondary antibodies. Under optimized conditions, the porous substrate offered high sensitivity toward target bacteria detection of 3 CFU mL^-1 and linear response of 10¹-10⁵ CFU mL^-1. Moreover, the selectivity and specificity of the designed sensing platform were cross-validated against other interfering bacteria without compromising its performance efficiencies. Finally, the applicability of the developed system for real-life conditions was elucidated in different milk samples (bovine, goat, sheep) with recovery values of 78-115% compared to the conventional culture technique. Considering the complex media analysis, the miniaturized SERS platform is highly reliable, rapid and accurate that could be applicable for routine on-site analysis of various emerging pathogens relevant to BM management.

Recent advances of Au@Ag core-shell SERS-based biosensors

The methodological advancements in surface-enhanced Raman scattering (SERS) technique with nanoscale materials based on noble metals, Au, Ag, and their bimetallic alloy Au-Ag, has enabled the highly efficient sensing of chemical and biological molecules at very low concentration values. By employing the innovative various type of Au, Ag nanoparticles and especially, high efficiency Au@Ag alloy nanomaterials as substrate in SERS based biosensors have revolutionized the detection of biological components including; proteins, antigens antibodies complex, circulating tumor cells, DNA, and RNA (miRNA), etc. This review is about SERS-based Au/Ag bimetallic biosensors and their Raman enhanced activity by focusing on different factors related to them. The emphasis of this research is to describe the recent developments in this field and conceptual advancements behind them. Furthermore, in this article we apex the understanding of impact by variation in basic features like effects of size, shape varying lengths, thickness of core-shell and their influence of large-scale magnitude and morphology. Moreover, the detailed information about recent biological applications based on these core-shell noble metals, importantly detection of receptor binding domain (RBD) protein of COVID-19 is provided.

Understanding the Excitation Wavelength Dependence and Thermal Stability of the SARS-CoV-2 Receptor-Binding Domain Using Surface-Enhanced Raman Scattering and Machine Learning

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.

Specific intracellular signature of SARS-CoV-2 infection using confocal Raman microscopy

SARS-CoV-2 infection remains spread worldwide and requires a better understanding of virus-host interactions. Here, we analyzed biochemical modifications due to SARS-CoV-2 infection in cells by confocal Raman microscopy. Obtained results were compared with the infection with another RNA virus, the measles virus. Our results have demonstrated a virus-specific Raman molecular signature, reflecting intracellular modification during each infection. Advanced data analysis has been used to distinguish non-infected versus infected cells for two RNA viruses. Further, classification between non-infected and SARS-CoV-2 and measles virus-infected cells yielded an accuracy of 98.9 and 97.2 respectively, with a significant increase of the essential amino-acid tryptophan in SARS-CoV-2-infected cells. These results present proof of concept for the application of Raman spectroscopy to study virus-host interaction and to identify factors that contribute to the efficient SARS-CoV-2 infection and may thus provide novel insights on viral pathogenesis, targets of therapeutic intervention and development of new COVID-19 biomarkers.

Heterogeneous Nanoplasmonic Amplifiers for Photocatalysis’s Application: A Theoretical Study

The higher cost of Ag and Au and their resonance frequency shift limitation opened the way to find an alternative solution by developing new nanohybrid antenna based on silicon and silicon dioxide coated with metallic nanoparticles. The latter has been recently solicited as a promising configuration for more large-scale plasmonic utilisation. This work reports a multitude of fascinating new phenomenon on LSPR on silicon antenna wires coated with core-shell nanospheres and the studying of the nanoplasmonics amplifiers to control optical and electromagnetic properties of materials. The LSPR modes and their interaction with the silicon nanowires are studied using numerical methods. The suggested configuration offers resonance covering the UV-visible and NIR regions, making them an adaptable addition to the nanoplasmonics toolbox.

Ultrafast Detection of SARS-CoV-2 Spike Protein (S) and Receptor-Binding Domain (RBD) in Saliva Using Surface-Enhanced Raman Spectroscopy

Controlling contagious diseases necessitates using diagnostic techniques that can detect infection in the early stages. Although different diagnostic tools exist, there are still challenges related to accuracy, rapidity, cost-effectiveness, and ease of use. Surface-enhanced Raman spectroscopy (SERS) is a rapid, simple, less expensive, and accurate method. We continue our previous work published on SERS detection of the SARS-CoV-2 receptor-binding domain (RBD) in water. In this work, we replace water with saliva to detect SARS-CoV-2 proteins at very low concentrations and during a very short time. We prepared a very low concentration of 10−9 M SARS-CoV-2 spike protein (S) and SARS-CoV-2 receptor-binding domain (RBD) in saliva to mimic a real case scenario. Then, we drop them on a SERS substrate. Using modified SERS measurements on the control and the sample containing the biomolecules, confirmed the sensitivity of the target identification. This technique provides different diagnostic solutions that are fast, simple, non-destructive and ultrasensitive. Simulation of the real-world of silicon wire covered with silver and gold, were performed using an effective and accurate tool, COMSOL Multiphysics software, for the enhancement properties study.

Rapid Optical Biosensing of SARS-CoV-2 Spike Proteins in Artificial Samples

Tests for SARS-CoV-2 are crucial for the mass surveillance of the incidence of infection. The long waiting time for classic nucleic acid test results highlights the importance of developing alternative rapid biosensing methods. Herein, we propose a fiber-optic biolayer interferometry-based biosensor (FO-BLI) to detect SARS-CoV-2 spike proteins, extracellular domain (ECD), and receptor-binding domain (RBD) in artificial samples in 13 min. The FO-BLI biosensor utilized an antibody pair to capture and detect the spike proteins. The secondary antibody conjugated with horseradish peroxidase (HRP) reacted with the enzyme substrate for signal amplification. Two types of substrates, 3,3'-diaminobenzidine (DAB) and an advanced 3-Amino-9-ethylcarbazole (i.e., AMEC), were applied to evaluate their capabilities in enhancing signals and reaching high sensitivity. After careful comparison, the AMEC-based FO-BLI biosensor showed better assay performance, which detected ECD at a concentration of 32-720 pM and RBD of 12.5-400 pM in artificial saliva and serum, respectively. The limit of detection (LoD) for SARS-CoV-2 ECD and RBD was defined to be 36 pM and 12.5 pM, respectively. Morphology of the metal precipitates generated by the AMEC-HRP reaction in the fiber tips was observed using field emission scanning electron microscopy (SEM). Collectively, the developed FO-BLI biosensor has the potential to rapidly detect SARS-CoV-2 antigens and provide guidance for "sample-collect and result-out on-site" mode.