Optical Detection of CoV-SARS-2 Viral Proteins to Sub-Picomolar Concentrations

Single-molecule detection of SARS-CoV-2 N protein on multilayered plasmonic nanotraps with surface-enhanced Raman spectroscopy

The spread of the SARS-CoV-2 virus has had an unprecedented impact, both by posing a serious risk to human health and by amplifying the burden on the global economy. The rapid identification of the SARS-CoV-2 virus has been crucial to preventing and controlling the spread of SARS-CoV-2 infections. In this study, we propose a multilayered plasmonic nanotrap (MPNT) device for the rapid identification of single particles of SARS-CoV-2 virus in ultra-high sensitivity by surface-enhanced Raman scattering (SERS). The MPNT device is composed of arrays of concentric cylindrical cavities with Ag/SiO2/Ag multilayers deposited on the top and at the bottom. By varying the diameter of the cylinders and the thickness of the multilayers, the resonant optical absorption and local electric field were optimized. The SERS enhancement factors of the proposed device are of the order of 108, which enable the rapid identification of SARS-CoV-2 N protein in concentrations as low as 1.25 × 10-15－12.5 × 10-15 g mL-1 within 1 min. The developed MPNT SERS device provides a label-free and rapid detection platform for SARS-CoV-2 virus. The general nature of the device makes it equally suitable to detect other infectious viruses.

Advances in nanobiosensors during the COVID-19 pandemic and future perspectives for the post-COVID era

The unprecedented threat of the highly contagious virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes exponentially increased infections of coronavirus disease 2019 (COVID-19), highlights the weak spots of the current diagnostic toolbox. In the midst of catastrophe, nanobiosensors offer a new opportunity as an alternative tool to fill a gap among molecular tests, rapid antigen tests, and serological tests. Nanobiosensors surpass the potential of antigen tests because of their enhanced sensitivity, thus enabling us to see antigens as stable and easy-to-access targets. During the first three years of the COVID-19 pandemic, a substantial number of studies have reported nanobiosensors for the detection of SARS-CoV-2 antigens. The number of articles on nanobiosensors and SARS-CoV-2 exceeds the amount of nanobiosensor research on detecting previous infectious diseases, from influenza to SARS-CoV and MERS-CoV. This unprecedented publishing pace also implies the significance of SARS-CoV-2 and the present pandemic. In this review, 158 studies reporting nanobiosensors for detecting SARS-CoV-2 antigens are collected to discuss the current challenges of nanobiosensors using the criteria of point-of-care (POC) diagnostics along with COVID-specific issues. These advances and lessons during the pandemic pave the way for preparing for the post-COVID era and potential upcoming infectious diseases.

Antibody- and aptamer-free SERS substrate for ultrasensitive and anti-interference detection of SARS-CoV-2 spike protein in untreated saliva

Sensitive and anti-interference detection of targeted signal(s) in body fluids is one of the paramount tasks in biosensing. Overcoming the complication and high cost of antibody/aptamer-modification, surface-enhanced Raman spectroscopy (SERS) based on antibody/aptamer-free (AAF) substrates has shown great promise, yet with rather limited detection sensitivity. Herein, we report ultrasensitive and anti-interference detection of SARS-CoV-2 spike protein in untreated saliva by an AAF SERS substrate, applying the evanescent field induced by the high-order waveguide modes of well-defined nanorods for SERS for the first time. A detection limit of 3.6 × 10-17 M and 1.6 × 10-16 M are obtained in phosphate buffered saline and untreated saliva, respectively; the detection limits are three orders of magnitude improved than the best records from AAF substrates. This work unlocks an exciting path to design AAF SERS substrates for ultrasensitive biosensing, not limited to detection of viral antigens.

Development of Rapid Aptamer-Based Screening Assay for the Detection of Covid-19 Variants

The development of a colorimetric severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection assay with the WHO published ASSURED criteria is reported, in which the biosensor should have the following characteristics of (i) being affordable for low-income communities, (ii) sensitive, (iii) specific, (iv) user-friendly to be used by non-skilled personnel, (v) rapid and robust, (vi) equipment-free, and (vii) delivered to the end-users as a simple and easy to use point-of-care tool. Early viral infection detection prevents virus spread and controls the epidemic. We herein report the development of a colorimetric assay in which SARS-COV-2 variants can be detected by colorimetric observation of color on the sensing cotton swab surface. Using the developed biosensor assay, it is possible to discriminate between the various SARS-CoV-2 variants with a LOD of 100 ng/mL within 4 min including sample preconcentration and incubation step. The results illustrated the development of a SARS-CoV-2 colorimetric biosensor that can be mass produced, with low-reagent cost, and can be read-out visually in the field by nonskilled personnel.

Aptamer-, heparin- or cocktail-based inhibition of S1-ACE2 protein complexes

The Spike protein (S1) from the Severe acute respiratory syndrome 2 virus binds to angiotensin converting enzyme 2 (ACE2) receptor to initiate infection. Hence, antiviral therapeutic targeting the S1-ACE2 interface is of interest. Herein, we compare the inhibition efficacy of an aptamer to heparin or their cocktail, against wild-type (WT), Omicron, Delta, and Lambda S1-ACE2 complexes. The aptamer-protein complexes had the dissociation constant K_D values in the 2-13 nM range. The aptamer half-maximal inhibitory concentration against WT S1-ACE was 17 nM, with the % inhibition in the 12-35% range. Several aptamer-S1 protein complexes were also stable at low pH with 60% inhibition. Despite the similarity in S1 sequences, the extent of inhibition (2-27%) with heparin was highly dependent on the type of S1 protein. More importantly, heparin did not inhibit the WT S1-ACE2 complex but was effective with mutants. The aptamer-heparin cocktail was less effective compared to aptamer or heparin, individually. Modelling data show that either a direct or proximal binding to RBD sites by aptamer or heparin prevents the ACE2 binding. Overall, heparin was as an effective inhibitor as aptamer against certain variants, and represents the more cost-effective neutralizing agent against emerging coronaviruses.

Emerging trends in point-of-care biosensing strategies for molecular architectures and antibodies of SARS-CoV-2

COVID-19, a highly contagious viral infection caused by the occurrence of severe acute respiratory syndrome coronavirus (SARS-CoV-2), has turned out to be a viral pandemic then ravaged many countries worldwide. In the recent years, point-of-care (POC) biosensors combined with state-of-the-art bioreceptors, and transducing systems enabled the development of novel diagnostic tools for rapid and reliable detection of biomarkers associated with SARS-CoV-2. The present review thoroughly summarises and discusses various biosensing strategies developed for probing SARS-CoV-2 molecular architectures (viral genome, S Protein, M protein, E protein, N protein and non-structural proteins) and antibodies as a potential diagnostic tool for COVID-19. This review discusses the various structural components of SARS-CoV-2, their binding regions and the bioreceptors used for recognizing the structural components. The various types of clinical specimens investigated for rapid and POC detection of SARS-CoV-2 is also highlighted. The importance of nanotechnology and artificial intelligence (AI) approaches in improving the biosensor performance for real-time and reagent-free monitoring the biomarkers of SARS-CoV-2 is also summarized. This review also encompasses existing practical challenges and prospects for developing new POC biosensors for clinical monitoring of COVID-19.

Aptamers Targeting Membrane Proteins for Sensor and Diagnostic Applications

Many biological processes (physiological or pathological) are relevant to membrane proteins (MPs), which account for almost 30% of the total of human proteins. As such, MPs can serve as predictive molecular biomarkers for disease diagnosis and prognosis. Indeed, cell surface MPs are an important class of attractive targets of the currently prescribed therapeutic drugs and diagnostic molecules used in disease detection. The oligonucleotides known as aptamers can be selected against a particular target with high affinity and selectivity by iterative rounds of in vitro library evolution, known as Systematic Evolution of Ligands by EXponential Enrichment (SELEX). As an alternative to antibodies, aptamers offer unique features like thermal stability, low-cost, reuse, ease of chemical modification, and compatibility with various detection techniques. Particularly, immobilized-aptamer sensing platforms have been under investigation for diagnostics and have demonstrated significant value compared to other analytical techniques. These "aptasensors" can be classified into several types based on their working principle, which are commonly electrochemical, optical, or mass-sensitive. In this review, we review the studies on aptamer-based MP-sensing technologies for diagnostic applications and have included new methodological variations undertaken in recent years.

Advanced and Smart Textiles during and after the COVID-19 Pandemic: Issues, Challenges, and Innovations

The COVID-19 pandemic has hugely affected the textile and apparel industry. Besides the negative impact due to supply chain disruptions, drop in demand, liquidity problems, and overstocking, this pandemic was found to be a window of opportunity since it accelerated the ongoing digitalization trends and the use of functional materials in the textile industry. This review paper covers the development of smart and advanced textiles that emerged as a response to the outbreak of SARS-CoV-2. We extensively cover the advancements in developing smart textiles that enable monitoring and sensing through electrospun nanofibers and nanogenerators. Additionally, we focus on improving medical textiles mainly through enhanced antiviral capabilities, which play a crucial role in pandemic prevention, protection, and control. We summarize the challenges that arise from personal protective equipment (PPE) disposal and finally give an overview of new smart textile-based products that emerged in the markets related to the control and spread reduction of SARS-CoV-2.

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.

Adsorption and Inactivation of SARS-CoV-2 on the Surface of Anatase TiO2(101)

We investigated the adsorption of severe acute respiratory syndrome corona virus 2 (SARS-CoV-2), the virus responsible for the current pandemic, on the surface of the model catalyst TiO₂(101) using atomic force microscopy, transmission electron microscopy, fluorescence microscopy, and X-ray photoelectron spectroscopy, accompanied by density functional theory calculations. Three different methods were employed to inactivate the virus after it was loaded on the surface of TiO₂(101): (i) ethanol, (ii) thermal, and (iii) UV treatments. Microscopic studies demonstrate that the denatured spike proteins and other proteins in the virus structure readsorb on the surface of TiO₂ under thermal and UV treatments. The interaction of the virus with the surface of TiO₂ was different for the thermally and UV treated samples compared to the sample inactivated via ethanol treatment. AFM and TEM results on the UV-treated sample suggested that the adsorbed viral particles undergo damage and photocatalytic oxidation at the surface of TiO₂(101) which can affect the structural proteins of SARS-CoV-2 and denature the spike proteins in 30 min. The role of Pd nanoparticles (NPs) was investigated in the interaction between SARS-CoV-2 and TiO₂(101). The presence of Pd NPs enhanced the adsorption of the virus due to the possible interaction of the spike protein with the NPs. This study is the first investigation of the interaction of SARS-CoV-2 with the surface of single crystalline TiO₂(101) as a potential candidate for virus deactivation applications. Clarification of the interaction of the virus with the surface of semiconductor oxides will aid in obtaining a deeper understanding of the chemical processes involved in photoinactivation of microorganisms, which is important for the design of effective photocatalysts for air purification and self-cleaning materials.

Investigation and comparison of graphene nanoribbon and carbon nanotube based SARS-CoV-2 detection sensors: An ab initio study

The rapid detection of SARS-CoV-2, the pathogen of the Covid-19 pandemic, is obviously of great importance for stopping the spread of the virus by detecting infected individuals. Here, we report the ab initio analysis results of graphene nanoribbon (GNR) and carbon nanotube (CNT) based SARS-CoV-2 detection sensors which are experimentally demonstrated in the literature. The investigated structures are the realistic molecular models of the sensors that are employing 1-pyrenebutyric acid N-hydroxysuccinimide ester as the antibody linker. Density functional theory in conjunction with non-equilibrium Green's function formalism (DFT-NEGF) is used to obtain the transmission spectra, current-voltage and resistance-voltage characteristics of the sensors before and after the attachment of the SARS-CoV-2 spike protein. The operation mechanism of the GNR and CNT based SARS-CoV-2 sensors are exposed using the transmission spectrum analysis. Moreover, it is observed that GNR based sensor has more definitive detection characteristics compared to its CNT based counterpart.

Long-Range SERS Detection of the SARS-CoV-2 Antigen on a Well-Ordered Gold Hexagonal Nanoplate Film

The development of an effective method for identifying severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) via direct viral protein detection is significant but challenging in combatting the COVID-19 epidemic. As a promising approach for direct detection, viral protein detection using surface-enhanced Raman scattering (SERS) is limited by the larger viral protein size compared to the effective electromagnetic field (E-field) range because only the analyte remaining within the E-field can achieve high detection sensitivity. In this study, we designed and fabricated a novel long-range SERS (LR-SERS) substrate with an Au nanoplate film/MgF2/Au mirror/glass configuration to boost the LR-SERS resulting from the extended E-field. On applying the LR-SERS to detect the SARS-CoV-2 spike protein (S protein), reagent-free detection achieved a low detection limit of 9.8 × 10-11 g mL-1 and clear discrimination from the SARS-CoV S protein. The developed technique also allows testing of the S protein in saliva with 98% sensitivity and 100% specificity.

Label-free electrochemical aptasensor for the detection of SARS-CoV-2 spike protein based on carbon cloth sputtered gold nanoparticles

The proliferation and transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), or the (COVID-19) disease, has become a threat to worldwide biosecurity. Therefore, early diagnosis of COVID-19 is crucial to combat the ongoing infection spread. In this study we propose a flexible aptamer-based electrochemical sensor for the rapid, label-free detection of SARS-CoV-2 spike protein (SP). A platform made of a porous and flexible carbon cloth, coated with gold nanoparticles, to increase the conductivity and electrochemical performance of the material, was assembled with a thiol functionalized DNA aptamer via S-Au bonds, for the selective recognition of the SARS-CoV-2 SP. The various steps for the sensor preparation were followed by using scanning electron microscopy, cyclic voltammetry and differential pulse voltammetry (DPV). The proposed platform displayed good mechanical stability, revealing negligible changes on voltammetric responses to bending at various angles. Quantification of SARS-CoV-2 SP was performed by DPV and chronopotentiometry (CP), exploiting the changes of the electrical signals due the [Fe(CN)₆]^3-/4- redox probe, when SARS-CoV-2 SP binds to the aptamer immobilized on the electrode surface. Current density, in DPV, and square root of the transition time, in CP, varied linearly with the log[ SARS-CoV-2 SP], providing lower limits of detection (LOD) of 0.11 ng/mL and 37.8 ng/mL, respectively. The sensor displayed good selectivity, repeatability, and was tested in diluted human saliva, spiked with different SARS-CoV-2 SP concentrations, providing LODs of 0.167 ng/mL and 46.2 ng/mL for DPV and CP, respectively.

Aptamer-based biosensors for virus protein detection

Virus threatens life health seriously. The accurate early diagnosis of the virus is vital for clinical control and treatment of virus infection. Aptamers are small single-stranded oligonucleotides (DNAs or RNAs). In this review, we summarized aptasensors for virus detection in recent years according to the classification of the viral target protein, and illustrated common detection mechanisms in the aptasensors (colorimetry, fluorescence assay, surface plasmon resonance (SPR), surface-enhanced raman spectroscopy (SERS), electrochemical detection, and field-effect transistor (FET)). Furthermore, aptamers against different target proteins of viruses were summarized. The relationships between the different biomarkers of the viruses and the detection methods, and their performances were revealed. In addition, the challenges and future directions of aptasensors were discussed. This review will provide valuable references for constructing on-site aptasensors for detecting viruses, especially the SARS-CoV-2.

In Situ Surface-Enhanced Raman Scattering Detection of a SARS-CoV-2 Biomarker Using Flexible and Transparent Polydimethylsiloxane Films with Embedded Au Nanoplates

Coronavirus disease 2019 (COVID-19) remains an ongoing issue worldwide and continues to disrupt daily life. Transmission of infection primarily occurs through secretions when in contact with infected individuals, but more recent evidence has shown that fomites are also a source of virus transmission, especially in cold-chain logistics. Traditional nucleic acid testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contamination in cold-chain logistics is time-consuming and inaccurate because of the multiplex sampling sites. Surface-enhanced Raman spectroscopy (SERS) provides a rapid, sensitive, and label-free detection route for various molecules, including viruses, through the identification of the characteristic peaks of their outer membrane proteins. In this study, we embedded arbitrarily orientated gold nanoplates (Au NPLs) in polydimethylsiloxane (PDMS) elastomer and used it as biosensor for the ultrasensitive detection of the SARS-CoV-2 spike protein in cold-chain logistics. This transparent and flexible substrate can be wrapped onto arbitrary surfaces and permits light penetration into the underlying contact surface, enabling in situ and point-of-care SERS diagnostics. The developed assay displayed high reproducibility (8.7%) and a low detection limit of 6.8 × 10-9 g mL-1, indicating its potential to serve as a promising approach with increased accuracy and sensitivity for the detection of the S protein.

Sensitive SARS-CoV-2 detection in wastewaters using a carbon nanodot-amplified electrochemiluminescence immunosensor

Given the great utility that having fast, efficient and cost-effective methods for the detection of SARS-CoV-2 in wastewater can have in controlling the pandemic caused by this virus, the development of new dependable and specific SARS-CoV-2 coronavirus sensing devices to be applied to wastewater is essential to promote public health interventions. Therefore, herein we propose a new method to detect SARS-CoV-2 in wastewater based on a carbon nanodots-amplified electrochemiluminescence immunosensor for the determination of the SARS-CoV-2 Spike S1 protein. For the construction of the immunosensor, N-rich carbon nanodots have been synthetized with a double function: to contribute as amplifiers of the electrochemiluminescent signal in presence of [Ru(bpy)₃]²⁺ and as antibody supports by providing functional groups capable of covalently interacting with the SARS-CoV-2 Spike S1 antibody. The proposed ECL immunosensor has demonstrated a high specificity in presence of other virus-related proteins and responded linearly to SARS-CoV-2 Spike S1 concentration over a wide range with a limit of detection of 1.2 pg/mL. The immunosensor has an excellent stability and achieved the detection of SARS-CoV-2 Spike S1 in river and urban wastewater, which supplies a feasible and reliable sensing platform for early virus detection and therefore to protect the population. The detection of SARS-CoV-2 Spike S1 in urban wastewater can be used as a tool to measure the circulation of the virus in the population and to detect a possible resurgence of COVID-19.

Single-Nanoparticle-Based Digital SERS Sensing Platform for the Accurate Quantitative Detection of SARS-CoV-2

To prevent the ongoing spread of the highly infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), accurate and early detection based on a rapid, ultrasensitive, and highly reliable sensing method is crucially important. Here, we present a bumpy core-shell surface-enhanced Raman spectroscopy (SERS) nanoprobe-based sensing platform with single-nanoparticle (SNP)-based digital SERS analysis. The tailorable bumpy core-shell SERS nanoprobe with an internal self-assembled monolayer of 4-nitrobenzenethiol Raman reporters, synthesized using HEPES biological buffer, generates a strong, uniform, and reproducible SERS signal with an SNP-level sensitive and narrowly distributed enhancement factor (2.1 × 108 to 2.2 × 109). We also propose an SNP-based digital SERS analysis method that provides direct visualization of SNP detection at ultralow concentrations and reliable quantification over a wide range of concentrations. The bumpy core-shell SERS nanoprobe-based sensing platform with SNP-based digital SERS analysis achieves the ultrasensitive and quantitative detection of the SARS-CoV-2 spike protein with a limit of detection of 7.1 × 10-16 M over a wide dynamic range from 3.7 × 10-15 to 3.7 × 10-8 M, far outperforming the conventional enzyme-linked immunosorbent assay method for the target protein. Furthermore, it can detect mutated spike proteins from the SARS-CoV-2 variants, representing the key mutations of Alpha, Beta, Gamma, Delta, and Omicron variants. Therefore, this sensing platform can be effectively and efficiently used for the accurate and early detection of SARS-CoV-2 and be adapted for the ultrasensitive and reliable detection of other highly infectious diseases.

Diagnostic Tools for Rapid Screening and Detection of SARS-CoV-2 Infection

The novel coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has severely impacted human health and the health management system globally. The ongoing pandemic has required the development of more effective diagnostic strategies for restricting deadly disease. For appropriate disease management, accurate and rapid screening and isolation of the affected population is an efficient means of containment and the decimation of the disease. Therefore, considerable efforts are being directed toward the development of rapid and robust diagnostic techniques for respiratory infections, including SARS-CoV-2. In this article, we have summarized the origin, transmission, and various diagnostic techniques utilized for the detection of the SARS-CoV-2 virus. These higher-end techniques can also detect the virus copy number in asymptomatic samples. Furthermore, emerging rapid, cost-effective, and point-of-care diagnostic devices capable of large-scale population screening for COVID-19 are discussed. Finally, some breakthrough developments based on spectroscopic diagnosis that could revolutionize the field of rapid diagnosis are discussed.

Controlled, partially exfoliated, self-supported functionalized flexible graphitic carbon foil for ultrasensitive detection of SARS-CoV-2 spike protein

This paper reports on an ultrasensitive and label-free electrochemical immunosensor for monitoring the SARS-CoV-2 spike protein (SARS-CoV-2 SP). A self-supported electrode, which can simultaneously serve as an antibody immobilization matrix and electron transport channel, was initially fabricated by a controlled partial exfoliation of a flexible graphitic carbon foil (GCF). Mild acidic treatment enabled the partial oxidation and exfoliation (down to a few layers) of the flexible GCF; this also provided a high percentage of oxygen functionality and an enhanced surface roughness. The substrate electrode was further functionalized with ethylenediamine (EDA) to provide a suitable platform with even a higher surface roughness, for the covalent immobilization of an anti-SARS-CoV-2 antibody. The change in the current response for the [Fe(CN)₆]^3-/4- redox couple, induced by the binding of SARS-CoV-2 SP to the antibody immobilized on the electrode surface, was used to determine the SARS-CoV-2 SP concentration. The immunosensor thus prepared could detect SARS-CoV-2 SP within 30 min with high reproducibility and specificity over a wide concentration range (0.2-100 ng/mL). Detection limits of 25 pg/mL and 27 pg/mL were found in a phosphate buffer solution (pH 7.4), and diluted blood plasma, respectively. The immunosensor was also employed to detect SARS-CoV-2 SP in artificial human saliva.

Label-Free Detection of the Receptor-Binding Domain of the SARS-CoV-2 Spike Glycoprotein at Physiologically Relevant Concentrations Using Surface-Enhanced Raman Spectroscopy

Surface-enhanced Raman scattering (SERS) spectroscopy is a surface- or cavity-enhanced variant of Raman scattering spectroscopy that allows the detection of analytes with a sensitivity down to single molecules. This method involves the use of SERS-active surfaces or cavities capable of concentrating incident radiation into small mode volumes containing the analyte. Here, we have engineered an ultranarrow metal-dielectric nano-cavity out of a film of the receptor-binding domain (RBD) of SARS-CoV-2 spike (S) glycoprotein and a silver surface, held together by interaction between reduced protein sulfhydryl groups and silver. The concentration of light in this nano-cavity allows the label-free recording of the characteristic Raman spectra of protein samples smaller than 1 pg. This is sufficient for the ultrasensitive detection of viral protein antigens at physiologically relevant levels. Moreover, the protein SERS signal can be increased by several orders of magnitude by coating the RBD film with a nanometer-thick silver shell, thereby raising the cavity Q-factor. This ensures a sub-femtogram sensitivity of the viral antigen detection. A simple theoretical model explaining the observed additional enhancement of the SERS signal from the silver-coated protein is proposed. Our study is the first to obtain the characteristic Raman and SERS spectra of the RBD of S glycoprotein, the key SARS-CoV-2 viral antigen, directly, without the use of Raman-reporter molecules. Thus, our approach allows label-free recording of the characteristic spectra of viral antigens at concentrations orders of magnitude lower than those required for detecting the whole virus in biological media. This makes it possible to develop a high-performance optical detection method and conformational analysis of the pathogen and its variants.

Surface-enhanced Raman scattering biosensors for detection of oncomiRs in breast cancer

Surface-enhanced Raman scattering (SERS) has emerged as one of the most promising platforms for various biosensing applications. These sensing systems encompass the advantages of specificity, ultra-high sensitivity, stability, low cost, repeatability, and easy-to-use methods. Moreover, their ability to offer a molecular fingerprint and identify the target analyte at low levels make SERS a promising technique for detecting circulating cancer biomarkers with greater sensitivity and reliability. Among the various circulating biomolecules, oncomiRs are emerging as prominent biomarkers for the early screening of breast cancers (BCs). In this review, we provide a comprehensive understanding of different SERS-based biosensors and their application to identify BC-specific oncomiRs. We also discuss different SERS-based sensing strategies, nano-analytical frameworks, and challenges to be addressed for effective clinical translation.

Optical imaging spectroscopy for rapid, primary screening of SARS-CoV-2: a proof of concept

Effective testing is essential to control the coronavirus disease 2019 (COVID-19) transmission. Here we report a-proof-of-concept study on hyperspectral image analysis in the visible and near-infrared range for primary screening at the point-of-care of SARS-CoV-2. We apply spectral feature descriptors, partial least square-discriminant analysis, and artificial intelligence to extract information from optical diffuse reflectance measurements from 5 µL fluid samples at pixel, droplet, and patient levels. We discern preparations of engineered lentiviral particles pseudotyped with the spike protein of the SARS-CoV-2 from those with the G protein of the vesicular stomatitis virus in saline solution and artificial saliva. We report a quantitative analysis of 72 samples of nasopharyngeal exudate in a range of SARS-CoV-2 viral loads, and a descriptive study of another 32 fresh human saliva samples. Sensitivity for classification of exudates was 100% with peak specificity of 87.5% for discernment from PCR-negative but symptomatic cases. Proposed technology is reagent-free, fast, and scalable, and could substantially reduce the number of molecular tests currently required for COVID-19 mass screening strategies even in resource-limited settings.

Aptameric nanobiosensors for the diagnosis of COVID-19: An update

COVID-19 pandemic has left a catastrophic effect on the world economy and human civilization. As an effective step towards controlling the transmission of viral infections during multiple waves of COVID-19, there is an urgent need to develop robust nanobiosensors for the detection of SARS-CoV-2 with high sensitivity, specificity, and fast analysis. Aptameric nanobiosensors are rapid and sensitive diagnostic platforms, capable of SARS-CoV-2 detection, which overcomes the limitations of the conventional techniques. This review article presents an outline of the aptameric nanobiosensors established for improved diagnosis of SARS-CoV-2 and the future perspectives are also covered.

Ultrasensitive Aptasensors for the Detection of Viruses Based on Opto-Electrochemical Readout Systems

Viral infections are becoming the foremost driver of morbidity, mortality and economic loss all around the world. Treatment for diseases associated to some deadly viruses are challenging tasks, due to lack of infrastructure, finance and availability of rapid, accurate and easy-to-use detection methods or devices. The emergence of biosensors has proven to be a success in the field of diagnosis to overcome the challenges associated with traditional methods. Furthermore, the incorporation of aptamers as bio-recognition elements in the design of biosensors has paved a way towards rapid, cost-effective, and specific detection devices which are insensitive to changes in the environment. In the last decade, aptamers have emerged to be suitable and efficient biorecognition elements for the detection of different kinds of analytes, such as metal ions, small and macro molecules, and even cells. The signal generation in the detection process depends on different parameters; one such parameter is whether the labelled molecule is incorporated or not for monitoring the sensing process. Based on the labelling, biosensors are classified as label or label-free; both have their significant advantages and disadvantages. Here, we have primarily reviewed the advantages for using aptamers in the transduction system of sensing devices. Furthermore, the labelled and label-free opto-electrochemical aptasensors for the detection of various kinds of viruses have been discussed. Moreover, numerous globally developed aptasensors for the sensing of different types of viruses have been illustrated and explained in tabulated form.

Aptamers-Diagnostic and Therapeutic Solution in SARS-CoV-2

The SARS-CoV-2 virus is currently the most serious challenge to global public health. Its emergence has severely disrupted the functioning of health services and the economic and social situation worldwide. Therefore, new diagnostic and therapeutic tools are urgently needed to allow for the early detection of the SARS-CoV-2 virus and appropriate treatment, which is crucial for the effective control of the COVID-19 disease. The ideal solution seems to be the use of aptamers—short fragments of nucleic acids, DNA or RNA—that can bind selected proteins with high specificity and affinity. They can be used in methods that base the reading of the test result on fluorescence phenomena, chemiluminescence, and electrochemical changes. Exploiting the properties of aptamers will enable the introduction of rapid, sensitive, specific, and low-cost tests for the routine diagnosis of SARS-CoV-2. Aptamers are excellent candidates for the development of point-of-care diagnostic devices and are potential therapeutic tools for the treatment of COVID-19. They can effectively block coronavirus activity in multiple fields by binding viral proteins and acting as carriers of therapeutic substances. In this review, we present recent developments in the design of various types of aptasensors to detect and treat the SARS-CoV-2 infection.

Glycosylation of Receptor Binding Domain of SARS-CoV-2 S-Protein Influences on Binding to Immobilized DNA Aptamers

Nucleic acid aptamers specific to S-protein and its receptor binding domain (RBD) of SARS-CoV-2 (severe acute respiratory syndrome-related coronavirus 2) virions are of high interest as potential inhibitors of viral infection and recognizing elements in biosensors. Development of specific therapy and biosensors is complicated by an emergence of new viral strains bearing amino acid substitutions and probable differences in glycosylation sites. Here, we studied affinity of a set of aptamers to two Wuhan-type RBD of S-protein expressed in Chinese hamster ovary cell line and Pichia pastoris that differ in glycosylation patterns. The expression system for the RBD protein has significant effects, both on values of dissociation constants and relative efficacy of the aptamer binding. We propose glycosylation of the RBD as the main force for observed differences. Moreover, affinity of a several aptamers was affected by a site of biotinylation. Thus, the robustness of modified aptamers toward new virus variants should be carefully tested.

Aptamer Sandwich Assay for the Detection of SARS-CoV-2 Spike Protein Antigen

The novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) emerged at the end of 2019, resulting in the ongoing COVID-19 pandemic. The high transmissibility of the virus and the substantial number of asymptomatic individuals have led to an exponential rise in infections worldwide, urgently requiring global containment strategies. Reverse transcription-polymerase chain reaction is the gold standard for the detection of SARS-CoV-2 infections. Antigen tests, targeting the spike (S) or nucleocapsid (N) viral proteins, are considered as complementary tools. Despite their shortcomings in terms of sensitivity and specificity, antigen tests could be deployed for the detection of potentially contagious individuals with high viral loads. In this work, we sought to develop a sandwich aptamer-based assay for the detection of the S protein of SARS-CoV-2. A detailed study on the binding properties of aptamers to the receptor-binding domain of the S protein in search of aptamer pairs forming a sandwich is presented. Screening of aptamer pairs and optimization of assay conditions led to the development of a laboratory-based sandwich assay able to detect 21 ng/mL (270 pM) of the protein with negligible cross-reactivity with the other known human coronaviruses. The detection of 375 pg of the protein in viral transport medium demonstrates the compatibility of the assay with clinical specimens. Finally, successful detection of the S antigen in nasopharyngeal swab samples collected from suspected patients further establishes the suitability of the assay for screening purposes as a complementary tool to assist in the control of the pandemic.

Localized surface plasmon resonance aptasensor for selective detection of SARS-CoV-2 S1 protein

In this work, we designed and developed a method to detect S1 spike protein of SARS-CoV-2. The portable Localized Surface Plasmon Resonance instrument equipped with a two-channel system was combined with the biotin-streptavidin platform on a nanogold surface to immobilize biotinylated aptamers. The proposed assay does not utilize antibodies or enzyme-based reagents, further simplifying the detection method. Using aptamer-protein bioaffinity interactions, the aptasensor selectively and specifically detected in real-time S1 spike protein, rather than S2 spike protein, RBD spike protein, or bovine serum albumin. The dynamic range and limit of detection of the aptasensor was determined to be 1 nM-100 nM and 0.26 nM, respectively. Notably, aptasensor detected preferentially S1 protein of SARS-CoV-2 compared to SARS-CoV and detected S1 protein with >95% recovery in artificial saliva, and serum albumin, excellent repeatability and shelf-life stability. The method may provide a low-cost, rapid, and real-time detection and monitoring of viruses in the general public.

SARS-CoV-2 spike protein detection through a plasmonic D-shaped plastic optical fiber aptasensor

A specific aptameric sequence has been immobilized on short polyethyleneglycol (PEG) interface on gold nano-film deposited on a D-shaped plastic optical fiber (POFs) probe, and the protein binding has been monitored exploiting the very sensitive surface plasmon resonance (SPR) phenomenon. The receptor-binding domain (RBD) of the SARS-CoV-2 spike glycoprotein has been specifically used to develop an aptasensor. Surface analysis techniques coupled to fluorescence microscopy and plasmonic analysis have been utilized to characterize the biointerface. Spanning a wide protein range (25 ÷ 1000 nM), the SARS-Cov-2 spike protein was detected with a Limit of Detection (LoD) of about 37 nM. Different interferents (BSA, AH1N1 hemagglutinin protein and MERS spike protein) have been tested confirming the specificity of our aptasensor. Finally, a preliminary test in diluted human serum encouraged its application in a point-of-care device, since POF-based aptasensor represent a potentially low-cost compact biosensor, characterized by a rapid response, a small size and could be an ideal laboratory portable diagnostic tool.

Rapid and Efficient Detection of the SARS-CoV-2 Spike Protein Using an Electrochemical Aptamer-Based Sensor

The availability of sensors able to rapidly detect SARS-CoV-2 directly in biological fluids in a single step would allow performing massive diagnostic testing to track in real time and contain the spread of COVID-19. Motivated by this, here, we developed an electrochemical aptamer-based (EAB) sensor able to achieve the rapid, reagentless, and quantitative measurement of the SARS-CoV-2 spike (S) protein. First, we demonstrated the ability of the selected aptamer to undergo a binding-induced conformational change in the presence of its target using fluorescence spectroscopy. Then, we engineered the aptamer to work as a bioreceptor in the EAB platform and we demonstrated its sensitivity and specificity. Finally, to demonstrate the clinical potential of the sensor, we tested it directly in biological fluids (serum and artificial saliva), achieving the rapid (minutes) and single-step detection of the S protein in its clinical range.

Nanobiotechnology enabled approaches for wastewater based epidemiology

The impacts of the ongoing coronavirus pandemic highlight the importance of environmental monitoring to inform public health safety. Wastewater based epidemiology (WBE) has drawn interest as a tool for analysis of biomarkers in wastewater networks. Wide scale implementation of WBE requires a variety of field deployable analytical tools for real-time monitoring. Nanobiotechnology enabled sensing platforms offer potential as biosensors capable of highly efficient and sensitive detection of target analytes. This review provides an overview of the design and working principles of nanobiotechnology enabled biosensors and recent progress on the use of biosensors in detection of biomarkers. In addition, applications of biosensors for analysis of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus are highlighted as they relate to the potential expanded use of biosensors for WBE-based monitoring. Finally, we discuss the opportunities and challenges in future applications of biosensors in WBE for effective monitoring and investigation of public health threats.

Aptamer Applications in Emerging Viral Diseases

Aptamers are single-stranded DNA or RNA molecules which are submitted to a process denominated SELEX. SELEX uses reiterative screening of a random oligonucleotide library to identify high-affinity binders to a chosen target, which may be a peptide, protein, or entire cells or viral particles. Aptamers can rival antibodies in target recognition, and benefit from their non-proteic nature, ease of modification, increased stability, and pharmacokinetic properties. This turns them into ideal candidates for diagnostic as well as therapeutic applications. Here, we review the recent accomplishments in the development of aptamers targeting emerging viral diseases, with emphasis on recent findings of aptamers binding to coronaviruses. We focus on aptamer development for diagnosis, including biosensors, in addition to aptamer modifications for stabilization in body fluids and tissue penetration. Such aptamers are aimed at in vivo diagnosis and treatment, such as quantification of viral load and blocking host cell invasion, virus assembly, or replication, respectively. Although there are currently no in vivo applications of aptamers in combating viral diseases, such strategies are promising for therapy development in the future.

SERS-Based Aptasensor for Rapid Quantitative Detection of SARS-CoV-2

During the COVID-19 pandemic, the development of sensitive and rapid techniques for detection of viruses have become vital. Surface-enhanced Raman scattering (SERS) is an appropriate tool for new techniques due to its high sensitivity. SERS materials modified with short-structured oligonucleotides (DNA aptamers) provide specificity for SERS biosensors. Existing SERS-based aptasensors for rapid virus detection are either inapplicable for quantitative determination or have sophisticated and expensive construction and implementation. In this paper, we provide a SERS-aptasensor based on colloidal solutions which combines rapidity and specificity in quantitative determination of SARS-CoV-2 virus, discriminating it from the other respiratory viruses.