Conventional PCR assisted single-component assembly of spherical nucleic acids for simple colorimetric detection of SARS-CoV-2

From Structure to Application: The Evolutionary Trajectory of Spherical Nucleic Acids

Since the proposal of the concept of spherical nucleic acids (SNAs) in 1996, numerous studies have focused on this topic and have achieved great advances. As a new delivery system for nucleic acids, SNAs have advantages over conventional deoxyribonucleic acid (DNA) nanostructures, including independence from transfection reagents, tolerance to nucleases, and lower immune reactions. The flexible structure of SNAs proves that various inorganic or organic materials can be used as the core, and different types of nucleic acids can be conjugated to realize diverse functions and achieve surprising and exciting outcomes. The special DNA nanostructures have been employed for immunomodulation, gene regulation, drug delivery, biosensing, and bioimaging. Despite the lack of rational design strategies, potential cytotoxicity, and structural defects of this technology, various successful examples demonstrate the bright and convincing future of SNAs in fields such as new materials, clinical practice, and pharmacy.

Smart Stimuli-Responsive Spherical Nucleic Acids: Cutting-Edge Platforms for Biosensing, Bioimaging, and Therapeutics

Spherical nucleic acids (SNAs) with exceptional colloidal stability, multiple modularity, and programmability are excellent candidates to address common molecular delivery-related issues. Based on this, the higher targeting accuracy and enhanced controllability of stimuli-responsive SNAs render them precise nanoplatforms with inestimable prospects for diverse biomedical applications. Therefore, tailored diagnosis and treatment with stimuli-responsive SNAs may be a robust strategy to break through the bottlenecks associated with traditional nanocarriers. Various stimuli-responsive SNAs are engineered through the incorporation of multifunctional modifications to meet biomedical demands with the development of nucleic acid functionalization. This review provides a comprehensive overview of prominent research in this area and recent advancements in the utilization of stimuli-responsive SNAs in biosensing, bioimaging, and therapeutics. For each aspect, SNA nanoplatforms that exhibit responsive behavior to both internal stimuli (including sequence, enzyme, redox reactions, and pH) and external stimuli (such as light and temperature) are highlighted. This review is expected to offer inspiration and guidance strategies for the rational design and development of stimuli-responsive SNAs in the field of biomedicine.

Revolutionizing SARS-CoV-2 omicron variant detection: Towards faster and more reliable methods

The emergence of the highly contagious Omicron variant of SARS-CoV-2 has inflicted significant damage during the ongoing COVID-19 pandemic. This new variant's significant sequence changes and mutations in both proteins and RNA have rendered many existing rapid detection methods ineffective in identifying it accurately. As the world races to control the spread of the virus, researchers are urgently exploring new diagnostic strategies to specifically detect Omicron variants with high accuracy and sensitivity. In response to this challenge, we have compiled a comprehensive overview of the latest reported rapid detection techniques. These techniques include strategies for the simultaneous detection of multiple SARS-CoV-2 variants and methods for selectively distinguishing Omicron variants. By categorizing these diagnostic techniques based on their targets, which encompass protein antigens and nucleic acids, we aim to offer a comprehensive understanding of the utilization of various recognition elements in identifying these targets. We also highlight the advantages and limitations of each approach. Our work is crucial in providing a more nuanced understanding of the challenges and opportunities in detecting Omicron variants and emerging variants.

Methods to functionalize gold nanoparticles with tandem-phosphorothioate DNA: role of physicochemical properties of the phosphorothioate backbone in DNA adsorption to gold nanoparticles

Perception of the differences in the physicochemical properties of phosphorothioate DNA (PS-DNA) and phosphodiester DNA (PO-DNA) greatly aids in understanding the AuNP-DNA binding process. Replacing one non-bridging oxygen atom of the anionic phosphodiester backbone with a sulfur atom leads to a major change in the DNA adsorption mechanism of AuNPs. In this work, we investigated and compared salt-aging, low pH-assisted, and freeze-thaw methods for conjugating phosphorothioate-modified oligonucleotides to AuNPs. The results obtained clearly demonstrate that only the pH-assisted method can successfully bind tandem phosphorothioate DNA to gold nanoparticles and sufficiently maintain the colloidal stability of AuNPs. When a phosphate group is converted to a phosphorothioate group, the negative charge of the phosphate group is located on the sulfur atom. Due to the soft nature of sulfur (a very weak H-bond acceptor), the negative charge on the sulfur atom cannot be shielded even with the gradual addition of salt to increase the ionic strength, so, the pH-assisted based method is the best for the functionalization of AuNPs with tandem-PS DNA.

Magnetic Bead Spherical Nucleic Acid Microstructure for Reliable DNA Preservation and Repeated DNA Reading

DNA is an attractive medium for long-term data storage because of its density, ease of copying, sustainability, and longevity. Recent advances have focused on the development of new encoding algorithms, automation, and sequencing technologies. Despite progress in these subareas, the most challenging hurdle in the deployment of DNA storage remains the reliability of preservation and the repeatability of reading. Herein, we report the construction of a magnetic bead spherical nucleic acid (MB-SNA) composite microstructure and its use as a cost-effective platform for reliable DNA preservation and repeated reading. MB-SNA has an inner core of silica@γ-Fe2O3@silica microbeads and an outer spherical shell of double-stranded DNA (dsDNA) with a density as high as 34 pmol/cm2. For MB-SNA, each strand of dsDNA stored a piece of data, and the high-density packing of dsDNA achieved high-capacity storage. MB-SNA was advantageous in terms of reliable preservation over free DNA. By accelerated aging tests, the data of MB-SNA is demonstrated to be readable after 0.23 million years of preservation at -18 °C and 50% relative humidity. Moreover, MB-SNA facilitated repeated reading by facile PCR-magnetic separation. After 10 cycles of PCR access, the retention rate of dsDNA for MB-SNA is demonstrated to be as high as 93%, and the accuracy of sequencing is more than 98%. In addition, MB-SNA makes cost-effective DNA storage feasible. By serial dilution, the physical limit for MB-SNA to achieve accurate reading is probed to be as low as two microstructures.

Construction of Very Low-Cost Loop Polymerase Chain Reaction System Based on Proportional-Integral-Derivative Temperature Control Optimization Algorithm and Its Application in Gene Detection

Real-time polymerase chain reaction (PCR) technology is essential in nucleic acid detection and point-of-care testing (POCT). However, nowadays, the classical qPCR instrument has the deficiency of its bulky volume, high cost, and inconvenience to use; hence, a low-cost and easy-to-use PCR equipment was thus developed consisting of a hardware subsystem as well as a software subsystem based on an improved proportional-integral-derivative (PID) system. The proposed system not only could hold self-setting reaction cycles of temperature rising and falling automatically but also the temperature during the constant temperature stage was regulated steady based on improved temperature control algorithm, which proved its great effect compared with the reaction temperature derived from an infrared thermal imaging camera. The experimental results in gene detection research also could indicate its applicability and stability of our developed PCR system by using the amplification curve analysis, the melting curve analysis, and agarose gel electrophoresis analysis compared with the commercial PCR instrument, which illustrates the great potential application value of the proposed PCR system.

Non-enzymatic signal amplification-powered point-of-care SERS sensor for rapid and ultra-sensitive assay of SARS-CoV-2 RNA

The development of rapid and ultra-sensitive detection technology of SARS-CoV-2 RNA for shortening the diagnostic window and achieving early detection of virus infections is a huge challenge to the efficient prevention and control of COVID-19. Herein, a novel ultra-sensitive surface-enhanced Raman spectroscopy (SERS) sensor powered by non-enzymatic signal amplification is proposed for rapid and reliable assay of SARS-CoV-2 RNA based on SERS-active silver nanorods (AgNRs) sensing chips and a specially designed smart unlocking-mediated target recycling signal amplification strategy. The SERS sensing was carried out by a one-pot hybridization of the lock probes (LPs), hairpin DNAs and SERS tags with SARS-CoV-2 RNA samples on an arrayed SERS sensing chip to achieve the recognition of SARS-CoV-2 RNA, the execution of nuclease-free unlocking-mediated target recycling signal amplification, and the combination of SERS tags to generate SERS signal. The SERS sensor for SARS-CoV-2 RNA can be achieved within 50 min with an ultra-high sensitivity low to 51.38 copies/mL, and has good selectivity in discriminating SARS-CoV-2 RNA against other respiratory viruses in representative clinical samples, which is well adapted for rapid, ultra-sensitive, multi-channel and point-of-care testing of viral nucleic acids, and is expected to achieve detection of SARS-CoV-2 infection in earlier detection windows for efficient COVID-19 prevention and control.

Sensitive colorimetric detection of miRNA-155 via G-quadruplex DNAzyme decorated spherical nucleic acid

Rapid and sensitive detection of biomarkers enables monitoring patients' health status and can enhance the early diagnosis of deadly diseases. In this work, we have developed a new colorimetric platform based on spherical nucleic acid (SNA) and G-quadruplex DNAzymes for the identification of specific miRNAs. The simple hybridization between the target miRNA and two capture probes (capture probe 1 located at AuNP surface and free capture probe 2) is the working principle of this biosensor. The hybridization and duplex formation among probes and miRNAs led to a significant decrease in the intensity of color change. A linear relationship between the decrease of colorimetric signal and the amount of target molecules was witnessed from 1 to 100 nM for miRNA-155. Using this method, we were able to detect concentrations of miRNA-155 as low as 0.7 nM. Furthermore, the proposed sensing platform can be utilized profitably to detect miRNA-155 in real human serum samples. We further investigated the applicability of the proposed method in a microfluidic system which displayed promising results. In this project, A G-quadruplex based SNAzyme was constructed to provide a fast and simple colorimetric method for miRNA detection. The SNAzyme actually employed as both target recognition element and catalytic nano labels for colorimetric detection.

Nucleic Acid Detection with Ion Concentration Polarization Microfluidic Chip for Reduced Cycle Numbers of Polymerase Chain Reaction

Nucleic acid detection is widely used in disease diagnosis, food safety, environmental monitoring and many other research fields. The continuous development of rapid and sensitive new methods to detective nucleic acid is very important for practical application. In this study, we developed a rapid nucleic-acid detection method using polymerase chain reaction (PCR) combined with electrokinetic preconcentration based on ion concentration polarization (ICP). Using a Nafion film, the proposed ICP microfluidic chip is utilized to enrich the nucleic acid molecules amplified by PCR thermal cycles. To demonstrate the capability of the microfluidic device and the hybrid nucleic-acid detection method, we present an animal-derived component detection experiment for meat product identification applications. With the reduced cycle numbers of 24 cycles, the detection can be completed in about 35 min. The experimental results show that this work can provide a microfluidic device and straightforward method for rapid detection of nucleic acids with reduced cycle numbers.

Recent advances in airborne pathogen detection using optical and electrochemical biosensors

The world is currently facing an adverse condition due to the pandemic of airborne pathogen SARS-CoV-2. Prevention is better than cure; thus, the rapid detection of airborne pathogens is necessary because it can reduce outbreaks and save many lives. Considering the immense role of diverse detection techniques for airborne pathogens, proper summarization of these techniques would be beneficial for humans. Hence, this review explores and summarizes emerging techniques, such as optical and electrochemical biosensors used for detecting airborne bacteria (Bacillus anthracis, Mycobacterium tuberculosis, Staphylococcus aureus, and Streptococcus pneumoniae) and viruses (Influenza A, Avian influenza, Norovirus, and SARS-CoV-2). Significantly, the first section briefly focuses on various diagnostic modalities applied toward airborne pathogen detection. Next, the fabricated optical biosensors using various transducer materials involved in colorimetric and fluorescence strategies for infectious pathogen detection are extensively discussed. The third section is well documented based on electrochemical biosensors for airborne pathogen detection by differential pulse voltammetry, cyclic voltammetry, square-wave voltammetry, amperometry, and impedance spectroscopy. The unique pros and cons of these modalities and their future perspectives are addressed in the fourth and fifth sections. Overall, this review inspected 171 research articles published in the last decade and persuaded the importance of optical and electrochemical biosensors for airborne pathogen detection.

Plasmonic Approaches for the Detection of SARS-CoV-2 Viral Particles

The ongoing highly contagious Coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), underlines the fundamental position of diagnostic testing in outbreak control by allowing a distinction of the infected from the non-infected people. Diagnosis of COVID-19 remains largely based on reverse transcription PCR (RT-PCR), identifying the genetic material of the virus. Molecular testing approaches have been largely proposed in addition to infectivity testing of patients via sensing the presence of viral particles of SARS-CoV-2 specific structural proteins, such as the spike glycoproteins (S1, S2) and the nucleocapsid (N) protein. While the S1 protein remains the main target for neutralizing antibody treatment upon infection and the focus of vaccine and therapeutic design, it has also become a major target for the development of point-of care testing (POCT) devices. This review will focus on the possibility of surface plasmon resonance (SPR)-based sensing platforms to convert the receptor-binding event of SARS-CoV-2 viral particles into measurable signals. The state-of-the-art SPR-based SARS-CoV-2 sensing devices will be provided, and highlights about the applicability of plasmonic sensors as POCT for virus particle as well as viral protein sensing will be discussed.

Review of COVID-19 testing and diagnostic methods

More than six billion tests for COVID-19 has been already performed in the world. The testing for SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) virus and corresponding human antibodies is essential not only for diagnostics and treatment of the infection by medical institutions, but also as a pre-requisite for major semi-normal economic and social activities such as international flights, off line work and study in offices, access to malls, sport and social events. Accuracy, sensitivity, specificity, time to results and cost per test are essential parameters of those tests and even minimal improvement in any of them may have noticeable impact on life in the many countries of the world. We described, analyzed and compared methods of COVID-19 detection, while representing their parameters in 22 tables. Also, we compared test performance of some FDA approved test kits with clinical performance of some non-FDA approved methods just described in scientific literature. RT-PCR still remains a golden standard in detection of the virus, but a pressing need for alternative less expensive, more rapid, point of care methods is evident. Those methods that may eventually get developed to satisfy this need are explained, discussed, quantitatively compared. The review has a bioanalytical chemistry prospective, but it may be interesting for a broader circle of readers who are interested in understanding and improvement of COVID-19 testing, helping eventually to leave COVID-19 pandemic in the past.

Advances in Nanomaterial-Based Platforms to Combat COVID-19: Diagnostics, Preventions, Therapeutics, and Vaccine Developments

The COVID-19 pandemic caused by the SARS-CoV-2, a ribonucleic acid (RNA) virus that emerged less than two years ago but has caused nearly 6.1 million deaths to date. Recently developed variants of the SARS-CoV-2 virus have been shown to be more potent and expanded at a faster rate. Until now, there is no specific and effective treatment for SARS-CoV-2 in terms of reliable and sustainable recovery. Precaution, prevention, and vaccinations are the only ways to keep the pandemic situation under control. Medical and scientific professionals are now focusing on the repurposing of previous technology and trying to develop more fruitful methodologies to detect the presence of viruses, treat the patients, precautionary items, and vaccine developments. Nanomedicine or nanobased platforms can play a crucial role in these fronts. Researchers are working on many effective approaches by nanosized particles to combat SARS-CoV-2. The role of a nanobased platform to combat SARS-CoV-2 is extremely diverse (i.e., mark to personal protective suit, rapid diagnostic tool to targeted treatment, and vaccine developments). Although there are many theoretical possibilities of a nanobased platform to combat SARS-CoV-2, until now there is an inadequate number of research targeting SARS-CoV-2 to explore such scenarios. This unique mini-review aims to compile and elaborate on the recent advances of nanobased approaches from prevention, diagnostics, treatment to vaccine developments against SARS-CoV-2, and associated challenges.

Point-of-care COVID-19 testing: colorimetric diagnosis using rapid and ultra-sensitive ramified rolling circle amplification

In this paper, we report a molecular diagnostic system—combining a colorimetric probe (RHthio-CuSO₄) for pyrophosphate sensing and isothermal gene amplification (ramified rolling circle amplification)—that operates with high selectivity and sensitivity for clinical point-of-care diagnosis of SARS-CoV-2. During the polymerase phase of the DNA amplification process, pyrophosphate was released from the nucleotide triphosphate as a side product, which was then sensed by our RHthio-CuSO₄ probe with a visible color change. This simple colorimetric diagnostic system allowed highly sensitive (1.13 copies/reaction) detection of clinical SARS-CoV-2 within 1 h, while also displaying high selectivity, as evidenced by its discrimination of two respiratory viral genomes (human rhino virus and respiratory syncytial virus) from that of SARS-CoV-2. All of the reactions in this system were performed at a single temperature, with positive identification being made by the naked eye, without requiring any instrumentation. The high sensitivity and selectivity, short detection time (1 h), simple treatment (one-pot reaction), isothermal amplification, and colorimetric detection together satisfy the requirements for clinical point-of-care detection of SARS-CoV-2. Therefore, we believe that this combination of a colorimetric probe and isothermal amplification will be useful for point-of-care testing to prevent the propagation of COVID-19.

The Integration of Gold Nanoparticles with Polymerase Chain Reaction for Constructing Colorimetric Sensing Platforms for Detection of Health-Related DNA and Proteins

Polymerase chain reaction (PCR) is the standard tool in genetic information analysis, and the desirable detection merits of PCR have been extended to disease-related protein analysis. Recently, the combination of PCR and gold nanoparticles (AuNPs) to construct colorimetric sensing platforms has received considerable attention due to its high sensitivity, visual detection, capability for on-site detection, and low cost. However, it lacks a related review to summarize and discuss the advances in this area. This perspective gives an overview of established methods based on the combination of PCR and AuNPs for the visual detection of health-related DNA and proteins. Moreover, this work also addresses the future trends and perspectives for PCR-AuNP hybrid biosensors.

Zinc associated nanomaterials and their intervention in emerging respiratory viruses: Journey to the field of biomedicine and biomaterials

Respiratory viruses represent a severe public health risk worldwide, and the research contribution to tackle the current pandemic caused by the SARS-CoV-2 is one of the main targets among the scientific community. In this regard, experts from different fields have gathered to confront this catastrophic pandemic. This review illustrates how nanotechnology intervention could be valuable in solving this difficult situation, and the state of the art of Zn-based nanostructures are discussed in detail. For virus detection, learning from the experience of other respiratory viruses such as influenza, the potential use of Zn nanomaterials as suitable sensing platforms to recognize the S1 spike protein in SARS-CoV-2 are shown. Furthermore, a discussion about the antiviral mechanisms reported for ZnO nanostructures is included, which can help develop surface disinfectants and protective coatings. At the same time, the properties of Zn-based materials as supplements for reducing viral activity and the recovery of infected patients are illustrated. Within the scope of noble adjuvants to improve the immune response, the ZnO NPs properties as immunomodulators are explained, and potential prototypes of nanoengineered particles with metallic cations (like Zn2+) are suggested. Therefore, using Zn-associated nanomaterials from detection to disinfection, supplementation, and immunomodulation opens a wide area of opportunities to combat these emerging respiratory viruses. Finally, the attractive properties of these nanomaterials can be extrapolated to new clinical challenges.

Visual naked-eye detection of SARS-CoV-2 RNA based on covalent organic framework capsules

The ongoing outbreak of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted that new diagnosis technologies are crucial for controlling the spread of the disease. Especially in the resources-limit region, conveniently operated detection methods such as "naked-eye" detection are urgently required that no instrument is needed. Herein, we have designed a novel and facile strategy to fabricate covalent organic framework (COF) capsules, which can be utilized to establish a new colorimetric assay for naked-eye detection of SARS-CoV-2 RNA. Specifically, we employ the digestible ZIF-90 as the sacrificial template to prepare the hollow COF capsules for horseradish peroxidase (HRP) encapsulation. The fabricated COF capsules can provide an appropriate microenvironment for the enzyme molecules, which may improve the conformational freedom of enzymes, enhance the mass transfer, and endow the enzyme with high environmental resistance. With such design, the proposed assay exhibits outstanding analytical performance for the detection of SARS-CoV-2 RNA in the linear range from 5 pM to 50 nM with a detection limit of 0.28 pM which can go parallel to qTR-PCR analysis. Our method also possesses excellent selectivity and reproducibility. Moreover, this method can also be served to analyze the clinical samples, and can successfully differentiate COVID-19 patients from healthy people, suggesting the promising potential in clinical diagnosis.

Spherical nucleic acids: Organized nucleotide aggregates as versatile nanomedicine

Spherical nucleic acids (SNAs) are composed of a nanoparticle core and a layer of densely arranged oligonucleotide shells. After the first report of SNA by Mirkin and coworkers in 1996, it has created a significant interest by offering new possibilities in the field of gene and drug delivery. The controlled aggregation of oligonucleotides on the surface of organic/inorganic nanoparticles improves the delivery of genes and nucleic acid-based drugs and alters and regulates the biological profiles of the nanoparticle core within living organisms. Here in this review, we present an overview of the recent progress of SNAs that has speeded up their biomedical application and their potential transition to clinical use. We start with introducing the concept and characteristics of SNAs as drug/gene delivery systems and highlight recent efforts of bioengineering SNA by imaging and treatmenting various diseases. Finally, we discuss potential challenges and opportunities of SNAs, their ongoing clinical trials, and future translation, and how they may affect the current landscape of clinical practices. We hope that this review will update our current understanding of SNA, organized oligonucleotide aggregates, for disease diagnosis and treatment.

A pH-engineering regenerative DNA tetrahedron ECL biosensor for the assay of SARS-CoV-2 RdRp gene based on CRISPR/Cas12a trans-activity

In this work, we constructed an exonuclease III cleavage reaction-based isothermal amplification of nucleic acids with CRISPR/Cas12a-mediated pH-induced regenerative Electrochemiluminescence (ECL) biosensor for ultrasensitive and specific detection of SARS-CoV-2 nucleic acids for SARS-CoV-2 diagnosis. The triple-stranded nucleic acid in this biosensor has an extreme dependence on pH, which makes our constructed biosensor reproducible. This is essential for effective large-scale screening of SARS-CoV-2 in areas where resources are currently relatively scarce. Using this pH-induced regenerative biosensor, we detected the SARS-CoV-2 RdRp gene with a detection limit of 43.70 aM. In addition, the detection system has good stability and reproducibility, and we expect that this method may provide a potential platform for the diagnosis of COVID-19.

SARS-CoV-2 detection with aptamer-functionalized gold nanoparticles

A rapid detection test for SARS-CoV-2 is urgently required to monitor virus spread and containment. Here, we describe a test that uses nanoprobes, which are gold nanoparticles functionalized with an aptamer specific to the spike membrane protein of SARS-CoV-2. An enzyme-linked immunosorbent assay confirms aptamer binding with the spike protein on gold surfaces. Protein recognition occurs by adding a coagulant, where nanoprobes with no bound protein agglomerate while those with sufficient bound protein do not. Using plasmon absorbance spectra, the nanoprobes detect 16 nM and higher concentrations of spike protein in phosphate-buffered saline. The time-varying light absorbance is examined at 540 nm to determine the critical coagulant concentration required to agglomerates the nanoprobes, which depends on the protein concentration. This approach detects 3540 genome copies/μl of inactivated SARS-CoV-2.

A minireview on nanoparticle-based sensors for the detection of coronaviruses

Coronaviruses (CoVs) are a class of viruses that cause respiratory tract infections in birds and mammals. Severe acute respiratory syndrome and Middle East respiratory syndrome are pathogenic human viruses. The ongoing coronavirus causing a pandemic of COVID-19 is a recently identified virus from this group. The first step in the control of spreading the disease is to detect and quarantine infected subjects. Consequently, the introduction of rapid and reliable detection methods for CoVs is crucial. To date, several methods were reported for the detection of coronaviruses. Nanoparticles play an important role in detection tools, thanks to their high surface-to-volume ratio and exclusive optical property enables the development of susceptible analytical nanoparticle-based sensors. The studies performed on using nanoparticles-based (mainly gold) sensors to detect CoVs in two categories of optical and electrochemical were reviewed here. Details of each reported sensor and its relevant analytical parameters are carefully provided and explained.

Nanotechnology-based approaches in the fight against SARS-CoV-2

The COVID-19 pandemic caused by highly-infectious virus namely severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in infection of millions of individuals and deaths across the world. The need of an hour is to find the innovative solution for diagnosis, prevention, and cure of the COVID-19 disease. Nanotechnology is emerging as one of the important tool for the same. In the present review we discuss the applications of nanotechnology-based approaches that are being implemented to speed up the development of diagnostic kits for SARS-CoV-2, development of personal protective equipments, and development of therapeutics of COVID-19 especially the vaccine development.

Application of Nanomaterials as an Advanced Strategy for the Diagnosis, Prevention, and Treatment of Viral Diseases

The coronavirus disease (COVID-19) pandemic poses serious global health concerns with the continued emergence of new variants. The periodic outbreak of novel emerging and re-emerging infectious pathogens has elevated concerns and challenges for the future. To develop mitigation strategies against infectious diseases, nano-based approaches are being increasingly applied in diagnostic systems, prophylactic vaccines, and therapeutics. This review presents the properties of various nanoplatforms and discusses their role in the development of sensors, vectors, delivery agents, intrinsic immunostimulants, and viral inhibitors. Advanced nanomedical applications for infectious diseases have been highlighted. Moreover, physicochemical properties that confer physiological advantages and contribute to the control and inhibition of infectious diseases have been discussed. Safety concerns limit the commercial production and clinical use of these technologies in humans; however, overcoming these limitations may enable the use of nanomaterials to resolve current infection control issues via application of nanomaterials as a platform for the diagnosis, prevention, and treatment of viral diseases.

Multiplex Nucleic Acid Assay of SARS-CoV-2 via a Lanthanide Nanoparticle-Tagging Strategy

Early diagnosis, early isolation, and early treatment are efficient solutions to control the COVID-19 pandemic. To achieve the accurate early diagnosis of SARS-CoV-2, a multiplex detection strategy is required for the cross-validation to solve the problem of "false negative" of the existing gold standard assay. Here, we present a multicomponent nucleic acid assay platform for SARS-CoV-2 detection based on lanthanide nanoparticle (LnNP)-tagging strategy. For targeting SARS-CoV-2's RNA fragments ORF1ab gene, RdRp gene, and E gene, three LnNP probes can be used simultaneously to identify three sites in one sample through elemental mass spectrometry detection with limits of detection of 1.2, 1.3, and 1.3 fmol, respectively. With the multisite cross-validation, we envision that this multiplex and sensitive detection platform may provide an effective strategy for SARS-CoV-2 fast screening with a high accuracy.

Surface plasmon resonance aptasensor based on niobium carbide MXene quantum dots for nucleocapsid of SARS-CoV-2 detection

A novel label-free surface plasmon resonance (SPR) aptasensor has been constructed for the detection of N-gene of SARS-CoV-2 by using thiol-modified niobium carbide MXene quantum dots (Nb2C-SH QDs) as the bioplatform for anchoring N-gene-targeted aptamer. In the presence of SARS-CoV-2 N-gene, the immobilized aptamer strands changed their conformation to specifically bind with N-gene. It thus increased the contact area or enlarged the distance between aptamer and the SPR chip, resulting in a change of the SPR signal irradiated by the laser (He-Ne) with the wavelength (λ) of 633 nm. Nb2C QDs were derived from Nb2C MXene nanosheets via a solvothermal method, followed by functionalization with octadecanethiol through a self-assembling method. Subsequently, the gold chip for SPR measurements was modified with Nb2C-SH QDs via covalent binding of the Au-S bond also by self-assembling interaction. Nb2C-SH QDs not only resulted in high bioaffinity toward aptamer but also enhanced the SPR response. Thus, the Nb2C-SH QD-based SPR aptasensor had low limit of detection (LOD) of 4.9 pg mL-1 toward N-gene within the concentration range 0.05 to 100 ng mL-1. The sensor also showed excellent selectivity in the presence of various respiratory viruses and proteins in human serum and high stability. Moreover, the Nb2C-SH QD-based SPR aptasensor displayed a vast practical application for the qualitative analysis of N-gene from different samples, including seawater, seafood, and human serum. Thus, this work can provide a deep insight into the construction of the aptasensor for detecting SARS-CoV-2 in complex environments. A novel label-free surface plasmon resonance aptasensor has been constructed to detect sensitively and selectively the N-gene of SARS-CoV-2 by using thiol-modified niobium carbide MXene quantum dots as the scaffold to anchor the N-gene-targeted aptamer.

Hairpin-Spherical Nucleic Acids for Diagnosing COVID-19: a Simple Method to Generalize the Conventional PCR for Molecular Assays

The COVID-19 pandemic revealed during the first global wave of this infectious disease that mass diagnostic testing was necessary to more rapidly detect infection in patients and control the pandemic. Therefore, extra research efforts to develop reliable and more accessible techniques for disease diagnosis are of supreme importance. Here, a target-responsive assembly of gold nanoparticle-core hairpin-spherical nucleic acids (AuNP-core H-SNAs) was implemented to modify the conventional polymerase chain reaction (PCR) assay for the "naked-eye" colorimetric detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA. Two hairpin DNA ligands are designed based on the two highly conserved regions within N and E genes of SARS-CoV-2 RNA by positioning two short palindromic arms (stem) on either side of a recognition sequence (loop). In the presence of a sequence-specific probe (activator), hairpin DNAs anchored to the surface of AuNPs unfold and expose the palindromic ends to the DNA-directed assembly of AuNPs. The sequence of the activator probes was chosen to be identical to the TaqMan probe in a real-time reverse transcription PCR (RT-PCR) assay for specifically targeting the N and E genes of SARS-CoV-2 RNA. They may either be degraded by the 5'-exonuclease activity of DNA polymerase during PCR cycles or stay intact depending on the presence or absence of the target template in the sample, respectively. Post-addition of H-SNA solutions to the final PCR products of some preconfirmed clinical samples for COVID-19 generated naked-eye-observable red and blue colors for positive and negative cases, respectively, with similar sensitivity to that of the real-time RT-PCR method.

Rational Engineering of the DNA Walker Amplification Strategy by Using a Au@Ti3C2@PEI-Ru(dcbpy)32+ Nanocomposite Biosensor for Detection of the SARS-CoV-2 RdRp Gene

The detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is crucial for preventing and controlling infectious diseases and disease treatment. In this work, a Au@Ti3C2@PEI-Ru(dcbpy)32+ nanocomposite-based electrochemiluminescence (ECL) biosensor was rationally designed, which realized sensitive detection of the RNA-dependent RNA polymerase (RdRp) gene of SARS-CoV-2. In addition, a DNA walker was also used to excise the hairpin DNAs under the action of Nb.BbvCI endonuclease. Furthermore, model DNA-Ag nanoclusters (model DNA-AgNCs) were used to quench the initial ECL signal. As a result, the ECL biosensor was used to sensitively detect the SARS-CoV-2 RdRp gene with a detection range of 1 fM to 100 pM and a limit of detection of 0.21 fM. It was indicated that the ECL biosensor had a great application potential for clinical medical detection. Furthermore, the DNA walker amplification also played a reliable candidate strategy for other detection methods.

Nanobiotechnology as a platform for the diagnosis of COVID-19: a review

A sensitive method for diagnosing coronavirus disease 2019 (COVID-19) is highly required to fight the current and future global health threats due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV 2). However, most of the current methods exhibited high false‐negative rates, resulting in patient misdiagnosis and impeding early treatment. Nanoparticles show promising performance and great potential to serve as a platform for diagnosing viral infection in a short time and with high sensitivity. This review highlighted the potential of nanoparticles as platforms for the diagnosis of COVID-19. Nanoparticles such as gold nanoparticles, magnetic nanoparticles, and graphene (G) were applied to detect SARS-CoV 2. They have been used for molecular-based diagnosis methods and serological methods. Nanoparticles improved specificity and shorten the time required for the diagnosis. They may be implemented into small devices that facilitate the self-diagnosis at home or in places such as airports and shops. Nanoparticles-based methods can be used for the analysis of virus-contaminated samples from a patient, surface, and air. The advantages and challenges were discussed to introduce useful information for designing a sensitive, fast, and low-cost diagnostic method. This review aims to present a helpful survey for the lesson learned from handling this outbreak to prepare ourself for future  pandemic.

Paper biosensors for detecting elevated IL-6 levels in blood and respiratory samples from COVID-19 patients

Decentralizing COVID-19 care reduces contagions and affords a better use of hospital resources. We introduce biosensors aimed at detecting severe cases of COVID-19 in decentralized healthcare settings. They consist of a paper immunosensor interfaced with a smartphone. The immunosensors have been designed to generate intense colorimetric signals when the sample contains ultralow concentrations of IL-6, which has been proposed as a prognosis biomarker of COVID-19. This is achieved by combining a paper-based signal amplification mechanism with polymer-filled reservoirs for dispensing antibody-decorated nanoparticles and a bespoken app for color quantification. With this design we achieved a low limit of detection (LOD) of 10^-3 pg mL^-1 and semi-quantitative measurements in a wide dynamic range between 10^-3 and 10² pg mL^-1 in PBS. The assay time is under 10 min. The low LOD allowed us to dilute blood samples and detect IL-6 with an LOD of 1.3 pg mL^-1 and a dynamic range up to 10² pg mL^-1. Following this protocol, we were able to stratify COVID-19 patients according to different blood levels of IL-6. We also report on the detection of IL-6 in respiratory samples (bronchial aspirate, BAS) from COVID-19 patients. The test could be easily adapted to detect other cytokines such as TNF-α and IL-8 by changing the antibodies decorating the nanoparticles accordingly. The ability of detecting cytokines in blood and respiratory samples paves the way for monitoring local inflammation in the lungs as well as systemic inflammation levels in the body.

Public health management during COVID-19 and applications of point-of-care based biomolecular detection approaches

The emergence of the novel human coronavirus, characterized as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a worldwide pandemic. The outbreak of SARS-CoV-2 was first reported at a local wet market in the city of Wuhan in the Hubei province of China at a local wet market. This virus is highly contagious, which gives it the potential for rapid transmission across the world. The transmission of SARS-CoV-2 can be triggered via respiratory droplets in the air from an infected individual to a healthy individual. Thus, to restrict the transmission of the virus, proper public health management and early diagnosis of infected individual is extremely essential. Considering this, the development of various point-of-care (POC) biomolecular assays lead to the importance of early diagnoses at a larger scale during this pandemic situation. Detecting a minimum level of specific target analytes to a particular disease with less instrumentation and minimum reagents, as well as immidiate outcomes, has appeared a challenging path for researchers. Apart from early-stage diagnosis, public awareness is also important to prevent the spread of the virus. Proper intensive care units, isolation rooms, maintaining hygiene, and wearing masks in public areas are necessary. In this chapter, we have discussed the public health management steps and current clinical diagnostics processes and various advanced technology including, molecular, serological, and nanobiosensing approaches for SARS-CoV-2 detection. Furthermore, we have highlighted the various challenges and limitations associated with health management and early diagnostics technologies during SARS-CoV-2 pandemic. Additionally, we have summarized various technical aspects of the development of such POC strategies including biomarkers selections, sensing platforms, unit fabrication, and device incorporation.