Detecting the Coronavirus (COVID-19)

Application of smart-responsive hydrogels in nucleic acid and nucleic acid-based target sensing: A review

In recent years, nucleic acid-related sensing and detection have become essential in clinical diagnostics, treatment and genotyping, especially in connection with the Human Genome Project and the COVID-19 pandemic. Many traditional nucleic acid-related sensing strategies have been employed in analytical chemistry, including fluorescence, colorimetric and chemiluminescence methods. However, their key limitation is the lack of understanding of the interaction during analysis, particularly at the 3D matrix level close to biological tissue. To address this issue, smart-responsive hydrogels are increasingly used in biosensing due to their hydrophilic and biocompatible properties. By combining smart-responsive hydrogels with traditional nucleic acid-related sensing, biological microenvironments can be mimicked, and targets can be easily accessed and diffused, making them ideal for nucleic acid sensing. This review focuses on utilizing smart-responsive hydrogels for nucleic acid-related sensing and detection, including nucleic acid detection, other nucleic acid-based analyte detection and nucleic acid-related sensing platforms applying nucleic acid as sensing tools in hydrogels. Additionally, the analytical mechanisms of smart-responsive hydrogels with the combination of various detection platforms such as optical and electrochemical techniques are described. The limitations of using smart-responsive hydrogels in nucleic acid-related sensing and proposed possible solutions are also discussed. Lastly, the future challenge of smart-responsive hydrogels in nucleic acid-related sensing is explored. Smart-responsive hydrogels can be used as biomimetic materials to simulate the extracellular matrix, achieve biosensing, and exhibit great potential in nucleic acid-related sensing. They serve as a valuable complement to traditional detection and analytical methods.

Microfluidic methods for the diagnosis of acute respiratory tract infections

Acute respiratory tract infections (ARTIs) are caused by sporadic or pandemic outbreaks of viral or bacterial pathogens, and continue to be a considerable socioeconomic burden for both developing and industrialized countries alike. Diagnostic methods and technologies serving as the cornerstone for disease management, epidemiological tracking, and public health interventions are evolving continuously to keep up with the demand for higher sensitivity, specificity and analytical throughput. Microfluidics is becoming a key technology in these developments as it allows for integrating, miniaturizing and automating bioanalytical assays at an unprecedented scale, reducing sample and reagent consumption and improving diagnostic performance in terms of sensitivity, throughput and response time. In this article, we describe relevant ARTIs-pneumonia, influenza, severe acute respiratory syndrome, and coronavirus disease 2019-along with their pathogenesis. We provide a summary of established methods for disease diagnosis, involving nucleic acid amplification techniques, antigen detection, serological testing as well as microbial culture. This is followed by a short introduction to microfluidics and how flow is governed at low volume and reduced scale using centrifugation, pneumatic pumping, electrowetting, capillary action, and propagation in porous media through wicking, for each of these principles impacts the design, functioning and performance of diagnostic tools in a particular way. We briefly cover commercial instruments that employ microfluidics for use in both laboratory and point-of-care settings. The main part of the article is dedicated to emerging methods deriving from the use of miniaturized, microfluidic systems for ARTI diagnosis. Finally, we share our thoughts on future perspectives and the challenges associated with validation, approval, and adaptation of microfluidic-based systems.

Helicoid Grating-Coupled Surface Plasmon Resonance Sensor

Ultrasensitive, rapid, and reliable biomolecular sensing is essential for biomedical diagnostics, requiring real-time monitoring and detection of trace samples. Optical sensing, particularly plasmonic biosensing, meets these demands through noninvasive, high-sensitivity detection based on the interaction between light and molecules. Here, we present novel plasmonic metamaterial-based sensing strategy, utilizing the circular dichroism (CD) response of grating-coupled surface plasmon resonance (SPR) from chiral nanoparticle grating structure (i.e., 2D helicoid crystal) on gold substrate. Strong chiroptic response of helicoids has been effectively expanded to produce a remarkable CD/greflection response in the SPR mode, achieved by spectral coupling of SPR with localized surface plasmon resonance (LSPR) in helicoids. This CD response, derived from the differential of left and right circularly polarized light, corrects optical fluctuations, enhancing sensitivity and reliability. Our SPR-CD-based approach achieves a sensitivity of 379.2 nm/RIU and detection limit of a few mM for d-glucose, offering a new paradigm for high-performance optical biosensors.

Evaluation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using a high figure-of-merit plasmonic multimode refractive index optical sensor

In recent years, following the outbreak of the COVID-19 pandemic, there has been a significant increase in cases of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) and related deaths worldwide. Despite the pandemic nearing its end due to the introduction of mass-produced vaccines against SARS-CoV-2, early detection and diagnosis of the virus remain crucial in preventing disease progression. This article explores the rapid identification of SARS-CoV-2 by implementing a multimode plasmonic refractive index (MMRI) optical sensor, developed based on the split ring resonator (SRR) design. The Finite Difference Time Domain (FDTD) numerical solution method simulates the sensor. The studied sensor demonstrates three resonance modes within the reflection spectrum ranging from 800 nm to 1400 nm. Its material composition and dimensional parameters are optimized to enhance the sensor's performance. The research indicates that all three resonance modes exhibit strong performance with high sensitivity and figures of merit. Notably, the first mode achieves an exceptional sensitivity of 557 nm/RIU, while the third mode exhibits a commendable sensitivity of 453 nm/RIU and a Figure of Merit (FOM) of 45 RIU-1. These findings suggest that the developed MMRI optical sensor holds significant potential for the early and accurate detection of SARS-CoV-2, contributing to improved disease management and control efforts.

Feasibility of snapshot testing using wearable sensors to detect cardiorespiratory illness (COVID infection in India)

The COVID-19 pandemic has challenged the current paradigm of clinical and community-based disease detection. We present a multimodal wearable sensor system paired with a two-minute, movement-based activity sequence that successfully captures a snapshot of physiological data (including cardiac, respiratory, temperature, and percent oxygen saturation). We conducted a large, multi-site trial of this technology across India from June 2021 to April 2022 amidst the COVID-19 pandemic (Clinical trial registry name: International Validation of Wearable Sensor to Monitor COVID-19 Like Signs and Symptoms; NCT05334680; initial release: 04/15/2022). An Extreme Gradient Boosting algorithm was trained to discriminate between COVID-19 infected individuals (n = 295) and COVID-19 negative healthy controls (n = 172) and achieved an F1-Score of 0.80 (95% CI = [0.79, 0.81]). SHAP values were mapped to visualize feature importance and directionality, yielding engineered features from core temperature, cough, and lung sounds as highly important. The results demonstrated potential for data-driven wearable sensor technology for remote preliminary screening, highlighting a fundamental pivot from continuous to snapshot monitoring of cardiorespiratory illnesses.

Use of NIR in COVID-19 Screening: Proof of Principles for Future Application

The COVID-19 pandemic that affected the world between 2019 and 2022 showed the need for new tools to be tested and developed to be applied in global emergencies. Although standard diagnostic tools exist, such as the reverse-transcription polymerase chain reaction (RT-PCR), these tools have shown severe limitations when mass application is required. Consequently, a pressing need remains to develop a rapid and efficient screening test to deliver reliable results. In this context, near-infrared spectroscopy (NIRS) is a fast and noninvasive vibrational technique capable of identifying the chemical composition of biofluids. This study aimed to develop a rapid NIRS testing methodology to identify individuals with COVID-19 through the spectral analysis of swabs collected from the oral cavity. Swab samples from 67 hospitalized individuals were analyzed using NIR equipment. The spectra were preprocessed, outliers were removed, and classification models were constructed using partial least-squares for discriminant analysis (PLS-DA). Two models were developed: one with all the original variables and another with a limited number of variables selected using ordered predictors selection (OPS-DA). The OPS-DA model effectively reduced the number of redundant variables, thereby improving the diagnostic metrics. The model achieved a sensitivity of 92%, a specificity of 100%, an accuracy of 95%, and an AUROC of 94% for positive samples. These preliminary results suggest that NIRS could be a potential tool for future clinical application. A fast methodology for COVID-19 detection would facilitate medical diagnoses and laboratory routines, helping to ensure appropriate treatment.

An emerging network for COVID-19 CT-scan classification using an ensemble deep transfer learning model

Over the past few years, the widespread outbreak of COVID-19 has caused the death of millions of people worldwide. Early diagnosis of the virus is essential to control its spread and provide timely treatment. Artificial intelligence methods are often used as powerful tools to reach a COVID-19 diagnosis via computed tomography (CT) samples. In this paper, artificial intelligence-based methods are introduced to diagnose COVID-19. At first, a network called CT6-CNN is designed, and then two ensemble deep transfer learning models are developed based on Xception, ResNet-101, DenseNet-169, and CT6-CNN to reach a COVID-19 diagnosis by CT samples. The publicly available SARS-CoV-2 CT dataset is utilized for our implementation, including 2481 CT scans. The dataset is separated into 2108, 248, and 125 images for training, validation, and testing, respectively. Based on experimental results, the CT6-CNN model achieved 94.66% accuracy, 94.67% precision, 94.67% sensitivity, and 94.65% F1-score rate. Moreover, the ensemble learning models reached 99.2% accuracy. Experimental results affirm the effectiveness of designed models, especially the ensemble deep learning models, to reach a diagnosis of COVID-19.

Accuracy improvement enzyme-linked immunosorbent assay using superparamagnetic/polyethylene glycol) nanoparticles for leishmaniasis diagnostic

Serodiagnosis methods have been used as platforms for diagnostic tests for many diseases. Due to magnetic nanoparticles' properties to quickly detach from an external magnetic field and particle size effects, these nanomaterials' functionalization allows the specific isolation of target analytes, enhancing accuracy parameters and reducing serodiagnosis time. Superparamagnetic iron oxide nanoparticles (MNPs) were synthesized and functionalized with polyethylene glycol (PEG) and then associated with the synthetic Leishmaniosis epitope. This nano-peptide antigen showed promising results. Regarding Tegumentary leishmaniasis diagnostic accuracy, the AUC was 0.8398 with sensibility 75% (95CI% 50.50 - 89.82) and specificity 87.50% (95CI% 71.93 - 95.03), and Visceral leishmaniasis accuracy study also present high performance, the AUC was 0.9258 with sensibility 87.50% (95CI% 63.98 - 97.78) and specificity 87.50% (95CI% 71.93 - 95.03). Our results demonstrate that the association of the antigen with MNPs accelerates and improves the diagnosis process. MNPs could be an important tool for enhancing serodiagnosis.

Infrared spectroscopy combined with chemometrics in transflectance mode: An alternative approach in the photodiagnosis of COVID-19 using saliva

The Coronavirus Disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has required the search for sensitive, rapid, specific, and lower-cost diagnostic methods to meet the high demand. The gold standard method of laboratory diagnosis is real-time reverse transcription polymerase chain reaction (RT-PCR). However, this method is costly and results can take time. In the literature, several studies have already described the potential of Fourier transform infrared spectroscopy (FTIR) as a tool in the biomedical field, including the diagnosis of viral infections, while being fast and inexpensive. In view of this, the objective of this study was to develop an FTIR model for the diagnosis of COVID-19. For this analysis, all private clients who had performed a face-to-face collection at the Univates Clinical Analysis Laboratory (LAC Univates) within a period of six months were invited to participate. Data from clients who agreed to participate in the study were collected, as well as nasopharyngeal secretions and a saliva sample. For the development of models, the RT-PCR result of nasopharyngeal secretions was used as a reference method. Absorptions with high discrimination (p < 0.001) between GI (28 patients, RT-PCR test positive to SARS-CoV-2 virus) and GII (173 patients who did not have the virus detected in the test) were most relevant at 3512 cm-1, 3385 cm-1 and 1321 cm-1 after 2nd derivative data transformation. To carry out the diagnostic modeling, chemometrics via FTIR and Discriminant Analysis of Orthogonal Partial Least Squares (OPLS-DA) by salivary transflectance mode with one latent variable and one orthogonal signal correction component were used. The model generated predictions with 100 % sensitivity, specificity and accuracy. With the proposed model, in a single application of an individual's saliva in the FTIR equipment, results related to the detection of SARS-CoV-2 can be obtained in a few minutes of spectral evaluation.

Rapid Nucleic Acid Diagnostic Technology for Pandemic Diseases

The recent global pandemic of coronavirus disease 2019 (COVID-19) has enormously promoted the development of diagnostic technology. To control the spread of pandemic diseases and achieve rapid screening of the population, ensuring that patients receive timely treatment, rapid diagnosis has become the top priority in the development of clinical technology. This review article aims to summarize the current rapid nucleic acid diagnostic technologies applied to pandemic disease diagnosis, from rapid extraction and rapid amplification to rapid detection. We also discuss future prospects in the development of rapid nucleic acid diagnostic technologies.

Fluorescence Biosensing Based on Bifurcated DNA Scaffold-Aggregated Ag Nanocluster via Responsive Conformation Switch of Quasi-Molecular Beacon

To address the limitations of typical hairpin-structural molecular beacons, exploring the ability of a quasi-molecular beacon (qMB) to create label-free fluorescence biosensors is intriguing and remains a challenge. Herein, we propose the first example of modular qMB with the feature of a stimulation-responsive conformation switch to develop an aggregated Ag nanocluster (aAgNC) in a bifurcated DNA scaffold for fluorescently sensing a specific initiator (I*). This qMB was well designed to program four functional modules: I*-recognizable element adopting metastable stem-loop bihairpin structure and two DNA splits (exposed C3GT4 and locked C4AC4T) of aAgNC template that is separated by a tunable hairpin spacer for the customized combination of selective recognition and signaling readout. When presenting I* in an assay route, the specific hybridization induces the directional disassembly of the bihairpin unit, on which the qMB is configurationally switched to liberate the locked split. Thus, the bifurcated parent template pair of C3GT4/C4AC4T is proximal, affording in situ nucleation and clustering of emissive aAgNC. By collecting the fluorescence signal, the quantitative detection of I* is achieved. Benefiting from the ingenious programming of qMB, the recognizing and signaling integration actuates the construction of a facile and convenient fluorescent biosensor featuring rapid reaction kinetics, a wide linear range, high sensitivity, and specificity. This would provide a new paradigm to exploit versatile qMB-based biosensing platforms via stimulation-responsive conformation switches for developing various DNA-scaffolded Ag clusters.

Research on accurate pipetting complementation model for high-throughput molecular detection platform

The incidence of infectious diseases has risen in recent years, leading to a significant surge in the demand for medical molecular detection. High-throughput molecular detection platforms play a crucial role in facilitating rapid and efficient molecular detection. Among the various techniques employed in high-throughput molecular detection, microliquid transfer stands out as one of the most frequently utilized methods. However, ensuring the accuracy of liquid transfer poses a challenge due to variations in the physical and chemical properties of different samples and reagents. In this study, a pipetting complementation model was developed specifically for the serum, paraffin oil, and throat swabs. The aim was to enhance the transfer accuracy of diverse liquids in the context of high-throughput molecular detection, ultimately ensuring detection reliability and stability. The experimental findings revealed notable improvements in pipetting accuracy after compensating for the three liquids. In particular, the pipetting error rates decreased by 52.5, 96, and 71.4% for serum, paraffin oil, and throat swabs, respectively. These results underscore the model's effectiveness in providing reliable support for the precise transfer of liquids on the high-throughput molecular detection platform.

A highly selective and sensitive electrochemical sensor for tetracycline resistant genes detection based on the non-covalent interaction of graphene oxide and nucleobase

Antibiotic resistance genes (ARGs) are causing worldwide environmental problems, however, the traditional analytical methods and test equipment for them are time-consuming and expensive. The electrochemical sensor using the non-covalent bond between graphene oxide (GO) and single-stranded tet (ss-tet) was established for specific tetracycline resistance genes (tet, composed of ss-tet and complementary ss-tet (ss-tet') in water) detection, which preparation time was only 35 min and far less than most reported sensors based on covalent bond. As the result of the detection for tet, the developed sensor not only had the low detection limit of 50.0 pM (8.1 × 102 copies·mL-1), the short detection time within 42 min, but also had satisfactory stability, excellent reproducibility, and highly selectivity (RSD < 4.43 %). Besides, it also had acceptable accuracy comparing to the real-time quantitative polymerase chain reaction (RT-qPCR) and PCR array in tet detection. Noticeably, it also had been successfully applied to tetA detection in different water samples. In brief, the prepared non-covalent bond sensor is simple, rapid, and suitable for highly selective and sensitive detection of the ARGs in actual water.

Toehold switch plus signal amplification enables rapid detection

Recent world events have led to an increased interest in developing rapid and inexpensive clinical diagnostic platforms for viral detection. Here, the development of a cell-free toehold switch-based biosensor, which does not require upstream amplification of target RNA, is described for the detection of RNA viruses. Toehold switches were designed to avoid interfering secondary structure in the viral RNA binding region, mutational hotspots, and cross-reacting sequences of other coronaviruses. Using these design criteria, toehold switches were targeted to a low mutation region of the SARS-CoV-2 genome nonstructural protein 2 (nsp2). The designs were tested in a cell-free system using trigger RNA based on the viral genome and a highly sensitive fluorescent reporter gene, mNeonGreen. The detection sensitivity of our best toehold design, CSU 08, was in the low picomolar range of target (trigger) RNA. To increase the sensitivity of our cell-free biosensor to a clinically relevant level, we developed a modular downstream amplification system that utilizes toehold switch activation of tobacco etch virus (TEV) protease expression. The TEV protease cleaves a quenched fluorescent reporter, both increasing the signal fold change between control and sample and increasing the sensitivity to a clinically relevant low femtomolar range for target RNA detection.

A Multichannel Fluorescence Isothermal Amplification Device with Integrated Internet of Medical Things for Rapid Sensing of Pathogens through Deep Learning

The landscape of diagnostic assessments has experienced a paradigm shift driven by the advent of isothermal amplification techniques on point-of-care testing (POCT). The development of compact, portable isothermal amplification devices further emphasizes their transformative influence on diagnostic approaches. However, in prioritizing portability, these devices may exhibit limitations in functionality, rendering them less effective in addressing urgent public health emergencies during sudden pathogen outbreaks. In this paper, an efficient isothermal fluorescence amplification device has been fabricated for the rapid detection of pathogens during public health crises. The device features multichannel capability for simultaneous detection of various targets, integrates with the Internet of Medical Things (IoMT) for remote control and data uploading, and includes a deep learning-based batch processing system for rapid (9.4 ms) and accurate discrimination of pathogen type with excellent accuracy. The device has been successfully employed to simultaneously detect Staphylococcus aureus (SA) and methicillin-resistant Staphylococcus aureus (MRSA) with limits of detection (LODs) of 18 CFU/mL (SA) and 20 CFU/mL (MRSA) within 35 min by multiplex RPA assay and CRISPR/Cas12a-mediated nucleic acid detection assay.

Streamlined Specimen Purification for Rapid COVID-19 Diagnosis Using Positively Charged Polymer Thin Film-Coated Surfaces and Chamber Digital PCR

The ongoing coronavirus disease 2019 (COVID-19) pandemic demands rapid and straightforward diagnostic tools to prevent early-stage viral transmission. Although nasopharyngeal swabs are a widely used patient sample collection method for diagnosing COVID-19, using these samples for diagnosis without RNA extraction increases the risk of obtaining false-positive and -negative results. Thus, multiple purification steps are necessary, which are time-consuming, generate significant waste, and result in substantial sample loss. To address these issues, we developed surface-modified polymerase chain reaction (PCR) tubes using the tertiary aminated polymer poly(2-dimethylaminomethylstyrene) (pDMAMS) via initiated chemical vapor deposition. Introducing the clinical samples into the pDMAMS-coated tubes resulted in approximately 100% RNA capture efficiency within 25 min, which occurred through electrostatic interactions between the positively charged pDMAMS surface and the negatively charged RNA. The captured RNA is then detected via chamber digital PCR, enabling a sensitive, accurate, and rapid diagnosis. Our platform provides a simple and efficient RNA extraction and detection strategy that allows detection from 22 nasopharyngeal swabs and 21 saliva specimens with 0% false negatives. The proposed method can facilitate the diagnosis of COVID-19 and contribute to the prevention of early-stage transmission.

Development and Analytical Evaluation of a Point-of-Care Electrochemical Biosensor for Rapid and Accurate SARS-CoV-2 Detection

The COVID-19 pandemic has underscored the critical need for rapid and accurate screening and diagnostic methods for potential respiratory viruses. Existing COVID-19 diagnostic approaches face limitations either in terms of turnaround time or accuracy. In this study, we present an electrochemical biosensor that offers nearly instantaneous and precise SARS-CoV-2 detection, suitable for point-of-care and environmental monitoring applications. The biosensor employs a stapled hACE-2 N-terminal alpha helix peptide to functionalize an in situ grown polypyrrole conductive polymer on a nitrocellulose membrane backbone through a chemical process. We assessed the biosensor's analytical performance using heat-inactivated omicron and delta variants of the SARS-CoV-2 virus in artificial saliva (AS) and nasal swab (NS) samples diluted in a strong ionic solution, as well as clinical specimens with known Ct values. Virus identification was achieved through electrochemical impedance spectroscopy (EIS) and frequency analyses. The assay demonstrated a limit of detection (LoD) of 40 TCID50/mL, with 95% sensitivity and 100% specificity. Notably, the biosensor exhibited no cross-reactivity when tested against the influenza virus. The entire testing process using the biosensor takes less than a minute. In summary, our biosensor exhibits promising potential in the battle against pandemic respiratory viruses, offering a platform for the development of rapid, compact, portable, and point-of-care devices capable of multiplexing various viruses. The biosensor has the capacity to significantly bolster our readiness and response to future viral outbreaks.

Detection of SARS-CoV-2 in saliva by a low-cost LSPR-based sensor

The SARS-CoV-2 pandemic started more than 3 years ago, but the containment of the spread is still a challenge. Screening is imperative for informed decision making by government authorities to contain the spread of the virus locally. The access to screening tests is disproportional, due to the lack of access to reagents, equipment, finances or because of supply chain disruptions. Low and middle-income countries have especially suffered with the lack of these resources. Here, we propose a low cost and easily constructed biosensor device based on localized surface plasmon resonance, or LSPR, for the screening of SARS-CoV-2. The biosensor device, dubbed "sensor" for simplicity, was constructed in two modalities: (1) viral detection in saliva and (2) antibody against COVID in saliva. Saliva collected from 18 patients were tested in triplicates. Both sensors successfully classified all COVID positive patients (among hospitalized and non-hospitalized). From the COVID negative patients 7/8 patients were correctly classified. For both sensors, sensitivity was determined as 100% (95% CI 79.5-100) and specificity as 87.5% (95% CI 80.5-100). The reagents and equipment used for the construction and deployment of this sensor are ubiquitous and low-cost. This sensor technology can then add to the potential solution for challenges related to screening tests in underserved communities.

Recent Advances in Quantum Dot-Based Lateral Flow Immunoassays for the Rapid, Point-of-Care Diagnosis of COVID-19

The COVID-19 pandemic has spurred demand for efficient and rapid diagnostic tools that can be deployed at point of care to quickly identify infected individuals. Existing detection methods are time consuming and they lack sensitivity. Point-of-care testing (POCT) has emerged as a promising alternative due to its user-friendliness, rapidity, and high specificity and sensitivity. Such tests can be conveniently conducted at the patient's bedside. Immunodiagnostic methods that offer the rapid identification of positive cases are urgently required. Quantum dots (QDs), known for their multimodal properties, have shown potential in terms of combating or inhibiting the COVID-19 virus. When coupled with specific antibodies, QDs enable the highly sensitive detection of viral antigens in patient samples. Conventional lateral flow immunoassays (LFAs) have been widely used for diagnostic testing due to their simplicity, low cost, and portability. However, they often lack the sensitivity required to accurately detect low viral loads. Quantum dot (QD)-based lateral flow immunoassays have emerged as a promising alternative, offering significant advancements in sensitivity and specificity. Moreover, the lateral flow immunoassay (LFIA) method, which fulfils POCT standards, has gained popularity in diagnosing COVID-19. This review focuses on recent advancements in QD-based LFIA for rapid POCT COVID-19 diagnosis. Strategies to enhance sensitivity using QDs are explored, and the underlying principles of LFIA are elucidated. The benefits of using the QD-based LFIA as a POCT method are highlighted, and its published performance in COVID-19 diagnostics is examined. Overall, the integration of quantum dots with LFIA holds immense promise in terms of revolutionizing COVID-19 detection, treatment, and prevention, offering a convenient and effective approach to combat the pandemic.

Carbon-based biosensors: Next-generation diagnostic tool for target-specific detection of SARS-CoV-2 (COVID-19)

Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) was declared a global pandemic in 2020. Having rapidly spread around the globe, with the emergence of new variants, there is a crucial need to develop diagnostic kits for its rapid detection. Since it validated accuracy and reliability, the reverse transcription polymerase chain reaction (RT-PCR) test has been declared the gold standard for disease detection. However, despite its reliability, the requirement of specialized facilities, reagents, and duration of a PCR run limits its usage for rapid detection. There is thus a continuous increase in the design and development of rapid, point-of-care (PoC), and cost-effective diagnostic kits. In this review, we discuss the potential of carbon-based biosensors for target-specific detection of coronavirus disease 19 (COVID-19) and present an overview of investigation within the timeframe of the last four years (2019-2022), which have developed novel platforms using carbon nanomaterial-based approaches for viral detection. The approaches discussed offer rapid, accurate, and cost-effective strategies for COVID-19 detection for healthcare personnel and research workers.

Improvements in skills and knowledge after a comprehensive ELISA teaching course for biotechnology undergraduates

As a universal and extensively adopted technique, enzyme-linked immunosorbent assay (ELISA) can be used to detect and quantify small molecules in many applications both clinical and analytical. However, generally, students experiment mechanically using commercial ELISA kits according to the instructions and eventually produce a standard curve to calculate the concentration of the sample to be measured, cannot understand the critical factors and process of method establishment. This study systematically introduced undergraduates to using the pathogen-specific antigen and establishing an indirect ELISA method to detect the diagnostic target pathogen Burkholderia pseudomallei. This course aimed to develop the experimental skills of the students and improve their scientific research knowledge, which fully embody the organic combination of scientific research and teaching. Students independently selected the diagnostic antigen target of interest, obtained the antigen proteins using genetic engineering techniques, and established an ELISA method through a series of conditional optimization experiments. In addition, typical student-generated data, experimental methods, and a student feedback interpretation are presented in this study. Overall, the students were able to combine abstract knowledge with practice and understand the principles and applications of antigen-antibody interactions, thus enabling them to gain practical experience in molecular biology techniques, and learn how to use this principle to establish an ELISA method for detecting infectious diseases.

Nanostructures for prevention, diagnosis, and treatment of viral respiratory infections: from influenza virus to SARS-CoV-2 variants

Viruses are a major cause of mortality and socio-economic downfall despite the plethora of biopharmaceuticals designed for their eradication. Conventional antiviral therapies are often ineffective. Live-attenuated vaccines can pose a safety risk due to the possibility of pathogen reversion, whereas inactivated viral vaccines and subunit vaccines do not generate robust and sustained immune responses. Recent studies have demonstrated the potential of strategies that combine nanotechnology concepts with the diagnosis, prevention, and treatment of viral infectious diseases. The present review provides a comprehensive introduction to the different strains of viruses involved in respiratory diseases and presents an overview of recent advances in the diagnosis and treatment of viral infections based on nanotechnology concepts and applications. Discussions in diagnostic/therapeutic nanotechnology-based approaches will be focused on H1N1 influenza, respiratory syncytial virus, human parainfluenza virus type 3 infections, as well as COVID-19 infections caused by the SARS-CoV-2 virus Delta variant and new emerging Omicron variant.

Electrochemical Biosensors for Whole Blood Analysis: Recent Progress, Challenges, and Future Perspectives

Whole blood, as one of the most significant biological fluids, provides critical information for health management and disease monitoring. Over the past 10 years, advances in nanotechnology, microfluidics, and biomarker research have spurred the development of powerful miniaturized diagnostic systems for whole blood testing toward the goal of disease monitoring and treatment. Among the techniques employed for whole-blood diagnostics, electrochemical biosensors, as known to be rapid, sensitive, capable of miniaturization, reagentless and washing free, become a class of emerging technology to achieve the target detection specifically and directly in complex media, e.g., whole blood or even in the living body. Here we are aiming to provide a comprehensive review to summarize advances over the past decade in the development of electrochemical sensors for whole blood analysis. Further, we address the remaining challenges and opportunities to integrate electrochemical sensing platforms.

Unlocking the Diagnostic Potential of Saliva: A Comprehensive Review of Infrared Spectroscopy and Its Applications in Salivary Analysis

Infrared (IR) spectroscopy is a noninvasive and rapid analytical technique that provides information on the chemical composition, structure, and conformation of biomolecules in saliva. This technique has been widely used to analyze salivary biomolecules, owing to its label-free advantages. Saliva contains a complex mixture of biomolecules including water, electrolytes, lipids, carbohydrates, proteins, and nucleic acids which are potential biomarkers for several diseases. IR spectroscopy has shown great promise for the diagnosis and monitoring of diseases such as dental caries, periodontitis, infectious diseases, cancer, diabetes mellitus, and chronic kidney disease, as well as for drug monitoring. Recent advancements in IR spectroscopy, such as Fourier-transform infrared (FTIR) spectroscopy and attenuated total reflectance (ATR) spectroscopy, have further enhanced its utility in salivary analysis. FTIR spectroscopy enables the collection of a complete IR spectrum of the sample, whereas ATR spectroscopy enables the analysis of samples in their native form, without the need for sample preparation. With the development of standardized protocols for sample collection and analysis and further advancements in IR spectroscopy, the potential for salivary diagnostics using IR spectroscopy is vast.

Multiplexed Nanopore-Based Nucleic Acid Sensing and Bacterial Identification Using DNA Dumbbell Nanoswitches

Multiplexed nucleic acid sensing methods with high specificity are vital for clinical diagnostics and infectious disease control, especially in the postpandemic era. Nanopore sensing techniques have developed in the past two decades, offering versatile tools for biosensing while enabling highly sensitive analyte measurements at the single-molecule level. Here, we establish a nanopore sensor based on DNA dumbbell nanoswitches for multiplexed nucleic acid detection and bacterial identification. The DNA nanotechnology-based sensor switches from an "open" into a "closed" state when a target strand hybridizes to two sequence-specific sensing overhangs. The loop in the DNA pulls two groups of dumbbells together. The change in topology results in an easily recognized peak in the current trace. Simultaneous detection of four different sequences was achieved by assembling four DNA dumbbell nanoswitches on one carrier. The high specificity of the dumbbell nanoswitch was verified by distinguishing single base variants in DNA and RNA targets using four barcoded carriers in multiplexed measurements. By combining multiple dumbbell nanoswitches with barcoded DNA carriers, we identified different bacterial species even with high sequence similarity by detecting strain specific 16S ribosomal RNA (rRNA) fragments.

Molecular-electromechanical system for unamplified detection of trace analytes in biofluids

Biological research and diagnostic applications normally require analysis of trace analytes in biofluids. Although considerable advancements have been made in developing precise molecular assays, the trade-off between sensitivity and ability to resist non-specific adsorption remains a challenge. Here, we describe the implementation of a testing platform based on a molecular-electromechanical system (MolEMS) immobilized on graphene field-effect transistors. A MolEMS is a self-assembled DNA nanostructure, containing a stiff tetrahedral base and a flexible single-stranded DNA cantilever. Electromechanical actuation of the cantilever modulates sensing events close to the transistor channel, improving signal-transduction efficiency, while the stiff base prevents non-specific adsorption of background molecules present in biofluids. A MolEMS realizes unamplified detection of proteins, ions, small molecules and nucleic acids within minutes and has a limit of detection of several copies in 100 μl of testing solution, offering an assay methodology with wide-ranging applications. In this protocol, we provide step-by-step procedures for MolEMS design and assemblage, sensor manufacture and operation of a MolEMS in several applications. We also describe adaptations to construct a portable detection platform. It takes ~18 h to construct the device and ~4 min to finish the testing from sample addition to result.

An ultra-sensitive one-pot RNA-templated DNA ligation rolling circle amplification-assisted CRISPR/Cas12a detector assay for rapid detection of SARS-CoV-2

Rapid, sensitive, and one-pot diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays an extremely important role in point-of-care testing (POCT). Herein, we report an ultra-sensitive and rapid one-pot enzyme-catalyzed rolling circle amplification-assisted CRISPR/FnCas12a assay, termed OPERATOR. OPERATOR employs a single well-designed single-strand padlock DNA, containing a protospacer adjacent motif (PAM) site and a sequence complementary to the target RNA which procedure converts and amplifies genomic RNA to DNA by RNA-templated DNA ligation and multiply-primed rolling circle amplification (MRCA). The MRCA amplicon of single-stranded DNA is cleaved by the FnCas12a/crRNA complex and detected via a fluorescence reader or lateral flow strip. OPERATOR presents outstanding advantages including ultra-sensitivity (1.625 copies per reaction), high specificity (100%), rapid reaction speed (∼30 min), easy operation, low cost, and on-spot visualization. Furthermore, we established a POCT platform by combining OPERATOR with rapid RNA release and a lateral flow strip without professional equipment. The high performance of OPERATOR in SARS-CoV-2 tests was confirmed using both reference materials and clinical samples, and the results suggest that is readily adaptable for point-of-care testing of other RNA viruses.

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.

Peptide nucleic acid and antifouling peptide based biosensor for the non-fouling detection of COVID-19 nucleic acid in saliva

The electrochemical biosensor with outstanding sensitivity and low cost is regarded as a viable alternative to current clinical diagnostic techniques for various disease biomarkers. However, their actual analytical use in complex biological samples is severely hampered due to the biofouling, as they are also highly sensitive to nonspecific adsorption on the sensing interfaces. Herein, we have constructed a non-fouling electrochemical biosensor based on antifouling peptides and the electroneutral peptide nucleic acid (PNA), which was used as the recognizing probe for the specific binding of the viral RNA of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Different from the negatively charged DNA probes that will normally weaken the biosensors' antifouling capabilities owing to the charge attraction of positively charged biomolecules, the neutral PNA probe will generate no side-effects on the biosensor. The biosensor demonstrated remarkable sensitivity in detecting SARS-CoV-2 viral RNA, possessing a broad linear range (1.0 fM - 1.0 nM) and a detection limit down to 0.38 fM. Furthermore, the sensing performance of the constructed electrochemical biosensor in human saliva was nearly similar to that in pure buffer, indicating satisfying antifouling capability. The combination of PNA probes with antifouling peptides offered a new strategy for the development of non-fouling sensing systems capable of assaying trace disease biomarkers in complicated biological media.

A straightforward one-step strategy for SARS-CoV-2 diagnosis and screening of variants of concern: a multicentre study

BACKGROUND

The prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) has changed unevenly over time around the world. Although whole genome sequencing is the gold standard for virus characterisation, the discovery of alpha VOC causing spike gene target failure (SGTF) result, when tested using an reverse transcription real-time polymerase chain reaction (RT-qPCR) assay, has provided a simple tool for tracking the frequencies of variants.

OBJECTIVES

The aim of this study was to investigate if a multiplex RT-qPCR assay (BioM 4Plex VOC) could be used to detect SARS-CoV-2 and to perform a VOC screening test in a single reaction tube. Here, we present the multicentre study evaluating this assay.

METHODS

Twelve laboratories have participated in the multicentre study. The BioM 4Plex VOC was distributed to them with detailed instructions of how to perform the test. They were asked to test the BioM 4Plex VOC in parallel with their routine Commercial SARS-CoV-2 diagnostic assay. Additionally, they were requested to select SARS-CoV-2-positive samples with genome sequenced and lineage definition according to PANGO lineage classification.

FINDINGS

The BioM 4Plex VOC and commercial RT-PCR assay are equally effective in detecting SARS-CoV-2. Results revealed a specificity of 96.5-100% [95% confidence interval (CI)], a sensitivity of 99.8-100% (95% CI), and an accuracy of 99.8-100% (95% CI). A 99% concordance rate was found between results from the BioM 4Plex VOC and that from available genome sequencing data.

MAIN CONCLUSIONS

The BioM 4Plex VOC provides an effective solution to detect SARS-CoV-2 infections and screening for VOCs in a single reaction. It is a straightforward method to help us monitor the frequency and distribution of VOCs and develop strategies to better cope with the pandemics.

Carrageenan from Gigartina skottsbergii: A Novel Molecular Probe to Detect SARS-CoV-2

The COVID-19 pandemic has caused an unprecedented health and economic crisis, highlighting the importance of developing new molecular tools to monitor and detect SARS-CoV-2. Hence, this study proposed to employ the carrageenan extracted from Gigartina skottsbergii algae as a probe for SARS-CoV-2 virus binding capacity and potential use in molecular methods. G. skottsbergii specimens were collected in the Chilean subantarctic ecoregion, and the carrageenan was extracted -using a modified version of Webber's method-, characterized, and quantified. After 24 h of incubation with an inactivated viral suspension, the carrageenan's capacity to bind SARS-CoV-2 was tested. The probe-bound viral RNA was quantified using the reverse transcription and reverse transcription loop-mediated isothermal amplification (RT-LAMP) methods. Our findings showed that carrageenan extraction from seaweed has a similar spectrum to commercial carrageenan, achieving an excellent proportion of binding to SARS-CoV-2, with a yield of 8.3%. Viral RNA was also detected in the RT-LAMP assay. This study shows, for the first time, the binding capacity of carrageenan extracted from G. skottsbergii, which proved to be a low-cost and highly efficient method of binding to SARS-CoV-2 viral particles.

Occurrence and transport of SARS-CoV-2 in wastewater streams and its detection and remediation by chemical-biological methods

This paper explains the transmission of SARS-CoV and influences of several environmental factors in the transmission process. The article highlighted several methods of collection, sampling and monitoring/estimation as well as surveillance tool for detecting SARS-CoV in wastewater streams. In this context, WBE (Wastewater based epidemiology) is found to be the most effective surveillance tool. Several methods of genomic sequencing are discussed in the paper, which are applied in WBE, like qPCR-based wastewater testing, metagenomics-based analysis, next generation sequencing etc. Additionally, several types of biosensors (colorimetric biosensor, mobile phone-based biosensors, and nanomaterials-based biosensors) showed promising results in sensing SARS-CoV in wastewater. Further, this review paper outlined the gaps in assessing the factors responsible for transmission and challenges in detection and monitoring along with the remediation and disinfection methods of this virus in wastewater. Various methods of disinfection of SARS-CoV-2 in wastewater are discussed (primary, secondary, and tertiary phases) and it is found that a suite of disinfection methods can be used for complete disinfection/removal of the virus. Application of ultraviolet light, ozone and chlorine-based disinfectants are also discussed in the context of treatment methods. This study calls for continuous efforts to gather more information about the virus through continuous monitoring and analyses and to address the existing gaps and identification of the most effective tool/ strategy to prevent SARS-CoV-2 transmission. Wastewater surveillance can be very useful in effective surveillance of future pandemics and epidemics caused by viruses, especially after development of new technologies in detecting and disinfecting viral pathogens more effectively.

Analysis of network public opinion on COVID-19 epidemic based on the WSR theory

Objective

To obtain the influencing factors of public opinion reactions and to construct a basic framework of the factors causing the occurrence of online public opinion in the epidemic area.

Methods

The hot news comments on microblogs during the epidemic in Shanghai were collected and analyzed with qualitative analysis, grounded theory, and the "Wuli-Shili-Renli" (WSR) methodology as an auxiliary method.

Results

(1) Three core categories of the Wuli system, the Shili system, and the Renli system, 15 main categories, and 86 categories that influence the development of network public opinion are obtained. (2) WSR Elements Framework Of Network Public Opinion (WSR-EFONPO) is established. (3) The WSR-EFONPO is explained.

Conclusion

The framework of factors for the occurrence of network public opinion is proposed, and the development process of network public opinion under COVID-19 is sorted out, which is of great theoretical value in guiding the public in the epidemic area to form reasonable behavior.

Analysis of critical protein-protein interactions of SARS-CoV-2 capping and proofreading molecular machineries towards designing dual target inhibitory peptides

In recent years, the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as the cause of the coronavirus disease (COVID-19) global pandemic, and its variants, especially those with higher transmissibility and substantial immune evasion, have highlighted the imperative for developing novel therapeutics as sustainable solutions other than vaccination to combat coronaviruses (CoVs). Beside receptor recognition and virus entry, members of the SARS-CoV-2 replication/transcription complex are promising targets for designing antivirals. Here, the interacting residues that mediate protein-protein interactions (PPIs) of nsp10 with nsp16 and nsp14 were comprehensively analyzed, and the key residues' interaction maps, interaction energies, structural networks, and dynamics were investigated. Nsp10 stimulates both nsp14's exoribonuclease (ExoN) and nsp16's 2'O-methyltransferase (2'O-MTase). Nsp14 ExoN is an RNA proofreading enzyme that supports replication fidelity. Nsp16 2'O-MTase is responsible for the completion of RNA capping to ensure efficient replication and translation and escape from the host cell's innate immune system. The results of the PPIs analysis proposed crucial information with implications for designing SARS-CoV-2 antiviral drugs. Based on the predicted shared protein-protein interfaces of the nsp16-nsp10 and nsp14-nsp10 interactions, a set of dual-target peptide inhibitors was designed. The designed peptides were evaluated by molecular docking, peptide-protein interaction analysis, and free energy calculations, and then further optimized by in silico saturation mutagenesis. Based on the predicted evolutionary conservation of the interacted target residues among CoVs, the designed peptides have the potential to be developed as dual target pan-coronavirus inhibitors.

An ultra-sensitive and specific nanoplasmonic-enhanced isothermal amplification platform for the ultrafast point-of-care testing of SARS-CoV-2

The novel mutations attributed by the high mutagenicity of the SARS-CoV-2 makes its prevention and treatment challenging. Developing an ultra-fast, point-of-care-test (POCT) protocol is critical for responding to large-scale spread of SARS-CoV-2 in public places and in resource-poor remote areas. Here, we developed a nanoplasmonic enhanced isothermal amplification (NanoPEIA) strategy that combines a nanoplasmonic sensor with isothermal amplification. The novel strategy provides an ideal easy-to operate detection platform for obtaining accurate, ultra-fast and high-throughput (96 samples can be tested together) data. For clinical samples with viral detection at Ct value <25, the entire process (including sample preparation, virus lysis, detection, and data analysis) can be completed within six minutes. The method is also appropriate for detection of SARS-CoV-2 γ-coronavirus mutants. The NanoPEIA method was validated using clinical samples from 21 patients with SARS-CoV-2 infection and 31 healthy individuals. The detection result on the 52 clinical samples for SARS-CoV-2 showed that the NanoPEIA platform had a 100% sensitivity for N and orf1ab genes, which was higher than those obtained using RT-qPCR (88.9% and 90.0%, respectively). The specificities of 31 clinical negative samples were 92.3% and 91.7% for the N gene and the orf1ab gene, respectively. The limits of detection (LoD) of the clinical samples were 28.3 copies/mL and 23.3 copies/mL for the N gene and the orf1ab gene, respectively. The efficient NanoPEIA detection strategy facilitates real-time detection and visualization within ultrashort durations and can be applied for POCT diagnosis in resource-poor and highly populated areas.

An ultrasensitive and rapid "sample-to-answer" microsystem for on-site monitoring of SARS-CoV-2 in aerosols using "in situ" tetra-primer recombinase polymerase amplification

Airborne transmissibility of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the urgent need for aerosol monitoring of SARS-CoV-2 to prevent sporadic outbreaks of COVID-19. The inadequate sensitivity of conventional methods and the lack of an on-site detection system limited the practical SARS-CoV-2 monitoring of aerosols in public spaces. We have developed a novel SARS-CoV-2-in-aerosol monitoring system (SIAMs) which consists of multiple portable cyclone samplers for collecting aerosols from several venues and a sensitive "sample-to-answer" microsystem employing an integrated cartridge for the analysis of SARS-CoV-2 in aerosols (iCASA) near the sampling site. By seamlessly combining viral RNA extraction based on a chitosan-modified quartz filter and "in situ" tetra-primer recombinase polymerase amplification (tpRPA) into an integrated microfluidic cartridge, iCASA can provide an ultra-high sensitivity of 20 copies/mL, which is nearly one order of magnitude greater than that of the commercial kit, and a short turnaround time of 25 min. By testing various clinical samples of nasopharyngeal swabs, saliva, and exhaled breath condensates obtained from 23 COVID-19 patients, we demonstrate that the positive rate of our system was 3.3 times higher than those of the conventional method. Combining with multiple portable cyclone samplers, we detected 52.2% (12/23) of the aerosol samples, six times higher than that of the commercial kit, collected from the isolation wards of COVID-19 patients, demonstrating the excellent performance of our system for SARS-CoV-2-in-aerosol monitoring. We envision the broad application of our microsystem in aerosol monitoring for fighting the COVID-19 pandemic.

Amplification Free Detection of SARS-CoV-2 Using Multi-Valent Binding

We present the development of electrochemical impedance spectroscopy (EIS)-based biosensors for sensitive detection of SARS-CoV-2 RNA using multi-valent binding. By increasing the number of probe-target binding events per target molecule, multi-valent binding is a viable strategy for improving the biosensor performance. As EIS can provide sensitive and label-free measurements of nucleic acid targets during probe-target hybridization, we used multi-valent binding to build EIS biosensors for targeting SARS-CoV-2 RNA. For developing the biosensor, we explored two different approaches including probe combinations that individually bind in a single-valent fashion and the probes that bind in a multi-valent manner on their own. While we found excellent biosensor performance using probe combinations, we also discovered unexpected signal suppression. We explained the signal suppression theoretically using inter- and intra-probe hybridizations which confirmed our experimental findings. With our best probe combination, we achieved a LOD of 182 copies/μL (303 aM) of SARS-CoV-2 RNA and used these for successful evaluation of patient samples for COVID-19 diagnostics. We were also able to show the concept of multi-valent binding with shorter probes in the second approach. Here, a 13-nt-long probe has shown the best performance during SARS-CoV-2 RNA binding. Therefore, multi-valent binding approaches using EIS have high utility for direct detection of nucleic acid targets and for point-of-care diagnostics.

Robustness of FTIR-Based Ultrarapid COVID-19 Diagnosis Using PLS-DA

The World Health Organization (WHO) declared the Omicron variant (B.1.1.529) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogen responsible for the Coronavirus disease 2019 (COVID-19) pandemic, as a variant of concern on 26 November 2021. By this time, 42% of the world's population had received at least one dose of the vaccine against COVID-19. As on 1 October 2022, only 68% of the world population got the first dose of the vaccine. Although the vaccination is incredibly protective against severe complications of the disease and death, the highly contagious Omicron variant, compared to the Delta variant (B.1.617.2), has led the whole world into more chaotic situations. Furthermore, the virus has a high mutation rate, and hence, the possibility of a new variant of concern in the future cannot be ruled out. To face such a challenging situation, paramount importance should be given to rapid diagnosis and isolation of the infected patient. Current diagnosis methods, including reverse transcription-polymerase chain reaction and rapid antigen tests, face significant burdens during a COVID-19 wave. However, studies reported ultrarapid, reagent-free, cost-efficient, and non-destructive diagnosis methods based on chemometrics for COVID-19 and COVID-19 severity diagnosis. These studies used a smaller sample cohort to construct the diagnosis model and failed to discuss the robustness of the model. The current study systematically evaluated the robustness of the diagnosis models trained using smaller (real and augmented spectra) and larger (augmented spectra) datasets. The Monte Carlo cross-validation and permutation test results suggest that diagnosis using models trained by larger datasets was accurate and statistically significant (Q ² > 99% and AUROC = 100%).

Nucleic acid testing of SARS-CoV-2: A review of current methods, challenges, and prospects

Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and has brought a huge threat to public health and the global economy. Rapid identification and isolation of SARS-CoV-2-infected individuals are regarded as one of the most effective measures to control the pandemic. Because of its high sensitivity and specificity, nucleic acid testing has become the major method of SARS-CoV-2 detection. A deep understanding of different diagnosis methods for COVID-19 could help researchers make an optimal choice in detecting COVID-19 at different symptom stages. In this review, we summarize and evaluate the latest developments in current nucleic acid detection methods for SARS-CoV-2. In particular, we discuss biosensors and CRISPR-based diagnostic systems and their characteristics and challenges. Furthermore, the emerging COVID-19 variants and their impact on SARS-CoV-2 diagnosis are systematically introduced and discussed. Considering the disease dynamics, we also recommend optional diagnostic tests for different symptom stages. From sample preparation to results readout, we conclude by pointing out the pain points and future directions of COVID-19 detection.

Novel reverse transcription-multiple inner primer loop-mediated isothermal amplification (RT-MIPLAMP) for visual and sensitive detection of SARS-CoV-2

Since the end of 2019, outbreaks of COVID-19 pandemics have continued in different areas worldwide, which exacerbates the need for rapid, sensitive and simple methods for diagnosis. Currently, COVID-19 diagnosis mainly relies on reverse transcription-polymerase chain reaction (RT-PCR), which requires sophisticated instruments. Reverse transcription-loop mediated isothermal amplification (RT-LAMP), due to its isothermal nature and high specificity, can be used as an alternative. In this paper, a novel visual reverse transcription-multiple inner primer loop-mediated isothermal amplification (RT-MIPLAMP) method is established based on RT-LAMP by adding a pair of inner primers. The RT-MIPLAMP method has a higher sensitivity and shorter reaction time compared with conventional RT-LAMP. By using RT-MIPLAMP, as low as 6 × 10³ copies per mL in vitro transcribed (IVT) N gene can be detected within 55 min. Meanwhile, as low as 6 × 10⁴ copies per mL IVT N gene is detectable with conventional RT-LAMP within 80 min. The feasibility of visual RT-MIPLAMP is also validated by detecting the N gene spiked into one healthy volunteer's saliva and the full-length RNA in pseudoviruses, indicating the great potential of visual RT-MIPLAMP for SARS-CoV-2 identification.

Novel bridge multi-species ELISA for detection of SARS-CoV-2 antibodies

Considering the course of the current SARS-CoV-2 pandemic, it is important to have serological tests for monitoring humoral immune response against SARS-CoV-2 infection and vaccination. Herein we describe a novel bridge enzyme-linked immunosorbent assay (b-ELISA) for SARS-CoV-2 antibodies detection in human and other species, employing recombinant Spike protein as a unique antigen, which is produced at high scale in insect larvae.

METHODS

Eighty two human control sera/plasmas and 169 COVID-19 patients' sera/plasmas, confirmed by rRT-PCR, were analyzed by the b-ELISA assay. In addition, a total of 27 animal sera (5 horses, 13 rats, 2 cats and 7 dogs) were employed in order to evaluate the b-ELISA in other animal species.

RESULTS

Out of the 169 patient samples, 129 were positive for IgG anti-SARS-CoV-2 and 40 were negative when they were tested by ELISA COVIDAR® IgG. When a cut-off value of 5.0 SDs was established, 124 out of the 129 COVID-19 positive samples were also positive by our developed b-ELISA (sensitivity: 96.12%). Moreover, the test was able to evaluate the humoral immune response in animal models and also detected as positive a naturally infected cat and two dogs with symptoms, whose owners had suffered the COVID-19 disease.

CONCLUSION

The obtained results demonstrate that the method developed herein is versatile, as it is able to detect antibodies against SARS-CoV-2 in different animal species without the need to perform and optimize a new assay for each species.

Advancements in Detection Approaches of Severe Acute Respiratory Syndrome Coronavirus 2

Diagnostic testing to identify individuals infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays a key role in selecting appropriate treatments, saving people's lives and preventing the global pandemic of COVID-19. By testing on a massive scale, some countries could successfully contain the disease spread. Since early viral detection may provide the best approach to curb the disease outbreak, the rapid and reliable detection of coronavirus (CoV) is therefore becoming increasingly important. Nucleic acid detection methods, especially real-time reverse transcription polymerase chain reaction (RT-PCR)-based assays are considered the gold standard for COVID-19 diagnostics. Some non-PCR-based molecular methods without thermocycler operation, such as isothermal nucleic acid amplification have been proved promising. Serologic immunoassays are also available. A variety of novel and improved methods based on biosensors, Clustered-Regularly Interspaced Short Palindromic Repeats (CRISPR) technology, lateral flow assay (LFA), microarray, aptamer etc. have also been developed. Several integrated, random-access, point-of-care (POC) molecular devices are rapidly emerging for quick and accurate detection of SARS-CoV-2 that can be used in the local hospitals and clinics. This review intends to summarize the currently available detection approaches of SARS-CoV-2, highlight gaps in existing diagnostic capacity, and propose potential solutions and thus may assist clinicians and researchers develop better technologies for rapid and authentic diagnosis of CoV infection.

Tellurium-Modified Nucleosides, Nucleotides, and Nucleic Acids with Potential Applications

Tellurium was successfully incorporated into proteins and applied to protein structure determination through X-ray crystallography. However, studies on tellurium modification of DNA and RNA are limited. This review highlights the recent development of Te-modified nucleosides, nucleotides, and nucleic acids, and summarizes the main synthetic approaches for the preparation of 5-PhTe, 2'-MeTe, and 2'-PhTe modifications. Those modifications are compatible with solid-phase synthesis and stable during Te-oligonucleotide purification. Moreover, the ideal electronic and atomic properties of tellurium for generating clear isomorphous signals give Te-modified DNA and RNA great potential applications in 3D crystal structure determination through X-ray diffraction. STM study also shows that Te-modified DNA has strong topographic and current peaks, which immediately suggests potential applications in nucleic acid direct imaging, nanomaterials, molecular electronics, and diagnostics. Theoretical studies indicate the potential application of Te-modified nucleosides in cancer therapy.

Knowledge about, acceptance of and willingness to use over-the-counter COVID-19 self-testing kits

Objectives

Early investments in new diagnostic technologies that allow for rapid and decentralized testing were critical in reducing SARS-CoV-2’s detrimental health and economic effects. This study evaluates public knowledge about, acceptance of and willingness to use COVID-19 self-testing kits.

Methods

An online descriptive cross-sectional questionnaire was used in this study. The final study population included all contacted national and resident adults, age 18 and over, who were willing to engage in the study. The survey was divided according to participants’ demographic information and 11 questions assessed the respondents’ understanding of and willingness to use COVID-19 self-testing kits. The statistical analysis was carried out using SPSS version 24. Multivariate linear regression models were used to identify the factors influencing respondents’ knowledge of and attitudes toward the acceptability of self-testing kits for COVID-19 and their willingness to use these kits.

Key findings

A total of 876 respondents participated in the study and completed the whole questionnaire. The average knowledge score on the acceptability of and willingness to use self-testing kits for COVID-19 was 70.2%, with a 95% confidence interval (CI) [69.1%, 71.4%]. Participants who were postgraduate, female and vaccinated against COVID-19, as well as employees and older participants, were jointly highly associated with higher levels of knowledge about, acceptance of and willingness to use self-testing kits for COVID-19. Moreover, participants who had been infected with COVID-19, were vaccinated against COVID-19 or were female, employees, older, Western or Arabic were jointly highly associated with positive attitudes about the acceptability of and willingness to use self-testing kits for COVID-19.

Conclusions

The majority of the respondents have acceptable levels of knowledge about, acceptance of and willingness to use self-testing kits for COVID-19. Nonetheless, future studies should consider the issues of pre- and post-test counselling, false negative results and the sale of unregulated testing kits. Additional information should be communicated so that people can make informed decisions and be protected from possible abuse of COVID-19 self-testing kits when they become available in pharmacies.

Cas12a-assisted RTF-EXPAR for accurate, rapid and simple detection of SARS-CoV-2 RNA

Developing highly accurate and simple approaches to rapidly identify and isolate SARS-CoV-2 infected patients is important for the control of the COVID-19 pandemic. We, herein, reported the performance of a Cas12a-assisted RTF-EXPAR strategy for the identification of SARS-CoV-2 RNA. This assay combined the advantages of RTF-EXPAR with CRISPR-Cas12a can detect SARS-CoV-2 within 40 min, requiring only isothermal control. Particularly, the simultaneous use of EXPAR amplification and CRISPR improved the detection sensitivity, thereby realizing ultrasensitive SARS-CoV-2 RNA detection with a detection limit of 3.77 aM (∼2 copies/μL) in an end-point fluorescence read-out fashion, and at 4.81 aM (∼3 copies/μL) level via a smartphone-assisted analysis system (RGB analysis). Moreover, Cas12a increases the specificity by intrinsic sequence-specific template recognition. Overall, this method is fast, sensitive, and accurate, needing minimal equipment, which holds great promise to meet the requirements of point-of-care molecular detection of SARS-CoV-2.

Application of Nanotechnology in COVID-19 Infection: Findings and Limitations

There is an urgent need to address the global mortality of the COVID-19 pandemic, as it reached 6.3 million as of July 2022. As such, the experts recommended the mass diagnosis of SARS-CoV-2 infection at an early stage using nanotechnology-based sensitive diagnostic approaches. The development of nanobiosensors for Point-of-Care (POC) sampling of COVID-19 could ensure mass detection without the need for sophisticated laboratories or expert personnel. The use of Artificial Intelligence (AI) techniques for POC detection was also proposed. In addition, the utilization of various antiviral nanomaterials such as Silver Nanoparticles (AgNPs) for the development of masks for personal protection mitigates viral transmission. Nowadays, nano-assisted vaccines have been approved for emergency use, but their safety and effectiveness in the mutant strain of the SARS-CoV-2 virus remain challenging. Methodology: Updated literature was sourced from various research indexing databases such as PubMed, SCOPUS, Science Direct, Research Gate and Google Scholars. Result: We presented the concept of novel nanotechnology researched discovery, including nano-devices, electrochemical biosensing, nano-assisted vaccine, and nanomedicines, for use in recent times, which could be a formidable step for future management of COVID-19.

Real-time COVID-19 detection via graphite oxide-based field-effect transistor biosensors decorated with Pt/Pd nanoparticles

Coronavirus 2019 (COVID-19) spreads an extremely infectious disease where there is no specific treatment. COVID-19 virus had a rapid and unexpected spread rate which resulted in critical difficulties for public health and unprecedented daily life disruption. Thus, accurate, rapid, and early diagnosis of COVID-19 virus is critical to maintain public health safety. A graphite oxide-based field-effect transistor (GO-FET) was fabricated and functionalized with COVID-19 antibody for the purpose of real-time detection of COVID-19 spike protein antigen. Thermal evaporation process was used to deposit the gold electrodes on the surface of the sensor substrate. Graphite oxide channel was placed between the gold electrodes. Bimetallic nanoparticles of platinum and palladium were generated via an ultra-high vacuum (UHV) compatible system by sputtering and inert-gas condensation technique. The biosensor graphite oxide channel was immobilized with specific antibodies against the COVID-19 spike protein to achieve selectivity and specificity. This technique uses the attractive semiconductor characteristics of the graphite oxide-based materials resulting in highly specific and sensitive detection of COVID-19 spike protein. The GO-FET biosensor was decorated with bimetallic nanoparticles of platinum and palladium to investigate the improvement in the sensor sensitivity. The in-house developed biosensor limit of detection (LOD) is 1 fg/mL of COVID-19 spike antigen in phosphate-buffered saline (PBS). Moreover, magnetic labelled SARS-CoV-2 spike antibody were studied to investigate any enhancement in the sensor performance. The results indicate the successful fabrication of a promising field effect transistor biosensor for COVID-19 diagnosis.

Ultrafast one-minute electronic detection of SARS-CoV-2 infection by 3CLpro enzymatic activity in untreated saliva samples

Since its onset in December 2019, severe acute respiratory syndrome coronavirus 2, SARS-CoV-2, has caused over 6.5 million deaths worldwide as of October 2022. Attempts to curb viral transmission rely heavily on reliable testing to detect infections since a large number of transmissions are carried through asymptomatic individuals. Many available detection methods fall short in terms of reliability or point-of-care applicability. Here, we report an electrochemical approach targeting a viral proteolytic enzyme, 3CLpro, as a marker of active infection. We detect proteolytic activity directly from untreated saliva within one minute of sample incubation using a reduction-oxidation pH indicator. Importantly, clinical tests of saliva samples from 50 subjects show accurate detection of SARS-CoV-2, with high sensitivity and specificity, validated by PCR testing. These, coupled with our platform's ultrafast detection, simplicity, low cost and point-of-care compatibility, make it a promising method for the real-world SARS-CoV-2 mass-screening.

Toward a Home Test for COVID-19 Diagnosis: DNA Machine for Amplification-Free SARS-CoV-2 Detection in Clinical Samples

Nucleic acid-based detection of RNA viruses requires an annealing procedure to obtain RNA/probe or RNA/primer complexes for unwinding stable structures of folded viral RNA. In this study, we designed a protein-enzyme-free nano-construction, named four-armed DNA machine (4DNM), that requires neither an amplification stage nor a high-temperature annealing step for SARS-CoV-2 detection. It uses a binary deoxyribozyme (BiDz) sensor incorporated in a DNA nanostructure equipped with a total of four RNA-binding arms. Additional arms were found to improve the limit of detection at least 10-fold. The sensor distinguished SARS-CoV-2 from other respiratory viruses and correctly identified five positive and six negative clinical samples verified by quantitative polymerase chain reaction (RT-qPCR). The strategy reported here can be used for the detection of long natural RNA and can become a basis for a point-of-care or home diagnostic test.