On the Challenges for the Diagnosis of SARS-CoV-2 Based on a Review of Current Methodologies

Advancements in SARS-CoV-2 detection: Navigating the molecular landscape and diagnostic technologies

According to information from the World Health Organization, the world has experienced about 430 million cases of COVID-19, a world-wide health crisis caused by the SARS-CoV-2 virus. This outbreak, originating from China in 2019, has led to nearly 6 million deaths worldwide. As the number of confirmed infections continues to rise, the need for cutting-edge techniques that can detect SARS-CoV-2 infections early and accurately has become more critical. To address this, the Federal Drug Administration (FDA) has issued emergency use authorizations (EUAs) for a wide range of diagnostic tools. These include tests based on detecting nucleic acids and antigen-antibody reactions. The quantitative real-time reverse transcription PCR (qRT-PCR) assay stands out as the gold standard for early virus detection. However, despite its accuracy, qRT-PCR has limitations, such as complex testing protocols and a risk of false negatives, which drive the continuous improvement in nucleic acid and serological testing approaches. The emergence of highly contagious variants of the coronavirus, such as Alpha (B.1.1.7), Delta (B.1.617.2), and Omicron (B.1.1.529), has increased the need for tests that can specifically identify these mutations. This article explores both nucleic acid-based and antigen-antibody serological assays, assessing the performance of recently approved FDA tests and those documented in scientific research, especially in identifying new coronavirus strains.

Engineered two-dimensional nanomaterials based diagnostics integrated with internet of medical things (IoMT) for COVID-19

More than four years have passed since an inimitable coronavirus disease (COVID-19) pandemic hit the globe in 2019 after an uncontrolled transmission of the severe acute respiratory syndrome (SARS-CoV-2) infection. The occurrence of this highly contagious respiratory infectious disease led to chaos and mortality all over the world. The peak paradigm shift of the researchers was inclined towards the accurate and rapid detection of diseases. Since 2019, there has been a boost in the diagnostics of COVID-19 via numerous conventional diagnostic tools like RT-PCR, ELISA, etc., and advanced biosensing kits like LFIA, etc. For the same reason, the use of nanotechnology and two-dimensional nanomaterials (2DNMs) has aided in the fabrication of efficient diagnostic tools to combat COVID-19. This article discusses the engineering techniques utilized for fabricating chemically active E2DNMs that are exceptionally thin and irregular. The techniques encompass the introduction of heteroatoms, intercalation of ions, and the design of strain and defects. E2DNMs possess unique characteristics, including a substantial surface area and controllable electrical, optical, and bioactive properties. These characteristics enable the development of sophisticated diagnostic platforms for real-time biosensors with exceptional sensitivity in detecting SARS-CoV-2. Integrating the Internet of Medical Things (IoMT) with these E2DNMs-based advanced diagnostics has led to the development of portable, real-time, scalable, more accurate, and cost-effective SARS-CoV-2 diagnostic platforms. These diagnostic platforms have the potential to revolutionize SARS-CoV-2 diagnosis by making it faster, easier, and more accessible to people worldwide, thus making them ideal for resource-limited settings. These advanced IoMT diagnostic platforms may help with combating SARS-CoV-2 as well as tracking and predicting the spread of future pandemics, ultimately saving lives and mitigating their impact on global health systems.

Hierarchical Nanobiosensors at the End of the SARS-CoV-2 Pandemic

Nanostructures have played a key role in the development of different techniques to attack severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Some applications include masks, vaccines, and biosensors. The latter are of great interest for detecting diseases since some of their features allowed us to find specific markers in secretion samples such as saliva, blood, and even tears. Herein, we highlight how hierarchical nanoparticles integrated into two or more low-dimensional materials present outstanding advantages that are attractive for photonic biosensing using their nanoscale functions. The potential of nanohybrids with their superlative mechanical characteristics together with their optical and optoelectronic properties is discussed. The progress in the scientific research focused on using nanoparticles for biosensing a variety of viruses has become a medical milestone in recent years, and has laid the groundwork for future disease treatments. This perspective analyzes the crucial information about the use of hierarchical nanostructures in biosensing for the prevention, treatment, and mitigation of SARS-CoV-2 effects.

The development of an electrochemical immunosensor utilizing chicken IgY anti-spike antibody for the detection of SARS-CoV-2

This paper introduces a novel approach for detecting the SARS-CoV-2 recombinant spike protein combining a label free electrochemical impedimetric immunosensor with the use of purified chicken IgY antibodies. The sensor employs three electrodes and is functionalized with an anti-S IgY antibody, ELISA and immunoblot assays confirmed the positive response of chicken immunized with SARS-CoV2 S antigen. The developed immunosensor is effective in detecting SARS-CoV-2 in nasopharyngeal clinical samples from suspected cases. The key advantage of this biosensor is its remarkable sensitivity, and its capability of detecting very low concentrations of the target analyte, with a detection limit of 5.65 pg/mL. This attribute makes it highly suitable for practical point-of-care (POC) applications, particularly in low analyte count clinical scenarios, without requiring amplification. Furthermore, the biosensor has a wide dynamic range of detection, spanning from 11.56 to 740 ng/mL, which makes it applicable for sample analysis in a typical clinical setting.

Performance of Grating Couplers Used in the Optical Switch Configuration

Surface plasmon resonance is an effect widely used for biosensing. Biosensors based on this effect operate in different configurations, including the use of diffraction gratings as couplers. Gratings are highly tunable and are easy to integrate into a fluidic system due to their planar configuration. We discuss the optimization of plasmonic grating couplers for use in a specific sensor configuration based on the optical switch. These gratings present a sinusoidal profile with a high depth/period ratio. Their interaction with a p-polarized light beam results in two significant diffracted orders (the 0th and the -1st), which enable differential measurements cancelling noise due to common fluctuations. The gratings are fabricated by combining laser interference lithography with nanoimprinting in a process that is aligned with the challenges of low-cost mass production. The effects of different grating parameters such as the period, depth and profile are theoretically and experimentally investigated.

Expanding the application of graphene vertical devices to dual femtomolar detection of SARS-CoV-2 receptor binding domain in serum and saliva

The emergence of the graphene-based hybrid electrical-electrochemical vertical device (EEVD) has introduced a promising nanostructured biosensor tailored for point-of-care applications. In this study, we present an innovative EEVD capable of simultaneously detecting the receptor binding domain (RBD) of the SARS-CoV-2 spike protein in both serum and saliva. The foundation of the EEVD lies in a poly-neutral red-graphene heterojunction, which has been enhanced with a bioconjugate of gold nanoparticles and antibodies. The biodevice demonstrates a remarkable limit of detection, registering at the femtomolar scale (2.86 fmol L-1 or 0.1 pg mL-1). Its sensitivity is characterized by a 6.1 mV/decade response, and its operational range spans 10-12 to 10-7 g mL-1 in both serum and saliva samples. With a 20.0 μL of biological samples and a rapid processing time of under 10 min, the EEVD achieves the feat of dual antigen detection. The tests achieved 100.0% specificity, accuracy, and sensitivity in saliva, and 100.0% specificity, 88.9% accuracy, and 80.0% sensitivity in serum. This study highlights the EEVD as a low-cost solution of rapid viral detection during the crucial initial phases of COVID-19 infections.

Development of extension-mediated self-folding isothermal amplification technology for SARS-CoV-2 diagnosis

The coronavirus disease (COVID-19) pandemic has highlighted the importance of rapid and accurate diagnosis, and loop-mediated isothermal amplification (LAMP) has become a popular method because of its powerful amplification ability using a simple instrument such as a heater or water bath. However, LAMP has limitations such as the complexity of primer design and the difficulty of designing sequence-specific probes, leading to non-specific amplicons and false-positive results. To overcome these limitations, we developed a novel isothermal amplification system called the Extension-mediated self-folding Isothermal amplification Technology (ExIT). ExIT uses a newly designed, self-folding primer (SP) with two key functions. Hairpin structures are formed when the extended strand of the SP hybridizes, exposing the priming site for continuous binding of the new SP. This results in exponential amplification with only two primers, unlike conventional LAMP primer systems. Additionally, an unnatural base was introduced into the SP, which terminated the extension of polymerase and generated a ssDNA amplicon. This makes it easier to design and apply probes, reducing the possibility of false-positive results even if non-specific amplicons are produced. Through this strategy, we confirmed a sensitivity of 90 copies (3.6 copies/μL) and verified the specificity by testing for the presence or absence of non-complementary targets. Therefore, the validation of the ExIT was completed. In conclusion, ExIT will be key to solving the complexity of conventional LAMP design and offers great potential for successfully introducing sequence-specific probes to improve false positives.

Simultaneous Detection of SARS-CoV-2 Nucleoprotein and Receptor Binding Domain by a Multi-Area Reflectance Spectroscopy Sensor

The COVID-19 pandemic has emphasized the urgent need for point-of-care methods suitable for the rapid and reliable diagnosis of viral infections. To address this demand, we report the rapid, label-free simultaneous determination of two SARS-CoV-2 proteins, namely, the nucleoprotein and the receptor binding domain peptide of S1 protein, by implementing a bioanalytical device based on Multi Area Reflectance Spectroscopy. Simultaneous detection of these two proteins is achieved by using silicon chips with adjacent areas of different silicon dioxide thickness on top, each of which is modified with an antibody specific to either the nucleoprotein or the receptor binding domain of SARS-CoV-2. Both areas were illuminated by a single probe that also collected the reflected light, directing it to a spectrometer. The online conversion of the combined reflection spectra from the two silicon dioxide areas into the respective adlayer thickness enabled real-time monitoring of immunoreactions taking place on the two areas. Several antibodies have been tested to define the pair, providing the higher specific signal following a non-competitive immunoassay format. Biotinylated secondary antibodies and streptavidin were used to enhance the specific signal. Both proteins were detected in less than 12 min, with detection limits of 1.0 ng/mL. The assays demonstrated high repeatability with intra- and inter-assay coefficients of variation lower than 10%. Moreover, the recovery of both proteins from spiked samples prepared in extraction buffer from a commercial self-test kit for SARS-CoV-2 collection from nasopharyngeal swabs ranged from 90.0 to 110%. The short assay duration in combination with the excellent analytical performance and the compact instrument size render the proposed device and assay suitable for point-of-care applications.

Reviewing methods of deep learning for diagnosing COVID-19, its variants and synergistic medicine combinations

The COVID-19 pandemic has necessitated the development of reliable diagnostic methods for accurately detecting the novel coronavirus and its variants. Deep learning (DL) techniques have shown promising potential as screening tools for COVID-19 detection. In this study, we explore the realistic development of DL-driven COVID-19 detection methods and focus on the fully automatic framework using available resources, which can effectively investigate various coronavirus variants through modalities. We conducted an exploration and comparison of several diagnostic techniques that are widely used and globally validated for the detection of COVID-19. Furthermore, we explore review-based studies that provide detailed information on synergistic medicine combinations for the treatment of COVID-19. We recommend DL methods that effectively reduce time, cost, and complexity, providing valuable guidance for utilizing available synergistic combinations in clinical and research settings. This study also highlights the implication of innovative diagnostic technical and instrumental strategies, exploring public datasets, and investigating synergistic medicines using optimised DL rules. By summarizing these findings, we aim to assist future researchers in their endeavours by providing a comprehensive overview of the implication of DL techniques in COVID-19 detection and treatment. Integrating DL methods with various diagnostic approaches holds great promise in improving the accuracy and efficiency of COVID-19 diagnostics, thus contributing to effective control and management of the ongoing pandemic.

A DNA framework-based dual signal amplification biosensor for portable detection of SARS-CoV-2 and its mutations

We developed a rapid and accurate biosensor to detect SARS-CoV-2 and distinguish its mutations. Benefitting from a DNA framework-modified ordered interface and a dual signal amplification strategy, our biosensor could detect SARS-CoV-2 with a detection limit down to 10 fM. It performed well on pseudo virus and SARS-CoV-2 RNA standard materials, revealing the potential application in disease diagnosis and spread, in combination with a home-made smartphone.

Development of nucleocapsid-specific monoclonal antibodies for SARS-CoV-2 and their ELISA diagnostics on an automatic microfluidic device

Coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has threatened public health globally, and the emergence of viral variants has exacerbated an already precarious situation. To prevent further spread of the virus and determine government action required for virus control, accurate and rapid immunoassays for SARS-CoV-2 diagnosis are urgently needed. In this study, we generated monoclonal antibodies (mAbs) against the SARS-CoV-2 nucleocapsid protein (NP), compared their reactivity using an enzyme-linked immunosorbent assay (ELISA), and selected four mAbs designated 1G6, 3E10, 3F10, and 5B6 which have higher reactivity to NP and viral lysates of SARS-CoV-2 than other mAbs. Using an epitope mapping assay, we identified that 1G6 detected the C-terminal domain of SARS-CoV-2 NP (residues 248-364), while 3E10 and 3F10 bound to the N-terminal domain (residues 47-174) and 3F10 detected the N-arm region (residues 1-46) of SARS-CoV-2 NP. Based on the epitope study and sandwich ELISA, we selected the 1G6 and 3E10 Abs as an optimal Ab pair and applied them for a microfluidics-based point-of-care (POC) ELISA assay to detect the NPs of SARS-CoV-2 and its variants. The integrated and automatic microfluidic system could operate the serial injection of the sample, the washing solution, the HRP-conjugate antibody, and the TMB substrate solution simply by controlling air purge via a single syringe. The proposed Ab pair-equipped microsystem effectively detected the NPs of SARS-CoV-2 variants as well as in clinical samples. Collectively, our proposed platform provides an advanced protein-based diagnostic tool for detecting SARS-CoV-2.

A fast RT-qPCR system significantly shortens the time for SARS-CoV-2 nucleic acid test

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a serious threat to global development. Rapid and accurate diagnosis is critical for containing the pandemic and treating patients in time. As the gold standard for SARS-CoV-2 diagnosis, the qualitative reverse transcription-PCR (RT-qPCR) test has long been criticized for its long detection time. In this study, we optimized the primers and probes targeting SARS-CoV-2 ORF1ab and N gene designed by the Chinese Center for Disease Control and Preventions (CDC) to increase their Tm values to meet the optimal elongation temperature of Taq DNA polymerase, thus greatly shortened the elongation time. The higher elongation temperature in turn narrowed the temperature range of the reaction and saved more time. In addition, by shortening the distance between the fluorophore at the 5' end and the quencher in the middle we got a probe with higher signal-to-noise ratio. Finally, by using all these measures and optimized RT-qPCR program we successfully reduced the time (nucleic acid extraction step is not included) for nucleic acid test from 74 min to 26 min.

Low-dimensionality carbon-based biosensors: the new era of emerging technologies in bioanalytical chemistry

Since the last decade, carbon nanomaterials have had a notable impact on different fields such as bioimaging, drug delivery, artificial tissue engineering, and biosensors. This is due to their good compatibility toward a wide range of chemical to biological molecules, low toxicity, and tunable properties. Especially for biosensor technology, the characteristic features of each dimensionality of carbon-based materials may influence the performance and viability of their use. Surface area, porous network, hybridization, functionalization, synthesis route, the combination of dimensionalities, purity levels, and the mechanisms underlying carbon nanomaterial interactions influence their applications in bioanalytical chemistry. Efforts are being made to fully understand how nanomaterials can influence biological interactions, to develop commercially viable biosensors, and to gain knowledge on the biomolecular processes associated with carbon. Here, we present a comprehensive review highlighting the characteristic features of the dimensionality of carbon-based materials in biosensing.

The ORF7a protein of SARS-CoV-2 initiates autophagy and limits autophagosome-lysosome fusion via degradation of SNAP29 to promote virus replication

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is closely related to various cellular aspects associated with autophagy. However, how SARS-CoV-2 mediates the subversion of the macroautophagy/autophagy pathway remains largely unclear. In this study, we demonstrate that overexpression of the SARS-CoV-2 ORF7a protein activates LC3-II and leads to the accumulation of autophagosomes in multiple cell lines, while knockdown of the viral ORF7a gene via shRNAs targeting ORF7a sgRNA during SARS-CoV-2 infection decreased autophagy levels. Mechanistically, the ORF7a protein initiates autophagy via the AKT-MTOR-ULK1-mediated pathway, but ORF7a limits the progression of autophagic flux by activating CASP3 (caspase 3) to cleave the SNAP29 protein at aspartic acid residue 30 (D30), ultimately impairing complete autophagy. Importantly, SARS-CoV-2 infection-induced accumulated autophagosomes promote progeny virus production, whereby ORF7a downregulates SNAP29, ultimately resulting in failure of autophagosome fusion with lysosomes to promote viral replication. Taken together, our study reveals a mechanism by which SARS-CoV-2 utilizes the autophagic machinery to facilitate its own propagation via ORF7a.Abbreviations: 3-MA: 3-methyladenine; ACE2: angiotensin converting enzyme 2; ACTB/β-actin: actin beta; ATG7: autophagy related 7; Baf A1: bafilomycin A₁; BECN1: beclin 1; CASP3: caspase 3; COVID-19: coronavirus disease 2019; GFP: green fluorescent protein; hpi: hour post-infection; hpt: hour post-transfection; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MERS: Middle East respiratory syndrome; MTOR: mechanistic target of rapamycin kinase; ORF: open reading frame; PARP: poly(ADP-ribose) polymerase; SARS-CoV-2: severe acute respiratory syndrome coronavirus 2; shRNAs: short hairpin RNAs; siRNA: small interfering RNA; SNAP29: synaptosome associated protein 29; SQSTM1/p62: sequestosome 1; STX17: syntaxin 17; TCID₅₀: tissue culture infectious dose; TEM: transmission electron microscopy; TUBB, tubulin, beta; ULK1: unc-51 like autophagy activating kinase 1.

Differential Sensing with Replicated Plasmonic Gratings Interrogated in the Optical Switch Configuration

A new plasmonic configuration is proposed for application in a sensor and demonstrated for the detection of variations in the bulk refractive index of solutions. The configuration consists of monitoring two diffracted orders resulting from the interaction of a TM-polarized optical beam incident on a grating coupler, operating based on an effect termed the "optical switch". The two monitored diffracted orders enable differential measurements which cancel the drift and perturbations common to both, leading to an improved detection limit, as demonstrated experimentally. The measured switch pattern associated with the grating coupler is in good agreement with theory. Bulk sensing is demonstrated under intensity interrogation via the sequential injection of solutions comprised of glycerol in water into a fluidic cell. A limit of detection of about 10-6 RIU was achieved. The optical switch configuration is easy to implement and is cost-effective, yielding a highly promising approach for the sensing and the real-time detection of biological species.

Portable high-throughput multimodal immunoassay platform for rapid on-site COVID-19 diagnostics

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as a causal agent of Coronavirus Disease 2019 (COVID-19) has led to the global pandemic. Though the real-time reverse transcription polymerase chain reaction (RT-PCR) acting as a gold-standard method has been widely used for COVID-19 diagnostics, it can hardly support rapid on-site applications or monitor the stage of disease development as well as to identify the infection and immune status of rehabilitation patients. To suit rapid on-site COVID-19 diagnostics under various application scenarios with an all-in-one device and simple detection reagents, we propose a high-throughput multimodal immunoassay platform with fluorescent, colorimetric, and chemiluminescent immunoassays on the same portable device and a multimodal reporter probe using quantum dot (QD) microspheres modified with horseradish peroxidase (HRP) coupled with goat anti-human IgG. The recombinant nucleocapsid protein fixed on a 96-well plate works as the capture probe. In the condition with the target under detection, both reporter and capture probes can be bound by such target. When illuminated by excitation light, fluorescence signals from QD microspheres can be collected for target quantification often at a fast speed. Additionally, when pursuing simple detection without using any sensing devices, HRP-catalyzed TMB colorimetric immunoassay is employed; and when pursuing highly sensitive detection, HRP-catalyzed luminol chemiluminescent immunoassay is established. Verified by the anti-SARS-CoV-2 N humanized antibody, the sensitivities of colorimetric, fluorescent, and chemiluminescent immunoassays are respectively 20, 80, and 640 times more sensitive than that of the lateral flow colloidal gold immunoassay strip. Additionally, such a platform can simultaneously detect multiple samples at the same time thus supporting high-throughput sensing; and all these detecting operations can be implemented on-site within 50 min relying on field-operable processing and field-portable devices. Such a high-throughput multimodal immunoassay platform can provide a new all-in-one solution for rapid on-site diagnostics of COVID-19 for different detecting purposes.

Achieving broad availability of SARS-CoV-2 detections via smartphone-based analysis

With the development of COVID-19, widely available tests are in great demand. Naked-eye SARS-CoV-2 test kits have recently been developed as home tests, but their sensitivity and accuracy are sometimes limited. Smartphones can convert various signals into digital information, potentially improving the sensitivity and accuracy of these home tests. Herein, we summarize smartphone-based detections for SARS-CoV-2. Optical detections of non-nucleic acids using various sensors and portable imaging systems, as well as nucleic acid analyses based on LAMP, CRISP, CATCH, and biosensors are discussed. Furthermore, different electrochemical detections were compared. We show results obtained using relatively complex equipment, complicated programming procedures, or custom smartphone apps, and describe methods for obtaining information with only simple setups and free software on smartphones. Then, the combined costs of typical smartphone-based detections are evaluated. Finally, the prospect of improving smartphone-based strategies to achieve broad availability of SARS-CoV-2 detection is proposed.

Systematically investigating the fluorescent signal readout of CRISPR-Cas12a for highly sensitive SARS-CoV-2 detection

The CRISPR/Cas system is widely used for molecular diagnostics after the discovery of trans-cleavage activity, especially now with the COVID-19 outbreak. However, the majority of contemporary trans-cleavage activity-based CRISPR/Cas biosensors exploited standard single-strand DNA (ssDNA) reporters, which were based on the FRET principle from pioneering research. An in-depth comparison and understanding of various fluorescent readout types are essential to facilitate the outstanding analytical performance of CRISPR probes. We investigated various types of fluorescent reporters of Cas12a comprehensively. Results show that trans-cleavage of Cas12a is not limited to ssDNA and dsDNA reporters, but can be extended to molecular beacons (MB). And MB reporters can achieve superior analytical performance compared with ssDNA and ds DNA reporters at the same conditions. Accordingly, we developed a highly-sensitive SARS-CoV-2 detection with the sensitivity as low as 100 fM were successfully achieved without amplification strategy. The model target of ORF1a could robustly identify the current widespread emerging SARS-CoV-2 variants. A real coronavirus GX/P2V instead of SARS-CoV-2 were chosen for practical application validation. And a minimum of 27 copies/mL was achieved successfully. This inspiration can also be applied to other Cas proteins with trans-cleavage activity, which provides new perspectives for simple, highly-sensitive and universal molecular diagnosis in various applications.

From research to market: correlation between publications, patent filings, and investments in development and production of technological innovations in biosensors

As the global population grows and science and technology development evolve, fulfilling basic human needs has been even more linked to technological solutions. In this review, we present an overview of the biosensor market and discuss the factors that make certain countries more competitive than others in terms of technology and innovation and how this is reflected in the trends in publication and patent filling. Additionally, we expose briefly how the COVID-19 pandemic acts as a catalyst for the integration of research and development, business, and innovation sectors to bring solutions and ideas that have been predicted as tendencies for the future.

Current trends in COVID-19 diagnosis and its new variants in physiological fluids: Surface antigens, antibodies, nucleic acids, and RNA sequencing

Rapid, highly sensitive, and accurate virus circulation monitoring techniques are critical to limit the spread of the virus and reduce the social and economic burden. Therefore, point-of-use diagnostic devices have played a critical role in addressing the outbreak of COVID-19 (SARS-CoV-2) viruses. This review provides a comprehensive overview of the current techniques developed for the detection of SARS-CoV-2 in various body fluids (e.g., blood, urine, feces, saliva, tears, and semen) and considers the mutations (i.e., Alpha, Beta, Gamma, Delta, Omicron). We classify and comprehensively discuss the detection methods depending on the biomarker measured (i.e., surface antigen, antibody, and nucleic acid) and the measurement techniques such as lateral flow immunoassay (LFIA), enzyme-linked immunosorbent assay (ELISA), reverse transcriptase-polymerase chain reaction (RT-PCR), reverse transcription loop-mediated isothermal amplification (RT-LAMP), microarray analysis, clustered regularly interspaced short palindromic repeats (CRISPR) and biosensors. Finally, we addressed the challenges of rapidly identifying emerging variants, detecting the virus in the early stages of infection, the detection sensitivity, selectivity, and specificity, and commented on how these challenges can be overcome in the future.

The Future of Point-of-Care Nucleic Acid Amplification Diagnostics after COVID-19: Time to Walk the Walk

Since the onset of the COVID-19 pandemic, over 610 million cases have been diagnosed and it has caused over 6.5 million deaths worldwide. The crisis has forced the scientific community to develop tools for disease control and management at a pace never seen before. The control of the pandemic heavily relies in the use of fast and accurate diagnostics, that allow testing at a large scale. The gold standard diagnosis of viral infections is the RT-qPCR. Although it provides consistent and reliable results, it is hampered by its limited throughput and technical requirements. Here, we discuss the main approaches to rapid and point-of-care diagnostics based on RT-qPCR and isothermal amplification diagnostics. We describe the main COVID-19 molecular diagnostic tests approved for self-testing at home or for point-of-care testing and compare the available options. We define the influence of specimen selection and processing, the clinical validation, result readout improvement strategies, the combination with CRISPR-based detection and the diagnostic challenge posed by SARS-CoV-2 variants for different isothermal amplification techniques, with a particular focus on LAMP and recombinase polymerase amplification (RPA). Finally, we try to shed light on the effect the improvement in molecular diagnostics during the COVID-19 pandemic could have in the future of other infectious diseases.

Directly immersible silicon photonic probes: Application to rapid SARS-CoV-2 serological testing

Silicon photonic probes based on broad-band Mach-Zehnder interferometry are explored for the first time as directly immersible immunosensors alleviating the need for microfluidics and pumps. Each probe includes two U-shaped waveguides allowing light in- and out-coupling from the same chip side through a bifurcated fiber and a mechanical coupler. At the opposite chip side, two Mach-Zehnder interferometers (MZI) are located enabling real-time monitoring of binding reactions by immersion of this chip side into a sample. The sensing arm windows of the two MZIs have different length resulting in two distinct peaks in the Fourier domain, the phase shift of which can be monitored independently through Fast Fourier Transform of the output spectrum. The photonic probes analytical potential was demonstrated through detection of antibodies against SARS-CoV-2 in human serum samples. For this, one MZI was functionalized with the Receptor Binding Domain (RBD) of SARS-CoV-2 Spike 1 protein, and the other with bovine serum albumin to serve as reference. The biofunctionalized probes were immersed for 10 min in human serum sample and then for 5 min in goat anti-human IgG Fc specific antibody solution. Using a humanized rat antibody against SARS-CoV-2 RBD, a detection limit of 20 ng/mL was determined. Analysis of human serum samples indicated that the proposed sensor discriminated completely non-infected/non-vaccinated from vaccinated individuals, and the antibodies levels determined correlated well with those determined in the same samples by ELISA. These results demonstrated the potential of the proposed sensor to serve as an efficient tool for expeditious point-of-care testing.

Advances in Biosensing Technologies for Diagnosis of COVID-19

The COVID-19 pandemic has severely impacted normal human life worldwide. Due to its rapid community spread and high mortality statistics, the development of prompt diagnostic tests for a massive number of samples is essential. Currently used traditional methods are often expensive, time-consuming, laboratory-based, and unable to handle a large number of specimens in resource-limited settings. Because of its high contagiousness, efficient identification of SARS-CoV-2 carriers is crucial. As the advantages of adopting biosensors for efficient diagnosis of COVID-19 increase, this narrative review summarizes the recent advances and the respective reasons to consider applying biosensors. Biosensors are the most sensitive, specific, rapid, user-friendly tools having the potential to deliver point-of-care diagnostics beyond traditional standards. This review provides a brief introduction to conventional methods used for COVID-19 diagnosis and summarizes their advantages and disadvantages. It also discusses the pathogenesis of COVID-19, potential diagnostic biomarkers, and rapid diagnosis using biosensor technology. The current advancements in biosensing technologies, from academic research to commercial achievements, have been emphasized in recent publications. We covered a wide range of topics, including biomarker detection, viral genomes, viral proteins, immune responses to infection, and other potential proinflammatory biomolecules. Major challenges and prospects for future application in point-of-care settings are also highlighted.

Two Years into the COVID-19 Pandemic: Lessons Learned

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible and virulent human-infecting coronavirus that emerged in late December 2019 in Wuhan, China, causing a respiratory disease called coronavirus disease 2019 (COVID-19), which has massively impacted global public health and caused widespread disruption to daily life. The crisis caused by COVID-19 has mobilized scientists and public health authorities across the world to rapidly improve our knowledge about this devastating disease, shedding light on its management and control, and spawned the development of new countermeasures. Here we provide an overview of the state of the art of knowledge gained in the last 2 years about the virus and COVID-19, including its origin and natural reservoir hosts, viral etiology, epidemiology, modes of transmission, clinical manifestations, pathophysiology, diagnosis, treatment, prevention, emerging variants, and vaccines, highlighting important differences from previously known highly pathogenic coronaviruses. We also discuss selected key discoveries from each topic and underline the gaps of knowledge for future investigations.

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 annealing procedure to obtain RNA/probe or RNA/primer complexes for unwinding stable structure of folded viral RNA. In this study, we designed a protein enzymes-free nano-construction, names four-armed DNA machine (4DNM), that requires neither amplification stage nor high temperature annealing step for SARS-CoV-2 detection. It uses binary deoxyribozyme (BiDz) sensor incorporated in a DNA nanostructure equipped with total of four RNA-binding arms. Additional arms improved limit of detection at least 10 times. 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 detection of long natural RNA and can become a basis for a point-of-care or home diagnostic test.

State-of-the-Art Smart and Intelligent Nanobiosensors for SARS-CoV-2 Diagnosis

The novel coronavirus appeared to be a milder infection initially, but the unexpected outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), commonly called COVID-19, was transmitted all over the world in late 2019 and caused a pandemic. Human health has been disastrously affected by SARS-CoV-2, which is still evolving and causing more serious concerns, leading to the innumerable loss of lives. Thus, this review provides an outline of SARS-CoV-2, of the traditional tools to diagnose SARS-CoV-2, and of the role of emerging nanomaterials with unique properties for fabricating biosensor devices to diagnose SARS-CoV-2. Smart and intelligent nanomaterial-enabled biosensors (nanobiosensors) have already proven their utility for the diagnosis of several viral infections, as various detection strategies based on nanobiosensor devices are already present, and several other methods are also being investigated by researchers for the determination of SARS-CoV-2 disease; however, considerably more is undetermined and yet to be explored. Hence, this review highlights the utility of various nanobiosensor devices for SARS-CoV-2 determination. Further, it also emphasizes the future outlook of nanobiosensing technologies for SARS-CoV-2 diagnosis.

Comparative Performance Evaluation of FilmArray BioFire RP2.1 and MAScIR 2.0 Assays for SARS-CoV-2 Detection

Background

RT-PCR is the gold standard for COVID-19 diagnosis, but the lack of standardization of assays, whose diagnostic performance may widely vary, complicates the interpretation of the discrepancies that may be encountered. Study design. We conducted a retrospective study over a ten-month period at the Central Laboratory of Virology of Ibn Sina University Hospital of Rabat. We included nasopharyngeal swabs, positive and negative for SARS-CoV-2 on FilmArray BioFire® Respiratory Panel 2.1 Plus, which were subjected to our laboratory's reference test, MAScIR SARS-CoV-2 M kit 2.0, initially or after a freeze-thaw cycle. The results were compared, and each discrepant sample with sufficient volume underwent the third test, using ARGENE® SARS-CoV-2 R-GENE kit.

Results

Of 80 SARS-CoV-2 negative samples on FilmArray, there were no discordant results, whereas of 80 SARS-CoV-2 positive samples on FilmArray, 21 had discordant results on MAScIR, and only 11 could be tested on ARGENE, revealing positive results in 6 cases. 12.7% and 76.5% correspond to the discordance rates for MAScIR (with one or both targets detected on FilmArray), while 14.3% and 100% correspond to those of ARGENE. As the estimated sensitivity and specificity of FilmArray, compared with MAScIR, were 100% and 79.2%, respectively, its lower limit of detection, and ARGENE assay results, made it difficult to distinguish between false positives on FilmArray and false negatives on MAScIR without further investigations.

Conclusion

The implementation of a new assay in our laboratory revealed discrepancies suggesting a lack of sensitivity of our laboratory's reference test, leading us consequently to retain the SARS-CoV-2 positive result of these discordant samples on FilmArray, regardless of the detection of one or both targets. Our study, which is, to our knowledge, the first comparing FilmArray RP2.1 and MAScIR 2.0 assays for SARS-CoV-2 detection, highlights the urgent need to standardize RT-PCR assays for COVID-19 diagnosis.

Virus Detection: From State-of-the-Art Laboratories to Smartphone-Based Point-of-Care Testing

Infectious virus outbreaks pose a significant challenge to public healthcare systems. Early and accurate virus diagnosis is critical to prevent the spread of the virus, especially when no specific vaccine or effective medicine is available. In clinics, the most commonly used viral detection methods are molecular techniques that involve the measurement of nucleic acids or proteins biomarkers. However, most clinic-based methods require complex infrastructure and expensive equipment, which are not suitable for low-resource settings. Over the past years, smartphone-based point-of-care testing (POCT) has rapidly emerged as a potential alternative to laboratory-based clinical diagnosis. This review summarizes the latest development of virus detection. First, laboratory-based and POCT-based viral diagnostic techniques are compared, both of which rely on immunosensing and nucleic acid detection. Then, various smartphone-based POCT diagnostic techniques, including optical biosensors, electrochemical biosensors, and other types of biosensors are discussed. Moreover, this review covers the development of smartphone-based POCT diagnostics for various viruses including COVID-19, Ebola, influenza, Zika, HIV, et al. Finally, the prospects and challenges of smartphone-based POCT diagnostics are discussed. It is believed that this review will aid researchers better understand the current challenges and prospects for achieving the ultimate goal of containing disease-causing viruses worldwide.

Recent Progress on Rapid Lateral Flow Assay-Based Early Diagnosis of COVID-19

The outbreak of the coronavirus disease 2019 (COVID-19) has resulted in enormous losses worldwide. Through effective control measures and vaccination, prevention and curbing have proven significantly effective; however, the disease has still not been eliminated. Therefore, it is necessary to develop a simple, convenient, and rapid detection strategy for controlling disease recurrence and transmission. Taking advantage of their low-cost and simple operation, point-of-care test (POCT) kits for COVID-19 based on the lateral flow assay (LFA) chemistry have become one of the most convenient and widely used screening tools for pathogens in hospitals and at home. In this review, we introduce essential features of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, compare existing detection methods, and focus on the principles, merits and limitations of the LFAs based on viral nucleic acids, antigens, and corresponding antibodies. A systematic comparison was realized through summarization and analyses, providing a comprehensive demonstration of the LFA technology and insights into preventing and curbing the COVID-19 pandemic.

In silico study of substrate chemistry effect on the tethering of engineered antibodies for SARS-CoV-2 detection: Amorphous silica vs gold

The influence of the properties of different solid substrates on the tethering of two antibodies, IgG1-CR3022 and IgG1-S309, which were specifically engineered for the detection of SARS-CoV-2, has been examined at the molecular level using conventional and accelerated Molecular Dynamics (cMD and aMD, respectively). Two surfaces with very different properties and widely used in immunosensors for diagnosis, amorphous silica and the most stable facet of the face-centered cubic gold structure, have been considered. The effects of such surfaces on the structure and orientation of the immobilized antibodies have been determined by quantifying the tilt and hinge angles that describe the orientation and shape of the antibody, respectively, and the dihedrals that measure the relative position of the antibody arms with respect to the surface. Results show that the interactions with amorphous silica, which are mainly electrostatic due to the charged nature of the surface, help to preserve the orientation and structure of the antibodies, especially of the IgG1-CR3022, indicating that the primary sequence of those antibodies also plays some role. Instead, short-range van der Waals interactions with the inert gold surface cause a higher degree tilting and fraying of the antibodies with respect to amorphous silica. The interactions between the antibodies and the surface also affect the correlation among the different angles and dihedrals, which increases with their strength. Overall, results explain why amorphous silica substrates are frequently used to immobilize antibodies in immunosensors.

Impact of COVID-19 Disease in Early Breast Cancer Management: A Summary of the Current Evidence

An expert panel on breast cancer and COVID-19 disease was convened to address the impact of the COVID-19 pandemic for early breast cancer (eBC) management.

Molecularly Imprinted Polymer Nanoparticles Enable Rapid, Reliable, and Robust Point-of-Care Thermal Detection of SARS-CoV-2

Rapid antigen tests are currently used for population screening of COVID-19. However, they lack sensitivity and utilize antibodies as receptors, which can only function in narrow temperature and pH ranges. Consequently, molecularly imprinted polymer nanoparticles (nanoMIPs) are synthetized with a fast (2 h) and scalable process using merely a tiny SARS-CoV-2 fragment (∼10 amino acids). The nanoMIPs rival the affinity of SARS-CoV-2 antibodies under standard testing conditions and surpass them at elevated temperatures or in acidic media. Therefore, nanoMIP sensors possess clear advantages over antibody-based assays as they can function in various challenging media. A thermal assay is developed with nanoMIPs electrografted onto screen-printed electrodes to accurately quantify SARS-CoV-2 antigens. Heat transfer-based measurements demonstrate superior detection limits compared to commercial rapid antigen tests and most antigen tests from the literature for both the alpha (∼9.9 fg mL-1) and delta (∼6.1 fg mL-1) variants of the spike protein. A prototype assay is developed, which can rapidly (∼15 min) validate clinical patient samples with excellent sensitivity and specificity. The straightforward epitope imprinting method and high robustness of nanoMIPs produce a SARS-CoV-2 sensor with significant commercial potential for population screening, in addition to the possibility of measurements in diagnostically challenging environments.

Considerations for the selection of tests for SARS-CoV-2 molecular diagnostics

During the course of 2020, the outbreak of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS‐CoV‐2) spread rapidly across the world. Clinical diagnostic testing for SARS-Cov-2 infection has relied on the real‐time Reverse Transcriptase Polymerase Chain Reaction and is considered the gold standard assay. Commercial vendors and laboratories quickly mobilised to develop diagnostic tests to detect the novel coronavirus, which was fundamentally important in the pandemic response. These SARS-Cov-2 assays were developed in line with the Food Drug Administration-Emergency Use Authorization guidance. Although new tests are continuously being developed, information about SARS-CoV-2 diagnostic molecular test accuracy has been limited and at times controversial. Therefore, the analytical and clinical performance of SARS-CoV-2 test kits should be carefully considered by the appropriate regulatory authorities and evaluated by independent laboratory validation. This would provide improved end-user confidence in selecting the most reliable and accurate diagnostic test. Moreover, it is unclear whether some of these rapidly developed tests have been subjected to rigorous quality control and assurance required under good manufacturing practice. Variable target gene regions selected for currently available tests, potential mutation in target gene regions, non-standardized pre-analytic phase, a lack of manufacturer independent validation data all create difficulties in selecting tests appropriate for different countries and laboratories. Here we provide information on test criteria which are important in the assessment and selection of SARS-CoV-2 molecular diagnostic tests and outline the potential issues associated with a proportion of the tests on the market.

Current perspective in metal oxide based photocatalysts for virus disinfection: A review

Nanotechnology holds huge potential for the prevention of various viral outbreaks that have increased at a disquieting rate over the past decades. Metal oxide nanomaterials with oxidative capability are the effective materials that provide platforms as well as tools for the well understanding of the mechanism, its detection, and treatment of various viral diseases like measles, influenza, herpes, ebola, current COVID-19 etc. In this inclusive review, we survey various previous research articles on different notable photoactive transition metal oxides that possess enough potential to act as antiviral agents for the deactivation of harmful viruses. We investigated and highlighted the plausible photocatalytic oxidative mechanism of photoactive transition metal oxides in degrading viral coatings, genomic RNA using suitable free radical generation. The key finding of the present review article including the discovery of a vision on the suitable photocatalytic transition metal oxides that have been proven to be excellent against harmful viruses and consequently combatting deadly CoV-2 in the environment. This review intends to provide conclusive remarks and a realistic outlook on other advanced photocatalytic metal oxides as a potential solution in battling other similar upcoming pandemics.

A point-of-care SARS-CoV-2 test based on reverse transcription loop-mediated isothermal amplification without RNA extraction with diagnostic performance same as RT-PCR

The global public health crisis and economic losses resulting from the current novel coronavirus disease (COVID-19) pandemic have been dire. The most used real-time reverse transcription polymerase chain reaction (RT-PCR) method needs expensive equipment, technical expertise, and a long turnaround time. Therefore, there is a need for a rapid, accurate, and alternative technique of diagnosis that is deployable at resource-poor settings like point-of-care. This study combines heat deactivation and a novel mechanical lysis method by bead beating for quick and simple sample preparation. Then, using an optimized reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay to target genes encoding the open reading frame 8 (ORF8), spike and nucleocapsid proteins of the novel coronavirus, SARS-CoV-2. The test results can be read simultaneously in fluorometric and colorimetric readouts within 40 min from sample collection. We also calibrated a template transfer tool to simplify sample addition into LAMP reactions when pipetting skills are needed. Most importantly, validation of the direct RT-LAMP system based on multiplexing primers S1:ORF8 in a ratio (1:0.8) using 143 patients’ nasopharyngeal swab samples showed a diagnostic performance of 99.30% accuracy, with 98.81% sensitivity and 100% selectivity, compared to commercial RT-PCR kits. Since our workflow does not rely on RNA extraction and purification, the time-to-result is two times faster than other workflows with FDA emergency use authorization. Considering all its strengths: speed, simplicity, accuracy and extraction-free, the system can be useful for optimal point-of-care testing of COVID-19.

N-gene-complementary antisense-oligonucleotide directed molecular aggregation of dual-colour carbon dots, leading to efficient fluorometric sensing of SARS-COV-2 RNA

The early stages of the COVID-19 pandemic punctuated the need for rapid, mass testing for early detection of viral infection. Carbon dots are easily synthesized, cost-effective fluorescent nanoparticles whose surface functionalities enable facile conjugation with biorecognition elements suitable for  molecular detection of viral RNA. Herein, we report that a pair of complementary antisense oligonucleotide (ASO) sequences can lead to a highly specific molecular aggregation of dual colour carbon dots (CDs) in the presence of SARS-CoV-2 RNA. The nanoprobes used ASOs highly specific to the N-gene of SARS-COV-2. When the ASOs are conjugated to blue and yellow citric acid-derived CDs, the combination of the ASO-CD pairs facilitates aggregation-induced emission enhancement (AIEE) of the measured fluorescence after hybridization with SARS-CoV-2 RNA. We found the sensor capable of differentiating between MERS-CoV and SARS-CoV-2 samples and was found to have a limit of detection of 81 copies per μL. Additionally, we used dialysis to demonstrate that the change in emission upon aggregation is dependent on the compositional heterogeneity of the conjugated-carbon dot mixture.

Purely electrical SARS-CoV-2 sensing based on single-molecule counting

The majority of RNA based COVID-19 diagnostics employ enzymatic amplification to achieve high sensitivity, but this relies on arbitrary thresholding, which complicates the comparison of test results and may lead to false outcomes. Here we introduce solid-state nanopore sensing for label-free quantification of SARS-CoV-2 RNA in clinical nasal swab samples. This PCR-free method involves reverse transcribing a target gene on the viral RNA before enzymatically digesting all but the resulting dsDNA. Ratiometric quantification of RNA abundance is achieved by single-molecule counting and length-based nanopore identification of dsDNA from a SARS-CoV-2 gene and a human reference gene. We graded nasal swab samples from >15 subjects and find that the SARS-CoV-2 ratiometric nanopore index correlates well with the reported RT-qPCR threshold cycle for positive classified samples. Remarkably, nanopore analysis also reports quantitative positive outcomes for clinical samples classified as negative by RT-qPCR, suggesting that the method may be used to diagnose COVID-19 in samples that may evade detection. We show that the sample preparation workflow can be implemented using a compact microfluidic device with integrated thermal control for semi-automated processing of extremely small sample volumes, offering a viable route towards automated, fast and affordable RNA quantification in a small and portable device.

SARS-CoV-2 Diagnostics Based on Nucleic Acids Amplification: From Fundamental Concepts to Applications and Beyond

COVID-19 pandemic ignited the development of countless molecular methods for the diagnosis of SARS-CoV-2 based either on nucleic acid, or protein analysis, with the first establishing as the most used for routine diagnosis. The methods trusted for day to day analysis of nucleic acids rely on amplification, in order to enable specific SARS-CoV-2 RNA detection. This review aims to compile the state-of-the-art in the field of nucleic acid amplification tests (NAATs) used for SARS-CoV-2 detection, either at the clinic level, or at the Point-Of-Care (POC), thus focusing on isothermal and non-isothermal amplification-based diagnostics, while looking carefully at the concerning virology aspects, steps and instruments a test can involve. Following a theme contextualization in introduction, topics about fundamental knowledge on underlying virology aspects, collection and processing of clinical samples pave the way for a detailed assessment of the amplification and detection technologies. In order to address such themes, nucleic acid amplification methods, the different types of molecular reactions used for DNA detection, as well as the instruments requested for executing such routes of analysis are discussed in the subsequent sections. The benchmark of paradigmatic commercial tests further contributes toward discussion, building on technical aspects addressed in the previous sections and other additional information supplied in that part. The last lines are reserved for looking ahead to the future of NAATs and its importance in tackling this pandemic and other identical upcoming challenges.

Immunoassay platform with surface-enhanced resonance Raman scattering for detecting trace levels of SARS-CoV-2 spike protein

The early diagnosis of Coronavirus disease (COVID-19) requires either an accurate detection of genetic material or a sensitive detection of viral proteins. In this work, we designed an immunoassay platform for detecting trace levels of SARS-CoV-2 spike (S) protein. It is based on surface-enhanced resonance Raman scattering (SERRS) of methylene blue (MB) adsorbed onto spherical gold nanoparticles (AuNPs) and coated with a 6 nm silica shell. The latter shell in the SERRS nanoprobe prevented aggregation and permitted functionalization with SARS-CoV-2 antibodies. Specificity of the immunoassay was achieved by combining this functionalization with antibody immobilization on the cover slides that served as the platform support. Different concentrations of SARS-CoV-2 antigen could be distinguished and the lack of influence of interferents was confirmed by treating SERRS data with the multidimensional projection technique Sammon's mapping. With SERRS using a laser line at 633 nm, the lowest concentration of spike protein detected was 10 pg/mL, achieving a limit of detection (LOD) of 0.046 ng/mL (0.60 pM). This value is comparable to the lowest concentrations in the plasma of COVID-19 patients at the onset of symptoms, thus indicating that the SERRS immunoassay platform may be employed for early diagnosis.

Spectroscopy: a versatile sensing tool for cost-effective and rapid detection of novel coronavirus (COVID-19)

The deadly novel coronavirus SARS-CoV-2 is responsible for COVID-19, which was first recognized in Wuhan, China, in December 2019. Rapid identification at primary stage of the novel coronavirus, SARS-CoV-2, is important to restrict it and prevent the pandemic. Real-time RT-PCR assays are the best diagnostic tests presently available for SARS-CoV-2 detection, which are highly sensitive, even though expensive equipment and trained technicians are necessary. Furthermore, the method has moderately long time bound. This deadly viral infection can also be detected by applying various spectroscopic techniques as spectroscopy can provide fast, precise identification and monitoring, leading to the overall understanding of its mutation rates, which will further facilitate antiviral drug development as well as vaccine development. It is an innovative and non-invasive technique for combating the spread of novel coronavirus. This review article demonstrates the application of various spectroscopic techniques to detect COVID-19 rapidly. Different spectroscopy-based detection protocols and additional development of new, novel sensors and biosensors along with diagnostic kits had been described here stressing the status of sensitive diagnostic systems to handle with the COVID-19 outbreak.

GRAPHICAL ABSTRACT

Spectroscopy: A versatile sensing tool for cost-effective and rapid detection of novel Coronavirus (COVID-19).

Diagnostic assay and technology advancement for detecting SARS-CoV-2 infections causing the COVID-19 pandemic

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-caused COVID-19 pandemic has transmitted to humans in practically all parts of the world, producing socio-economic turmoil. There is an urgent need for precise, fast, and affordable diagnostic testing to be widely available for detecting SARS-CoV-2 and its mutations in various phases of the disease. Early diagnosis with great precision has been achieved using real-time polymerase chain reaction (RT-PCR) and similar other molecular methods, but theseapproaches are costly and involve rigorous processes that are not easily obtainable. Conversely, immunoassays that detect a small number of antibodies have been employed for quick, low-cost tests, but their efficiency in diagnosing infected people has been restricted. The use of biosensors in the detection of SARS-CoV-2 is vital for the COVID-19 pandemic’s control. This review gives an overview of COVID-19 diagnostic approaches that are currently being developed as well as nanomaterial-based biosensor technologies, to aid future technological advancement and innovation. These approaches can be integrated into point-of-care (POC) devices to quickly identify a large number of infected patients and asymptomatic carriers. The ongoing research endeavors and developments in complementary technologies will play a significant role in curbing the spread of the COVID-19 pandemic and fill the knowledge gaps in current diagnostic accuracy and capacity.

True or False: What are the factors that influence COVID-19 diagnosis by RT-qPCR?

Introduction

The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease has had a catastrophic impact on the world resulting in several deaths. Since World Health Organization declared the pandemic status of the disease, several molecular diagnostic kits have been developed to help the tracking of viruses spread.

Areas Covered

This review aims to describe and evaluate the currently reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) diagnosis kit. Several processes used in COVID-19 diagnostic procedures are detailed in further depth to demonstrate optimal practices. Therefore, we debate the main factors that influence the viral detection of SARS-COV-2 and how they can affect the diagnosis of patients.

Expert Opinion

Here is highlighted and discussed several factors that can interfere in the RT-PCR analysis, such as the viral load of the sample, collection site, collection methodology, sample storage, transport, primer, and probe mismatch/dimerization in different brand kits. This is a pioneer study to discuss the factor that could lead to the wrong interpretation of RT-qPCR diagnosis of SARS-CoV-2. This study aimed to help the readers to understand what very likely is behind a bad result of SARS-CoV-2 detection by RT-PCR and what could be done to reach a reliable diagnosis.

SARS-CoV-2 monitoring by automated target-driven molecular machine-based engineering

Biosensors based on nucleic acid-structured electrochemiluminescence are rapidly developing for medical diagnostics. Here, we build an automated DNA molecular machine on Ti₃C₂/polyethyleneimine-Ru(dcbpy)₃ ²⁺@Au composite, which alters the situation that a DNA molecular machine requires laying down motion tracks. We use this DNA molecular machine to transduce the target concentration information to enhance the electrochemiluminescence signal based on DNA hybridization calculations. Complex bioanalytical processes are centralized in a single nucleic acid probe unit, thus eliminating the tedious steps of laying down motion tracks required by the traditional molecular machine. We found a detection limit of 0.68 pM and a range of 1 pM to 1 nM for the analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) specific DNA target. Recoveries range between 96.4 and 104.8% for the analysis of SARS-CoV-2 in human saliva.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10311-022-01434-9.

Point-of-care COVID-19 diagnostics powered by lateral flow assay

Since its first discovery in December 2019, the global coronavirus disease 2019 (COVID-19) pandemic caused by the novel coronavirus (SARS-CoV-2) has been posing a serious threat to human life and health. Diagnostic testing is critical for the control and management of the COVID-19 pandemic. In particular, diagnostic testing at the point of care (POC) has been widely accepted as part of the post restriction COVID-19 control strategy. Lateral flow assay (LFA) is a popular POC diagnostic platform that plays an important role in controlling the COVID-19 pandemic in industrialized countries and resource-limited settings. Numerous pioneering studies on the design and development of diverse LFA-based diagnostic technologies for the rapid diagnosis of COVID-19 have been done and reported by researchers. Hundreds of LFA-based diagnostic prototypes have sprung up, some of which have been developed into commercial test kits for the rapid diagnosis of COVID-19. In this review, we summarize the crucial role of rapid diagnostic tests using LFA in targeting SARS-CoV-2-specific RNA, antibodies, antigens, and whole virus. Then, we discuss the design principle and working mechanisms of these available LFA methods, emphasizing their clinical diagnostic efficiency. Ultimately, we elaborate the challenges of current LFA diagnostics for COVID-19 and highlight the need for continuous improvement in rapid diagnostic tests.

Diagnostics of SARS-CoV-2 infection using electrical impedance spectroscopy with an immunosensor to detect the spike protein

Mass testing for the diagnostics of COVID-19 has been hampered in many countries owing to the high cost of the methodologies to detect genetic material of SARS-CoV-2. In this paper, we report on a low-cost immunosensor capable of detecting the spike protein of SARS-CoV-2, including in samples of inactivated virus. Detection is performed with electrical impedance spectroscopy using an immunosensor that contains a monolayer film of carboxymethyl chitosan as matrix, coated with an active layer of antibodies specific to the spike protein. In addition to a low limit of detection of 0.179 fg/mL within an almost linear behavior from 10⁻²⁰ g/mL to 10⁻¹⁴ g/mL, the immunosensor was highly selective. For the samples with the spike protein could be distinguished in multidimensional projection plots from samples with other biomarkers and analytes that could be interfering species for healthy and infected patients. The excellent analytical performance of the immunosensors was validated with the distinction between control samples and those containing inactivated SARS-CoV-2 at different concentrations. The mechanism behind the immunosensor performance is the specific antibody-protein interaction, as confirmed with the changes induced in C–H stretching and protein bands in polarization-modulated infrared reflection absorption spectra (PM-IRRAS). Because impedance spectroscopy measurements can be made with low-cost portable instruments, the immunosensor proposed here can be applied in point-of-care diagnostics for mass testing even in places with limited resources.

Magnetically Enhanced Liquid SERS for Ultrasensitive Analysis of Bacterial and SARS-CoV-2 Biomarkers

In this work, it is shown that surface-enhanced Raman scattering (SERS) measurements can be performed using liquid platforms to perform bioanalysis at sub-pM concentrations. Using magnetic enrichment with gold-coated magnetic nanoparticles, the high sensitivity was verified with nucleic acid and protein targets. The former was performed with a DNA fragment associated with the bacteria Staphylococcus aureus, and the latter using IgG antibody, a biomarker for COVID-19 screening. It is anticipated that this work will inspire studies on ultrasensitive SERS analyzers suitable for large-scale applications, which is particularly important for in vitro diagnostics and environmental studies.

A Review of THz Technologies for Rapid Sensing and Detection of Viruses including SARS-CoV-2

Virus epidemics such as Ebola virus, Zika virus, MERS-coronavirus, and others have wreaked havoc on humanity in the last decade. In addition, a coronavirus (SARS-CoV-2) pandemic and its continuously evolving mutants have become so deadly that they have forced the entire technical advancement of healthcare into peril. Traditional ways of detecting these viruses have been successful to some extent, but they are costly, time-consuming, and require specialized human resources. Terahertz-based biosensors have the potential to lead the way for low-cost, non-invasive, and rapid virus detection. This review explores the latest progresses in terahertz technology-based biosensors for the virus, viral particle, and antigen detection, as well as upcoming research directions in the field.

Bioelectrochemical platforms to study and detect emerging pathogens

The ongoing SARS-CoV-2 pandemic has emphasized the importance of technologies to rapidly detect emerging pathogens and understand their interactions with hosts. Platforms based on the combination of biological recognition and electrochemical signal transduction, generally termed bioelectrochemical platforms, offer unique opportunities to both sense and study pathogens. Improved bio-based materials have enabled enhanced control over the biotic-abiotic interface in these systems. These improvements have generated platforms with the capability to elucidate biological function rather than simply detect targets. This advantage is a key feature of recent bioelectrochemical platforms applied to infectious disease. Here, we describe developments in materials for bioelectrochemical platforms to study and detect emerging pathogens. The incorporation of host membrane material into electrochemical devices has provided unparalleled insights into the interaction between viruses and host cells, and new capture methods have enabled the specific detection of bacterial pathogens, such as those that cause secondary infections with SARS-CoV-2. As these devices continue to improve through the merging of hi-tech materials and biomaterials, the scalability and commercial viability of these devices will similarly improve.

Ultrasensitive, high-throughput, and rapid simultaneous detection of SARS-CoV-2 antigens and IgG/IgM antibodies within 10 min through an immunoassay biochip

COVID-19 is now a severe threat to global health. Facing this pandemic, we developed a space-encoding microfluidic biochip for high-throughput, rapid, sensitive, simultaneous quantitative detection of SARS-CoV-2 antigen proteins and IgG/IgM antibodies in serum. The proposed immunoassay biochip integrates the advantages of graphene oxide quantum dots (GOQDs) and microfluidic chip and is capable of conducting multiple SARS-CoV-2 antigens or IgG/IgM antibodies of 60 serum samples simultaneously with only 2 μL sample volume of each patient. Fluorescence intensity of antigens and IgG antibody detection at emission wavelength of ~680 nm was used to quantify the target concentration at excitation wavelength of 632 nm, and emission wavelength of ~519 nm was used during the detection of IgM antibodies at excitation wavelength of 488 nm. The method developed has a large linear quantification detection regime of 5 orders of magnitude, an ultralow detection limit of ~0.3 pg/mL under optimized conditions, and less than 10-min qualitative detection time. The proposed biosensing platform will not only greatly facilitate the rapid diagnosis of COVID-19 patients, but also provide a valuable screening approach for infected patients, medical therapy, and vaccine recipients.