Integrated microfluidic device using a single universal aptamer to detect multiple types of influenza viruses

Aptamer selection via versatile microfluidic platforms and their diverse applications

Aptamers are synthetic oligonucleotides that bind with high affinity and specificity to various targets, making them invaluable for diagnostics, therapeutics, and biosensing. Microfluidic platforms can improve the efficiency and scalability of aptamer selection, especially through advancements in systematic evolution of ligands by exponential enrichment (SELEX) methods. Microfluidic SELEX methods are less time-consuming and labor-intensive and include critical steps like library preparation, binding, partitioning, and amplification. This review examines the contributions of microfluidic technology to SELEX-based aptamer identification, with alternative methods like conditional SELEX, in vivo-like SELEX and Non-SELEX for selecting aptamers and also discusses critical SELEX steps over the past decade. This work also examined the integrated microfluidic systems for SELEX, highlighting innovations such as conditional SELEX and in vivo-like SELEX. These advancements provide potential solutions to existing challenges in aptamer selection using conventional SELEX, especially concerning biological samples. A trend toward non-SELEX methods was also reviewed and discussed, wherein nucleic acid amplification was eliminated to improve aptamer selection. Microfluidic platforms have demonstrated versatility not only in aptamer selection but also in various detection applications; they allow for precise control of liquid flow and have been essential in the advancement of therapeutic aptamers, facilitating accurate screening, enhancing drug delivery systems, and enabling targeted therapeutic interventions. Although advances in microfluidic technology are expected to enhance aptamer-based diagnostics, therapeutics, and biosensing, challenges still persist, especially in up-scaling microfluidic systems for various clinical applications. The advantages and limitations of integrating microfluidic platforms with aptamer development are further addressed, emphasizing areas for future research. We also present a perspective on the future of microfluidic systems and aptamer technologies, highlighting their increasing significance in healthcare and diagnostics.

Influenza viruses and SARS-CoV-2 diagnosis via sensitive testing methods in clinical application

The identification of influenza viruses and SARS-CoV-2 has garnered increasing attention due of their longstanding global menace to human life and health. The point-of-care test is a potential approach for identifying influenza viruses and SARS-CoV-2 in clinical settings, leading to timely discovery, documentation, and treatment. The primary difficulties encountered with conventional detection techniques for influenza viruses and SARS-CoV-2 are the limited or inadequate ability to identify the presence of the viruses, the lack of speed, precision, accuracy, sensitivity, and specificity, often resulting in a failure to promptly notify disease control authorities. Recently, point-of-care test methods, along with nucleic acid amplification, optics, electrochemistry, lateral/vertical flow, and minimization, have been demonstrated the characteristics of reliability, sensitivity, specificity, stability, and portability. A point-of-care test offers promising findings in the early detection of influenza viruses and SARS-CoV-2 in both scientific research and practical use. In this review, we will go over the principles, advantages, limitations, and real-world applications of point-of-care diagnostics. The significance of constraints of detection, throughput, sensitivity, and specificity in the analysis of clinical samples in settings with restricted resources is underscored. This discussion concludes with their prospects and challenges.

Highly-Efficient Selection of Aptamers for Quantitative Fluorescence Detecting Multiple IAV Subtypes

Influenza A virus (IAV) can cause infectious respiratory diseases in humans and animals. IAVs mutate rapidly through antigenic drift and shift, resulting in the emergence of numerous IAV subtypes and significant challenges for IAV detection. Therefore, achieving the simultaneous detection of multiple IAVs is crucial. In this work, three specific aptamers targeting the hemagglutination (HA) protein of the influenza A H5N1, H7N9, and H9N2 viruses were screened using a multichannel magnetic microfluidic chip. The aptamers exhibit nanomolar affinity and excellent specificity for the HA protein of H5N1, H7N9, and H9N2 viruses. Furthermore, three specific aptamers were truncated and labeled with different fluorescence markers to realize fluorescence quantitative detection of influenza A H5N1, H7N9, and H9N2 viruses through an aptamer sandwich assay in 1 h. The limit of detection (LOD) of the developed method is 0.38 TCID50/mL for the H5N1 virus, 0.75 TCID50/mL for the H7N9 virus, and 1.14 TCID50/mL for the H9N2 virus. The detection method has excellent specificity, strong anti-interference ability, and good reproducibility. This work provides a sensitive quantitative detection method for the H5N1, H7N9, and H9N2 viruses, enabling quantitative fluorescence detection for multiple IAV subtypes.

Aptamer-Protein Interactions: From Regulation to Biomolecular Detection

Serving as the basis of cell life, interactions between nucleic acids and proteins play essential roles in fundamental cellular processes. Aptamers are unique single-stranded oligonucleotides generated by in vitro evolution methods, possessing the ability to interact with proteins specifically. Altering the structure of aptamers will largely modulate their interactions with proteins and further affect related cellular behaviors. Recently, with the in-depth research of aptamer-protein interactions, the analytical assays based on their interactions have been widely developed and become a powerful tool for biomolecular detection. There are some insightful reviews on aptamers applied in protein detection, while few systematic discussions are from the perspective of regulating aptamer-protein interactions. Herein, we comprehensively introduce the methods for regulating aptamer-protein interactions and elaborate on the detection techniques for analyzing aptamer-protein interactions. Additionally, this review provides a broad summary of analytical assays based on the regulation of aptamer-protein interactions for detecting biomolecules. Finally, we present our perspectives regarding the opportunities and challenges of analytical assays for biological analysis, aiming to provide guidance for disease mechanism research and drug discovery.

Highly-specific aptamer targeting SARS-CoV-2 S1 protein screened on an automatic integrated microfluidic system for COVID-19 diagnosis

Variants of the severe acute respiratory syndrome coronavirus (SARS-CoV-2) have evolved such that it may be challenging for diagnosis and clinical treatment of the pandemic coronavirus disease-19 (COVID-19). Compared with developed SARS-CoV-2 diagnostic tools recently, aptamers may exhibit some advantages, including high specificity/affinity, longer shelf life (vs. antibodies), and could be easily prepared. Herein an integrated microfluidic system was developed to automatically carry out one novel screening process based on the systematic evolution of ligands by exponential enrichment (SELEX) for screening aptamers specific with SARS-CoV-2. The new screening process started with five rounds of positive selection (with the S1 protein of SARS-CoV-2). In addition, including non-target viruses (influenza A and B), human respiratory tract-related cancer cells (adenocarcinoma human alveolar basal epithelial cells and dysplastic oral keratinocytes), and upper respiratory tract-related infectious bacteria (including methicillin-resistant Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter baumannii, and Klebsiella pneumoniae), and human saliva were involved to increase the specificity of the screened aptamer during the negative selection. Totally, all 10 rounds could be completed within 20 h. The dissociation constant of the selected aptamer was determined to be 63.0 nM with S1 protein. Limits of detection for Wuhan and Omicron clinical strains were found to be satisfactory for clinical applications (i.e. 4.80 × 10¹ and 1.95 × 10² copies/mL, respectively). Moreover, the developed aptamer was verified to be capable of capturing inactivated SARS-CoV-2 viruses, eight SARS-CoV-2 pseudo-viruses, and clinical isolates of SARS-CoV-2 viruses. For high-variable emerging viruses, this developed integrated microfluidic system can be used to rapidly select highly-specific aptamers based on the novel SELEX methods to deal with infectious diseases in the future.

Recent Advances in DNA Nanotechnology-Enabled Biosensors for Virus Detection

Virus-related infectious diseases are serious threats to humans, which makes virus detection of great importance. Traditional virus-detection methods usually suffer from low sensitivity and specificity, are time-consuming, have a high cost, etc. Recently, DNA biosensors based on DNA nanotechnology have shown great potential in virus detection. DNA nanotechnology, specifically DNA tiles and DNA aptamers, has achieved atomic precision in nanostructure construction. Exploiting the programmable nature of DNA nanostructures, researchers have developed DNA nanobiosensors that outperform traditional virus-detection methods. This paper reviews the history of DNA tiles and DNA aptamers, and it briefly describes the Baltimore classification of virology. Moreover, the advance of virus detection by using DNA nanobiosensors is discussed in detail and compared with traditional virus-detection methods. Finally, challenges faced by DNA nanobiosensors in virus detection are summarized, and a perspective on the future development of DNA nanobiosensors in virus detection is also provided.

Aptamer-based biosensors for virus protein detection

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

Aptamers: A prospective tool for infectious diseases diagnosis

It is well known that people's health is seriously threatened by various pathogens (such as Mycobacterium tuberculosis, Treponema pallidum, Novel coronavirus, HIV, Mucor, etc.), which leads to heavy socioeconomic burdens. Therefore, early and accurate pathogen diagnosis is essential for timely and effective therapies. Up to now, diagnosing human contagious diseases at molecule and nano levels is remarkably difficult owing to insufficient valid probes when it comes to determining the biological markers of pathogens. Aptamers are a set of high‐specificity and high‐sensitivity plastic oligonucleotides screened in vitro via the selective expansion of ligands by exponential enrichment (SELEX). With the advent of aptamer‐based technologies, their merits have aroused mounting academic interest. In recent years, as new detection and treatment tools, nucleic acid aptamers have been extensively utilized in the field of biomedicine, such as pathogen detection, new drug development, clinical diagnosis, nanotechnology, etc. However, the traditional SELEX method is cumbersome and has a long screening cycle, and it takes several months to screen out aptamers with high specificity. With the persistent development of SELEX‐based aptamer screening technologies, the application scenarios of aptamers have become more and more extensive. The present research briefly reviews the research progress of nucleic acid aptamers in the field of biomedicine, especially in the diagnosis of contagious diseases.

Enzyme linked oligonucleotide assay for the sensitive detection of SARS-CoV-2 variants

The exponential spread of COVID-19 has prompted the need to develop a simple and sensitive diagnostic tool. Aptamer-based detection assays like ELONA are promising since they are inexpensive and sensitive. Aptamers have advantages over antibodies in wide modification, small size, in vitro selection, and stability under stringent conditions, which aid in scalable and reliable detection. In this work, we used aptamers against SARS-CoV-2 RBD S protein to design a simple and sensitive ELONA detection tool. Screening CoV2-RBD-1C and CoV2-RBD-4C aptamers and optimizing assay conditions led to the development of a direct ELONA that can detect SARS-CoV-2 RBD S glycoprotein in buffer solution and 0.1 % human nasal fluid with a detection limit of 2.16 ng/mL and 1.02 ng/mL, respectively. We detected inactivated Alpha, Wuhan, and Delta variants of SARS-CoV-2 with the detection limit of 3.73, 5.72, and 6.02 TCID₅₀/mL, respectively. Using the two aptamers as capture and reporter elements, we designed a more sensitive sandwich assay to identify the three SARS-CoV-2 variants employed in this research. As predicted, a lower detection limit was obtained. Sandwich assay LOD was 2.31 TCID₅₀/mL for Alpha, 1.15 TCID₅₀/mL for Wuhan, and 2.96 TCID₅₀/mL for Delta. The sensitivity of sandwich ELONA was validated using Alpha and Wuhan variants spiked in 0.1% human nasal fluid sample condition and were detected in 1.41 and 1.79 TCID₅₀/mL LOD, respectively. SEM was used to visualize the presence of viral particles in the Delta variant sample. The effective detection of SARS-CoV-2 in this study confirms the potential of our aptamer-based technique as a screening tool.

Selection and Characterization of Single-Stranded DNA Aptamers of Diagnostic Potential against the Whole Zika Virus

Zika virus became a major public health problem in early 2015, when cases of Guillain–Barré syndrome and microcephaly were associated with viral infection. Currently, ZIKV is endemic in all tropical areas of the world, and the chance for future Zika epidemics remains very real and accurate diagnosis is crucial. The aim of this work was to select specific ssDNA aptamers that bind to the entire Zika virus and can be used to compose specific diagnostics, without cross-reactivity with other flaviviruses. Zika virus was cultivated in Vero cells and used as a target for aptamer selection. Aptamers specific for the ZIKV were selected using whole-virus SELEX, with counterselection for other flavivirus. Secondary and tertiary structures were evaluated and the molecular anchoring between the aptamers and target were simulated by the HDOCK server. Aptamer interaction was evaluated by ELISA/ELASA and the dissociation constant (Kd) was calculated by thermophoresis. Four ZIKV-specific aptamers were selected. The best two were further characterized and proved to be specific for ZIKV. Aptamers are capable of binding specifically to the ZIKV and differentiate from Dengue virus. The aptamers selected in this work can be used as capture agents in the composition of diagnostic tests to specifically detect ZIKV infection.

An overview of advancement in aptasensors for influenza detection

INTRODUCTION

The platforms for early identification of infectious diseases such as influenza has seen a surge in recent years as delayed diagnosis of such infections can lead to dreadful effects causing large numbers of deaths. The time taken in detection of an infectious disease may vary from a few days to a few weeks depending upon the choice of the techniques. So, there is an urgent need for advanced methodologies for early diagnosis of the influenza.

AREAS COVERED

The emergence of "Aptasensor" synergistically with biosensors for diagnosis has opened a new era for sensitive, selective and early detection approaches. This review described various conventional as well as advanced methods based on artificial immunogenic nucleotide sequences complementing a part of the virus, i.e., aptamers based aptasensors for influenza diagnosis and the challenges faced in their commercialization.

EXPERT OPINION

Although numerous traditional methods are available for influenza detection but mostly associated with low sensitivity, specificity, high cost, trained personnel, and animals required for virus culture/ antibody raising as the major drawbacks. Aptamers can be manufactured invitro as 'chemical antibodies' at commercial level, no animal required. Following these advantages, aptamers can pave the way for an efficient diagnostic technique as compared to other existing conventional methods..

Aptamers for Viral Detection and Inhibition

Recent times have experienced more than ever the impact of viral infections in humans. Viral infections are known to cause diseases not only in humans but also in plants and animals. Here, we have compiled the literature review of aptamers selected and used for detection and inhibition of viral infections in all three categories: humans, animals, and plants. This review gives an in-depth introduction to aptamers, different types of aptamer selection (SELEX) methodologies, the benefits of using aptamers over commonly used antibody-based strategies, and the structural and functional mechanism of aptasensors for viral detection and therapy. The review is organized based on the different characterization and read-out tools used to detect virus-aptasensor interactions with a detailed index of existing virus-targeting aptamers. Along with addressing recent developments, we also discuss a way forward with aptamers for DNA nanotechnology-based detection and treatment of viral diseases. Overall, this review will serve as a comprehensive resource for aptamer-based strategies in viral diagnostics and treatment.

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

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

Advanced Point-of-Care Testing Technologies for Human Acute Respiratory Virus Detection

The ever-growing global threats to human life caused by the human acute respiratory virus (RV) infections have cost billions of lives, created a significant economic burden, and shaped society for centuries. The timely response to emerging RVs could save human lives and reduce the medical care burden. The development of RV detection technologies is essential for potentially preventing RV pandemic and epidemics. However, commonly used detection technologies lack sensitivity, specificity, and speed, thus often failing to provide the rapid turnaround times. To address this problem, new technologies are devised to address the performance inadequacies of the traditional methods. These emerging technologies offer improvements in convenience, speed, flexibility, and portability of point-of-care test (POCT). Herein, recent developments in POCT are comprehensively reviewed for eight typical acute respiratory viruses. This review discusses the challenges and opportunities of various recognition and detection strategies and discusses these according to their detection principles, including nucleic acid amplification, optical POCT, electrochemistry, lateral flow assays, microfluidics, enzyme-linked immunosorbent assays, and microarrays. The importance of limits of detection, throughput, portability, and specificity when testing clinical samples in resource-limited settings is emphasized. Finally, the evaluation of commercial POCT kits for both essential RV diagnosis and clinical-oriented practices is included.

Aptamer-based biosensors and their implications in COVID-19 diagnosis

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a novel infectious member of the coronavirus family, has caused millions of cases of infection and deaths all over the world, and been declared a pandemic by the World Health Organization. Conventional laboratory-based diagnostic testing has faced extreme difficulties in meeting the overwhelming demand for testing worldwide, and this has brought about a pressing need for cost-effective rapid diagnosis. There has been a surge in the number of prototypes of diagnostic kits developed, although many of these have been found to be lacking in terms of their accuracy and sensitivity. One type of chip-based diagnostic platform is the aptamer-based biosensor. Aptamers are artificially synthesized oligonucleotides that are capable of specifically binding to a target antigen. As of now, some aptamers have been reported for SARS-CoV-2. Although many ultrasensitive aptasensors have been developed for viruses, few have been successfully adapted for SARS-CoV-2 detection. Our review discusses the recent developments in the domain of SARS-CoV-2 specific aptamer isolation, the design of electrochemical and optical aptasensors, and the implications of aptasensor-based COVID-19 diagnosis.

Aptamer Applications in Emerging Viral Diseases

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

Recent Advances and a Roadmap to Aptamer-Based Sensors for Bloodstream Infections

The present review is intended to describe bloodstream infections (BSIs), the major pathogens responsible for BSIs, conventional tests and their limitations, commercially available methods used, and the aptamer and nanomaterials-based approaches developed so far for the detection of BSIs. The advantages associated with aptamers and the aptamer-based sensors, the comparison between the aptamers and the antibodies, and the various types of aptasensors developed so far for the detection of bloodstream infections have been described in detail in the present review. Also, the future outlook and roadmap toward aptamer-based sensors and the challenges associated with the aptamer development have also been concluded in this review.

Aptamers for Anti-Viral Therapeutics and Diagnostics

Viral infections cause a host of fatal diseases and seriously affect every form of life from bacteria to humans. Although most viral infections can receive appropriate treatment thereby limiting damage to life and livelihood with modern medicine and early diagnosis, new types of viral infections are continuously emerging that need to be properly and timely treated. As time is the most important factor in the progress of many deadly viral diseases, early detection becomes of paramount importance for effective treatment. Aptamers are small oligonucleotide molecules made by the systematic evolution of ligands by exponential enrichment (SELEX). Aptamers are characterized by being able to specifically bind to a target, much like antibodies. However, unlike antibodies, aptamers are easily synthesized, modified, and are able to target a wider range of substances, including proteins and carbohydrates. With these advantages in mind, many studies on aptamer-based viral diagnosis and treatments are currently in progress. The use of aptamers for viral diagnosis requires a system that recognizes the binding of viral molecules to aptamers in samples of blood, serum, plasma, or in virus-infected cells. From a therapeutic perspective, aptamers target viral particles or host cell receptors to prevent the interaction between the virus and host cells or target intracellular viral proteins to interrupt the life cycle of the virus within infected cells. In this paper, we review recent attempts to use aptamers for the diagnosis and treatment of various viral infections.

Microfluidic-based virus detection methods for respiratory diseases

With the recent SARS-CoV-2 outbreak, the importance of rapid and direct detection of respiratory disease viruses has been well recognized. The detection of these viruses with novel technologies is vital in timely prevention and treatment strategies for epidemics and pandemics. Respiratory viruses can be detected from saliva, swab samples, nasal fluid, and blood, and collected samples can be analyzed by various techniques. Conventional methods for virus detection are based on techniques relying on cell culture, antigen-antibody interactions, and nucleic acids. However, these methods require trained personnel as well as expensive equipment. Microfluidic technologies, on the other hand, are one of the most accurate and specific methods to directly detect respiratory tract viruses. During viral infections, the production of detectable amounts of relevant antibodies takes a few days to weeks, hampering the aim of prevention. Alternatively, nucleic acid-based methods can directly detect the virus-specific RNA or DNA region, even before the immune response. There are numerous methods to detect respiratory viruses, but direct detection techniques have higher specificity and sensitivity than other techniques. This review aims to summarize the methods and technologies developed for microfluidic-based direct detection of viruses that cause respiratory infection using different detection techniques. Microfluidics enables the use of minimal sample volumes and thereby leading to a time, cost, and labor effective operation. Microfluidic-based detection technologies provide affordable, portable, rapid, and sensitive analysis of intact virus or virus genetic material, which is very important in pandemic and epidemic events to control outbreaks with an effective diagnosis.

Optimization of aptamer selection on an automated microfluidic system with cancer tissues

Cancer is among the world's most deadly inflictions, and early diagnosis is critical. Aptamers have shown utility as cancer probes since they can be screened rapidly in vitro against cancer tissues using systematic evolution of ligands by exponential enrichment (SELEX) process. However, bench-top SELEX procedures are relatively labor-intensive and time-consuming; ideally, they could instead be carried out on microfluidic devices, yet this requires optimization of buffer and reaction conditions. Herein an integrated microfluidic system (IMS) was established to automatically carry out the optimization of aptamer selection. A "formulation chip" was developed that could mix salt solutions at differing final concentrations, and the resulting optimal binding buffer was transferred to another "optimization-SELEX chip" for the following tissue-SELEX. Two aptamers were successfully screened; one of which, H-45, exhibited high specificity and affinity towards ovarian cancer tissue samples, suggesting that this IMS might be a promising device for screening of cancer associated aptamers for cancer diagnosis.

Electrochemical aptasensors for the detection of hepatocellular carcinoma-related biomarkers

Recent progress in electrochemical aptasensors for the detection of HCC-related biomarkers, including cancer cells, proteins, cell-derived exosomes, and nucleic acids, is reviewed.

Microfluidic devices for detection of RNA viruses

There is a long way to go before the coronavirus disease 2019 (Covid-19) outbreak comes under control. qRT-PCR is currently used for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of Covid-19, but it is expensive, time-consuming, and not as sensitive as it should be. Finding a rapid, easy-to-use, and cheap diagnostic method is necessary to help control the current outbreak. Microfluidic systems provide a platform for many diagnostic tests, including RT-PCR, RT-LAMP, nested-PCR, nucleic acid hybridization, ELISA, fluorescence-Based Assays, rolling circle amplification, aptamers, sample preparation multiplexer (SPM), Porous Silicon Nanowire Forest, silica sol-gel coating/bonding, and CRISPR. They promise faster, cheaper, and easy-to-use methods with higher sensitivity, so microfluidic devices have a high potential to be an alternative method for the detection of viral RNA. These devices have previously been used to detect RNA viruses such as H1N1, Zika, HAV, HIV, and norovirus, with acceptable results. This paper provides an overview of microfluidic systems as diagnostic methods for RNA viruses with a focus on SARS-CoV-2.

The Latest Achievements in the Construction of Influenza Virus Detection Aptasensors

Aptamers are short fragments of nucleic acids, DNA or RNA that have the ability to bind selected proteins with high specificity and affinity. These properties allow them to be used as an element of biosensors for the detection of specific proteins, including viral ones, which makes it possible to design valuable diagnostic tools. The influenza virus causes a huge number of human and animal deaths worldwide every year, and contributes to remarkable economic losses. In addition, in 2020, a new threat appeared-the SARS-Cov-2 pandemic. Both disease entities, especially in the initial stage of infection, are almost identical in terms of signs and symptoms. Therefore, a diagnostic solution is needed that will allow distinguishing between both pathogens, with high sensitivity and specificity; it should be cheap, quick and possible to use in the field, for example, in a doctor's office. All the mentioned properties are met by aptasensors in which the detection elements are specific aptamers. We present here the latest developments in the construction of various types of aptasensors for the detection of influenza virus. Aptasensor operation is based on the measurement of changes in electric impedance, fluorescence or electric signal (impedimetric, fluorescence and electrochemical aptasensors, respectively); it allows both qualitative and quantitative determinations. The particularly high advancement for detecting of influenza virus concerns impedimetric aptasensors.

An automated detection of influenza virus based on 3-D magnetophoretic separation and magnetic label

Automated detection of the influenza virus is important for the prevention of infectious viruses. Herein, assisted by three-dimensional (3-D) magnetophoretic separation and magnetic label, an automated detection device was constructed for H7N9 influenza virus hemagglutinin. Multi-layer glass slides were used to generate a 3-D microchannel network with two-level channels, realizing 3-D magnetophoretic separation with a magnetic field in the vertical direction to microchannels for the sample treatment. After the immunomagnetic separation, a magnetic-tagged complex was captured in an antibody-modified glass capillary, where magnetic beads further as a label could cause the voltage change of the miniature tube liquid sensor to obtain the detection signal. Moreover, the whole detection process and detection results were controlled and read through a liquid crystal display (LCD) screen to improve the automation. Finally, the detection limit was calculated to be 8.4 ng mL^-1 for H7N9 hemagglutinin and had good specificity and reproducibility. These results indicate that this detection device proposes promising automated avenues for the early detection of infectious diseases.

The research of aptamer biosensor technologies for detection of microorganism

The activities and transmissions of microorganisms are closely related to human, and all kinds of diseases caused by pathogenic microorganisms have attracted attention in the world and brought many challenges to human health and public health. The traditional microbial detection technologies have characteristics of longer detection cycle and complicated processes, therefore, which can no longer meet the detection requirements in the field of public health. At present, it is the focus to develop and design a novel, rapid, and simple microbial detection method in the field of public health. Herein, this article summarized the development of aptamer biosensor technologies for detection of microorganism in the aspect of bacteria, viruses, and toxins in detail, including optical aptamer sensors such as fluorometry and colorimetry, electrochemical aptamer sensors, and other technologies combined with aptamer. KEY POINTS: • Aptamer biosensor is a good platform for microbial detection. • Aptamer biosensors include optical sensors and electrochemical sensors. • Aptamer sensors have been widely used in the detection of bacteria, viruses, and other microorganisms.

A structure-free digital microfluidic platform for detection of influenza a virus by using magnetic beads and electromagnetic forces

H1N1, a subtype of influenza A virus, has emerged as a global threat in the past decades. Due to its highly infectious nature, an accurate and rapid detection assay is urgently required. Therefore, this study presents a new type of digital microfluidic platform for H1N1 virus detection by utilizing a one-aptamer/two-antibodies assay on magnetic beads. The droplets containing magnetic beads were driven by electromagnetic forces on a structure-free, super-hydrophobic surface to automate the entire assay within 40 min. With different levels of hydrophobic modification, the droplets could be easily controlled and positioned without any assisted microstructure. The tunable electromagnetic forces could be adjusted for three kinds of operating modes for the manipulations of beads and droplets, including movement of droplets containing magnetic beads, mixing of two droplets and beads extraction out of droplets. When compared with previous studies, the manipulations of droplets and magnetic particles in this study are more flexible as they can be easily adjusted by fine-tuning the magnetic flux density. Furthermore, the magnetic beads also served as three-dimensional substrates for the new enzyme-linked immunosorbent assay (ELISA)-like assay. The magnetic beads were conjugated with aptamers, which have high specificity towards H1N1 viruses such that they could be specifically captured and detected. The horseradish peroxidase-conjugated secondary antibody was then used to activate tyramide-tetramethylrhodamine (TTMR) such that fluorescent signals could be amplified. With this approach, the limit of detection was experimentally found to be 0.032 hemagglutination units/reaction, which is sensitive enough for clinical diagnostics. This kind of digital microfluidic platform with the ELISA-like assay could effectively reduce the consumption of samples and reagents such that the volume of all droplets including the H1N1 sample, antibodies, TTMR and wash buffers was only 20 μL. This is the first time that a digital microfluidic platform was demonstrated such that the entire diagnostic process for influenza A H1N1 viruses could be performed by using electromagnetic forces, which could be promising for rapid and accurate diagnosis of influenza.

Label-free peptide nucleic acid biosensor for visual detection of multiple strains of influenza A virus suitable for field applications

Accurate and rapid diagnosis of Influenza A viruses (IAVs) is challenging because of multiple strains circulating in humans and animal populations, and the emergence of new strains. In this study, we demonstrate a simple and rapid strategy for visual detection of multiple strains of IAVs (H1 to H16 subtypes) using peptide nucleic acid (PNA) as a biosensor and unmodified gold nanoparticles (AuNPs) as a reporter. The design principle of the assay is based on the color change on account of free PNA-induced aggregation of AuNPs in the presence of non-complementary viral RNA sequence and vice-versa. The assay could detect IAV RNA with a visual limit of detection of 2.3 ng. The quantification of RNA with a considerable accuracy on a simple spectrophotometer was achieved on plotting the PNA-induced colorimetric changes (absorption ratio of A₆₄₀/A₅₂₀) in the presence of a varying concentration of complementary RNA. As a proof-of-concept, the visual assay was validated on 419 avian clinical samples and receiver operating characteristic (ROC) curve analysis showed a high diagnostic specificity (96.46%, 95% CI = 93.8 to 98.2) and sensitivity (82.41%, 95% CI = 73.9 to 89.1) when RT-qPCR was used as reference test. Hence, the simplicity, rapidity, and universality of this strategy make it a potential candidate visual assay for clinical diagnosis and surveillance of IAVs, especially in the resource-limited settings. The proposed strategy establishes new avenues for developing a simple and rapid diagnostic system for viral infections and biomolecules.

Application of Aptamers in Virus Detection and Antiviral Therapy

Viral infections can cause serious diseases for humans and animals. Accurate and early detection of viruses is often crucial for clinical diagnosis and therapy. Aptamers are mostly single-stranded nucleotide sequences that are artificially synthesized by an in vitro technology known as the Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Similar to antibodies, aptamers bind specifically to their targets. However, compared with antibody, aptamers are easy to synthesize and modify and can bind to a broad range of targets. Thus, aptamers are promising for detecting viruses and treating viral infections. In this review, we briefly introduce aptamer-based biosensors (aptasensors) and describe their applications in rapid detection of viruses and as antiviral agents in treating infections. We summarize available data about the use of aptamers to detect and inhibit viruses. Furthermore, for the first time, we list aptamers specific to different viruses that have been screened out but have not yet been used for detecting viruses or treating viral infections. Finally, we analyze barriers and developing perspectives in the application of aptamer-based virus detection and therapeutics.

An integrated microfluidic system for rapid detection and multiple subtyping of influenza A viruses by using glycan-coated magnetic beads and RT-PCR

The influenza A (InfA) virus, which poses a significant global public health threat, is routinely classified into "subtypes" based on viral hemagglutinin (HA) and neuraminidase (NA) antigens. Because there are nearly 200 viral subtypes, current diagnostic approaches require multiplexing or array systems to cover various subtypes of HA and NA. A microfluidic chip featuring a HA × NA array was consequently developed herein for diagnosis and subtyping of InfA viruses via the use of glycan-coated magnetic beads followed by reverse transcription (RT) polymerase chain reaction (PCR). Up to 12 InfA subtypes were simultaneously detected in an automated fashion in less than 100 minutes on this microfluidic platform, representing a significant improvement in analysis speed compared to benchtop RT-PCR and chip-based microarray systems. The limits of detection of the RT-PCR assays ranged from 40 to 3000 copy numbers for the different subtypes of InfA viruses, around two orders of magnitude higher than in previous studies using microfluidic technologies. In summary, the array-type microfluidic chip system provides a rapid, sensitive, and fully automated approach for detection and multiple subtyping of InfA.

Encoded particle microfluidic platform for rapid multiplexed screening and characterization of aptamers against influenza A nucleoprotein

Aptamers represent interesting bioreceptor alternatives to antibodies when developing a bioassay and are selected by the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) process. After selection, an extensive characterization process is essential to verify the binding affinity and specificity of aptamer candidates, which is the most time-consuming and costly step. In this study, we assessed a new microfluidic platform, namely Evalution™, as a rapid and high throughput aptamer characterization platform. To do this, we first selected aptamers against influenza A nucleoprotein (infA NP) by performing magnetic bead-based SELEX. The selected aptamer candidates were subsequently screened using Evalution™ for their binding kinetics and specificity towards infA NP. All aptamers showed dissociation constants (K_D) in the low nanomolar range (from 13 to 41 nM), and differential binding behavior towards control proteins, such as BSA and influenza B nucleoprotein (infB NP). Among 5 selected candidates, one aptamer (NP5) exhibited a significant discrimination between infA NP and infB NP and was further used to benchmark the kinetic analysis of Evalution™ (K_D = 41 nM) with an SPR platform (K_D = 17 nM). These results suggested that NP5 has the potential to be used for developing sensitive and infA NP specific aptamer-based assay. Moreover, the presented platform proved to be an efficient aptamer characterization tool for performing typical aptamer characterization experiments like binding kinetics (due to the real-time monitoring feature) and specificity assessment in a high-throughput manner due to the multiplexing capacity.

Microfluidic and Paper-Based Devices for Disease Detection and Diagnostic Research

Recent developments in microfluidic devices, nanoparticle chemistry, fluorescent microscopy, and biochemical techniques such as genetic identification and antibody capture have provided easier and more sensitive platforms for detecting and diagnosing diseases as well as providing new fundamental insight into disease progression. These advancements have led to the development of new technology and assays capable of easy and early detection of pathogenicity as well as the enhancement of the drug discovery and development pipeline. While some studies have focused on treatment, many of these technologies have found initial success in laboratories as a precursor for clinical applications. This review highlights the current and future progress of microfluidic techniques geared toward the timely and inexpensive diagnosis of disease including technologies aimed at high-throughput single cell analysis for drug development. It also summarizes novel microfluidic approaches to characterize fundamental cellular behavior and heterogeneity.

A new amplified fluorescent aptasensor based on hairpin structure of G-quadruplex oligonucleotide-Aptamer chimera and silica nanoparticles for sensitive detection of aflatoxin B1 in the grape juice

As one of the most toxic mycotoxins, aflatoxin B₁ (AFB₁) is a major food pollutant which can pose a high risk to human health. In this work, an accurate fluorescent sensing method was proposed for AFB₁ determination, based on hairpin structure of G-quadruplex oligonucleotide-Aptamer chimera, silica nanoparticles coated with streptavidin (SNPs-Streptavidin) and N-methyl mesoporphyrin IX (NMM). The hairpin structure of chimera and SNPs-Streptavidin allowed AFB₁ detection with high sensitivity and specificity. Moreover, the developed sensor could detect AFB₁ in 30 min. The relative fluorescence intensity increased as AFB₁ concentrations increased with a linear range of 30-900 pg/mL and a limit of detection (LOD) of 8 pg/mL. The constructed aptasensor was successfully employed to assess AFB₁ spiked grape juice and human serum samples. The analytical recovery of AFB₁ in the grape juice samples ranged from 95 to 106%, implying the great potential of the presented aptasensor in food product analysis.

Recent Microdevice-Based Aptamer Sensors

Since the systematic evolution of ligands by exponential enrichment (SELEX) method was developed, aptamers have made significant contributions as bio-recognition sensors. Microdevice systems allow for low reagent consumption, high-throughput of samples, and disposability. Due to these advantages, there has been an increasing demand to develop microfluidic-based aptasensors for analytical technique applications. This review introduces the principal concepts of aptasensors and then presents some advanced applications of microdevice-based aptasensors on several platforms. Highly sensitive detection techniques, such as electrochemical and optical detection, have been integrated into lab-on-a-chip devices and researchers have moved towards the goal of establishing point-of-care diagnoses for target analyses.

The potential of aptamers for cancer research

Aptamers are promising alternatives to antibodies and can be used as high affinity agents for the cancer detection and the targeted drug transportation. In this manuscript, we highlight the advantages of aptamers, such as high affinities, specificity and excellent chemical stabilities, which are likely to benefit for the diagnosis of cancer in its early stages and then achieve molecular-level treatment. Also, we discuss the challenges and problems in the current application of aptamers.

A novel fluorescent aptasensor for ultrasensitive detection of microcystin-LR based on single-walled carbon nanotubes and dapoxyl

To assure water safety and protect human health, precise and simple analytical approaches are highly desired to determine low concentrations of microcystin-leucine-arginine (MC-LR), a toxin, in both water and serum samples. Herein, a simple, rapid and accurate aptamer-based fluorescent sensor was used for selective recognition of MC-LR, based on single-walled carbon nanotubes (SWNTs) as immobilizers, dapoxyl as a fluorescent dye, DAP-10 as a specific aptamer for dapoxyl and unmodified MC-LR aptamer (Apt) as a sensing ligand. The sensing method was developed to produce a remarkable fluorescence intensity difference in the absence and presence of MC-LR. Moreover, the Apt was used without any modification. In the absence of MC-LR, the dapoxyl could bind to DAP-10, leading to a strong fluorescence intensity. In the presence of MC-LR, DAP-10 bound to the surface of SWNTs, resulting in a very weak fluorescence intensity. Under optimized conditions, the presented fluorescent analytical approach showed high selectivity toward MC-LR with a limit of detection (LOD) of 138 pM. This new method indicated excellent analytical performance for MC-LR detection in tap water and serum samples with LODs of 135 and 168 pM, respectively.

Use of Aptamers as Diagnostics Tools and Antiviral Agents for Human Viruses

Appropriate diagnosis is the key factor for treatment of viral diseases. Time is the most important factor in rapidly developing and epidemiologically dangerous diseases, such as influenza, Ebola and SARS. Chronic viral diseases such as HIV-1 or HCV are asymptomatic or oligosymptomatic and the therapeutic success mainly depends on early detection of the infective agent. Over the last years, aptamer technology has been used in a wide range of diagnostic and therapeutic applications and, concretely, several strategies are currently being explored using aptamers against virus proteins. From a diagnostics point of view, aptamers are being designed as a bio-recognition element in diagnostic systems to detect viral proteins either in the blood (serum or plasma) or into infected cells. Another potential use of aptamers is for therapeutics of viral infections, interfering in the interaction between the virus and the host using aptamers targeting host-cell matrix receptors, or attacking the virus intracellularly, targeting proteins implicated in the viral replication cycle. In this paper, we review how aptamers working against viral proteins are discovered, with a focus on recent advances that improve the aptamers' properties as a real tool for viral infection detection and treatment.