Micro- and nanotechnology for viral detection

Nanotechnology-based diagnostic methods for coronavirus: From nucleic acid extraction to amplification

The recent emergence of human coronaviruses (CoVs) causing severe acute respiratory syndrome (SARS) is posing a great threat to global public health. Therefore, the rapid and accurate identification of pathogenic viruses plays a vital role in selecting appropriate treatments, saving people's lives and preventing epidemics. Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are natural biopolymers composed of nucleotides that store, transmit, and express genetic information. Applications of nucleic acid detection range from genotyping and genetic prognostics, to expression profiling and detection of infectious disease. The nucleic acid detection for infectious diseases is widely used, as evidenced by the widespread use of COVID-19 tests for the containment of the pandemic. Nanotechnology influences all medical disciplines and has been considered as an essential tool for novel diagnostics, nanotherapeutics, vaccines, medical imaging, and the utilization of biomaterials for regenerative medicine. In this review, the recent advances in the development of nanotechnology-based diagnostic methods for coronavirus, and their applications in nucleic acid detection are discussed in detail. The techniques for the amplification of nucleic acids are summarized, as well as the use of magnetic nanoparticles for nucleic acid extraction. Besides, current challenges and future prospects are proposed, along with the great potential of nanotechnology for the effective diagnosis of coronavirus.

Functional Nanomaterials Enhancing Electrochemical Biosensors as Smart Tools for Detecting Infectious Viral Diseases

Electrochemical biosensors are known as analytical tools, guaranteeing rapid and on-site results in medical diagnostics, food safety, environmental protection, and life sciences research. Current research focuses on developing sensors for specific targets and addresses challenges to be solved before their commercialization. These challenges typically include the lowering of the limit of detection, the widening of the linear concentration range, the analysis of real samples in a real environment and the comparison with a standard validation method. Nowadays, functional nanomaterials are designed and applied in electrochemical biosensing to support all these challenges. This review will address the integration of functional nanomaterials in the development of electrochemical biosensors for the rapid diagnosis of viral infections, such as COVID-19, middle east respiratory syndrome (MERS), influenza, hepatitis, human immunodeficiency virus (HIV), and dengue, among others. The role and relevance of the nanomaterial, the type of biosensor, and the electrochemical technique adopted will be discussed. Finally, the critical issues in applying laboratory research to the analysis of real samples, future perspectives, and commercialization aspects of electrochemical biosensors for virus detection will be analyzed.

Recent Developments in Nanotechnology-Based Biosensors for the Diagnosis of Coronavirus

The major challenge in today's world is that medical research is facing the existence of a vast number of viruses and their mutations, which from time to time cause outbreaks. Also, the continuous and spontaneous mutations occurring in the viruses and the emergence of resistant virus strains have become serious medical hazards. So, in view of the growing number of diseases, like the recent COVID-19 pandemic that has caused the deaths of millions of people, there is a need to improve rapid and sensitive diagnostic strategies to initiate timely treatment for such conditions. In the cases like COVID-19, where a real cure due to erratic and ambiguous signs is not available, early intervention can be life-saving. In the biomedical and pharmaceutical industries, nanotechnology has evolved exponentially and can overcome multiple obstacles in the treatment and diagnosis of diseases. Nanotechnology has developed exponentially in the biomedical and pharmaceutical fields and can overcome numerous challenges in the treatment and diagnosis of diseases. At the nano stage, the molecular properties of materials such as gold, silver, carbon, silica, and polymers get altered and can be used for the creation of reliable and accurate diagnostic techniques. This review provides insight into numerous diagnostic approaches focused on nanoparticles that could have been established for quick and early detection of such diseases.

Advances in Nanotechnology as a Potential Alternative for Plant Viral Disease Management

Plant viruses cause enormous losses in agricultural production accounting for about 47% of the total overall crop losses caused by plant pathogens. More than 50% of the emerging plant diseases are reported to be caused by viruses, which are inevitable or unmanageable. Therefore, it is essential to devise novel and effective management strategies to combat the losses caused by the plant virus in economically important crops. Nanotechnology presents a new tendency against the increasing challenges in the diagnosis and management of plant viruses as well as plant health. The application of nanotechnology in plant virology, known as nanophytovirology, includes disease diagnostics, drug delivery, genetic transformation, therapeutants, plant defense induction, and bio-stimulation; however, it is still in the nascent stage. The unique physicochemical properties of particles in the nanoscale allow greater interaction and it may knock out the virus particles. Thus, it opens up a novel arena for the management of plant viral diseases. The main objective of this review is to focus on the mounting collection of tools and techniques involved in the viral disease diagnosis and management and to elucidate their mode of action along with toxicological concerns.

Direct detection of virus-like particles using color images of plasmonic nanostructures

We propose a measurement method for sensitive and label-free detections of virus-like particles (VLPs) using color images of nanoplasmonic sensing chips. The nanoplasmonic chip consists of 5×5 gold nanoslit arrays and the gold surface is modified with specific antibodies for spike protein. The resonant wavelength of the 430-nm-period gold nanoslit arrays underwater environment is about 570 nm which falls between the green and red bands of the color CCD. The captured VLPs by the specific antibodies shift the plasmonic resonance of the gold nanoslits. It results in an increased brightness of green pixels and decreased brightness of red pixels. The image contrast signals of (green - red) / (red + green) show good linearity with the surface particle density. The experimental tests show the image contrast method can detect 100-nm polystyrene particles with a surface density smaller than 2 particles/µm². We demonstrate the application for direct detection of SARS-CoV-2 VLPs using a simple scanner platform. A detection limit smaller than 1 pg/mL with a detection time less than 30 minutes can be achieved.

Micro and Nanoscale Technologies for Diagnosis of Viral Infections

Viral infection is one of the leading causes of mortality worldwide. The growth of globalization significantly increases the risk of virus spreading, making it a global threat to future public health. In particular, the ongoing coronavirus disease 2019 (COVID-19) pandemic outbreak emphasizes the importance of devices and methods for rapid, sensitive, and cost-effective diagnosis of viral infections in the early stages by which their quick and global spread can be controlled. Micro and nanoscale technologies have attracted tremendous attention in recent years for a variety of medical and biological applications, especially in developing diagnostic platforms for rapid and accurate detection of viral diseases. This review addresses advances of microneedles, microchip-based integrated platforms, and nano- and microparticles for sampling, sample processing, enrichment, amplification, and detection of viral particles and antigens related to the diagnosis of viral diseases. Additionally, methods for the fabrication of microchip-based devices and commercially used devices are described. Finally, challenges and prospects on the development of micro and nanotechnologies for the early diagnosis of viral diseases are highlighted.

Nucleic Acid Testing of SARS-CoV-2

The coronavirus disease 2019 (COVID-19) has caused a large global outbreak. It is accordingly important to develop accurate and rapid diagnostic methods. The polymerase chain reaction (PCR)-based method including reverse transcription-polymerase chain reaction (RT-PCR) is the most widely used assay for the detection of SARS-CoV-2 RNA. Along with the RT-PCR method, digital PCR has emerged as a powerful tool to quantify nucleic acid of the virus with high accuracy and sensitivity. Non-PCR based techniques such as reverse transcription loop-mediated isothermal amplification (RT-LAMP) and reverse transcription recombinase polymerase amplification (RT-RPA) are considered to be rapid and simple nucleic acid detection methods and were reviewed in this paper. Non-conventional molecular diagnostic methods including next-generation sequencing (NGS), CRISPR-based assays and nanotechnology are improving the accuracy and sensitivity of COVID-19 diagnosis. In this review, we also focus on standardization of SARS-CoV-2 nucleic acid testing and the activity of the National Metrology Institutes (NMIs) and highlight resources such as reference materials (RM) that provide the values of specified properties. Finally, we summarize the useful resources for convenient COVID-19 molecular diagnostics.

Electrochemical diagnostics of infectious viral diseases: Trends and challenges

Infectious diseases caused by viruses can elevate up to undesired pandemic conditions affecting the global population and normal life function. These in turn impact the established world economy, create jobless situations, physical, mental, emotional stress, and challenge the human survival. Therefore, timely detection, treatment, isolation and prevention of spreading the pandemic infectious diseases not beyond the originated town is critical to avoid global impairment of life (e.g., Corona virus disease - 2019, COVID-19). The objective of this review article is to emphasize the recent advancements in the electrochemical diagnostics of twelve life-threatening viruses namely - COVID-19, Middle east respiratory syndrome (MERS), Severe acute respiratory syndrome (SARS), Influenza, Hepatitis, Human immunodeficiency virus (HIV), Human papilloma virus (HPV), Zika virus, Herpes simplex virus, Chikungunya, Dengue, and Rotavirus. This review describes the design, principle, underlying rationale, receptor, and mechanistic aspects of sensor systems reported for such viruses. Electrochemical sensor systems which comprised either antibody or aptamers or direct/mediated electron transfer in the recognition matrix were explicitly segregated into separate sub-sections for critical comparison. This review emphasizes the current challenges involved in translating laboratory research to real-world device applications, future prospects and commercialization aspects of electrochemical diagnostic devices for virus detection. The background and overall progress provided in this review are expected to be insightful to the researchers in sensor field and facilitate the design and fabrication of electrochemical sensors for life-threatening viruses with broader applicability to any desired pathogens.

Detection of RNA viruses from influenza and HIV to Ebola and SARS-CoV-2: a review

RNA-based viruses likely make up the highest pandemic threat among all known pathogens in about the last 100 years, since the Spanish Flu of 1918 with 50 M deaths up to COVID-19. Nowadays, an efficient and affordable testing strategy for such viruses have become the paramount target for the fields of virology and bioanalytical chemistry. The detection of the viruses (influenza, hepatitis, HIV, Zika, SARS, Ebola, SARS-CoV-2, etc.) and human antibodies to these viruses is described and tabulated in terms of the reported methods of detection, time to results, accuracy and specificity, if they are reported. The review is focused, but not limited to publications in the last decade. Finally, the limits of detection for each representative publication are tabulated by detection methods and discussed. These methods include PCR, lateral flow immunoassays, LAMP-based methods, ELISA, electrochemical methods (e.g., amperometry, voltammetry), fluorescence spectroscopy, AFM, SPR and SERS spectroscopy, silver staining and CRISPR-Cas based methods, bio-barcode detection, and resonance light scattering. The review is likely to be interesting for various scientists, and particularly helpful with information for establishing interdisciplinary research.

Integration of FISH and Microfluidics

Suitable molecular methods for a faster microbial identification in food and clinical samples have been explored and optimized during the last decades. However, most molecular methods still rely on time-consuming enrichment steps prior to detection, so that the microbial load can be increased and reach the detection limit of the techniques.In this chapter, we describe an integrated methodology that combines a microfluidic (lab-on-a-chip) platform, designed to concentrate cell suspensions and speed up the identification process in Saccharomyces cerevisiae , and a peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) protocol optimized and adapted to microfluidics. Microfluidic devices with different geometries were designed, based on computational fluid dynamics simulations, and subsequently fabricated in polydimethylsiloxane by soft lithography. The microfluidic designs and PNA-FISH procedure described here are easily adaptable for the detection of other microorganisms of similar size.

A review of monoclonal antibodies in COVID-19: Role in immunotherapy, vaccine development and viral detection

The harmful COVID-19 pandemic caused by the SARS-CoV-2 coronavirus imposes the scientific community to develop or find conventional curative drugs, protective vaccines, or passive immune strategies rapidly and efficiently. Passive immunity is based on recovering hyper-immune plasma from convalescent patients, or monoclonal antibodies with elevated titer of neutralizing antibodies with high antiviral activity, that have potential for both treatment and prevention. In this review, we focused on researching the potentiality of monoclonal antibodies for the prevention and treatment of COVID-19 infection. Our research review includes antibody-based immunotherapy, using human monoclonal antibodies targeting SARS-CoV-2 viral protein regions, specifically the spike protein regions, and using hyper-immune plasma from convalescent COVID-19 patients, in which monoclonal antibodies act as immunotherapy for the cytokine storm syndrome associated with the COVID-19 infection. In addition, we will demonstrate the role of the monoclonal antibodies in the development of candidate vaccines for SARS-CoV-2. Moreover, the recent progress of the diagnostic mouse monoclonal antibodies' role will be highlighted, as an accurate and rapid diagnostic assay, in the antigen detection of SARS-CoV-2. In brief, the monoclonal antibodies are the potential counter measures that may control SARS-CoV-2, which causes COVID-19 disease, through immunotherapy and vaccine development, as well as viral detection.

Two-Dimensional Material-Based Biosensors for Virus Detection

Viral infections are one of the major causes of mortality and economic losses worldwide. Consequently, efficient virus detection methods are crucial to determine the infection prevalence. However, most detection methods face challenges related to false-negative or false-positive results, long response times, high costs, and/or the need for specialized equipment and staff. Such issues can be overcome by access to low-cost and fast response point-of-care detection systems, and two-dimensional materials (2DMs) can play a critical role in this regard. Indeed, the unique and tunable physicochemical properties of 2DMs provide many advantages for developing biosensors for viral infections with high sensitivity and selectivity. Fast, accurate, and reliable detection, even at early infection stages by the virus, can be potentially enabled by highly accessible surface interactions between the 2DMs and the analytes. High selectivity can be obtained by functionalization of the 2DMs with antibodies, nucleic acids, proteins, peptides, or aptamers, allowing for specific binding to a particular virus, viral fingerprints, or proteins released by the host organism. Multiplexed detection and discrimination between different virus strains are also feasible. In this Review, we present a comprehensive overview of the major advances of 2DM-based biosensors for the detection of viruses. We describe the main factors governing the efficient interactions between viruses and 2DMs, making them ideal candidates for the detection of viral infections. We also critically detail their advantages and drawbacks, providing insights for the development of future biosensors for virus detection. Lastly, we provide suggestions to stimulate research in the fast expanding field of 2DMs that could help in designing advanced systems for preventing virus-related pandemics.

Highly sensitive SERS assay of DENV gene via a cascade signal amplification strategy of localized catalytic hairpin assembly and hybridization chain reaction

Pathogenic viruses with worldwide distribution, high incidence and great harm are significantly and increasingly threatening human health. However, there is still lack of sufficient, highly sensitive and specific detection methods for on-time and early diagnosis of virus infection. In this work, taking dengue virus (DENV) as an example, a highly sensitive SERS assay of DENV gene was proposed via a cascade signal amplification strategy of localized catalytic hairpin assembly (LCHA) and hybridization chain reaction (HCR). The SERS assay was performed by two steps, i.e., the operation of cascade signal amplification strategy and the following SERS measurements by transferring the products on SERS-active AgNRs arrays. The sensitivity of the cascade signal amplification strategy is significantly amplified, which is 4.5 times that of individual CHA, and the signal-to-noise ratio is also improved to 5.4 relative to 1.8 of the CHA. The SERS sensing possesses a linear calibration curve from 1 fM to 10 nM with the limit of detection low to 0.49 fM, and has good specificity, uniformity and recovery, which indicates that the highly sensitive SERS assay provides an attractive tool for reliable, early diagnosis of DENV gene and is worth to be popularized in a wide detection of other viruses.

How can nanotechnology help to combat COVID-19? Opportunities and urgent need

Incidents of viral outbreaks have increased at an alarming rate over the past decades. The most recent human coronavirus known as COVID-19 (SARS-CoV-2) has already spread around the world and shown R0 values from 2.2 to 2.68. However, the ratio between mortality and number of infections seems to be lower in this case in comparison to other human coronaviruses (such as severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV)). These outbreaks have tested the limits of healthcare systems and have posed serious questions about management using conventional therapies and diagnostic tools. In this regard, the use of nanotechnology offers new opportunities for the development of novel strategies in terms of prevention, diagnosis and treatment of COVID-19 and other viral infections. In this review, we discuss the use of nanotechnology for COVID-19 virus management by the development of nano-based materials, such as disinfectants, personal protective equipment, diagnostic systems and nanocarrier systems, for treatments and vaccine development, as well as the challenges and drawbacks that need addressing.

Betanodavirus and VER Disease: A 30-year Research Review

The outbreaks of viral encephalopathy and retinopathy (VER), caused by nervous necrosis virus (NNV), represent one of the main infectious threats for marine aquaculture worldwide. Since the first description of the disease at the end of the 1980s, a considerable amount of research has gone into understanding the mechanisms involved in fish infection, developing reliable diagnostic methods, and control measures, and several comprehensive reviews have been published to date. This review focuses on host–virus interaction and epidemiological aspects, comprising viral distribution and transmission as well as the continuously increasing host range (177 susceptible marine species and epizootic outbreaks reported in 62 of them), with special emphasis on genotypes and the effect of global warming on NNV infection, but also including the latest findings in the NNV life cycle and virulence as well as diagnostic methods and VER disease control.

Detecting Biothreat Agents: From Current Diagnostics to Developing Sensor Technologies

Although a fundamental understanding of the pathogenicity of most biothreat agents has been elucidated and available treatments have increased substantially over the past decades, they still represent a significant public health threat in this age of (bio)terrorism, indiscriminate warfare, pollution, climate change, unchecked population growth, and globalization. The key step to almost all prevention, protection, prophylaxis, post-exposure treatment, and mitigation of any bioagent is early detection. Here, we review available methods for detecting bioagents including pathogenic bacteria and viruses along with their toxins. An introduction placing this subject in the historical context of previous naturally occurring outbreaks and efforts to weaponize selected agents is first provided along with definitions and relevant considerations. An overview of the detection technologies that find use in this endeavor along with how they provide data or transduce signal within a sensing configuration follows. Current "gold" standards for biothreat detection/diagnostics along with a listing of relevant FDA approved in vitro diagnostic devices is then discussed to provide an overview of the current state of the art. Given the 2014 outbreak of Ebola virus in Western Africa and the recent 2016 spread of Zika virus in the Americas, discussion of what constitutes a public health emergency and how new in vitro diagnostic devices are authorized for emergency use in the U.S. are also included. The majority of the Review is then subdivided around the sensing of bacterial, viral, and toxin biothreats with each including an overview of the major agents in that class, a detailed cross-section of different sensing methods in development based on assay format or analytical technique, and some discussion of related microfluidic lab-on-a-chip/point-of-care devices. Finally, an outlook is given on how this field will develop from the perspective of the biosensing technology itself and the new emerging threats they may face.

Gene module analysis of juvenile myelomonocytic leukemia and screening of anticancer drugs

Juvenile myelomonocytic leukemia (JMML) is a rare but severe primary hemopoietic system tumor of childhood, most frequent in children 4 years and younger. There are currently no specific anticancer therapies targeting JMML, and the underlying gene expression changes have not been revealed. To define molecular targets and possible biomarkers for early diagnosis, optimal treatment, and prognosis, we conducted microarray data analysis using the Gene Expression Omnibus, and constructed protein‑protein interaction networks of all differentially expressed genes. Modular bioinformatics analysis revealed four core functional modules for JMML. We analyzed the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway functions associated with these modules. Using the CMap database, nine potential anticancer drugs were identified that modulate expression levels of many JMML‑associated genes. In addition, we identified possible miRNAs and transcription factors regulating these differentially expressed genes. This study defines a new research strategy for developing JMML‑targeted chemotherapies.

Nanotechnology: The new perspective in precision agriculture

Nanotechnology is an interdisciplinary research field. In recent past efforts have been made to improve agricultural yield through exhaustive research in nanotechnology. The green revolution resulted in blind usage of pesticides and chemical fertilizers which caused loss of soil biodiversity and developed resistance against pathogens and pests as well. Nanoparticle-mediated material delivery to plants and advanced biosensors for precision farming are possible only by nanoparticles or nanochips. Nanoencapsulated conventional fertilizers, pesticides and herbicides helps in slow and sustained release of nutrients and agrochemicals resulting in precise dosage to the plants. Nanotechnology based plant viral disease detection kits are also becoming popular and are useful in speedy and early detection of viral diseases. In this article, the potential uses and benefits of nanotechnology in precision agriculture are discussed. The modern nanotechnology based tools and techniques have the potential to address the various problems of conventional agriculture and can revolutionize this sector.

Recent advances in M13 bacteriophage-based optical sensing applications

Recently, M13 bacteriophage has started to be widely used as a functional nanomaterial for various electrical, chemical, or optical applications, such as battery components, photovoltaic cells, sensors, and optics. In addition, the use of M13 bacteriophage has expanded into novel research, such as exciton transporting. In these applications, the versatility of M13 phage is a result of its nontoxic, self-assembling, and specific binding properties. For these reasons, M13 phage is the most powerful candidate as a receptor for transducing chemical or optical phenomena of various analytes into electrical or optical signal. In this review, we will overview the recent progress in optical sensing applications of M13 phage. The structural and functional characters of M13 phage will be described and the recent results in optical sensing application using fluorescence, surface plasmon resonance, Förster resonance energy transfer, and surface enhanced Raman scattering will be outlined.

Nanomaterial-based sensors for the detection of biological threat agents

The danger posed by biological threat agents and the limitations of modern detection methods to rapidly identify them underpins the need for continued development of novel sensors. The application of nanomaterials to this problem in recent years has proven especially advantageous. By capitalizing on large surface/volume ratios, dispersability, beneficial physical and chemical properties, and unique nanoscale interactions, nanomaterial-based biosensors are being developed with sensitivity and accuracy that are starting to surpass traditional biothreat detection methods, yet do so with reduced sample volume, preparation time, and assay cost. In this review, we start with an overview of bioagents and then highlight the breadth of nanoscale sensors that have recently emerged for their detection.

Nonlinear electrical impedance spectroscopy of viruses using very high electric fields created by nanogap electrodes

Our living sphere is constantly exposed to a wide range of pathogenic viruses, which can be either known, or of novel origin. Currently, there is no methodology for continuously monitoring the environment for viruses in general, much less a methodology that allows the rapid and sensitive identification of a wide variety of viruses responsible for communicable diseases. Traditional approaches, based on PCR and immunodetection systems, only detect known or specifically targeted viruses. We here describe a simple device that can potentially detect any virus between nanogap electrodes using nonlinear impedance spectroscopy. Three test viruses, differing in shape and size, were used to demonstrate the general applicability of this approach: baculovirus, tobacco mosaic virus (TMV), and influenza virus. We show that each of the virus types responded differently in the nanogap to changes in the electric field strength, and the impedance of the virus solutions differed depending both on virus type and virus concentration. These preliminary results show that the three virus types can be distinguished and their approximate concentrations determined. Although further studies are required, the proposed nonlinear impedance spectroscopy method may achieve a sensitivity comparable to that of more traditional, but less versatile, virus detection systems.

A generic microfluidic biosensor of G protein-coupled receptor activation – impedance measurements of reversible morphological changes of reverse transfected HEK293 cells on microelectrodes

Flowcell with micro-IDEs (250–500 μm) covered with both stable and reverse transfected cells overexpressing membrane receptors to demonstrate impedance responses to serial injections of analyte.

Carbon nanotube-based lateral flow biosensor for sensitive and rapid detection of DNA sequence

In this article, we describe a carbon nanotube (CNT)-based lateral flow biosensor (LFB) for rapid and sensitive detection of DNA sequence. Amine-modified DNA detection probe was covalently immobilized on the shortened multi-walled carbon nanotubes (MWCNTs) via diimide-activated amidation between the carboxyl groups on the CNT surface and amine groups on the detection DNA probes. Sandwich-type DNA hybridization reactions were performed on the LFB and the captured MWCNTs on test zone and control zone of LFB produced the characteristic black bands, enabling visual detection of DNA sequences. Combining the advantages of lateral flow chromatographic separation with unique physical properties of MWCNT (large surface area), the optimized LFB was capable of detecting of 0.1 nM target DNA without instrumentation. Quantitative detection could be realized by recording the intensity of the test line with the Image J software, and the detection limit of 40 pM was obtained. This detection limit is 12.5 times lower than that of gold nanoparticle (GNP)-based LFB (0.5 nM, Mao et al. Anal. Chem. 2009, 81, 1660-1668). Another important feature is that the preparation of MWCNT-DNA conjugates was robust and the use of MWCNT labels avoided the aggregation of conjugates and tedious preparation time, which were often met in the traditional GNP-based nucleic acid LFB. The applications of MWCNT-based LFB can be extended to visually detect protein biomarkers using MWCNT-antibody conjugates. The MWCNT-based LFB thus open a new door to prepare a new generation of LFB, and shows great promise for in-field and point-of-care diagnosis of genetic diseases and for the detection of infectious agents.

DNA fluorescence shift sensor: a rapid method for the detection of DNA hybridization using silver nanoclusters

DNA-templated silver nanoclusters (AgNC) are a class of subnanometer sized fluorophores with good photostability and brightness. It has been applied as a diagnostic tool mainly for deoxyribonucleic acid (DNA) detection. Integration of DNA oligomers to generate AgNCs is interesting as varying DNA sequences can result in different fluorescence spectra. This allows a simple fluorescence shifting effect to occur upon DNA hybridization with the hybridization efficiency being a pronominal factor for successful shifting. The ability to shift the fluorescence spectra as a result of hybridization overcomes the issue of background intensities in most fluorescent based assays. Here we describe an optimized method for the detection of single-stranded and double-stranded synthetic forkhead box P3 (FOXP3) target by hybridization with the DNA fluorescence shift sensor. The system forms a three-way junction by successful hybridization of AgNC, G-rich strand (G-rich) to the target DNA, which generated a shift in fluorescence spectra with a marked increase in fluorescence intensity. The DNA fluorescence shift sensor presents a rapid and specific alternative to conventional DNA detection.

Fluorescent silver nanoclusters as DNA probes

Fluorescent silver nanoclusters (few atoms, quantum sized) have attracted much attention as promising substitutes for conventional fluorophores. Due to their unique environmental sensitivities, new fluorescent probes have been developed based on silver nanoclusters for the sensitive and specific detection of DNA. In this review we present the recent discoveries of activatable and color-switchable properties of DNA-templated silver nanoclusters and discuss the strategies to use these new properties in DNA sensing.

Micro-scale blood plasma separation: from acoustophoresis to egg-beaters

Plasma is a rich mine of various biomarkers including proteins, metabolites and circulating nucleic acids. The diagnostic and therapeutic potential of these analytes has been quite recently uncovered, and the number of plasma biomarkers will still be growing in the coming years. A significant part of the blood plasma preparation is still handled manually, off-chip, via centrifugation or filtration. These batch methods have variable waiting times, and are often performed under non-reproducible conditions that may impair the collection of analytes of interest, with variable degradation. The development of miniaturised modules capable of automated and reproducible blood plasma separation would aid in the translation of lab-on-a-chip devices to the clinical market. Here we propose a systematic review of major plasma analytes and target applications, alongside existing solutions for micro-scale blood plasma extraction, focusing on the approaches that have been biologically validated for specific applications.

Stochastic model-assisted development of efficient low-dose viral transduction in microfluidics

Adenoviruses are commonly used in vitro as gene transfer vectors in multiple applications. Nevertheless, issues such as low infection efficiency and toxicity effects on host cells have not been resolved yet. This work aims at developing a new versatile tool to enhance the expression of transduced genes while working at low viral doses in a sequential manner. We developed a microfluidic platform with automatically controlled sequential perfusion stages, which includes 10 independent channels. In addition, we built a stochastic mathematical model, accounting for the discrete nature of cells and viruses, to predict not only the percentage of infected cells, but also the associated infecting-virus distribution in the cell population. Microfluidic system and mathematical model were coupled to define an efficient experimental strategy. We used human foreskin fibroblasts, infected by replication-incompetent adenoviruses carrying EGFP gene, as the testing system. Cell characterization was performed through fluorescence microscopy, followed by image analysis. We explored the effect of different aspects: perfusion, multiplicity of infection, and temporal patterns of infection. We demonstrated feasibility of performing efficient viral transduction at low doses, by repeated pulses of cell-virus contact. This procedure also enhanced the exogenous gene expression in the sequential microfluidic infection system compared to a single infection at a higher, nontoxic, viral dose.

DNA/RNA Detection Using DNA-Templated Few-Atom Silver Nanoclusters

DNA-templated few-atom silver nanoclusters (DNA/Ag NCs) are a new class of organic/inorganic composite nanomaterials whose fluorescence emission can be tuned throughout the visible and near-IR range by simply programming the template sequences. Compared to organic dyes, DNA/Ag NCs can be brighter and more photostable. Compared to quantum dots, DNA/Ag NCs are smaller, less prone to blinking on long timescales, and do not have a toxic core. The preparation of DNA/Ag NCs is simple and there is no need to remove excess precursors as these precursors are non-fluorescent. Our recent discovery of the fluorogenic and color switching properties of DNA/Ag NCs have led to the invention of new molecular probes, termed NanoCluster Beacons (NCBs), for DNA detection, with the capability to differentiate single-nucleotide polymorphisms by emission colors. NCBs are inexpensive, easy to prepare, and compatible with commercial DNA synthesizers. Many other groups have also explored and taken advantage of the environment sensitivities of DNA/Ag NCs in creating new tools for DNA/RNA detection and single-nucleotide polymorphism identification. In this review, we summarize the recent trends in the use of DNA/Ag NCs for developing DNA/RNA sensors.

Integration of gold nanoparticles in PDMS microfluidics for lab-on-a-chip plasmonic biosensing of growth hormones

Gold nanoparticles were synthesized in a poly(dimethylsiloxane) (PDMS) microfluidic chip by using an in-situ method, on the basis of reductive properties of the cross-linking agent of PDMS. The proposed integrated device was further used as a sensitive and low-cost LSPR-based biosensor for the detection of polypeptides. Synthesis of nanoparticles in the microfluidic environment resulted in improvement of size distribution with only 8% variation, compared with the macro-environment that yields about 67% variation in size. The chemical kinetics of the in-situ reaction in the microfluidic environment was studied in detail and compared with the reaction carried out at the macro-scale. The effect of temperature and gold precursor concentration on the kinetics of the reaction was investigated and the apparent activation energy was estimated to be Ea*=30 kJ/mol. The sensitivity test revealed that the proposed sensor has a high sensitivity of 74 nm/RIU to the surrounding medium. The sensing of bovine growth hormone also known as bovine somatotropin (bST) shows that the proposed biosensor can reach a detection limit of as low as 3.7 ng/ml (185 pM). The results demonstrate the successful integration of microfluidics and nanoparticles which provides a potential alternative for protein detection in clinical diagnostics.

Applications of microfluidics for molecular diagnostics

Diagnostic assays implemented in microfluidic devices have developed rapidly over the past decade and are expected to become commonplace in the next few years. Hundreds of microfluidics-based approaches towards clinical diagnostics and pathogen detection have been reported with a general theme of rapid and customizable assays that are potentially cost-effective. This chapter reviews microfluidics in molecular diagnostics based on application areas with a concise review of microfluidics in general. Basic principles of microfabrication are briefly reviewed and the transition to polymer fabricated devices is discussed. Most current microfluidic diagnostic devices are designed to target a single disease, such as a given cancer or a variety of pathogens, and there will likely be a large market for these focused devices; however, the future of molecular diagnostics lies in highly multiplexed microfluidic devices that can screen for potentially hundreds of diseases simultaneously.

Cell-Based Biosensors: Electrical Sensing in Microfluidic Devices

Cell-based biosensors provide new horizons for medical diagnostics by adopting complex recognition elements such as mammalian cells in microfluidic devices that are simple, cost efficient and disposable. This combination renders possible a new range of applications in the fields of diagnostics and personalized medicine. The review looks at the most recent developments in cell-based biosensing microfluidic systems with electrical and electrochemical transduction, and relevance to medical diagnostics.

An integrated chip capable of performing sample pretreatment and nucleic acid amplification for HIV-1 detection

This study reports on a microfluidic system equipped with a sample pretreatment device and a nucleic acid amplification device for the rapid diagnosis of the human immunodeficiency virus-1 (HIV-1). The system analyzed proviral deoxyribonucleic acid (DNA) from an HIV-infected Jurkat T cell line. In order to ensure accurate diagnosis among other prevalent B-type strains, simultaneous detections of four conserved HIV-1 B-type DNA fragments were performed in this integrated microfluidic system. The entire protocol including cell lysis, extraction of DNA, polymerase chain reaction (PCR), and optical detection were successfully integrated in order to perform a rapid, automated diagnosis. Experimental results showed that four primer sets with conserved HIV-1 B-type sequences specific for the 167-bp RU5 promoter region, the 424-bp int, the 117-bp tat, and the 162-bp vpr coding regions were successfully amplified from the respective regions of the proviral DNA, even from a single infected cell. This accurate real-time detection was achieved within 95 min using the integrated optical system.

Microfluidic reactors for diagnostics applications

Diagnostic assays are an important part of health care, both in the clinic and in research laboratories. In addition to improving treatments and clinical outcomes, rapid and reliable diagnostics help track disease epidemiology, curb infectious outbreaks, and further the understanding of chronic illness. Disease markers such as antigens, RNA, and DNA are present at low concentrations in biological samples, such that the majority of diagnostic assays rely on an amplification reaction before detection is possible. Ideally, these amplification reactions would be sensitive, specific, inexpensive, rapid, integrated, and automated. Microfluidic technology currently in development offers many advantages over conventional benchtop reactions that help achieve these goals. The small reaction volumes and energy consumption make reactions cheaper and more efficient in a microfluidic reactor. Additionally, the channel architecture could be designed to perform multiple tests or experimental steps on one integrated, automated platform. This review explores the current research on microfluidic reactors designed to aid diagnostic applications, covering a broad spectrum of amplification techniques and designs.

Label-free virus detection using silicon photonic microring resonators

Viruses represent a continual threat to humans through a number of mechanisms, which include disease, bioterrorism, and destruction of both plant and animal food resources. Many contemporary techniques used for the detection of viruses and viral infections suffer from limitations such as the need for extensive sample preparation or the lengthy window between infection and measurable immune response, for serological methods. In order to develop a method that is fast, cost-effective, and features reduced sample preparation compared to many other virus detection methods, we report the application of silicon photonic microring resonators for the direct, label-free detection of intact viruses in both purified samples as well as in a complex, real-world analytical matrix. As a model system, we demonstrate the quantitative detection of Bean pod mottle virus, a pathogen of great agricultural importance, with a limit of detection of 10 ng/mL. By simply grinding a small amount of leaf sample in buffer with a mortar and pestle, infected leaves can be identified over a healthy control with a total analysis time of less than 45 min. Given the inherent scalability and multiplexing capability of the semiconductor-based technology, we feel that silicon photonic microring resonators are well-positioned as a promising analytical tool for a number of viral detection applications.

Challenges in environmental detection of human viral pathogens

There is substantial potential for human exposure to viruses in environmental matrixes. Identification of virally contaminated environmental reservoirs requires assays with sufficient sensitivity to detect low copy numbers of viral targets. However, low detection sensitivity frequently requires sample concentration during which inhibitors to downstream assays co-isolate with desired target. Conventional detection assays (e.g., cell culture, polymerase chain reaction) require a priori selection of appropriate cell lines or primers and probes based on the viruses anticipated to be present in the sample. This can underestimate exposure risks by excluding unidentified or unknown virus. Emerging methods including nonspecific adsorption/elution, filtration, and total nucleic acid sequencing, that are capable of concentrating, purifying, and detecting total virus and/or total virus nucleic acid will aid in estimates of exposure risk, source tracking, intervention efficacy, and evaluation of virus fate and transport. Development and implementation of novel virus detection techniques must integrate quality assurance guidelines to validate results and provide opportunities for interstudy comparison.

Polymer based biosensor for rapid electrochemical detection of virus infection of human cells

The demand in the field of medical diagnostics for simple, cost efficient and disposable devices is growing. Here, we present a label free, all-polymer electrochemical biosensor for detection of acute viral disease. The dynamics of a viral infection in human cell culture was investigated in a micro fluidic system on conductive polymer PEDOT:TsO microelectrodes by electrochemical impedance spectroscopy and video time lapse microscopy. Employing this sensitive, real time electrochemical technique, we could measure the immediate cell response to cytomegalovirus, and detect an infection within 3h, which is several hours before the cytopathic effect is apparent with conventional imaging techniques. Atomic force microscopy and scanning ion conductance microscopy imaging consolidate the electrochemical measurements by demonstrating early virus induced changes in cell morphology of apparent programmed cell death.

Microfluidic blood filtration device

Rapid decentralized biomedical diagnostics have become increasingly necessary in a medical environment of growing costs and mounting demands on healthcare personnel and infrastructure. Such diagnostics require low-cost novel devices that can operate at bedside or in doctor offices using small amounts of sample that can be extracted and processed on the spot. Thus, point-of-care sample preparation is an important component of the necessary diagnostic paradigm shift. We therefore introduce a microfluidic device which produces plasma from whole blood. The device is inexpensive, reliable, easy to fabricate, and requires only 3.5 kPa pressure to operate. The device is fully compatible with microfluidic diagnostic chips. The output 23-gauge microtube of the former can be directly plugged into the input ports of the latter allowing immediate applicability in practice as a sample-prep pre-stage to a variety of emergent microfluidic diagnostic devices. In addition, the shown approach of filter encapsulation in elastomer has principle importance as it is compatible with and applicable to microfluidic sample-prep integration with analytical stages within the same elastomeric chip. This can eventually lead to finger-prick blood tests in point-of-care settings.

Microfluidics in macro-biomolecules analysis: macro inside in a nano world

Use of microfluidic devices in the life sciences and medicine has created the possibility of performing investigations at the molecular level. Moreover, microfluidic devices are also part of the technological framework that has enabled a new type of scientific information to be revealed, i.e. that based on intensive screening of complete sets of gene and protein sequences. A deeper bioanalytical perspective may provide quantitative and qualitative tools, enabling study of various diseases and, eventually, may offer support for the development of accurate and reliable methods for clinical assessment. This would open the way to molecule-based diagnostics, i.e. establish accurate diagnosis and disease prognosis based on identification and/or quantification of biomacromolecules, for example proteins or nucleic acids. Finally, the development of disposable and portable devices for molecule-based diagnosis would provide the perfect translation of the science behind life-science research into practical applications dedicated to patients and health practitioners. This review provides an analytical perspective of the impact of microfluidics on the detection and characterization of bio-macromolecules involved in pathological processes. The main features of molecule-based diagnostics and the specific requirements for the diagnostic devices are discussed. Further, the techniques currently used for testing bio-macromolecules for potential diagnostic purposes are identified, emphasizing the newest developments. Subsequently, the challenges of this type of application and the status of commercially available devices are highlighted, and future trends are noted.

Concentration and purification of human immunodeficiency virus type 1 virions by microfluidic separation of superparamagnetic nanoparticles

The low concentration and complex sample matrix of many clinical and environmental viral samples presents a significant challenge in the development of low cost, point-of-care viral assays. To address this problem, we investigated the use of a microfluidic passive magnetic separator combined with on-chip mixer to both purify and concentrate whole-particle human immunodeficiency virus type 1 (HIV-1) virions. Virus-containing plasma samples are first mixed to allow specific binding of the viral particles with antibody-conjugated superparamagnetic nanoparticles, and several passive mixer geometries were assessed for their mixing efficiencies. The virus-nanoparticle complexes are then separated from the plasma in a novel magnetic separation chamber, where packed micrometer-sized ferromagnetic particles serve as high magnetic gradient concentrators for an externally applied magnetic field. Thereafter, a viral lysis buffer was flowed through the chip and the released HIV proteins were assayed off-chip. Viral protein extraction efficiencies of 62% and 45% were achieved at 10 and 30 muL/min throughputs, respectively. More importantly, an 80-fold concentration was observed for an initial sample volume of 1 mL and a 44-fold concentration for an initial sample volume of 0.5 mL. The system is broadly applicable to microscale sample preparation of any viral sample and can be used for nucleic acid extraction as well as 40-80-fold enrichment of target viruses.