A lab-on-a-chip for the concurrent electrochemical detection of SARS-CoV-2 RNA and anti-SARS-CoV-2 antibodies in saliva and plasma

A rapid and ultrasensitive RPA-assisted CRISPR-Cas12a/Cas13a nucleic acid diagnostic platform with a smartphone-based portable device

The spread of infectious diseases can be controlled by early identification of the source of infection and timely diagnosis to stop transmission. Real-time fluorescence quantitative polymerase chain reaction (PCR) is the current gold standard for pathogen diagnosis, with high detection sensitivity and accuracy. However, due to the need for specialized equipment, laboratories, and personnel, it is difficult to achieve rapid and immediate diagnosis during large-scale infectious disease outbreaks. Herein, an optimized CRISPR-based nucleic acid detection method was developed that reduces the CRISPR detection time to 15 min while maintaining high sensitivity. By using nucleic acid extraction-free and lyophilization techniques, the 'sample-in-result-out' detection of the two target genes of SARS-CoV-2, the human internal reference gene, and the negative quality control sample can be completed in 20 min, with a sensitivity of 0.5 copies/μL. Additionally, to facilitate the application, a smartphone-based reverse transcription-recombinase polymerase amplification (RT-RPA)-assisted CRISPR-rapid, portable nucleic acid detection device was developed, integrating functions such as heating, centrifugation, mixing, optical detection and result output. Process control, output, and uploading of detection results were conducted through smartphones. The device is not dependent on a power supply and can perform on-site rapid virus detection in resource-limited settings. Real-time uploading of results helps to rapidly implement epidemic prevention and control measures, providing an innovative means of detection, control, and prevention of virus-based infectious diseases. This important work provides a new and effective tool to manage potential future outbreaks of infectious diseases.

Hydrogel-based 3D printing technology: From interfacial engineering to precision medicine

Advances in 3D printing technology and the development of hydrogel-based inks have significantly enhanced the potential of precision medicine, promoting progress in medical diagnosis and treatment. The development of 3D printing enables the fabrication of complex gradient structures that emulate natural tissue environments, while advancements in interface engineering facilitate the precise control of interface properties, thereby enhancing the performance of hydrogels in biomedical applications. This review focuses on the latest advancements in three critical 3D printing application areas: efficient real-time detection, drug delivery systems, and regenerative medicine. The application of 3D printing technology enhances nucleic acid-based molecular diagnostic platforms and wearable biosensors for real-time monitoring of physiological parameters, thereby providing robust support for early disease diagnosis. Additionally, it facilitates the development of targeted and controlled drug delivery systems, which offer promising methods for efficient drug utilization, and enables the construction of complex tissue and organ structures with bioactivity and functionality, providing new solutions for regenerative medicine. Collectively, these advancements propel the ongoing progress and development of precision medicine. Furthermore, the challenges associated with 3D printing technology in these three major applications are discussed along with an outlook on prospects.

Catalytic hairpin assembly-and-cyclization aptasensing for AND-logic detection of protein- and RNA-targets in ribonucleoprotein

Both immunological and molecular diagnostics are essential in disease control. However, due to the different technical routes, existing diagnostic tools mainly focus on either immunological or molecular targets at a time, resulting in restricted information for assessment. Herein, we report a DNA operational amplifier circuit for AND-logic analysis of nucleoprotein and RNA of SARS-CoV-2 ribonucleoprotein. The operator is realized using an aptamer-hairpin probe and a padlock-hairpin probe for nucleoprotein- and ligase-catalyzed hairpin assembly-and-cyclization (CHAC). Given approximately 1000 nucleoproteins per virion in coronavirus, a rolling circle amplification (RCA)-based preamplifier is applied to adjust the input bias by converting the target sequence into an aptamer-hairpin input for CHAC. After CHAC, cyclized padlock-hairpin probes trigger another round of RCA as a post-operator amplifier, producing amplicon coils that aggregate detection probe-modified magnetic nanoparticles. These stepwise homogeneous reaction processes are conducted in a single tube for optomagnetic sensing, offering detection limits of 0.07 ng/mL and 1.5 fM for the protein and the molecular targets of SARS-CoV-2, respectively. The stability, specificity, and accuracy of the circuit are validated by testing serum samples, salmon sperm samples, biased inputs, and 33 clinical nasopharyngeal swab specimens, demonstrating the practicability of simultaneously analyzing immunological and molecular targets for accurate diagnostics.

Bioelectroanalytical Technologies for Advancing the Frontiers To Democratize Personalized Desired Health

The breakthroughs experienced in the development of cutting-edge, reliable, and multipurpose (bio)electroanalytical technologies and their successful incursion into underexplored scenarios have demonstrated their unique potential to act as enablers of the ongoing transformation from reactive to predictive, preventive, personalized, and participatory healthcare, currently known as "P4" medicine. This transformation, more than a vision, is a necessity to achieve a new generation of more efficient, sustainable, and tailored to individual needs healthcare. This promising outlook is the focus of this Perspective, which in addition to highlighting some of the most shocking related research over the last 5 years, offers a prospective and insightful view of the opportunities and imminent advances that shape the future of these fascinating technologies.

Nanoparticle-supported, rapid, digital quantification of neutralizing antibodies against SARS-CoV-2 variants

The measurement of neutralizing immune responses to viral infection is essential, given the heterogeneity of human immunity and the emergence of new virus strains. However, neutralizing antibody (nAb) assays often require high-level biosafety containment, sophisticated instrumentation, and long detection times. Here, as a proof-of-principle, we designed a nanoparticle-supported, rapid, electronic detection (NasRED) assay to assess the neutralizing potency of monoclonal antibodies (mAbs) against SARS-CoV-2. The gold nanoparticles (AuNPs) coated with human angiotensin-converting enzyme 2 (ACE2) protein as nAb potency reporters were mixed with the mAbs to be tested, as well as streptavidin-conjugated multivalent spike (S) protein or their receptor binding domains (RBD). High-affinity and ACE2-competitive nAbs alter the S (or RBD)-to-ACE2 binding level and modulate AuNP cluster formation and precipitation. The amount of free-floating AuNP reporters is quantified by a semiconductor-based readout system that measures the AuNPs' optical extinction, producing nAb signals that can differentiate SARS-CoV-2 variants (Wuhan-Hu-1, Gamma, and Omicron). The modular design nature, short assay time (less than 30 min), and portable and inexpensive readout system make this NasRED-nAb assay applicable to measuring vaccine potency, immune responses to infection, and the efficacy of antibody-based therapies.

A tube-based biosensor for DNA and RNA detection

Affordable, sensitive, and simplified DNA/RNA detection is important for disease diagnosis and enables timely medical intervention measures. Usually, high sensitivity depends on expensive instruments and sophisticated procedures, making sensitivity contradict affordability and simplicity. Here, we proposed an ultra-sensitive single-tube biosensor (USTB) where users can visually detect targets by observing the liquid motion state in a glass tube. The developed instrument-free USTB performed low-cost ($0.1), fast (1 min), and ultra-sensitive detection for both the DNA/RNA fragments (≤1 aM) and the clinical positive samples, which commercial reverse transcription polymerase chain reaction (RT-PCR) and PCR kits could not effectively recognize. Furthermore, USTB is promising to be easily applied to detect other-type biomarkers by the designed smart sensing unit.

Interfacial engineering for biomolecule immobilisation in microfluidic devices

Microfluidic devices are used for various applications in biology and medicine. From on-chip modelling of human organs for drug screening and fast and straightforward point-of-care (POC) detection of diseases to sensitive biochemical analysis, these devices can be custom-engineered using low-cost techniques. The microchannel interface is essential for these applications, as it is the interface of immobilised biomolecules that promote cell capture, attachment and proliferation, sense analytes and metabolites or provide enzymatic reaction readouts. However, common microfluidic materials do not facilitate the stable immobilisation of biomolecules required for relevant applications, making interfacial engineering necessary to attach biomolecules to the microfluidic surfaces. Interfacial engineering is performed through various immobilisation mechanisms and surface treatment techniques, which suitably modify the surface properties like chemistry and energy to obtain robust biomolecule immobilisation and long-term storage stability suitable for the final application. In this review, we provide an overview of the status of interfacial engineering in microfluidic devices, covering applications, the role of biomolecules, their immobilisation pathways and the influence of microfluidic materials. We then propose treatment techniques to optimise performance for various biological and medical applications and highlight future areas of development.

Lab-in-a-Tip: a multiplex immunoassay platform based on a self-assembled barcoded protein array

High throughput immunoassay is increasingly crucial for both scientific and clinical applications. Here we propose a "Lab-in-a-Tip" (LIT) concept to fabricate a pipette tip containing a high-density protein array and other essential reagents. The protein array is made by self-assembling digitally encoded microparticles inside the modified tip. Mounted on a robotic workstation, it automates liquid-handling steps. Notably, compared with Luminex, the current gold standard in multiplex immunoassays, such a design enables LIT to demonstrate multiple advantages in terms of analytical sensitivity, speed, and throughput. It detects analyte concentrations as low as fg/ml, representing a sensitivity improvement of two orders of magnitude over Luminex. Incubation time is reduced to 15 minutes from Luminex's 210 minutes. Furthermore, LIT requires only 10 µl of sample, one-fifth of what Luminex needs. This makes LIT ideal for rapid diagnostics and studies with limited biological samples, greatly expanding its application scope.

Deep-Learning-Assisted Microfluidic Immunoassay via Smartphone-Based Imaging Transcoding System for On-Site and Multiplexed Biosensing

Point-of-care testing (POCT) with multiplexed capability, ultrahigh sensitivity, affordable smart devices, and user-friendly operation is critically needed for clinical diagnostics and food safety. This study presents a deep-learning-assisted microfluidic immunoassay platform that uses a smartphone-based imaging transcoding system, polystyrene microsphere-based encoding, and artificial-intelligence-assisted decoding. Microspheres of varying sizes act as multiprobes, with their quantities correlating to target concentrations after an immunoreaction and separation-filtration within the microfluidic chip. A smartphone with intelligent decoding software captures images of multiprobes from the chip and performs classification, counting, and concentration calculations. The "encoding-decoding" strategy and integrated microfluidic chip design allow these processes to be completed in simple steps, eliminating the need for additional immunomagnetic separation. As a proof of concept, this platform successfully detected multiple respiratory viruses and antibiotics in various real samples with high sensitivity within 30 min, demonstrating great potential as a smart, universal toolkit for next-generation POCT applications.

Target-driven functionalized DNA hydrogel capillary sensor for SARS-CoV-2 dual-mode detection

Coronavirus disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused secondary pandemic, which still poses a serious threat to physical health and economic development. Herein, the target-driven functionalized DNA hydrogel capillary sensor based on cascade signal amplification and carbon coated cobalt manganese modified by prussian blue and platinum nanoparticles (MnCo@C-Pt-PB NPs) has been successfully developed for dual-mode detection of SARS-CoV-2. The cascade signal amplification triggered by target RNA causes the permeability of the DNA hydrogel loaded in the capillary to be destroyed, thereby releasing the embedded MnCo@C-Pt-PB NPs as signal molecules into 3,3',5,5'-tetramethylbenzidine/hydrogen peroxide (TMB/H2O2) solution under the driving of capillarity. The colorless TMB is then catalyzed to blue oxidation products (oxTMB) due to peroxidase-like activity of MnCo@C-Pt-PB NPs, and MnCo@C-Pt-PB NPs and oxTMB with photothermal properties synergistically increase the system temperature under near-infrared irradiation, which are recorded by portable devices to achieve dual-mode detection. Signals intensity are proportional to the logarithm of T-RNA concentration in a wide detection range (100 aM-100 pM), with a detection limit of 100 aM. Moreover, the reliability of the developed method in oropharyngeal swabs samples has also been validated. The signal conversion and amplification function of functionalized DNA hydrogel enhances the convenience, sensitivity and versatility of the developed method, which is promising to be applied in environmental safety, molecular diagnostic assays and disease prevention.

Rapid Bacterial/Viral Infections Typing Strategy Using a Portable Dual-Channel Electrochemical Biosensor Based on One-Step Assembly of Immunomagnetic Beads

Amidst multiple epidemics, a rapid, sensitive, economical, and portable infection diagnosis strategy is crucial for primary medical care, particularly through the analysis of pathogen sources to determine appropriate antibiotic use. C-reactive protein (CRP) and serum amyloid A (SAA) are host-related biomarkers, and their combined detection can effectively distinguish between bacterial and viral infections, which holds great significance for the diagnosis of unknown pathogens. In this work, a portable dual-channel electrochemical biosensor based on a one-step assembly of immunomagnetic beads was proposed for the on-site combined detection of plasma CRP and SAA, which streamlined the operation and shortened the minimum detection time to less than 3 min. The biosensor exhibited excellent linearity in the detection of 3.125-1250 ng/mL CRP and 31.25-1250 ng/mL SAA, with detection limits of 0.91 and 12 ng/mL, respectively, falling within the clinically relevant reference range. Through simulated sample tests, the biosensor effectively distinguished between bacterial infection, viral infection, and healthy plasma samples. The actual sample tests demonstrated a high correlation and comparable medical value to enzyme-linked immunosorbent assay. Overall, this proposed strategy showed potential to aid in infection diagnosis and enable rapid combined detection of multiple biomarkers.

Recent Advances in Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-Associated Proteins System-Based Biosensors

High-sensitivity and high-specificity biodetection is critical for advancing applications in life sciences, biosafety, food safety, and environmental monitoring. CRISPR/Cas systems have emerged as transformative tools in biosensing due to their unparalleled specificity, programmability, and unique enzymatic activities. They exhibit two key cleavage behaviors: precise ON-target cleavage guided by specific protospacers, which ensures accurate target recognition, and bystander cleavage activity triggered upon target binding, which enables robust signal amplification. These properties make CRISPR/Cas systems highly versatile for designing biosensors for ultra-sensitive detection. This review comprehensively explores recent advancements in CRISPR/Cas system-based biosensors, highlighting their impact on improving biosensing performance. We discuss the integration of CRISPR/Cas systems with diverse signal readout mechanisms, including electrochemical, fluorescent, colorimetric, surface-enhanced Raman scattering (SERS), and so on. Additionally, we examine the development of integrated biosensing systems, such as microfluidic devices and portable biosensors, which leverage CRISPR/Cas technology for point-of-care testing (POCT) and high-throughput analysis. Furthermore, we identify unresolved challenges, aiming to inspire innovative solutions and accelerate the translation of these technologies into practical applications for diagnostics, food, and environment safety.

Comparative Analysis of Machine Learning Algorithms Used for Translating Aptamer-Antigen Binding Kinetic Profiles to Diagnostic Decisions

Current approaches for classifying biosensor data in diagnostics rely on fixed decision thresholds based on receiver operating characteristic (ROC) curves, which can be limited in accuracy for complex and variable signals. To address these limitations, we developed a framework that facilitates the application of machine learning (ML) to diagnostic data for the binary classification of clinical samples, when using real-time electrochemical measurements. The framework was applied to a real-time multimeric aptamer assay (RT-MAp) that captures single-frequency (12.6 Hz) impedance data during the binding of viral protein targets to trimeric aptamers. The impedance data collected from 172 COVID-19 saliva samples were processed through multiple nonlinear regression models to extract nine key features from the transient signals. These features were then used to train three supervised ML algorithms─support vector machine (SVM), artificial neural network (ANN), and random forest (RF)─using a 75:25 training-testing ratio. Traditional ROC-based classification achieved an accuracy of 83.6%, while ML-based models significantly improved performance, with SVM, ANN, and RF achieving accuracies of 86.0%, 100%, and 100%, respectively. The ANN model demonstrated superior performance in handling complex and high-variance biosensor data, providing a robust and scalable solution for improving diagnostic accuracy in point-of-care settings.

Optical Nanopore Blockade Sensors for Multiplexed Detection of Proteins

Enduring challenges for quantitative analysis in nanopore sensing are the detection of low biomarker concentrations in reasonable time frames and the detection of multiple biomarkers in the same sample. Herein we report an optical blockade nanopore sensor strategy that can detect more than a protein at femtomolar concentrations in rapid time (approximately 12 min). This is done using a nanopore array functionalized with an aptamer that can bind to two different but related target proteins. The assay then monitors two different colors of fluorescent particles modified with antibodies specific to the protein of interest, as they block the nanopores using a wide-field microscope. By distinguishing specific and nonspecific blockade events for each nanoparticle based on whether they can be easily pulled out of the nanopores using an electric field, we can simultaneously quantify the concentrations of vascular endothelial growth factor (VEGF) and platelet-derived growth factor (PDGF) down to femtomolar concentrations.

Polymerase Chain Reaction Chips for Biomarker Discovery and Validation in Drug Development

Polymerase chain reaction (PCR) chips are advanced, microfluidic platforms that have revolutionized biomarker discovery and validation because of their high sensitivity, specificity, and throughput levels. These chips miniaturize traditional PCR processes for the speed and precision of nucleic acid biomarker detection relevant to advancing drug development. Biomarkers, which are useful in helping to explain disease mechanisms, patient stratification, and therapeutic monitoring, are hard to identify and validate due to the complexity of biological systems and the limitations of traditional techniques. The challenges to which PCR chips respond include high-throughput capabilities coupled with real-time quantitative analysis, enabling researchers to identify novel biomarkers with greater accuracy and reproducibility. More recent design improvements of PCR chips have further expanded their functionality to also include digital and multiplex PCR technologies. Digital PCR chips are ideal for quantifying rare biomarkers, which is essential in oncology and infectious disease research. In contrast, multiplex PCR chips enable simultaneous analysis of multiple targets, therefore simplifying biomarker validation. Furthermore, single-cell PCR chips have made it possible to detect biomarkers at unprecedented resolution, hence revealing heterogeneity within cell populations. PCR chips are transforming drug development, enabling target identification, patient stratification, and therapeutic efficacy assessment. They play a major role in the development of companion diagnostics and, therefore, pave the way for personalized medicine, ensuring that the right patient receives the right treatment. While this tremendously promising technology has exhibited many challenges regarding its scalability, integration with other omics technologies, and conformity with regulatory requirements, many still prevail. Future breakthroughs in chip manufacturing, the integration of artificial intelligence, and multi-omics applications will further expand PCR chip capabilities. PCR chips will not only be important for the acceleration of drug discovery and development but also in raising the bar in improving patient outcomes and, hence, global health care as these technologies continue to mature.

High-throughput multiplexed serology via the mass-spectrometric analysis of isotopically barcoded beads

In serology, each sample is typically tested individually, one antigen at a time. This is costly and time consuming. Serology techniques should ideally allow recurrent measurements in parallel in small sample volumes and be inexpensive and fast. Here we show that mass cytometry can be used to scale up multiplexed serology testing by leveraging polystyrene beads uniformly loaded with combinations of stable isotopes. We generated 18,480 unique isotopically barcoded beads to simultaneously detect, in a single tube with 924 serum samples, the levels of immunoglobulins G and M against 19 proteins from SARS-CoV-2 (a total of 36,960 tests in 400 nl of sample volume and 30 μl of reaction volume). As a rapid, high-throughput and cost-effective technique, serology by mass cytometry may contribute to the effective management of public health emergencies originating from infectious diseases.

An ultra-sensitive fluorescence biosensor with rolling circle amplification and CRISPR/Cas12a one-pot system for FEN1 detection

Flap endonuclease 1 (FEN1), a structure-specific nuclease, has been reported to be widely involved in the development of cancer, and recognized as a new biomarker for cancer. However, there remains a deficiency in the availability of simple, rapid and reliable biosensors for its detection. We have constructed a cascade signal amplification fluorescence biosensor for ultra-sensitive and rapid detection of FEN1. This biosensor relied on FEN1-induced production of the 5' flap DNA, and combined rolling circle amplification (RCA) and CRISPR/Cas12a one-pot system (RCOS). By utilizing branched dsDNA substrates to provoke FEN1 activity, the 5' flap DNA was cleaved and isolated through magnetic separation. Subsequently, these DNA fragments initiated the RCA and CRISPR/Cas12a one-pot exponential amplification reaction, activating the cis and trans-cleavage activity of Cas12a and resulting in a significant fluorescence signal for readout. By combining RCA and CRISPR/Cas12a one-pot cascade signal amplification, the detection signal was remarkable enhanced. The RCOS exhibited excellent sensitivity with a limit of detection (LOD) of 4.1 × 10-7 U/μL, which was more sensitive and expeditious than many other approaches. Furthermore, the biosensor successfully facilitated accurate determination of FEN1 in cell extracts and plasma samples, revealing the potential clinical application and providing a dependable and rapid approach for FEN1 inhibitor screening. Compared with traditional methods, this approach has several benefits including improving the selectivity and sensitivity for FEN1 assay, reducing the complex operation process, and providing a method for the FEN1 inhibition screening.

Rapid and comprehensive detection of viral antibodies and nucleic acids via an acoustofluidic integrated molecular diagnostics chip: AIMDx

Precise and rapid disease detection is critical for controlling infectious diseases like COVID-19. Current technologies struggle to simultaneously identify viral RNAs and host immune antibodies due to limited integration of sample preparation and detection. Here, we present acoustofluidic integrated molecular diagnostics (AIMDx) on a chip, a platform enabling high-speed, sensitive detection of viral immunoglobulins [immunoglobulin A (IgA), IgG, and IgM] and nucleic acids. AIMDx uses acoustic vortexes and Gor'kov potential wells at a 1/10,000 subwavelength scale for concurrent isolation of viruses and antibodies while excluding cells, bacteria, and large (>200 nanometers) vesicles from saliva samples. The chip facilitates on-chip viral RNA enrichment, lysis in 2 minutes, and detection via transcription loop-mediated isothermal amplification, alongside electrochemical sensing of antibodies, including mucin-masked IgA. AIMDx achieved nearly 100% recovery of viruses and antibodies, a 32-fold RNA detection improvement, and an immunity marker sensitivity of 15.6 picograms per milliliter. This breakthrough provides a transformative tool for multiplex diagnostics, enhancing early infectious disease detection.

Direct detection of 4-dimensions of SARS-CoV-2: infection (vRNA), infectivity (antigen), binding antibody, and functional neutralizing antibody in saliva

We developed a 4-parameter clinical assay using Electric Field Induced Release and Measurement (EFIRM) technology to simultaneously assess SARS-CoV-2 RNA (vRNA), nucleocapsid antigen, host binding (BAb) and neutralizing antibody (NAb) levels from a drop of saliva with performance that equals or surpasses current EUA-approved tests. The vRNA and antigen assays achieved lower limit of detection (LOD) of 100 copies/reaction and 3.5 TCID₅₀/mL, respectively. The vRNA assay differentiated between acutely infected (n = 10) and infection-naïve patients (n = 33) with an AUC of 0.9818, sensitivity of 90%, and specificity of 100%. The antigen assay similarly differentiated these patient populations with an AUC of 1.000. The BAb assay detected BAbs with an LOD of 39 pg/mL and distinguished acutely infected (n = 35), vaccinated with prior infection (n = 13), and vaccinated infection-naïve patients (n = 13) from pre-pandemic (n = 81) with AUC of 0.9481, 1.000, and 0.9962, respectively. The NAb assay detected NAbs with a LOD of 31.6 Unit/mL and differentiated between COVID-19 recovered or vaccinated patients (n = 31) and pre-pandemic controls (n = 60) with an AUC 0.923, sensitivity of 87.10%, and specificity of 86.67%. Our combo assay represents a significant technological advancement to simultaneously address SARS-CoV-2 infection and immunity, and it lays the foundation for tackling potential future pandemics.

Isothermal nucleic acid amplification for monitoring hand-foot-and-mouth disease: current status and future implications

With the global prevalence of the hand-foot-and-mouth disease (HFMD) epidemic, the development of reliable point-of-care testing (POCT) is crucial for the timely identification and prevention of outbreaks. Isothermal nucleic acid amplification techniques (INAATs) have attracted much attention because of their high efficiency for rapid diagnosis. In this work, we systematically summarize the current status of INAATs for HFMD and discuss advantages and drawbacks of various INAATs for HFMD. The INAATs for HFMD detection mainly include loop-mediated isothermal amplification (LAMP), simultaneous amplification and testing (SAT), and recombinase polymerase amplification (RPA). Among them, LAMP has excelled in several diagnostic metrics and has made significant progress in the field of POCT. SAT has been effective in overcoming the problem of RNA degradation. RPA is suited for on-site testing due to its rapid amplification rate and low reaction temperature. In addition, this study explores the potential of INAATs in lateral flow strips (LFS) test and microfluidic devices for HFMD. LFS is typically used for qualitative analysis and supports multiple detection. Microfluidics can integrate necessary processes of sample pre-processing, amplification, and signal output, enabling high-throughput qualitative or quantitative detection and demonstrating the potential of monitoring HFMD. We hope the current work will provide insights into INAATs for monitoring HFMD and serve as a reference for the implementation of on-site EV detection for public health.

Microfluidic methods for the diagnosis of acute respiratory tract infections

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

Sensors for surveillance of RNA viruses: a One Health perspective

RNA viruses, especially those capable of cross-species transmission, pose a serious threat to human, animal, and environmental health, as exemplified by the 2024 outbreak of the highly pathogenic avian influenza H5N1 virus in cattle, unpasteurised milk, and workers on dairy farms in the USA. This escalating risk of a new RNA virus pandemic highlights the urgent need to implement One Health strategies. However, the centralised virus detection systems currently in use fall short of meeting the required level of virus surveillance and infection diagnosis, particularly in resource-limited regions. In this context, the latest advancements in RNA virus-sensing technologies offer promising solutions. Through interdisciplinary collaboration, these sensors can achieve sensitivity and reliability similar to that of standard laboratory equipment and offer several advantages, such as compact size, affordability, and operational simplicity. In this Review, we highlight the latest advances in sensing technologies for detecting different biomarkers of viral infections (RNA, antigens, and antibodies). We further compare the sensing principles and performances of these technologies and discuss the possibility of deployment of these sensors in the One Health approach and the challenges expected in this pursuit. In conclusion, the widespread use of RNA virus sensors is expected to enhance the effectiveness of surveillance systems for infectious diseases.

Microfluidic biosensors for biomarker detection in body fluids: a key approach for early cancer diagnosis

Early detection of cancer significantly improves patient outcomes, with biomarkers offering a promising avenue for earlier and more precise diagnoses. Microfluidic biosensors have emerged as a powerful tool for detecting these biomarkers in body fluids, providing enhanced sensitivity, specificity, and rapid analysis. This review focuses on recent advances in microfluidic biosensors from 2018 to 2024, detailing their operational principles, fabrication techniques, and integration with nanotechnology for cancer biomarker detection. Additionally, we have reviewed recent innovations in several aspects of microfluidic biosensors, such as novel detection technologies, nanomaterials and novel microfluidic chip structures, which significantly enhance detection capabilities. We highlight key biomarkers pertinent to early cancer detection and explore how these innovations in biosensor technology contribute to the evolving landscape of personalized medicine. We further explore how these technologies could be incorporated into clinical cancer diagnostic workflows to improve early detection and treatment outcomes. These innovations could help enable more precise and personalized cancer diagnostics. In addition, this review addresses several important issues such as enhancing the scalability and sensitivity of these biosensors in clinical settings and points out future possibilities of combining artificial intelligence diagnostics with microfluidic biosensors to optimize their practical applications. This overview aims to guide future research and clinical applications by addressing current challenges and identifying opportunities for further development in the field of biomarker research.

CRISPR/Cas13a analysis based on NASBA amplification for norovirus detection

Human norovirus (HuNoV) is a leading cause of foodborne diseases worldwide, making rapid and accurate detection crucial for prevention and control. In recent years, the CRISPR/Cas13a system, known for its single-base resolution in RNA recognition and unique collateral cleavage activity, is particularly suitable for sensitive and rapid RNA detection. However, isothermal amplification-based CRISPR/Cas13 assays often require an external transcription step, complicating the detection process. In our study, an efficient diagnostic technique based on the NASBA/Cas13a system was established to identify conserved regions at the ORF1-ORF2 junction of norovirus. The RNA amplification techniques [Nucleic Acid Sequence-Based Amplification (NASBA)] integrates reverse transcription and transcription steps, enabling sensitive, accurate, and rapid enrichment of low-abundance RNA. Furthermore, the CRISPR/Cas13a system provides secondary precise recognition of the amplified products, generating a fluorescence signal through its activated accessory collateral cleavage activity. We optimized the reaction kinetics parameters of Cas13a and achieved a detection limit as low as 51pM. The conditions for the cascade reaction involving CRISPR analysis and RNA amplification were optimized. Finally, we validated the reliability and accuracy of the NASBA/Cas13a method by detecting norovirus in shellfish, achieving results comparable to qRT-PCR in a shorter time and detecting viral loads as low as 10 copies/μL.

Digital CRISPR-Powered Biosensor Concept without Target Amplification Using Single-Impact Electrochemistry

The rapid and reliable detection and quantification of nucleic acids is crucial for various applications, including infectious disease and cancer diagnostics. While conventional methods, such as the quantitative polymerase chain reaction are widely used, they are limited to the laboratory environment due to their complexity and the requirement for sophisticated equipment. In this study, we present a novel amplification-free digital sensing strategy by combining the collateral cleavage activity of the Cas12a enzyme with single-impact electrochemistry. In doing so, we modified silver nanoparticles using a straightforward temperature-assisted cofunctionalization process to subsequently detect the collision events of particles released by the activated Cas12a as distinct current spikes on a microelectrode array. The functionalization resulted in stable DNA-AgNP conjugates, making them suitable for numerous biosensor applications. Thus, our study demonstrates the potential of clustered regularly interspaced short palindromic repeats-based diagnostics combined with impact-based digital sensing for a rapid and amplification-free quantification of nucleic acids.

Compact highly sensitive photothermal RT-LAMP chip for simultaneous multidisease detection

Developing instant detection systems with disease diagnostic capabilities holds immense importance for remote or resource-limited areas. However, the task of creating these systems-which are simultaneously easy to operate, rapid in detection, and cost-effective-remains a challenge. In this study, we present a compact highly sensitive photothermal reverse transcriptase-loop-mediated isothermal amplification (RT-LAMP) chip (SPRC) designed for the detection of multiple diseases. The nucleic acid (NA) amplification on the chip is achieved through LAMP driven by either LED illumination or simple sunlight focusing. SPRC performs sample addition and amplification within a limited volume and autonomous enrichment of NA during the sample addition process, achieving a limit of detection (LOD) as low as 0.2 copies per microliter. Through 120 clinical samples, we achieved an accuracy of 95%, with a specificity exceeding 97.5%. Overall, SPRC has achieved promising progress in the application of point-of-care testing (POCT) by using light energy to simultaneously detect multiple diseases.

Nanoparticle-Supported, Rapid, Digital Quantification of Neutralizing Antibodies Against SARS-CoV-2 Variants

The measurement of neutralizing immune responses to viral infection is essential, given the heterogeneity of human immunity and the emergence of new virus strains. However, neutralizing antibody (nAb) assays often require high-level biosafety containment, sophisticated instrumentation, and long detection times. Here, as a proof-of-principle, we designed a nanoparticle-supported, rapid, electronic detection (NasRED) assay to assess the neutralizing potency of monoclonal antibodies (mAbs) against SARS-CoV-2. The gold nanoparticles (AuNPs) coated with human angiotensin-converting enzyme 2 (ACE2) protein as nAb potency reporters were mixed with the mAbs to be tested, as well as streptavidin-conjugated multivalent spike (S) protein or their receptor binding domains (RBD). High-affinity and ACE2-competitive nAbs alter the S (or RBD)-to-ACE2 binding level and modulate AuNP cluster formation and precipitation. The amount of free-floating AuNP reporters is quantified by a semiconductor-based readout system that measures the AuNPs' optical extinction, producing nAb signals that can differentiate SARS-CoV-2 variants (Wuhan-Hu-1, Gamma, and Omicron). The modular design nature, short assay time (less than 30 minutes), and portable and inexpensive readout system make this NasRED-nAb assay applicable to measuring vaccine potency, immune responses to infection, and the efficacy of antibody-based therapies.

Direct Zeptomole Detection of RNA Biomarkers by Ultrabright Fluorescent Nanoparticles on Magnetic Beads

Nucleic acids are important biomarkers in cancer and viral diseases. However, their ultralow concentration in biological/clinical samples makes direct target detection challenging, because it leads to slow hybridization kinetics with the probe and its insufficient signal-to-noise ratio. Therefore, RNA target detection is done by molecular (target) amplification, notably by RT-PCR, which is a tedious multistep method that includes nucleic acid extraction and reverse transcription. Here, a direct method based on ultrabright dye-loaded polymeric nanoparticles in a sandwich-like hybridization assay with magnetic beads is reported. The ultrabright DNA-functionalized nanoparticle, equivalent to ≈10 000 strongly emissive rhodamine dyes, is hybridized with the magnetic bead to the RNA target, providing the signal amplification for the detection. This concept (magneto-fluorescent sandwich) enables high-throughput detection of DNA and RNA sequences of varied lengths from 48 to 1362 nt with the limit of detection down to 0.3 fm using a plate reader (15 zeptomoles), among the best reported for optical sandwich assays. Moreover, it allows semi-quantitative detection of SARS-CoV-2 viral RNA directly in clinical samples without a dedicated RNA extraction step. The developed technology, combining ultrabright nanoparticles with magnetic beads, addresses fundamental challenges in RNA detection; it is expected to accelerate molecular diagnostics of diseases.

A drug-mediated organic electrochemical transistor for robustly reusable biosensors

Reusable point-of-care biosensors offer a cost-effective solution for serial biomarker monitoring, addressing the critical demand for tumour treatments and recurrence diagnosis. However, their realization has been limited by the contradictory requirements of robust reusability and high sensing capability to multiple interactions among transducer surface, sensing probes and target analytes. Here we propose a drug-mediated organic electrochemical transistor as a robust, reusable epidermal growth factor receptor sensor with striking sensitivity and selectivity. By electrostatically adsorbing protonated gefitinib onto poly(3,4-ethylenedioxythiophene):polystyrene sulfonate and leveraging its strong binding to the epidermal growth factor receptor target, the device operates with a unique refresh-in-sensing mechanism. It not only yields an ultralow limit-of-detection concentration down to 5.74 fg ml-1 for epidermal growth factor receptor but, more importantly, also produces an unprecedented regeneration cycle exceeding 200. We further validate the potential of our devices for easy-to-use biomedical applications by creating an 8 × 12 diagnostic drug-mediated organic electrochemical transistor array with excellent uniformity to clinical blood samples.

Affinity molecular assay for detecting Candida albicans using chitin affinity and RPA-CRISPR/Cas12a

Invasive fungal infections (IFIs) pose a significant threat to immunocompromised individuals, leading to considerable morbidity and mortality. Prompt and accurate diagnosis is essential for effective treatment. Here we develop a rapid molecular diagnostic method that involves three steps: fungal enrichment using affinity-magnetic separation (AMS), genomic DNA extraction with silicon hydroxyl magnetic beads, and detection through a one-pot system. This method, optimized to detect 30 CFU/mL of C. albicans in blood and bronchoalveolar lavage (BAL) samples within 2.5 h, is approximately 100 times more sensitive than microscopy-based staining. Initial validation using clinical samples showed 93.93% sensitivity, 100% specificity, and high predictive values, while simulated tests demonstrated 95% sensitivity and 100% specificity. This cost-effective, highly sensitive technique offers potential for use in resource-limited clinical settings and can be easily adapted to differentiate between fungal species and detect drug resistance.

Digital Quantification and Ultrasensitive Detection of Single Influenza Virus Using Microgel-in-Droplet Enzyme-Linked Immunosorbent Assay

Detection and quantification of viral particles (VPs) facilitate both diagnostics of pathogenic viruses and quality control testing of virus-based products. However, existing technologies fail to afford concurrent ultrasensitive detection and large-scale absolute quantification of VPs. Here, we propose a digital Microgel-in-Droplet enzyme-linked immunosorbent assay (ELISA) system that enables the processing and monitoring of millions of ELISA reactions at the single-VP level by incorporating droplet microfluidics with sandwich ELISA. Upon validating the microfluidic workflow and optimizing ELISA parameters, we demonstrate ultrasensitive VP detection at a limit of detection of 56 PFU/test. Leveraging a fluorescence-based screening platform, we further realize high-throughput digital counting of VPs with a linear detection range of 500-64 000 PFU/test. The precision is comparable to that of the gold standard, the plaque assay, across a wide range of virus concentrations. We anticipate that our system will provide a novel paradigm for the absolute enumeration of various types of viral particles.

CRISPR for companion diagnostics in low-resource settings

New point-of-care tests (POCTs), which are especially useful in low-resource settings, are needed to expand screening capacity for diseases that cause significant mortality: tuberculosis, multiple cancers, and emerging infectious diseases. Recently, clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostic (CRISPR-Dx) assays have emerged as powerful and versatile alternatives to traditional nucleic acid tests, revealing a strong potential to meet this need for new POCTs. In this review, we discuss CRISPR-Dx assay techniques that have been or could be applied to develop POCTs, including techniques for sample processing, target amplification, multiplex assay design, and signal readout. This review also describes current and potential applications for POCTs in disease diagnosis and includes future opportunities and challenges for such tests. These tests need to advance beyond initial assay development efforts to broadly meet criteria for use in low-resource settings.

Harnessing CRISPR/Cas Systems for DNA and RNA Detection: Principles, Techniques, and Challenges

The emergence of CRISPR/Cas systems has revolutionized the field of molecular diagnostics with their high specificity and sensitivity. This review provides a comprehensive overview of the principles and recent advancements in harnessing CRISPR/Cas systems for detecting DNA and RNA. Beginning with an exploration of the molecular mechanisms of key Cas proteins underpinning CRISPR/Cas systems, the review navigates the detection of both pathogenic and non-pathogenic nucleic acids, emphasizing the pivotal role of CRISPR in identifying diverse genetic materials. The discussion extends to the integration of CRISPR/Cas systems with various signal-readout techniques, including fluorescence, electrochemical, and colorimetric, as well as imaging and biosensing methods, highlighting their advantages and limitations in practical applications. Furthermore, a critical analysis of challenges in the field, such as target amplification, multiplexing, and quantitative detection, underscores areas requiring further refinement. Finally, the review concludes with insights into the future directions of CRISPR-based nucleic acid detection, emphasizing the potential of these systems to continue driving innovation in diagnostics, with broad implications for research, clinical practice, and biotechnology.

Revolutionizing Drug Discovery: The Impact of Distinct Designs and Biosensor Integration in Microfluidics-Based Organ-on-a-Chip Technology

Traditional drug development is a long and expensive process with high rates of failure. This has prompted the pharmaceutical industry to seek more efficient drug development frameworks, driving the emergence of organ-on-a-chip (OOC) based on microfluidic technologies. Unlike traditional animal experiments, OOC systems provide a more accurate simulation of human organ microenvironments and physiological responses, therefore offering a cost-effective and efficient platform for biomedical research, particularly in the development of new medicines. Additionally, OOC systems enable quick and real-time analysis, high-throughput experimentation, and automation. These advantages have shown significant promise in enhancing the drug development process. The success of an OOC system hinges on the integration of specific designs, manufacturing techniques, and biosensors to meet the need for integrated multiparameter datasets. This review focuses on the manufacturing, design, sensing systems, and applications of OOC systems, highlighting their design and sensing capabilities, as well as the technical challenges they currently face.

Simplified Electrochemical Approach for End-Point Yet Quantitative Detection of Nucleic Acids in Resource-Limited Settings

Nucleic acid detection plays a crucial role in various aspects of health care, necessitating accessible and reliable quantification methods, especially in resource-limited settings. This work presents a simplified electrochemical approach for end-point yet quantitative nucleic acid detection. By elevating the concentration of redox species and choosing potential as the signals, we achieved enhanced signal robustness, even in the presence of interfering substances. Leveraging this robustness, we accurately measured pH-induced redox potential changes in methylene blue solution for end-point nucleic acid detection after loop-mediated isothermal amplification (LAMP). Our method demonstrated quantitative detection of the SARS-CoV-2 N gene and human ATCB gene and successful discrimination of the human BRAF V600E mutation, comparable in sensitivity to commercial kits. The developed user-friendly electrochemical method offers a simplified and reliable approach for end-point yet quantitative detection of nucleic acids, potentially expanding the benefits of nucleic acid testing in resource-limited settings.

Capillary-driven microchip integrated with nickel phosphide hybrid-modified electrode for the electrochemical detection of glucose

BACKGROUND

Transition metal phosphides with properties similar to platinum metal have received increasing attention for the non-enzymatic detection of glucose. However, the requirement of highly corrosive reagent during sample pretreatment would impose a potential risk to the human body, limiting their practical applications.

RESULTS

In this study, we report a self-powered microfluidic device for the non-enzymatic detection of glucose using nickel phosphide (Ni2P) hybrid as the catalyst. The Ni2P hybrid is synthesized by pyrolysis of metal-organic framework (MOF)-based precursor and in-situ phosphating process, showing two linear detection ranges (1 μM-1 mM, 1 mM-6 mM) toward glucose with the detection limit of 0.32 μM. The good performance of Ni2P hybrid for glucose is attributed to the synergistic effect of Ni2P active sites and N-doped porous carbon matrix. The microchip is integrated with a NaOH-loaded paper pad and a capillary-based micropump, enabling the automatic NaOH redissolution and delivery of sample solution into the detection chamber. Under the optimized condition, the Ni2P hybrid-based microchip realized the detection of glucose in a user-friendly way. Besides, the feasibility of using this microchip for glucose detection in real serum samples has also been validated.

SIGNIFICANCE

This article presents a facile fabrication method utilizing a MOF template to synthesize a Ni2P hybrid catalyst. By leveraging the synergy between the Ni2P active sites and the N-doped carbon matrix, an exceptional electrochemical detection performance for glucose has been achieved. Additionally, a self-powered chip device has been developed for convenient glucose detection based on the pre-established high pH environment on the chip.

Harnessing the power of clustered regularly interspaced short palindromic repeats (CRISPR) based microfluidics for next-generation molecular diagnostics

CRISPR-based (Clustered regularly interspaced short palindromic repeats-based) technologies have revolutionized molecular biology and diagnostics, offering unprecedented precision and versatility. However, challenges remain, such as high costs, demanding technical expertise, and limited quantification capabilities. To overcome these limitations, innovative microfluidic platforms are emerging as powerful tools for enhancing CRISPR diagnostics. This review explores the exciting intersection of CRISPR and microfluidics, highlighting their potential to revolutionize healthcare diagnostics. By integrating CRISPR's specificity with microfluidics' miniaturization and automation, researchers are developing more sensitive and portable diagnostic tools for a range of diseases. These microfluidic devices streamline sample processing, improve diagnostic performance, and enable point-of-care applications, allowing for rapid and accurate detection of pathogens, genetic disorders, and other health conditions. The review discusses various CRISPR/Cas systems, including Cas9, Cas12, and Cas13, and their integration with microfluidic platforms. It also examines the advantages and limitations of these systems, highlighting their potential for detecting DNA and RNA biomarkers. The review also explores the key challenges in developing and implementing CRISPR-driven microfluidic diagnostics, such as ensuring robustness, minimizing cross-contamination, and achieving robust quantification. Finally, it highlights potential future directions for this rapidly evolving field, emphasizing the transformative potential of these technologies for personalized medicine and global health.

Rolosense: Mechanical Detection of SARS-CoV-2 Using a DNA-Based Motor

Assays that detect viral infections play a significant role in limiting the spread of diseases such as SARS-CoV-2. Here, we present Rolosense, a virus sensing platform that leverages the motion of 5 μm DNA-based motors on RNA fuel chips to transduce the presence of viruses. Motors and chips are modified with aptamers, which are designed for multivalent binding to viral targets and lead to stalling of motion. Therefore, the motors perform a "mechanical test" of the viral target and stall in the presence of whole virions, which represents a unique mechanism of transduction distinct from conventional assays. Rolosense can detect SARS-CoV-2 spiked in artificial saliva and exhaled breath condensate with a sensitivity of 103 copies/mL and discriminates among other respiratory viruses. The assay is modular and amenable to multiplexing, as demonstrated by our one-pot detection of influenza A and SARS-CoV-2. As a proof of concept, we show that readout can be achieved using a smartphone camera with a microscopic attachment in as little as 15 min without amplification reactions. Taken together, these results show that mechanical detection using Rolosense can be broadly applied to any viral target and has the potential to enable rapid, low-cost point-of-care screening of circulating viruses.

Sample preparation and detection methods in point-of-care devices towards future at-home testing

Timely and accurate diagnosis is critical for effective healthcare, yet nearly half the global population lacks access to basic diagnostics. Point-of-care (POC) testing offers partial solutions by enabling low-cost, rapid diagnosis at the patient's location. At-home POC devices have the potential to advance preventive care and early disease detection. Nevertheless, effective sample preparation and detection methods are essential for accurate results. This review surveys recent advances in sample preparation and detection methods at POC. The goal is to provide an in-depth understanding of how these technologies can enhance at-home POC devices. Lateral flow assays, nucleic acid tests, and virus detection methods are at the forefront of POC diagnostic technology, offering rapid and sensitive tools for identifying and measuring pathogens, biomarkers, and viral infections. By illuminating cutting-edge research on assay development for POC diagnostics, this review aims to accelerate progress towards widely available, user-friendly, at-home health monitoring tools that empower individuals in personalized healthcare in the future.

Advancing Microfluidic Immunity Testing Systems: New Trends for Microbial Pathogen Detection

Pathogenic microorganisms play a crucial role in the global disease burden due to their ability to cause various diseases and spread through multiple transmission routes. Immunity tests identify antigens related to these pathogens, thereby confirming past infections and monitoring the host's immune response. Traditional pathogen detection methods, including enzyme-linked immunosorbent assays (ELISAs) and chemiluminescent immunoassays (CLIAs), are often labor-intensive, slow, and reliant on sophisticated equipment and skilled personnel, which can be limiting in resource-poor settings. In contrast, the development of microfluidic technologies presents a promising alternative, offering automation, miniaturization, and cost efficiency. These advanced methods are poised to replace traditional assays by streamlining processes and enabling rapid, high-throughput immunity testing for pathogens. This review highlights the latest advancements in microfluidic systems designed for rapid and high-throughput immunity testing, incorporating immunosensors, single molecule arrays (Simoas), a lateral flow assay (LFA), and smartphone integration. It focuses on key pathogenic microorganisms such as SARS-CoV-2, influenza, and the ZIKA virus (ZIKV). Additionally, the review discusses the challenges, commercialization prospects, and future directions to advance microfluidic systems for infectious disease detection.

Automated and ultrasensitive point-of-care glycoprotein detection using boronate-affinity enhanced organic electrochemical transistor patch

Quantifying trace glycoproteins in biofluids requires ultrasensitive components, but feedback is not available in the current portable platforms of point-of-care (POC) diagnosis technologies. A compact and ultrasensitive bioelectrochemical patch was based on boronate-affinity amplified organic electrochemical transistors (BAAOECTs) for POC use was developed to overcome this dilemma. Benefit from the cascading signal enhancement deriving from boronate-affinity targeting multiple regions of glycoprotein and OECTs' inherent signal amplification capability, the BAAOECTs achieved a detection limit of 300 aM within 25 min, displaying about 3 orders of magnitude improvement in sensitivity compared with the commercial electrochemical luminescence (ECL) kit. By using a microfluidic chip, a microcontroller module, and a wireless sensing system, the testing workflows of the above patch was automated, allowing for running the sample-to-answer pipeline even in a resource-limited environment. The reliability of such portable biosensing platform is well recognized in clinical diagnostic applications of heart failure. Overall, the remarkable enhanced sensitivity and automated workflow of BAAOECTs biosensing platform provide a prospective and generalized design policy for expanding the POC diagnosis capabilities of glycoproteins.

CRISPR-Based Assays for Point-of-Need Detection and Subtyping of Influenza

The high disease burden of influenza virus poses a significant threat to human health. Optimized diagnostic technologies that combine speed, sensitivity, and specificity with minimal equipment requirements are urgently needed to detect the many circulating species, subtypes, and variants of influenza at the point of need. Here, we introduce such a method using Streamlined Highlighting of Infections to Navigate Epidemics (SHINE), a clustered regularly interspaced short palindromic repeats (CRISPR)-based RNA detection platform. Four SHINE assays were designed and validated for the detection and differentiation of clinically relevant influenza species (A and B) and subtypes (H1N1 and H3N2). When tested on clinical samples, these optimized assays achieved 100% concordance with quantitative RT-PCR. Duplex Cas12a/Cas13a SHINE assays were also developed to detect two targets simultaneously. This study demonstrates the utility of this duplex assay in discriminating two alleles of an oseltamivir resistance (H275Y) mutation as well as in simultaneously detecting influenza A and human RNAse P in patient samples. These assays have the potential to expand influenza detection outside of clinical laboratories for enhanced influenza diagnosis and surveillance.

Fully integrated and automated centrifugal microfluidic chip for point-of-care multiplexed molecular diagnostics

Public health events caused by pathogens have imposed significant economic and societal burdens. However, conventional methods still face challenges including complex operations, the need for trained operators, and sophisticated instruments. Here, we proposed a fully integrated and automated centrifugal microfluidic chip, also termed IACMC, for point-of-care multiplexed molecular diagnostics by harnessing the advantages of active and passive valves. The IACMC incorporates multiple essential components including a pneumatic balance module for sequential release of multiple reagents, a pneumatic centrifugation-assisted module for on-demand solution release, an on-chip silicon membrane module for nucleic acid extraction, a Coriolis force-mediated fluid switching module, and an amplification module. Numerical simulation and visual validation were employed to iterate and optimize the chip's structure. Upon sample loading, the chip automatically executes the entire process of bacterial sample lysis, nucleic acid capture, elution quantification, and isothermal LAMP amplification. By optimizing crucial parameters including centrifugation speed, direction of rotation, and silicone membrane thickness, the chip achieves exceptional sensitivity (twenty-five Salmonella or forty Escherichia coli) and specificity in detecting Escherichia coli and Salmonella within 40 min. The development of IACMC will drive advancements in centrifugal microfluidics for point-of-care testing and holds potential for broader applications in precision medicine including high-throughput biochemical analysis immune diagnostics, and drug susceptibility testing.

Ultra-Sensitive Detection of the SARS-CoV-2 Nucleocapsid Protein via a Clustered Regularly Interspaced Short Palindromic Repeat/Cas12a-Mediated Immunoassay

Tracking trace protein analytes in precision diagnostics is an ongoing challenge. Here, we developed an ultrasensitive detection method for the detection of SARS-CoV-2 nucleocapsid (N) protein by combining enzyme-linked immunosorbent assay (ELISA) with the clustered regularly interspaced short palindromic repeat/CRISPR-associated protein (CRISPR/Cas) system. First, the SARS-CoV-2 N protein bound by the capture antibody adsorbed on the well plate was sequentially coupled with the primary antibody, biotinylated secondary antibody, and streptavidin (SA), followed by biotin primer binding to SA. Subsequently, rolling circle amplification was initiated to generate ssDNA strands, which were targeted by CRISPR/Cas12a to cleave the FAM-ssDNA-BHQ1 probe in trans to generate fluorescence signals. We observed a linear relationship between fluorescence intensity and the logarithm of N protein concentration ranging from 3 fg/mL to 3 × 107 fg/mL. The limit of detection (LOD) was 1 fg/mL, with approximately nine molecules in 1 μL of the sample. This detection sensitivity was 4 orders magnitude higher than that of commercially available ELISA kits (LOD: 5.7 × 104 fg/mL). This method was highly specific and sensitive and could accurately detect SARS-CoV-2 pseudovirus and clinical samples, providing a new approach for ultrasensitive immunoassay of protein biomarkers.

Identifying SARS-CoV-2 Variants Using Single-Molecule Conductance Measurements

The global COVID-19 pandemic has highlighted the need for rapid, reliable, and efficient detection of biological agents and the necessity of tracking changes in genetic material as new SARS-CoV-2 variants emerge. Here, we demonstrate that RNA-based, single-molecule conductance experiments can be used to identify specific variants of SARS-CoV-2. To this end, we (i) select target sequences of interest for specific variants, (ii) utilize single-molecule break junction measurements to obtain conductance histograms for each sequence and its potential mutations, and (iii) employ the XGBoost machine learning classifier to rapidly identify the presence of target molecules in solution with a limited number of conductance traces. This approach allows high-specificity and high-sensitivity detection of RNA target sequences less than 20 base pairs in length by utilizing a complementary DNA probe capable of binding to the specific target. We use this approach to directly detect SARS-CoV-2 variants of concerns B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617.2 (Delta), and B.1.1.529 (Omicron) and further demonstrate that the specific sequence conductance is sensitive to nucleotide mismatches, thus broadening the identification capabilities of the system. Thus, our experimental methodology detects specific SARS-CoV-2 variants, as well as recognizes the emergence of new variants as they arise.

CRISPR/Cas12a antifouling nanocomposite electrochemical biosensors enable amplification-free detection of Monkeypox virus in complex biological fluids

The escalating global threat of infectious diseases, including monkeypox virus (MPXV), necessitates advancements in point-of-care diagnostics, moving beyond the constraints of conventional methods tethered to centralized laboratories. Here, we introduce multiple CRISPR RNA (crRNA)-based biosensors that can directly detect MPXV within 35 minutes without pre-amplification, leveraging the enhanced sensitivity and antifouling attributes of the BSA-based nanocomposite. Multiple crRNAs, strategically targeting diverse regions of the F3L gene of MPXV, are designed and combined to amplify Cas12a activation and its collateral cleavage of reporter probes. Notably, our electrochemical sensors exhibit the detection limit of 669 fM F3L gene without amplification, which is approximately a 15-fold improvement compared to fluorescence detection. This sensor also shows negligible changes in peak current after exposure to complex biological fluids, such as whole blood and serum, maintaining its sensitivity at 682 fM. This sensitivity is nearly identical to the conditions when only the F3L gene was present in PBS. In summary, our CRISPR-based electrochemical biosensors can be utilized as a high-performance diagnostic tool in resource-limited settings, representing a transformative leap forward in point-of-care testing. Beyond infectious diseases, the implications of this technology extend to various molecular diagnostics, establishing itself as a rapid, accurate, and versatile platform for detection of target analytes.

A universal nucleic acid detection platform combing CRISPR/Cas12a and strand displacement amplification with multiple signal readout

Rapid and sensitive detection of nucleic acids has become crucial in various fields. However, most current nucleic acid detection methods can only be used in specific scenarios, such as RT-qPCR, which relies on fluorometer for signal readout, limiting its application at home or in the field due to its high price. In this paper, a universal nucleic acid detection platform combing CRISPR/Cas12a and strand displacement amplification (CRISPR-SDA) with multiple signal readout was established to adapt to different application scenarios. Nucleocapsid protein gene of SARS-CoV-2 (N gene) and hepatitis B virus (HBV) DNA were selected as model targets. The proposed strategy achieved the sensitivity of 53.1 fM, 0.15 pM, and 1 pM for N gene in fluorescence mode, personal glucose meter (PGM) mode and lateral flow assay (LFA) mode, respectively. It possessed the ability to differentiate single-base mismatch and the presence of salmon sperm DNA with a mass up to 105-fold of the targets did not significantly interfere with the assay signal. The general and modular design idea made CRISPR-SDA as simple as building blocks to construct nucleic acid sensing methods to meet different requirements by simply changing the SDA template and selecting suitable signal report probes, which was expected to find a breadth of applications in nucleic acids detection.

Electrochemical Sensors and Biosensors for Identification of Viruses: A Critical Review

Due to their life cycle, viruses can disrupt the metabolism of their hosts, causing diseases. If we want to disrupt their life cycle, it is necessary to identify their presence. For this purpose, it is possible to use several molecular-biological and bioanalytical methods. The reference selection was performed based on electronic databases (2020-2023). This review focused on electrochemical methods with high sensitivity and selectivity (53% voltammetry/amperometry, 33% impedance, and 12% other methods) which showed their great potential for detecting various viruses. Moreover, the aforementioned electrochemical methods have considerable potential to be applicable for care-point use as they are portable due to their miniaturizability and fast speed analysis (minutes to hours), and are relatively easy to interpret. A total of 2011 articles were found, of which 86 original papers were subsequently evaluated (the majority of which are focused on human pathogens, whereas articles dealing with plant pathogens are in the minority). Thirty-two species of viruses were included in the evaluation. It was found that most of the examined research studies (77%) used nanotechnological modifications. Other ones performed immunological (52%) or genetic analyses (43%) for virus detection. 5% of the reports used peptides to increase the method's sensitivity. When evaluable, 65% of the research studies had LOD values in the order of ng or nM. The vast majority (79%) of the studies represent proof of concept and possibilities with low application potential and a high need of further research experimental work.

Intrinsic RNA Targeting Triggers Indiscriminate DNase Activity of CRISPR-Cas12a

The CRISPR-Cas12a system has emerged as a powerful tool for next-generation nucleic acid-based molecular diagnostics. However, it has long been believed to be effective only on DNA targets. Here, we investigate the intrinsic RNA-enabled trans-cleavage activity of AsCas12a and LbCas12a and discover that they can be directly activated by full-size RNA targets, although LbCas12a exhibits weaker trans-cleavage activity than AsCas12a on both single-stranded DNA and RNA substrates. Remarkably, we find that the RNA-activated Cas12a possesses higher specificity in recognizing mutated target sequences compared to DNA activation. Based on these findings, we develop the "Universal Nuclease for Identification of Virus Empowered by RNA-Sensing" (UNIVERSE) assay for nucleic acid testing. We incorporate a T7 transcription step into this assay, thereby eliminating the requirement for a protospacer adjacent motif (PAM) sequence in the target. Additionally, we successfully detect multiple PAM-less targets in HIV clinical samples that are undetectable by the conventional Cas12a assay based on double-stranded DNA activation, demonstrating unrestricted target selection with the UNIVERSE assay. We further validate the clinical utility of the UNIVERSE assay by testing both HIV RNA and HPV 16 DNA in clinical samples. We envision that the intrinsic RNA targeting capability may bring a paradigm shift in Cas12a-based nucleic acid detection and further enhance the understanding of CRISPR-Cas biochemistry.

Rapid and on-site wireless immunoassay of respiratory virus aerosols via hydrogel-modulated resonators

Rapid and accurate detection of respiratory virus aerosols is highlighted for virus surveillance and infection control. Here, we report a wireless immunoassay technology for fast (within 10 min), on-site (wireless and battery-free), and sensitive (limit of detection down to fg/L) detection of virus antigens in aerosols. The wireless immunoassay leverages the immuno-responsive hydrogel-modulated radio frequency resonant sensor to capture and amplify the recognition of virus antigen, and flexible readout network to transduce the immuno bindings into electrical signals. The wireless immunoassay achieves simultaneous detection of respiratory viruses such as severe acute respiratory syndrome coronavirus 2, influenza A H1N1 virus, and respiratory syncytial virus for community infection surveillance. Direct detection of unpretreated clinical samples further demonstrates high accuracy for diagnosis of respiratory virus infection. This work provides a sensitive and accurate immunoassay technology for on-site virus detection and disease diagnosis compatible with wearable integration.