Fast and sensitive CRISPR detection by minimized interference of target amplification

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.

The nucleic acid detection using CRISPR/Cas biosensing system with micro-nano modality for point-of-care applications

Nucleic acid detection is considered the golden standard for diagnosing infectious diseases caused by various pathogens, including viruses, bacteria, and parasites. PCR and other amplification-based technologies are highly sensitive and specific, allowing for accurate detection and identification of low-level causative pathogens by targeting and amplifying their unique genetic segment (DNA or RNA). However, it is important to recognize that machinery-dependent diagnostic methods may only sometimes be available or practical in resource-limited settings, where direct implementation can be challenging. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-based diagnostics offer a promising alternative for nucleic acid detection. These methods provide gene sequence-specific targeting, multiplexing capability, rapid result disclosure, and ease of operation, making them suitable for point-of-care (POC) applications. CRISPR-Cas-based nucleic acid detection leverages the intrinsic gene-editing capabilities of CRISPR systems to detect specific DNA or RNA sequences with high precision, ensuring high specificity in identifying pathogens. When integrated with micro- and nano-technologies, CRISPR-based diagnostics gain additional benefits, including automated microfluidic processes, enhanced multiplexed detection, improved sensitivity through nanoparticle integration, and combined detection strategies. In this review, we analyze the motivations for tailoring the CRISPR-Cas system with microfluidic formats or nanoscale materials for nucleic acid biosensing and detection. We discuss and categorize current achievements in such systems, highlighting their differences, commonalities, and opportunities for addressing challenges, particularly for POC diagnostics. Micro- and nano-technologies can significantly enhance the practical utility of the CRISPR-Cas system, enabling more comprehensive diagnostic and surveillance capabilities. By integrating these technologies, CRISPR-based diagnostics can achieve higher levels of automation, sensitivity, and multiplexing, making them invaluable tools in the global effort to diagnose and control infectious diseases.

Engineered CRISPR/Cas Ribonucleoproteins for Enhanced Biosensing and Bioimaging

CRISPR-Cas systems represent a highly programmable and precise nucleic acid-targeting platform, which has been strategically engineered as a versatile toolkit for biosensing and bioimaging applications. Nevertheless, their analytical performance is constrained by inherent functional and activity limitations of natural CRISPR/Cas systems, underscoring the critical role of molecular engineering in enhancing their capabilities. This review comprehensively examines recent advancements in engineering CRISPR/Cas ribonucleoproteins (RNPs) to enhance their functional capabilities for advanced molecular detection and cellular imaging. We explore innovative strategies for developing enhanced CRISPR/Cas RNPs, including Cas protein engineering through protein mutagenesis and fusion techniques, and guide RNA engineering via chemical and structural modifications. Furthermore, we evaluate these engineered RNPs' applications in sensitive biomarker detection and live-cell genomic DNA and RNA monitoring, while analyzing the current challenges and prospective developments in CRISPR-Cas RNP engineering for advanced biosensing and bioimaging.

Harnessing crRNA Transformer for Facile and Specific Nucleic Acid Detection

CRISPR/Cas systems have emerged as promising tools for nucleic acid detection. However, their practical applications have been limited by poor specificity and the need for additional preprocessing steps. Inspired by the concept of transformers, we found that changing the forms of crRNA with spatial arrangement may endow CRISPR/Cas with an enhanced performance for nucleic acid detection. Specifically, we rationally designed two crRNA transformers─swap crRNA and split crRNA─and found that they direct the CRISPR/Cas system for cis- and trans- cleavage with enhanced specificity and decreased Cas binding affinity and possess both DNA and RNA detection abilities. Based on these findings, our strategy enabled the identification of clinical prostatic cancer in a one-step reaction, with a remarkable sensitivity of 90.0% and specificity of 96.0%. Our study deepens the understanding of CRISPR/Cas systems and introduces a promising strategy for simple nucleic acid detection with enhanced specificity, sensitivity, and functionality in clinical molecular diagnosis.

CrRNA Conformation-Engineered CRISPR-Cas12a System for Robust and Ultrasensitive Nucleic Acid Detection

Despite the widespread application of the CRISPR-Cas12a system in vitro diagnostics due to its high programmability and distinctive trans-cleavage activity, the susceptibility of its crRNA component to degradation and sensitivity to storage and working conditions poses a significant challenge to improving the practical efficacy of these diagnostic systems. Here, we show that engineered crRNA with a covalently closed circular structure (C-crRNA) can replace traditional linear crRNA to form functional complexes with Cas12a protein, significantly enhancing the anti-interference ability of the CRISPR-Cas12a system while maintaining its sensitivity and specificity. Based on this finding, a circular crRNA-mediated CRISPR molecular diagnostic (CRCD) toolkit is developed and successfully integrated with a standard nucleic acid amplification technique to detect synthesized Human Papillomavirus type 16 (HPV-16) plasmids down to 10 aM sensitivity levels. Furthermore, the CRCD system is applied for ultrasensitive detection of 40 HPV-16 and 40 influenza A viruses in clinical samples, with results consistent with those from PANTHER detection and quantitative real-time polymerase chain reaction (qRT-PCR). In conclusion, this strategy introduces a novel paradigm for engineering crRNA to program Cas12a, which has the potential to revolutionize the use of crRNA in CRISPR-based molecular diagnostics.

A compact, palm-sized isothermal fluorescent diagnostic intelligent IoT device for personal health monitoring and beyond via one-tube/one-step LAMP-CRISPR assay

The demand for accurate, user-friendly, and sensitive at-home nucleic acid testing solutions is rising due to occasional outbreaks of various infectious diseases and a growing desire for an improved quality of life. In response, we developed the WeD-mini, a compact, palm-sized isothermal fluorescent diagnostic IoT device that weighs just 61 g. The WeD-mini features a uniquely designed, highly sensitive optical sensing system, ultra-low power consumption, a minimalist industrial design, and an intelligent operating algorithm. It integrates real-time fluorescence detection and automatic result interpretation via a smartphone, with results seamlessly uploaded to the 'EzDx Cloud' for comprehensive health management and spatio-temporal disease mapping. The device supports various assays that operate at different temperatures and with varying fluorescence emission intensities, such as RPA (39 °C, low intensity), LAMP (65 °C, high intensity), and LAMP-PfAgo (65/95 °C, high intensity), while maintaining precise temperature control and exceptional fluorescence detection sensitivity. Additionally, we engineered a more thermostable AapCRISPR-Cas12b variant that operates effectively at 63 °C, enhancing compatibility with LAMP to create a robust One-Tube/One-Step LAMP-CRISPR assay. Adaptable for at-home testing of SARS-CoV-2 and influenza viruses, the WeD-mini achieved 100% sensitivity and specificity with the newly established One-Tube/One-Step LAMP-CRISPR assay. Furthermore, the WeD-mini shows potential applications in detecting meat adulteration, monitoring respiratory diseases in pets, and conducting wastewater surveillance, making it suitable for a wide range of personal and public health use cases.

A minimal transcription template-based amplification-free CRISPR-Cas13a strategy for DNA detection

CRISPR-Cas13a has shown great potential for the rapid and accurate detection of pathogen nucleic acids. However, conventional CRISPR-Cas13a-based assays typically require pre-amplification, which can introduce aerosol contamination and operational complexities. In this study, we developed a Minimalist transcription template-based Amplification-free CRISPR-Cas13a strategy for DNA detection (MAD). This strategy facilitates the release of pathogen DNA and its annealing with primers from nasopharyngeal swab samples in a straightforward manner, followed by T7 transcription and CRISPR-Cas13a detection, completing the entire process within 40 min. MAD eliminates the need for DNA extraction and pre-amplification while maintaining high sensitivity after optimization, allowing for result visualization via lateral flow strips. Furthermore, evaluation of 167 clinical pediatric samples identified 18 positive cases of human adenovirus, demonstrating a 99.4% concordance in detection compared to standard qPCR. We believe that MAD offers new insights into CRISPR-Cas diagnostics and, due to its simplicity, rapidity, and safety, is poised for widespread application in clinical practice.

Oligonucleotide subsets selection by single nucleotide resolution barcode identification

Effective subset selection from complex oligonucleotide libraries is crucial for genomics, synthetic biology, and DNA data storage. The polymerase chain reaction, foundational for amplifying target subsets is limited by primer design and length for specificity, which constrains the scalability of oligo libraries and increases the synthesis burden for primers. We introduce an oligo subset selection methodology that utilizes sequence-specific cyclic nucleotide synthesis and blocking of the template oligos. This approach eliminates the need for primers for selective hybridization and enables the encoding and selection of hundreds of subsets with barcode lengths of fewer than five nucleotides. Moreover, cyclic selection enables a hierarchical data structure in the oligo library, enhancing the programmability. This advancement offers a scalable and cost-effective solution for handling complex oligo libraries.

Using CRISPR for viral nucleic acid detection

Pathogenic microorganisms, such as viruses, have threatened human health and will continue to contribute to future epidemics and pandemics, highlighting the importance of developing effective diagnostics. To contain viral outbreaks within populations, fast and early diagnosis of infected individuals is essential. Although current standard methods are highly sensitive and specific, like RT-qPCR, some can have slow turnaround times, which can hinder the prevention of viral transmission. The discovery of CRISPR-Cas systems in bacteria and archaea initially revolutionized the world of genome editing. Intriguingly, CRISPR-Cas enzymes also have the ability to detect nucleic acids with high sensitivity and specificity, which sparked the interest of researchers to also explore their potential in diagnosis of viral pathogens. In particular, the CRISPR-Cas13 system has been used as a tool for detecting viral nucleic acids. Cas13's capability to detect both target RNA and non-specific RNAs has led to the development of detection methods that leverage these characteristics through designing specific detection read-outs. Optimization of viral sample collection, amplification steps and the detection process within the Cas13 detection workflow has resulted in assays with high sensitivity, rapid turnaround times and the capacity for large-scale implementation. This review focuses on the significant innovations of various CRISPR-Cas13-based viral nucleic acid detection methods, comparing their strengths and weaknesses while highlighting Cas13's great potential as a tool for viral diagnostics.

Tunable control of Cas12 activity promotes universal and fast one-pot nucleic acid detection

The CRISPR-based detection methods have been widely applied, yet they remain limited by the non-universal nature of one-pot diagnostic approaches. Here, we report a universal one-pot fluorescent method for the detection of epidemic pathogens, delivering results within 15-20 min. This method uses heparin sodium to precisely tunes the cis-cleavage capability of Cas12 via interference with the Cas12a-crRNA binding process, thereby generating significant fluorescence due to the accumulation of isothermal amplification products. Additionally, this universal assay accommodates both classic and suboptimal PAMs, as well as various Cas12a subtypes such as LbCas12a, AsCas12a, and AapCas12b. Such a robust method demonstrates sensitivity and specificity exceeding 95% in the detection of monkeypox pseudovirus, influenza A virus, and SARS-CoV-2 from saliva or wastewater samples, when compared with qPCR or RT-qPCR. Moreover, the cost of heparin sodium per thousand uses is $0.01 to $0.04 only. Collectively, this universal and fast one-pot approach based on heparin sodium offers potential possibilities for point-of-care testing.

The current status and future prospects of CRISPR-based detection of monkeypox virus: A review

BACKGROUND

The current pandemic of 2022 global mpox (formerly known as monkeypox), caused by infection with monkeypox virus (MPXV), has now reached over 120 countries. This constitutes a critical public health issue requiring effective disease management and surveillance. Rapid and reliable diagnosis is conducive to the control of infection, early intervention, and timely treatment. Clinical laboratories use various conventional diagnostic methods for detecting MPXV, including PCR, which can be regarded as a gold-standard diagnostic method. However, the application of PCR is limited by its requirements for high-cost equipment, skilled professionals, and a laboratory setting.

RESULTS

Clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostic systems have provided promising prospects for the rapid, sensitive, and specific detection of infectious diseases, especially in point-of-care settings. Over the past 2 years, an increasing number of researchers have concentrated on the application of the CRISPR method to mpox diagnosis. In the majority of cases, a two-step method was chosen, with CRISPR/Cas12a and recombinase polymerase amplification (RPA) as pre-amplification methods, followed by a fluorescence readout. Different strategies have been applied to overcome the encountered limitations of CRISPR detection, but no consensus on an integrated solution has been achieved. Thus, the application of the CRISPR/Cas system in mpox detection requires further exploration and improvement.

SIGNIFICANCE

This review discusses contemporary studies on MPXV CRISPR detection systems and the strategies proposed to address the challenges faced by CRISPR diagnosis with the hope of helping the development of CRISPR detection methods and improving pathogen detection technologies.

Trends in developing one-pot CRISPR diagnostics strategies

The integration of nucleic acid amplification (NAA) with the CRISPR detection system has led to significant advancements and opportunities for development in molecular diagnostics. Nevertheless, the incompatibility between CRISPR cleavage and NAA has significantly impeded the commercialization of this technology. Currently, several one-pot detection strategies based on CRISPR systems have been devised to address concerns regarding aerosol contamination risk and operational complexity associated with step-by-step detection as well as the sensitivity limitation of conventional one-pot methods. In this review, we provide a comprehensive introduction and outlook of the various solutions of the one-pot CRISPR assay for practitioners who are committed to developing better CRISPR nucleic acid detection technologies to promote the progress of molecular diagnostics.

SlipChip Enables the Integration of CRISPR-Cas12a and RPA for Fast and Stand-Alone HPV Detection

Human papillomavirus (HPV) screening is vital for the early detection and prevention of cervical cancer. However, existing methods often face challenges related to speed, simplicity, and multiplexing, especially in resource-limited settings. Here we developed a portable SlipChip-based multiplexed and rapid nucleic acid testing platform, named SMART, designed to simultaneously detect HPV16 and HPV18. SMART allows seamless integration of the RPA and Cas12a assays on the SlipChip and includes a heating membrane to regulate the on-chip assay temperatures. This allows SMART to operate as a stand-alone platform without additional control instruments. The platform also features an All-in-One imaging mode for rapid on-chip data acquisition, enhancing its performance. SMART enables sensitive detection of HPV16 and HPV18 DNA across multiple samples in just 36 min with a detection limit of approximately 6 copies per reaction. Testing of 56 clinical samples at risk of HPV infection validated SMART's performance, showing 97.7% sensitivity and 100% specificity. In summary, SMART offers a stand-alone system capable of rapidly distinguishing between the two most harmful HPV subtypes, showcasing the significant potential for rapid, multiplexed nucleic acid testing in various applications.

Collateral nuclease activity of TnpB triggered by high temperature enables fast and sensitive nucleic acid detection

TnpB proteins encoded in the IS200/IS605 family are RNA-guided endonuclease which can be harnessed in genome editing. However, the collateral nuclease activity of TnpB remains poorly understood, which limits the development of TnpB-based diagnostic tools. Here we showed that TnpB from a thermophilic archaeon exhibits enhanced collateral ssDNA cleavage activity (trans-cleavage) activated by high temperature. Mutations either in the TAM or seed sequences of the target DNA impair the trans-cleavage activity, which indicates its potential to be employed in molecular diagnostic. Importantly, by optimizing the length and the sequences of the collateral substrates, we have developed a new nucleic acid detection method based on TnpB with a sensitivity of 29 cp μl-1 in 30 min, which we name it TESD (TnpB Enable fast and Sensitive Detection). In summary, our findings illustrate the collateral nuclease activity of a TnpB from thermophiles and provide a novel platform for molecular diagnostics.

A Novel High-Throughput Sample-in-Result-Out Device for the Rapid Detection of Viral Nucleic Acids

Clustered regularly interspaced short palindromic repeats (CRISPR) molecular diagnostic technology is one of the most reliable diagnostic tools for infectious diseases due to its short reaction time, high sensitivity, and excellent specificity. However, compared with fluorescent polymerase chain reaction (PCR) technology, CRISPR molecular diagnostic technology lacks high-throughput automated instrumentation and standardized detection reagents for high sensitivity, limiting its large-scale clinical application. In this study, a high-throughput automated device was developed by combining reagent lyophilization, extraction-free technology, and a one-pot consumable system. This innovative approach enabled the rapid sample-in-result-out detection of 48 samples in 25 min and demonstrated high sensitivity and specificity for the qualitative analysis of clinical samples. The obtained results show that the detection limit of the designed system for African swine fever virus (ASFV) is 0.5 copies/μL. As a proof concept, a single-tube dual-target nucleic acid detection method was developed, achieving a detection limit of 5 copies/μL for the ORF1ab and N genes of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) within 45 min. The method is highly specific, reliable, and stable, providing a feasible solution for the clinical application of CRISPR nucleic acid detection technology.

One-pot diagnostic methods based on CRISPR/Cas and Argonaute nucleases: strategies and perspectives

CRISPR/Cas and Argonaute (Ago) proteins, which target specific nucleic acid sequences, can be applied as diagnostic tools. Despite high specificity and efficiency, achieving sensitive detection often necessitates a preamplification step that involves opening the lid and multistep operation, which may elevate the risk of contamination and prove inadequate for point-of-care testing. Hence, various one-pot detection strategies have been developed that enable preamplification and sensing in a single operation. We outline the challenges of one-pot detection with Cas and Ago proteins, present several main implementation strategies, and discuss future prospects. This review offers comprehensive insights into this vital field and explores potential improvements to detection methods that will be beneficial for human health.

CRISPR/Cas and Argonaute-powered lateral flow assay for pathogens detection

Pathogens contamination is a pressing global public issue that has garnered significant attention worldwide, especially in light of recent outbreaks of foodborne illnesses. Programmable nucleases like CRISPR/Cas and Argonaute hold promise as tools for nucleic acid testing owning to programmability and the precise target sequence specificity, which has been utilized for the development pathogens detection. At present, fluorescence, as the main signal output method, provides a simple response mode for sensing analysis. However, the dependence of fluorescence output on large instruments and correct analysis of output data limited its use in remote areas. Lateral flow strips (LFS), emerging as a novel flexible substrate, offer a plethora of advantages, encompassing easy-to-use, rapidity, visualization, low-cost, portability, etc. The integration of CRISPR/Cas and Argonaute with LFS, lateral flow assay (LFA), rendered a new and on-site mode for pathogens detection. In the review, we introduced two programmable nucleases CRISPR/Cas and Argonaute, followed by the structure, principle and advantages of LFA. Then diversified engineering detection pattens for viruses, bacteria, parasites, and fungi based on CRISPR/Cas and Argonaute were introduced and summarized. Finally, the challenge and perspectives involved in on-site diagnostic assays were discussed.

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.

Y-switch: a spring-loaded synthetic gene switch for robust DNA/RNA signal amplification and detection

Nucleic acid tests (NATs) are essential for biomedical diagnostics. Traditional NATs, often complex and expensive, have prompted the exploration of toehold-mediated strand displacement (TMSD) circuits as an economical alternative. However, the wide application of TMSD-based reactions is limited by 'leakage'-the spurious activation of the reaction leading to high background signals and false positives. Here, we introduce the Y-Switch, a new TMSD cascade design that recognizes a custom nucleic acid input and generates an amplified output. The Y-Switch is based on a pair of thermodynamically spring-loaded DNA modules. The binding of a predefined nucleic acid target triggers an intermolecular reaction that activates a T7 promoter, leading to the perpetual transcription of a fluorescent aptamer that can be detected by a smartphone camera. The system is designed to permit the selective depletion of leakage byproducts to achieve high sensitivity and zero-background signal in the absence of the correct trigger. Using Zika virus (ZIKV)- and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-derived nucleic acid sequences, we show that the assay generates a reliable target-specific readout. Y-Switches detect native RNA under isothermal conditions without reverse transcription or pre-amplification, with a detection threshold as low as ∼200 attomole. The modularity of the assay allows easy re-programming for the detection of other targets by exchanging a single sequence domain. This work provides a low-complexity and high-fidelity synthetic biology tool for point-of-care diagnostics and for the construction of more complex biomolecular computations.

Mini-Program Enabled IoT Intelligent Molecular Diagnostic Device for Co-Detection and Spatiotemporal Mapping of Infectious Disease Pathogens

Effective detection of infectious pathogens is crucial for disease prevention and control. We present an innovative Internet of Things (IoT) molecular diagnostic device featuring a WeChat mini-program for simultaneous detection and spatiotemporal mapping of respiratory pathogens. Leveraging social software's widespread usage, our device integrates seamlessly with WeChat, eliminating the need for app downloads and installations. Through a comprehensive detection system, including a user-friendly mini-program, a portable Point-of-Care fluorescence detector, and a diagnostic information management platform (EzDx Cloud), we demonstrate high sensitivity and specificity in detecting common respiratory viruses. Our SARS-CoV-2/H1N1 combo test kit, developed using a novel one-tube/one-step loop-mediated isothermal amplification-CRISPR method, shows remarkable performance. We address challenges in at-home nucleic acid testing by providing a cost-effective solution capable of detecting multiple pathogens simultaneously. Our system's versatility accommodates various assays operating at different temperatures and fluorescence intensities, offering significant advantages over traditional methods. Moreover, integration with EzDx Cloud facilitates disease monitoring and early warning systems, enhancing public health management. This study highlights the potential of our IoT molecular diagnostic device in revolutionizing infectious disease detection and control, with wide-ranging applications in both human and animal population.

Ratiometric Readout of Bacterial Infections via a Lyophilized CRISPR-Cas12a Sensor with Color-Changeable Bioluminescence

The healthcare burden imposed by bacterial infections demands robust and accessible diagnostic methods that can be performed outside hospitals and centralized laboratories. Here, we report Pathogen Assay with Ratiometric Luminescence (PEARL), a sensitive and easy-to-operate platform for detecting pathogenic bacteria. The PEARL leveraged a color-changeable CRISPR-Cas12a sensor and recombinase polymerase amplification to elicit ratiometric bioluminescence responses to target inputs. This platform enabled robust and visualized identification of attomolar bacteria genome deoxyribonucleic acid according to the color changes of the reactions. In addition, the components of the color-changeable Cas12a sensor could be lyophilized for 3 month storage at ambient temperature and then be fully activated with the amplicons derived from crude bacterial lysates, reducing the requirements for cold-chain storage and tedious handling steps. We demonstrated that the PEARL assay is applicable for identifying the infections caused by Pseudomonas aeruginosa in different clinical specimens, including sputa, urines, and swabs derived from wounds. These results revealed the potential of PEARL to be used by untrained personnel, which will facilitate decentralized pathogen diagnosis in community- and resource-limited regions.

Development of a novel Cas13a/Cas12a-mediated 'one-pot' dual detection assay for genetically modified crops

INTRODUCTION

Genetically modified (GM) crops have been widely cultivated across the world and the development of rapid, ultrasensitive, visual multiplex detection platforms that are suitable for field deployment is critical for GM organism regulation.

OBJECTIVE

In this study, we developed a novel one-pot system, termed MR-DCA (Multiplex RPA and Dual CRISPR assay), for the simultaneous detection of CaMV35S and NOS genetic targets in GM crops. This innovative approach combined Multiplex RPA (recombinase polymerase amplification) with the Dual CRISPR (clustered regularly interspaced short palindromic repeat) assay technique, to provide a streamlined and efficient method for GM crop detection.

METHODS

The RPA reaction used for amplification CaMV35S and NOS targets was contained in the tube base, while the dual CRISPR enzymes were placed in the tube cap. Following centrifugation, the dual CRISPR (Cas13a/Cas12a) detection system was initiated. Fluorescence visualization was used to measure CaMV35S through the FAM channel and NOS through the HEX channel. When using lateral flow strips, CaMV35S was detected using rabbit anti-digoxin (blue line), whilst NOS was identified using anti-mouse FITC (red line). Line intensity was quantified using Image J and depicted graphically.

RESULTS

Detection of the targets was completed in 35 min, with a limit of detection as low as 20 copies. In addition, two analysis systems were developed and they performed well in the MR-DCA assay. In an analysis of 24 blind samples from GM crops with a wide genomic range, MR-DCA gave consistent results with the quantitative PCR method, which indicated high accuracy, applicability and semi-quantitative ability.

CONCLUSION

The development of MR-DCA represents a significant advancement in the field of GM detection, offering a rapid, sensitive and portable method for multiple target detection that can be used in resource-limited environments.

Detection of Parasites in the Field: The Ever-Innovating CRISPR/Cas12a

The rapid and accurate identification of parasites is crucial for prompt therapeutic intervention in parasitosis and effective epidemiological surveillance. For accurate and effective clinical diagnosis, it is imperative to develop a nucleic-acid-based diagnostic tool that combines the sensitivity and specificity of nucleic acid amplification tests (NAATs) with the speed, cost-effectiveness, and convenience of isothermal amplification methods. A new nucleic acid detection method, utilizing the clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) nuclease, holds promise in point-of-care testing (POCT). CRISPR/Cas12a is presently employed for the detection of Plasmodium falciparum, Toxoplasma gondii, Schistosoma haematobium, and other parasites in blood, urine, or feces. Compared to traditional assays, the CRISPR assay has demonstrated notable advantages, including comparable sensitivity and specificity, simple observation of reaction results, easy and stable transportation conditions, and low equipment dependence. However, a common issue arises as both amplification and cis-cleavage compete in one-pot assays, leading to an extended reaction time. The use of suboptimal crRNA, light-activated crRNA, and spatial separation can potentially weaken or entirely eliminate the competition between amplification and cis-cleavage. This could lead to enhanced sensitivity and reduced reaction times in one-pot assays. Nevertheless, higher costs and complex pre-test genome extraction have hindered the popularization of CRISPR/Cas12a in POCT.