Loop-mediated isothermal amplification of DNA

RT-RPA-assisted scaffold RNA transcription amplification activation Cas12a trans-cleavage strategy for one-pot miRNA detection

Split crRNA is utilized in the CRISPR system as a highly specific and sensitive tool for nucleic acid identification in molecular diagnostics. Here, we introduce a novel one-pot RT-RPA-assisted Scaffold RNA Transcription Amplification Activation Cas12a Trans-cleavage (ScRNA-TAAT) strategy for miRNA detection. Capable of completing miRNA detection in 50 min with a detection limit of 2.66 aM. The miRNA was amplified into double-stranded DNA amplicons with a T7 promoter using RT-RPA, which is subsequently transcribed into RNA trigger. A split T7 promoter extension sequence with template binds to the RNA trigger, assembly a three-way linker to initiate transcription of the scaffold RNA. The three-way linker with sticky ends joins to its RNA products, assembling a DNA-RNA complex that acts as both a spacer RNA and an activator. Simultaneously, the DNA-RNA hybrid complexes and scaffold RNA could replace the split crRNA and combined with Cas12a, forming an active ribonucleoprotein (RNP) complex with trans-cleavage activity comparable to that of the wild-type Cas12a RNP. Furthermore, we have successfully integrated the ScRNA-TAAT strategy into lateral flow analysis, enabling the visual detection of miRNAs. The assay's exceptional specificity and universality are highlighted by its application to complex biological matrices, including serum and cell lysates. The simplicity, sensitivity, and adaptability of the ScRNA TAAT assay render it a promising candidate for point-of-care testing and high sensitivity in molecular diagnostics.

Sensitive and rapid visual detection of Orientia tsutsugamushi with Recombinase assisted dipstick detection platform

Orientia tsutsugamushi, the causative agent of scrub typhus, poses a global threat, particularly in rural areas where standard PCR methods are impractical. To enable timely management of scrub typhus, we developed a rapid, simple, sensitive, and specific molecular detection method suitable for low-resource settings with minimal instrumentation. The developed platform enabled rapid detection of OT (≤25 minutes). For Gilliam and Karp strain of OT, the limit of detection was ≥1 gene copy, with 96.9 % clinical specificity and 100 % sensitivity. Primer artefact removal reduced background noise. The minimal concentration detected 91 ag µL-1 for Karp and 3 ag µL-1 for Gilliam genome. The assay showed no cross-reactivity with other acute febrile or acute encephalitis syndrome related etiologies. The developed assay holds considerable promise for clinicians, facilitating prompt diagnosis and management of ST cases in settings with constrained resources.

Nucleic acid-mediated SERS Biosensors: Signal enhancement strategies and applications

Surface Enhanced Raman Spectroscopy (SERS) is a powerful spectroscopic analysis technique applied in various fields due to its high selectivity, ultra-high sensitivity, and non-destructiveness. As natural biological macromolecules, nucleic acids perform a significant role in SERS biosensing. In this review, we first summarize how nucleic acids mediate the signal enhancement of SERS biosensors from three aspects: substrate self-assembly, analyte biorecognition, and molecular amplification. Among them, SERS substrates can be self-assembled by both DNA modification and coordination or electrostatic interactions. In the field of biorecognition, analyte biorecognition based on three nucleic acid recognition elements can enhance SERS signals by regulating the distance of analytes or Raman reporter molecules to the SERS substrate. In addition, nucleic acid-based enzyme and enzyme-free amplification can enhance SERS signals by enlarging the quantity of analytes or its nucleic acid intermediates. Subsequently, multidimensional applications of nucleic acid-mediated SERS signal enhancement in biomedicine, food safety, and environmental monitoring are listed. Finally, the current challenges and future exploration of nucleic acid-mediated SERS signal enhancement are discussed.

Handheld ISFET Lab-on-Chip detection of YAP1 nucleic acid and AR-FL and AR-V7 mRNA from liquid biopsies for prostate cancer prognosis

Prostate cancer (PCa) is a highly prevalent disease, causing the second largest amount of male cancer deaths worldwide. Currently, the prostate specific antigen (PSA) test remains the standard serum prognostic and diagnostic monitoring biomarker but it lacks specificity and sensitivity. PSA testing can lead to invasive biopsies which can result in under detection of clinically significant disease and potential overtreatment of indolent disease. Promising circulating biomarkers could facilitate less invasive and more accurate tests, but present challenges in robust quantitation and deployment in clinical settings. This work presents the detection of circulating YAP1 nucleic acid, androgen receptor (AR-FL) and AR-V7 mRNA for PCa prognostics in blood plasma from PCa patients. Sensitive detection of circulating YAP1 nucleic acid, AR-FL and AR-V7 mRNA extracted from PCa clinical samples was achieved with a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay. Optimisation of mRNA extraction methodologies for reliable detection of circulating mRNA for RT-LAMP and RT-qPCR detection took place. Multiplex testing of circulating AR-FL mRNA and YAP1 nucleic acid on an ISFET Lab-on-Chip platform was readily achieved with bio-electronic signal detection taking place within 15 min. Detection of AR-V7 and AR-FL mRNA could also be achieved simultaneously with the handheld device. Evaluation of clinical data indicated that circulating YAP1 nucleic acid presence in extracted RNA from the blood plasma of patients correlated with more advanced clinical cancer staging (p = 0.043) and PSA at diagnosis (p = 0.035). The work presents potential for Point-of-Care detection of circulating mRNA from clinical samples for PCa prognostics.

Evaluation of loop mediated isothermal amplification, quantitative real-time PCR, conventional PCR methods for identifying Ascaris lumbricoides in human stool samples

Ascariasis, caused by Ascaris lumbricoides, is a widespread parasitic infection. Traditional diagnostic methods, such as microscopy, can miss infections with low worm burdens, leading to false negatives. This study compares four diagnostic methods-microscopy, conventional PCR, real-time PCR, and loop-mediated isothermal amplification (LAMP)-for detecting A. lumbricoides in 400 stool samples from children aged 2-16. Microscopy methods (direct wet mount, Kato-Katz, and concentration) detected 17, 23, and 21 positive samples, respectively. Molecular techniques identified 23 positive samples by conventional PCR, 29 by real-time PCR, and 25 by LAMP. Notably, real-time PCR detected two samples missed by microscopy, while conventional PCR failed to detect three samples positive by real-time PCR and LAMP. In limit-of-detection assays, conventional PCR detected A. lumbricoides DNA down to 150 pg, while qPCR and LAMP could detect as low as 15 fg. For egg number analysis, conventional PCR detected DNA from 100 eggs, while qPCR and LAMP identified DNA from just 10 eggs. The methods specifically targeted A. lumbricoides, without cross-reacting with other co-occurring parasites. Sensitivity and specificity analysis revealed that microscopy had sensitivities of 81.3 %, while conventional PCR, qPCR, and LAMP had sensitivities of 81.1 %, 99.2 %, and 88.1 %, respectively. Microscopy and conventional PCR had 100 % specificity, while qPCR and LAMP had 99.2 % and 99.9 % specificity. While Kato-Katz is advantageous for detecting active infections, molecular techniques, particularly LAMP's field applicability in resource-limited settings makes it a promising tool for surveillance and control of low-intensity infections.

A fluorescence biosensor for detecting LncRNA MALAT1 based on isothermal amplification by cyclic extension

BACKGROUND

Long non-coding RNA (lncRNA) Metastasis-Associated Lung Adenocarcinoma Transcript 1 (MALAT1), a crucial regulator of gene expression, has emerged as a highly promising biomarker in the progression of various cancers. The clinical detection of lncRNA MALAT1 primarily relies on Reverse Transcription-Polymerase Chain Reaction (RT-PCR), which requires skilled operators and large, expensive thermal cycling equipment. These limitations have restricted the application of RT-PCR, particularly in resource-constrained settings.

RESULTS

In this study, we developed a novel signal amplification method, termed Isothermal Amplification by Cyclic Extension (IACE), based on the linear extension of a single-stranded DNA probe. IACE operates through the continuous extension of Probe 1 (a) into long single-stranded DNA with multiple repetitive sequences, facilitated by Probe 2 (a∗a∗) and Bst DNA polymerase. We found that the single-stranded DNA product of IACE could directly activate the CRISPR-Cas12a system without requiring a protospacer adjacent motif (PAM). By integrating IACE with a three-way junction structure and a nicking enzyme, we established a one-step signal amplification strategy for the detection of lncRNA MALAT1, achieving a detection limit as low as 37.5 fM using the CRISPR-Cas system.

SIGNIFICANCE

The biosensor developed in the present study simplifies workflows, minimizes contamination risks, and demonstrates exceptional detection performance in tumor patient samples, highlighting its potential to advance clinical tumor diagnostic approaches.

CRISPR Digital Sensing: From Micronano-Collaborative Chip to Biomolecular Detection

The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) sensing technology proved to be valuable during the COVID-19 pandemic through its sensitivity, specificity, robustness, and versatility. However, issues such as overreliance on amplification, susceptibility to false positives, lack of quantification strategies, and complex operation procedures have hindered its broader application in bioanalysis and clinical diagnostics. The collision between micronano-collaborative chips and CRISPR technology has effectively addressed these bottlenecks, offering innovative solutions for diagnosis and treatment. Unlike conventional micronano chips, micronano digital chips enhance CRISPR's response to trace amounts of target molecules by leveraging highly controllable local environments and compartmentalized microreactors. This advancement improves detection efficiency and revolutionizes traditional in vitro bioanalytical processes. First, the working principles, fabrication techniques, and performance metrics of CRISPR-based digital droplet microfluidics and microarray chips are examined. Then, the applications of CRISPR digital sensing chips in bioassays are reviewed, emphasizing their importance in advancing in vitro detection systems for gene editing. Finally, the prospects of CRISPR digital sensing technology are explored, particularly its potential for body surface biomonitoring and its broader development opportunities in the biomedical field.

Point-of-care analysis for foodborne pathogens in food samples based on a fully enclosed microfluidic chip cartridge

Foodborne pathogens endanger public health and rapid, sensitive, and accurate detection of them is vital. Portable, highly integrated detection devices have great application prospects in the screening and analysis of foodborne pathogens. In this study, a fully automated detection device based on a fully enclosed microfluidic chip cartridge was successfully designed. This device integrates multiple functions, including nucleic acid extraction, reagent preparation, LAMP reaction, and signal detection. By simply adding a sample, it can simultaneously detect four types of foodborne pathogens, making it advantageous for the analysis of complex samples and improving detection accuracy. Additionally, freeze-dried reagents are integrated into the fully enclosed microfluidic chip cartridge, which allows the reagents to be transported and stored at room temperature, greatly reducing the cost of detection. It has been successfully applied in actual samples contaminated with multiple foodborne pathogens and has excellent stability. The entire detection process can be completed in 45 minutes, with a sensitivity of approximately 500 CFU mL-1. Therefore, the automated microfluidic device would be adequate for point-of-care testing (POCT) with high simplicity and high speed, providing an advanced genetic analysis microsystem for foodborne pathogen detection.

Detection of TuMV by a toehold switch sensor coupled with NASBA amplification in Pseudostellaria heterophylla

Pseudostellaria heterophylla (P. heterophylla) is a perennial herb that has been used as a medicinal food for hundreds of years in China. Viral infections during the production of P. heterophylla severely reduce the yield and quality. Turnip mosaic virus (TuMV) is a common and highly variable viral pathogen in P. heterophylla plants. A high-efficiency diagnostic system is urgently needed to control and alleviate TuMV infection. However, the current detection methods still have various deficiencies that limit their field application. Here, a cell-free expression system relying on nucleic acid sequence-based amplification (NASBA) with toehold switch sensors and a visual reporter for color change was developed and introduced for TuMV detection in P. heterophylla. After designing and screening the approach, the selected sensitive sensor was able to detect 1 pM TuMV RNA fragments within 40 min, and the detection limit was less than 10 fM if the time was extended to 90 min. The sensor exhibited high specificity, with no cross-reactivity detected when tested against cucumber mosaic virus, another prevalent viral pathogen in P. heterophylla. In addition, in in-field samples, TuMV was successfully detected directly from both purified and crude RNA extracts in approximately 3 h. This cell-free synthetic biology tool is rapid, sensitive, specific and field-applicable and provides high-capacity and low-cost diagnostics for TuMV in P. heterophylla, as well as various viruses in herbs and other host plants.

Kinetic analysis and engineering of thermostable Cas12a for nucleic acid detection

Cas12a trans nuclease activity has been leveraged for nucleic acid detection, often coupled with isothermal amplification to increase sensitivity. However, due to the lack of highly efficient thermostable Cas12a orthologs, use of Cas12a in one-pot combination with high temperature (55-65°C) amplification, such as loop-mediated isothermal amplification (LAMP), has remained challenging. Here, we attempt to address this challenge by comparative study of the thermostable, but poorly trans-active YmeCas12a (from Yellowstone metagenome) with the mesophilic, highly trans-active LbaCas12a (from Lachnospiraceae bacterium ND 2006). Kinetic characterizations identified that poor trans substrate affinity (high Km) is the key limiting factor in YmeCas12a trans activity. We engineered YmeCas12a by structure-guided mutagenesis and fusion to DNA-binding domains to increase its affinity to the trans substrate. The most successful combinatorial variant showed 5-50-fold higher catalytic efficiency with the trans substrate depending on the target site. With the improved variant, we demonstrate efficient nucleic acid detection in combination with LAMP in a single reaction workflow, setting the basis for development of point-of-care tests.

Enhancing Biosecurity in Mollusc Aquaculture: A Review of Current Isothermal Nucleic Acid Detection Methods

The growing human population has increased the need for food beyond what terrestrial sources can provide. This boosts aquaculture demand for molluscs, fish, and crustaceans. Molluscs are popular for their nutritional benefits, making them a profitable industry. Despite a 3% annual growth in mollusc populations, recent high mortality rates and population losses due to poor feeding practices and water pollution have made them more disease-prone. Limited treatment options exist for mollusc diseases in aquaculture systems. Hence, developing rapid, sensitive, and cost-effective diagnostic tools for field use is essential to identify and prevent infections promptly. Recently developed isothermal nucleic acid amplification technologies, like loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA), offer rapid results within an hour. This review examines these isothermal diagnostic techniques for mollusc pathogens and their potential for field application.

Development of recombinase polymerase amplification combined with a lateral flow dipstick assay for rapid and simple detection of Tylenchulus semipenetrans in soil

BACKGROUND

Tylenchulus semipenetrans, the causal agent of citrus slow decline disease, is one of the most destructive plant-parasitic nematodes in all citrus-growing regions of the world, causing significant reductions in citrus growth and yield. Accurate and rapid detection of T. semipenetrans is critical for the diagnosis and effective control of the disease.

RESULTS

We developed a rapid, visual, isothermal detection method using recombinase polymerase amplification combined with a lateral flow dipstick (RPA-LFD) assay to detect T. semipenetrans in soil. The primers and a probe were designed based on sequence differences in the internal transcribed spacer region 1 (ITS1) of ribosomal DNA (rDNA) among T. semipenetrans and four other Tylenchulus species. The RPA reaction can be performed in 10-25 min at a constant temperature ranging from 30 to 45 °C, and the result can be read directly on the LFD within 3 min. Under the optimized conditions, the RPA-LFD assay could specifically detect T. semipenetrans with a sensitivity as low as 10-2 second-stage juveniles/0.5 g soil, which was 10-fold more sensitive than that of the conventional PCR assay. Furthermore, we combined a soil DNA extraction method with the RPA-LFD assay to achieve simple and rapid detection of T. semipenetrans in natural field soil samples within 1 h.

CONCLUSION

The developed RPA-LFD assay is a simple, rapid, specific, sensitive and visual method for detecting T. semipenetrans. It shows great potential for on-site rapid detection applications, especially in resource-limited settings. © 2025 Society of Chemical Industry.

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.

Development of a HiFi-LAMP Assay for Detection of Human Pegivirus Type 1 RNA

Human pegivirus (HPgV) is a blood-borne RNA virus belonging to the family Flaviviridae, and contains two types HPgV-1 and HPgV-2. HPgV-1 infection does not cause acute diseases in healthy individuals but was demonstrated to play beneficial roles in individuals coinfected with HIV-1. HPgV-1 has a high prevalence in blood donors and the general population worldwide. The long-term consequence of HPgV-1 infection in healthy individuals remains unknown. High prevalence of HPgV-1 in blood donors raises concerns about the risk of transfusion transmission. Development of rapid and accurate point-of-care testing (POCT) of HPgV-1 will facilitate the screening of HPgV-1 infection among blood donors. Here, we reported a novel high-fidelity loop-mediated isothermal amplification (HiFi-LAMP) assay for detection of HPgV-1 and evaluated its performance in 175 healthy adults from Taizhou, China. The assay exhibits high specificity and sensitivity with limits of detection (LODs) of 122.6-135.7 copies of viral RNA/25 μL reaction for various HPgV-1 variants and can be completed within 30 min. Clinical validation showed that the assay had a 100% concordance with a previously described RT-qPCR assay for 175 sera from healthy adults, showing 100% sensitivity and specificity. Furthermore, we reported a 28.0% (111/397) prevalence of HPgV-1 in healthy adults in Taizhou, China, with no significant differences between genders and ages. The prevalence is obviously higher than a pooled HPgV-1 prevalence of 3.3% in blood donors in China. The novel HPgV-1 HiFi-LAMP assay offers a robust, rapid, and cost-effective tool for HPgV-1 surveillance to mitigate transfusion risk, especially in resource-limited areas. High prevalence of HPgV-1 in healthy adults underscores its potential public health relevance.

Differential detection of ovine Theileria species using loop-mediated isothermal amplification combined with nanoparticle-based lateral flow biosensor

Ovine theileriosis is an important tick-borne protozoan disease. It has been reported that three Theileria species are responsible for ovine theileriosis in China, which are T. luwenshuni, T. uilenbergi, and T. ovis. Here, we established three detection techniques based on loop-mediated isothermal amplification (LAMP) and nanoparticle-based lateral flow biosensor (LFB) for the infection of the three Theileria species. Three LAMP primer sets were designed targeting the nucleotide sequences of the 28S rRNA gene of T. luwenshuni, T. uilenbergi, and T. ovis. We used LAMP coupled with real-time fluorescence detection to optimize the concentrations of dNTP Mix, MgSO4, and Bst 2.0 DNA polymerase, as well as the reaction temperature of the LAMP assay, and then combined LAMP with LFB (LAMP-LFB). The entire detection assay process, including genomic DNA extraction (40 min), LAMP reaction (40 min), and LFB readout (<5 min), can be completed within 85 min. The established assays can specifically detect species of T. luwenshuni, T. uilenbergi, and T. ovis infection without cross-reaction with other Theileria, Babesia, and Anaplasma species. The detection limits of the LAMP-LFB assays for T. luwenshuni, T. uilenbergi, and T. ovis plasmid templates were 2.72 × 102 copies/μL, 2.96 × 103 copies/μL, and 3.05 × 101 copies/μL, respectively. Finally, we compared the established LAMP-LFB assay with the traditional PCR assay. The results showed that the total coincidence rates were 96.67 % (T. luwenshuni), 96.67 % (T. uilenbergi), and 93.33 % (T. ovis), respectively. In general, we developed a rapid, simple, sensitive, and specific technique for differential detection of T. luwenshuni, T. uilenbergi, and T. ovis infection in small ruminants.

Mycoplasma pneumoniae: evolving diagnostic methods for a known pathogen

Mycoplasma pneumoniae causes community-acquired pneumonia and extrapulmonary manifestations. It is an important cause of atypical pneumonia in children and can be associated with cyclical epidemics. This manuscript reviews the performance of current M. pneumoniae diagnostic methods, including culture-based, serological and nucleic acid amplification testing. The added value of molecular typing and genome sequencing in controlling M. pneumoniae epidemics is also considered, especially in characterising the evolving epidemiology and detecting genes and mutations associated with antimicrobial resistance, studies of which are lacking in Australia at present.

Enhancing the forensic sexual assault investigations with LAMP-based male DNA detection

Sexual assault is a terrible crime that demands a comprehensive and skilled investigation to gather the perpetrator's biological material. To collect all possible physical and biological evidence, forensic investigation is crucial and should be conducted as soon as possible. The primary focus of such investigations is the detection of male-specific materials. This study presents a novel assay utilizing the LAMP technique to detect male DNA. The assay underwent validation following the SWGDAM guidelines and was subsequently tested on 92 casework samples from sexual assault cases. To evaluate its performance, the outcomes of three distinct tests: acid phosphatase, microscopic examination, and the LAMP assay, were compared against the Y-STR profiling results. The LAMP assay exhibited remarkable efficiency, comparable to Y-STR profiling. These findings emphasize the LAMP technique's potential as a valuable tool for male DNA detection in forensic casework. Further research and validation studies are essential to fully explore its practical applications and enhance its utility in criminal investigations.

Development of a Visual Loop-Mediated Isothermal Amplification Assay for Rapid Detection of Morganella morganii

Morganella morganii is a Gram-negative bacterium associated with foodborne diseases and histamine toxicity in fish, posing significant public health concerns. Traditional detection methods, such as polymerase chain reaction (PCR), often require costly equipment, restricting their applicability in resource-limited environments. In this study, we present the development of a cost-effective and user-friendly colorimetric loop-mediated isothermal amplification (LAMP) assay. We designed six primers targeting the urease gene and optimized the assay to produce visual results using a pH-sensitive phenol red dye. The LAMP assay delivers results in 25 min and can detect M. morganii at concentrations as low as 5 pg (1.16 × 106 copies/reaction) and 2.6 × 105 CFU/mL (2.5 × 106 copies/reaction) in pure cultures, demonstrating high specificity, with no cross-reactivity against 10 other bacterial strains. A comparison with PCR methods using 30 samples revealed a 100% concordance rate, indicating robust diagnostic agreement. Additionally, the assay successfully identified M. morganii in spiked aquaculture water samples at concentrations up to 107 CFU/mL. In summary, this LAMP assay operates at a constant temperature and provides clear visual results, serving as a potential rapid detection method for applications in aquaculture settings.

Veterinary application of LAMP: a simple and visual detection tool for feline sporotrichosis

Early diagnosis of sporotrichosis, along with the surveillance of fungal circulation in both human and domestic animal populations, is critical for global health. Although the gold standard method is microbiological culture followed by microscopic analysis of the fungus, this methodology requires a long period and skilled professionals for pathogen identification. We developed a molecular assay and conducted a preliminary evaluation using clinical samples using Loop-Mediated Isothermal Amplification (LAMP) technology that detects Sporothrix schenckii and Sporothrix brasiliensis fungi, with results in 30 min. Results are visually interpreted and do not require DNA extraction, making it a promising tool for point-of-care diagnosis in veterinary settings.

Recombinase polymerase amplification assay for sensitive and rapid detection of invasive fall armyworm, Spodoptera frugiperda

The fall armyworm, Spodoptera frugiperda, is an invasive, polyphagous pest that threatens approximately 353 plant species across 72 families worldwide. Due to morphological similarities with other noctuid pests during the early larval, pupal, and adult stages, traditional identification methods are labour-intensive and require specialist expertise. Rapid, reliable detection is essential given the pest's potential for widespread destruction. Through genome-wide in-silico analysis, this study identified a unique region within a signal peptide gene of S. frugiperda, which served as the basis for developing PCR, LAMP, and RPA-based assays for detection. The PCR assay produced a specific 550 bp amplicon for S. frugiperda, showing no cross-reactivity with negative controls. In the LAMP assay, positive samples exhibited a sky-blue colour, while negative samples turned violet when hydroxynaphthol blue dye was used. The RPA assay, with SYBR green dye, displayed bright green in positive samples and brick-red in negatives. Sensitivity tests demonstrated that PCR detected as low as 1 pg/µL, while LAMP and RPA achieved a higher sensitivity of 100 fg/µL. This study introduces the first RPA colorimetric assay for S. frugiperda, providing a time-efficient, cost-effective option that requires minimal equipment, ideal for field detection, thereby supporting timely pest monitoring and management.

Fast and visual RT-LAMP assay for detection of oropouche virus

BACKGROUND

The epidemic potential of Oropouche virus (OROV) highlights the urgent need for rapid and accessible diagnostic methods to improve testing capacity and reduce result turnaround times, especially in tropical regions where OROV prevalence is rising.

OBJECTIVE

To develop and validate a rapid, cost-effective diagnostic assay for OROV detection suitable for use in resource-limited and field settings.

METHODS

A reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was designed and optimized for OROV detection. The assay's performance was evaluated in terms of sensitivity, specificity, time to result, and ease of visual interpretation based on colorimetric changes.

RESULTS

The RT-LAMP assay produced results within 30 to 35 minutes and enabled straightforward visual detection through a clear color change. Its detection limit was comparable to that of real-time PCR, the current gold standard for molecular diagnosis. The assay's simplicity and minimal equipment requirements make it well-suited for decentralized testing environments.

CONCLUSIONS

This RT-LAMP assay represents a rapid, sensitive, and accessible tool for OROV diagnosis, with significant potential to enhance outbreak response and surveillance efforts in endemic regions.

One-step narrow-thermal-cycling strand exchange amplification for sensitive detection of porcine reproductive and respiratory syndrome virus

Porcine reproductive and respiratory syndrome (PRRS), which is primarily characterized by respiratory and reproductive dysfunction, is an epidemic disease caused by porcine reproductive and respiratory syndrome virus (PRRSV) that has the potential to economically devastate the global swine industry. Rapid and accurate detection of PRRSV is critical for effective control of PRRS in swine. In this study, a novel one-step, highly sensitive and specific accelerated strand exchange amplification (ASEA) method for the detection of PRRSV was developed. The detection limit of the ASEA method was determined to be 6 copies µL-1 of PRRSV RNA reference material or PRRSV in spiked swine blood. The ASEA method demonstrated the capacity to discern the currently circulating PRRSV genotypes without cross-reactivity with other porcine-derived pathogens that manifest similar clinical signs. The ASEA method exhibited a detection time of 35 min, and its clinical applicability was validated through the analysis of 5 inactivated blood samples and 62 clinical samples. The method's potential extends beyond the diagnosis of PRRSV, as it can also be applied to the rapid diagnosis of other RNA pathogens. This capacity is expected to make significant contributions to future epidemic prevention and surveillance efforts.

A label-free and naked-eye fluorescence turn-on assay for one-pot LAMP detection of foodborne pathogens using AuNCs-Cu2+ complex

Loop-mediated isothermal amplification (LAMP) is a rapid and sensitive approach for foodborne pathogen detection; however, a simple, user-friendly, and naked-eye readable readout method remains a challenge. Herein, we synthesized bovine serum albumin stabilized gold nanoclusters (BSA-AuNCs), which exhibit fluorescence quenching upon copper ions (Cu2+) binding and fluorescence recovery in the presence of phosphate ions (PPi). Leveraging this property, we developed a label-free fluorescence turn-on assay for naked-eye LAMP detection by monitoring PPi accumulation under UV light. To mitigate potential cross-contamination risks inherent in LAMP workflows, we integrated the BSA-AuNCs-Cu2+ complex into the reaction lid, enabling a closed, one-pot detection system. This method demonstrated high sensitivity, detecting Salmonella enterica at concentrations as low as 101 CFU/mL within 40 min (excluding nucleic acid extraction process). With its customizable primers and naked-eye visual detection capability, this assay offers a versatile and practical tool for rapid pathogen screening in diverse applications.

Establishment and application of an indirect enzyme-linked immunosorbent assay based on tandem expression PrgH-PagN protein to detect Salmonella infection in ducks

Salmonella, an important foodborne zoonotic pathogen, can be transmitted both vertically and horizontally. It is difficult to control and effectively decontaminate Salmonella, and it poses a serious threat to food safety. Therefore, to prevent the spread of salmonellosis, there is an urgent need for a rapid, accurate and sensitive assay to detect the prevalence of Salmonella in duck flocks. In this study, we utilized biological software to predictively screen the highly conserved Salmonella-specific proteins SpiC, PrgH and PagN. The recombinant proteins PrgH, SpiC, PagN were screened for sensitivity based on individual proteins and pairwise combinations (SpiC + PrgH, SpiC + PagN and PrgH + PagN). A specific and sensitive dual-protein combination, PrgH + PagN, was used as an antigen. Subsequently, PrgH-PagN was produced by tandem expression and employed as the coating antigen in an indirect ELISA (iELISA) for detecting Salmonella antibodies in duck serum. The optimal antigen coating concentration was determined to be 1 μg/ml, with a critical value of OD450 = 0.154. The cross-reactivity test results showed no evidence of cross-reactivity with known positive serums from ducks infected with S. Enteritidis, S. Typhimurium, S. Kottbus, E. coli, Streptococcus or Staphylococcus. Screening of 611 duck serums was performed to determine an overall positive rate of 22.09%. The final compliance rate of 93.1% was determined by comparison with that of the commercial kit. In conclusion, the PrgH-PagN-iELISA established in the present study was an accurate and reliable method, with high sensitivity and specificity for detecting antibody responses to systemic Salmonella infections in ducks.

Detection of Mycobacterium ulcerans with IS2404 loop-mediated isothermal amplification and a fluorescent reporter probe

An exquisitely sensitive quantitative PCR (qPCR) assay targeting the high-copy number insertion sequence, IS2404, is the gold standard diagnostic test for Mycobacterium ulcerans, the agent of the neglected tropical skin disease Buruli ulcer. Here, we designed and tested an alternative M. ulcerans diagnostic test, a fluorescent probe-based, loop-mediated isothermal amplification (P-LAMP) assay that also targets IS2404. Benchmarked against IS2404 qPCR, P-LAMP was equally specific and nearly as sensitive (analytical sensitivity of four vs two M. ulcerans genome copies). Clinical and environmental specimen validation against IS2404 qPCR showed P-LAMP had 100% sensitivity and specificity. P-LAMP was twice as fast as qPCR with an average time-to-positive at the limit-of-detection of 19 minutes. P-LAMP targeting IS2404 is a versatile assay that addresses the performance issues of previously described IS2404 LAMP formats. This study tackles a key research priority for Buruli ulcer and represents another avenue for the development of rapid and accessible molecular diagnostics for this neglected tropical disease.IMPORTANCEBuruli ulcer is a neglected tropical disease caused by infection with Mycobacterium ulcerans. Correct diagnosis is essential before appropriate treatment for Buruli ulcer can be started. Development of a portable, easy-to-use diagnostic test for M. ulcerans has been identified by the World Health Organization as a research priority. Buruli ulcer most commonly occurs in remote, rural areas; therefore, an ideal test is one that can be used at (or near) the point of care (community health centres) without the need for specialized laboratories. Here, we describe a molecular test using loop-mediated isothermal amplification (LAMP) to detect DNA specific to M. ulcerans and show that this new test has equivalent performance to the gold standard M. ulcerans PCR test currently used worldwide. Our new test is rapid (30 minutes to run), simple to perform, and could be further developed into a robust, portable format to provide accessible and affordable M. ulcerans diagnostics anywhere.

CRISPR/Cas-powered nucleic acid amplification and amplification-free biosensors for public safety detection: Principles, advances and prospects

Rapid, accurate, cost-effective, and efficient ultrasensitive detection strategies are essential for public health safety (including food safety, disease prevention and environmental governance). The CRISPR/CRISPR-associated (Cas) detection is a cutting-edge technology that has been widely used in the detection of public health safety due to its targeted cleavage properties (signal amplification), attomolar level sensitivity, high specificity (recognizing single-base mismatches), and rapid turnover time. However, the current research about CRISPR/Cas-based biosensors is not clear, such as mechanism problem and application differences of integrating CRISPR/Cas system with other technologies, and how to further innovate and develop in the future. Therefore, further detailed analysis and comparative discussion of CRISPR/Cas-based biosensors is needed. Currently, CRISPR/Cas system powered biosensors can be mainly categorized into two types: CRISPR/Cas system powered nucleic acid amplification biosensors and CRISPR/Cas system powered nucleic acid amplification-free biosensors. The two biosensors have different characteristics and advantages. This paper first provides an in-depth investigation of the enzymatic mechanism of CRISPR/Cas system at the molecular level. Then, this paper summarizes the principles and recent advances of CRISPR/Cas system powered nucleic acid amplification biosensors and CRISPR/Cas system powered nucleic acid amplification-free biosensors and discusses their integration mechanisms in depth. More, the differences and application-oriented between the two biosensors are further discussed. Finally, the application orientation and future perspectives of the two biosensors are discussed, and unique insights into the future development of CRISPR/Cas system are provided.

Colorimetric loop-mediated isothermal amplification (cLAMP) assay for the genotyping of a thrombophilia genetic risk factor, MTHFR (C677T)

Methylenetetrahydrofolate reductase (MTHFR) is an enzyme involved in regulating serum homocysteine and folate levels. A single nucleotide polymorphism (SNP) of MTHFR (rs1801133; C677T) is strongly associated with an increased risk of thrombophilia, heart attack, stroke, and dementia. Genotyping this SNP is vital; however, techniques need to be simplified. This study developed a colorimetric loop-mediated isothermal amplification (cLAMP) technique to genotype the C677T in thrombophilia-susceptible individuals. The results were compared with those of kompetitive allele-specific PCR (KASP) and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assays. The cLAMP assay successfully detected the C677T SNPs in the MTHFR gene. The results agreed with the KASP and PCR-RFLP results. The MTHFR-cLAMP assay is a simple, rapid, and affordable technique for colorimetric genotyping. This is the first study describing visual detection of a SNP associated with thrombophilia. The assay can also be used in screening other SNPs at low-resource centers and hospitals for point-of-care testing.

Hydrogel-based electrochemical LAMP sensor for rapid, contamination-free and ultrasensitive point-of-care detection of Vibrio parahaemolyticus

We report in this work a sure-seal hydrogel-based sensor based on electrochemistry (EC) and loop-mediated isothermal amplification (LAMP) for real-time or end-point monitoring of the amplicon of Vibrio parahaemolyticus. Thanks to the nanoconfinement effect of the porous hydrogel, the LAMP can be significantly accelerated, allowing either real-time or endpoint detection within 15 min with a sensitivity down to 2.11 copies per reaction. A portable device was fabricated by integrating the hydrogel-based EC-LAMP sensor with a flexible and wireless electrochemical system, which enabled the point-of-care detection of Vibrio parahaemolyticus.

Viral Challenges in Wheat: Comprehensive Diagnosis and Innovative Management Approaches

Wheat (Triticum aestivum L.) is a staple crop cultivated globally, providing essential nutrition to billions. However, viral diseases pose a major challenge, causing yield losses of up to 80% and significant economic damage. More than 50 distinct viruses infect wheat, with key threats including wheat streak mosaic virus (WSMV), barley yellow dwarf viruses (BYDVs), high plains wheat mosaic virus (HPWMoV), soilborne wheat mosaic virus (SBWMV), and wheat yellow mosaic virus (WYMV). These viruses are primarily transmitted by vectors such as wheat curl mites (Aceria tosichella), aphids, and soilborne fungi like Polymyxa graminis. Diagnosing wheat viral infections is challenging due to overlapping symptoms with other plant stresses and the microscopic nature of viruses. Recent advancements in molecular and serological diagnostics, including Enzyme-Linked Immunosorbent Assay (ELISA), RT-Polymerase Chain Reaction (RT-PCR), CRISPR-based detection, and biosensors, have improved virus identification and monitoring. Since chemical treatments are ineffective, integrated management strategies such as breeding virus-resistant varieties, controlling vector populations, adjusting cultural practices, and utilizing RNA interference (RNAi) are essential for mitigating disease spread. This review provides a comprehensive analysis of wheat viral diseases, focusing on cutting-edge diagnostic tools and sustainable management approaches. By addressing knowledge gaps and highlighting future research directions, it aims to support the development of virus-resistant wheat, ensuring global food security.

Self-priming isothermal polymerization engineered in-situ copper nanoparticles generation for one-tube biomarkers sensing

BACKGROUND

On the one hand, for most of isothermal polymerization-based biosensing, the detection signals are uniformly originated from non-specific fluorescent staining that usually leads to high background or false positive, which limited their applications in molecular diagnostics. On the other hand, in virtue of characteristic advantages including but not limited to short preparation time (<5 min), large Stokes shift (>230 nm) and high template dependence, DNA-templated copper nanoparticles (CuNPs) enable low-cost and label-free signal transduction in low-background fluorescent sensing, which thus are ideal candidates for signal sources in promising molecular diagnostics.

RESULTS

Herein, we developed highly sensitive and label-free methods for one-tube biomarkers sensing based on self-priming isothermal polymerization (SPIP) engineered in-situ generation of DNA-templated CuNPs. As the core element for SPIP, a dumbbell-shaped primary DNA is rationally designed to consist of adenine/thymine (AT)-rich stem-loop structure and phosphorothioate (PS)-modified DNA hairpin. Once initiated by polymerase, enzymatic extension and self-folding alternately occurred on the primary DNA, which resulted in accumulation of numerous AT-rich templates repeatedly included in the elongated dsDNA products, and ultimately enabled rapid formation of fluorescent CuNPs. By virtue of alkaline phosphatase (ALP)-catalyzed dephosphorylation to generate 3'-OH available for polymerization, the strategy of SPIP engineered CuNPs generation was successfully adapted to sensitive ALP detection. Moreover, by utilizing apurinic/apyrimidinic endonuclease 1 (APE1)-triggered conformation transformation of probe DNA to produce primary DNA, sensitive APE1 sensing was also realized with this self-contained isothermal amplification approach.

SIGNIFICANCE

Benefiting from the robustness and simplicity of SPIP engineered CuNPs generation, the sensing methods enabled accurate analysis of real samples including ALP assay in clinical human serum and APE1 determination in normal and cancer cells. In brief, this work provides a new vision for nano-signal amplification and a promising sensing strategy for molecular diagnostics.

One-Pot Detection of miRNA by Dual Rolling Circle Amplification at Ambient Temperature with High Specificity and Sensitivity

Rolling circle amplification (RCA) at ambient temperature is prone to false positive signals during nucleic acid detection, which makes it challenging to establish an efficient RCA detection method. The false positive signals are primarily caused by binding of non-target nucleic acids to the circular single-stranded template, leading to non-specific amplification. Here, we present an RCA method for miRNA detection at 37 °C using two circular ssDNAs, each of which is formed by ligating the intramolecularly formed nick (without any splint) in a secondary structure. The specific target recognition is realized by utilizing low concentrations (0.1 nM) of circular ssDNA1 (C1). A phosphorothioate modification is present at G*AATTC on C1 to generate a nick for primer extension during the primer self-generated rolling circle amplification (PG-RCA). The fragmented amplification products are used as primers for the following RCA that serves as signal amplification using circular ssDNA2 (C2). Notably, the absence of splints and the low concentration of C1 significantly inhibits non-target binding, thus minimizing false positive signals. A high concentration (10 nM) of C2 is used to carry out linear rolling circle amplification (LRCA), which is highly specific. This strategy demonstrates a good linear response to 0.01-100 pM of miRNA with a detection limit of 7.76 fM (miR-155). Moreover, it can distinguish single-nucleotide mismatch in the target miRNA, enabling the rapid one-pot detection of miRNA at 37 °C. Accordingly, this method performs with high specificity and sensitivity. This approach is suitable for clinical serum sample analysis and offers a strategy for developing specific biosensors and diagnostic tools.

A fluorescence and colorimetric dual-mode LAMP method for detection of Vibrio parahaemolyticus

Conventional nucleic acid detection technology for foodborne pathogens relies on advanced analyzers and professional technicians, but in areas with limited resources, this method limits the rapid detection of pathogens, which highlights the importance of developing a method suitable for on-site detection. A dual-mode detection method was proposed for Vibrio parahaemolyticus (V. parahaemolyticus) based on loop-mediated isothermal amplification (LAMP), which integrates fluorescence detection and visual colorimetric detection. This method was developed for instant on-site detection. When the experimental conditions are available, the fluorescence detection method can be selected for quantitative determination, and when the resources are limited, the visual colorimetric method can be used for qualitative determination. The dual-mode LAMP method has been shown to achieve comparable sensitivity to real-time fluorescent LAMP, with the capacity to detect 1 pg μL-1 of V. parahaemolyticus DNA with high specificity. In order to enhance the objectivity of detection, an RGB image analysis method was developed, and a simple judgment strategy was proposed: when the B/G value is less than 1.3 and the R/G value is less than 0.8, the result can be judged as positive. In addition, the real samples were tested, and the accuracy rate of the visual colorimetric detection mode was found to be 96%. The RGB analysis method reduced the subjective error of naked eye colorimetry, and the accuracy rate was equivalent to that of the real-time fluorescence mode, reaching 98%. This method provides a novel and sensitive idea for on-site instant detection.

Molecular methods for rapid detection and identification of foodborne pathogenic bacteria

Foodborne pathogenic bacteria are one of the main factors causing food safety issues. The rapid and accurate detection of pathogenic bacteria using molecular techniques is an effective and powerful strategy for preventing and controlling outbreaks of foodborne diseases, thereby ensuring food safety. This article summarizes the rapid and efficient molecular diagnostic techniques for detecting pathogenic bacteria, including polymerase chain reaction and its derivatives, isothermal amplification, DNA hybridization, genomic sequencing, and Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/CRISPR-associated (CRISPR/Cas)-based detection technique. Through a comparative analysis of the technical principles, advantages, and potential limitations of these diagnostic methods, as well as an outlook on the future development directions for molecular biological detection technology, which will provide a valuable reference for developing more accurate, convenient, and sensitive methods for foodborne pathogens detection, and will help better address the challenges posed by foodborne diseases, thereby ensuring public health and safety.

Detection of Cancer Biomarkers: Review of Methods and Applications Reported from Analytical Perspective

One in five deaths in developed countries is related to cancer. The cancer prevalence is likely to grow with aging population. The affordable and accurate early diagnostics of cancer based on detection of cancer biomarkers at low concentration during its early stages is one of the most efficient way to decrease mortality and human suffering from cancer. The data from 201 analytical papers are tabulated in 9 tables, illustrated in 8 figures and used for comparative analysis of methods applied for cancer biomarker detection, including polymerase chain reaction, Loop-mediated isothermal amplification (LAMP), mass spectrometry, enzyme-linked immunosorbent assay, electroanalytical methods, immunoassays, surface enhanced Raman scattering, Fourier Transform Infrared and others in terms of above-mentioned performance parameters. Median and/or average limit of detection (LOD) are calculated and compared between different analytical methods. We also described and compared LOD of the methods used for detection of three frequently detected cancer biomarkers: carcinoembryonic antigen, prostate-specific antigen and alpha-fetoprotein. Among those methods of detection, the reported electrochemical sensors often demonstrate relatively high sensitivity/low LOD while they often have a moderate instrumental cost and fast time to results. The review tabulates, compares and discusses analytical papers, which report LOD of cancer biomarkers and comprehensive quantitative comparison of various analytical methods is made. The discussion of those techniques applied for cancer biomarker detection included brief summary of pro and cons for each of those methods.

Bringing the heat: Thermostable analogs of Bst polymerase allow high-temperature LAMP

BACKGROUND

Loop-mediated isothermal amplification (LAMP) is a nucleic acid amplification method that gained prominence during the early months of the COVID-19 pandemic due to its simplicity, sensitivity and robustness. However, this technique is susceptible to non-specific amplifications, raising concerns about false-positive results and reduced diagnostic accuracy. A primary contributor to false-positive testing is primer dimerization, which can theoretically be mitigated by performing reactions at higher temperatures. Unfortunately, the strand-displacing DNA polymerases typically used in LAMP, such as Bst, exhibit reduced efficiency at elevated temperatures. To address this limitation, we hypothesised that naturally occurring thermophilic analogs of Bst may be capable of supporting LAMP at higher temperatures, thereby improving reaction specificity.

METHODS

Bioinformatics and recombinant enzyme production allowed the identification and synthesis of several Bst analogs. These were tested in real-time LAMP assays to detect diverse targets, in a wide range of reaction temperatures (63°C-75°C) and in the presence of typical qPCR inhibitors.

RESULTS

Three polymerases-Bst_7, Bst_8 and Bst_15-demonstrated exceptional activity and robust stability at higher temperature conditions (up to 72.5°C), while displaying considerable resistance to common qPCR inhibitors.

CONCLUSIONS

The identified thermophilic Bst analogs represent a potential solution for the mitigation of non-specific amplification in LAMP, further boosting the application of this technique in molecular diagnostic settings.

Loop-Mediated Isothermal Amplification Assay for Visual Detection of Salmonella enterica Serovar Typhimurium in Food Animal Meat Products

Detection of Salmonella, a highly diverse foodborne pathogen, is paramount to ensure safety and protection of the animal industry and its consumers. Salmonella enterica serovar Typhimurium is among the most important non-typhoidal serovars causing gastroenteritis worldwide. However, traditional serovar identification is labor- and resource-intensive, while typical molecular tools require expensive reagents and equipment. Hence, this study developed and optimized a calcein-based and closed-tube loop-mediated isothermal amplification (LAMP)-based assay to detect S. Typhimurium following enrichment steps compared with an optimized PCR assay. The PCR assay showed 100% specificity in silico confirmed through DNA sequencing. For actual specificity testing, both PCR and LAMP showed 100% specificity to S. Typhimurium. For DNA sensitivity, while PCR showed a limit of detection of 22 pg/μL, LAMP showed a 100-fold higher sensitivity at 220 fg/μL. Meanwhile, for pure culture sensitivity, both assays detected at least 4.98 × 104 CFU/mL. Parallel testing of 208 raw meat samples from wet markets in Metro Manila, Philippines, showed corroboration and statistical association of the optimized PCR and LAMP with 89.42% and 90.87% positivity rates for S. Typhimurium, respectively. Hence, the developed closed-tube and calcein-based LAMP assay is potentially a powerful yet simple, sensitive, and fast method for S. Typhimurium detection.

Optimization of human T-cell lymphotropic virus type 1 (HTLV-1) serological and molecular diagnosis for alternative blood samples

HTLV-1 is a bloodborne virus that poses diagnostic challenges and can cause severe complications. Diagnosis is made by serological and molecular assays that are laborious in some conditions. This study aims to optimize methods for molecular and serological diagnosis using less invasive samples and rapid assays. A total of 125 individuals donated whole blood, dried blood spots (DBS), and serum samples. Loop mediated isothermal amplification (LAMP) was used for HTLV-1 detection in whole blood (extracted, in natura, and inactivated) and DBS samples while electrochemiluminescence assay (ECLIA) was used to detect anti-HTLV1/2 in serum and DBS. HTLV LAMP presented the highest performance in whole blood (extracted) with sensitivity of 92 % and specificity of 100 %. LAMP for inactivated samples had a sensitivity of 47.4 % and specificity of 100 %, whereas in natura samples had a sensitivity of 50 % and specificity of 100 %. The whole blood HTLV-1 LAMP had a limit detection of 0.02 ng/µL and 100 % precision. DBS LAMP carried out after DNA extraction yielded similar results, with a sensitivity 43 of 90 % (36/40). The average DNA concentration was 5.05 ± 5.2 ng/µL. For anti-HTLV1/2 testing, DBS yielded sensitivity of 97.6 % (86/88) and total specificity (0/29). The mean SD of optical density to cut off (OD/CO) value was 37.2 ± 36.8 in reactive samples and 0.3 ± 0.05 in negative samples. In conclusion, DBS testing demonstrated high sensitivity and specificity for detecting anti-HTLV-1 and HTLV DNA, which could facilitate the diagnosis of this infection.

Development of an RT-LAMP Assay for Detecting tet(M) in Enterococcus Species: Enhancing AMR Surveillance Within the One Health Sectors

The increasing prevalence of antimicrobial-resistant (AMR) bacteria in humans, animals, and the environment underscores the necessity for a rapid, sensitive, and specific method to identify resistance genes. Objectives: This study aims to develop a reliable detection tool for identifying the tetracycline-resistant gene tet(M) in Enterococcus species using a real-time loop-mediated isothermal amplification (RT-LAMP) assay. Real-time visualization through a turbidimeter enabled precise estimation of time-to-positivity for gene detection. Methodology: Six primers were designed using PrimerExplorer v.5, and the assay was optimized across different temperatures and incubation times. Validation was conducted by testing 52 tet(M)-positive clinical enterococci isolates and spiking urine samples from a healthy volunteer and a cow with tet(M)-positive Enterococcus species. Results: The tet(M) gene was detected as early as 33 min, with optimal amplification occurring within 60 min at 60 °C. The assay demonstrated 100% specificity with the established primers. The sigmoidal graphs were corroborated with visual confirmation methods, including a green color change (visible to the naked eye), green fluorescence (under UV light), and a 200 bp PCR product observed via agarose gel electrophoresis. Notably, the tet(M) RT-LAMP assay exhibited a detection limit of 0.001 pg/μL, significantly surpassing conventional PCR, which had a detection limit of 0.1 pg/μL. Conclusions: This rapid, cost-effective, highly sensitive, and specific tet(M) RT-LAMP assay holds significant promise as a surveillance tool for antimicrobial resistance monitoring within a One Health framework, particularly in low-resource countries.

Modeling a Standard Loop-Mediated Isothermal Amplification Reaction and Its Modification Involving Additional Inner Primers

Loop-mediated isothermal amplification (LAMP) was developed a quarter of a century ago, but it is still not exactly clear how this reaction proceeds. Only a few articles have focused on the kinetics of LAMP and the types of products formed. In this work, 10 types were identified and named. A basic dumbbell structure, Z6_dmb(1), consists of six zones and triggers the LAMP cycle. Due to self-priming, Z6_dmb(1) transforms into hairpin structure Z9_hp(1) and then into linearized strand Z9_li(1), carrying also strand Z6_dmb(2). Through similar transformations, it again generates strand Z6_dmb(1), completing the first LAMP cycle and starting a new one. The next stage of the exponential phase starts from two Z15_hp hairpin structures generated in the LAMP cycle, which next turn into Z15_li → Z27_hp → Z27_li → Z51_hp → and so forth. Modeling of a new type of the reaction, namely, pseudo-hemi-nested LAMP (phn-LAMP), was carried out. phn-LAMP involves three inner primers: two forward (FIP and extraFIP) and one backward inner primer, or vice versa. phn-LAMP has an advantage over LAMP involving loop or stem primers and over MIP-LAMP (multiple inner primers).

Reference Gene-Assisted LAMP-LFD for Sensitive and Specific Detection of Soy DNA as a Marker for Allergen Presence in Complex Food Products

Sensitive, selective screening for allergenic ingredients with internal control is crucial to identify food adulteration and remove allergens from the food chain. Here, loop-mediated isothermal amplification combined with a lateral flow device (LAMP-LFD) was developed for the fast and easy detection of soy DNA. The integrated quality controls included a regular control line to ensure proper implementation (extraction and amplification control) and a second LAMP-LFD assay for the cytochrome oxidase gene, which is a housekeeping gene in plants. The developed LAMP assay showed a limit of detection of only 5 pg DNA input per reaction, for both pure soy and spiked food samples. The test was subsequently implemented for the examination of 32 real food products with different compositions and declared soy contents, and benchmarked against qPCR. Then, this system was combined with a digital cube reader, allowing direct interpretation of the test results, facilitating the point-of-need applicability.

Current diagnosing strategies for Mycobacterium tuberculosis and its drug resistance: a review

Tuberculosis (TB), caused by Mycobacterium tuberculosis (MTB), remains a major global health threat, compounded by the rise of extensively drug-resistant (XDR) and multidrug-resistant (MDR) strains. This review critically examines the current landscape of laboratory diagnostic methods for MTB, encompassing both established techniques and recent advancements. We explore the growth and genetic characteristics of MTB that underpin drug resistance development and detection. We then provide a comparative analysis of smear microscopy, culture-based methods, antigen detection, molecular diagnostics (including nucleic acid amplification tests and whole-genome sequencing), spectroscopic techniques (such as Raman spectroscopy), and mass spectrometry-based approaches. Notably, this review focuses on pathogen-based diagnostic methods, excluding host immune response assays. The strengths and limitations of each method are evaluated in terms of sensitivity, specificity, turnaround time, cost-effectiveness, and suitability for resource-limited settings. Finally, we discuss the future of TB diagnostics, emphasizing the need for integrated, multi-modal platforms, the incorporation of artificial intelligence (AI) for enhanced data analysis, and the development of affordable, point-of-care testing to improve accessibility and impact in high-burden regions. Overcoming current diagnostic challenges is essential for improving patient outcomes and achieving global TB elimination goals.

Establishment and Application of a Rapid Detection Method of Cyprinid Herpesvirus 2 (CyHV-2) in Aquacultural Waters by Using a Novel One-Pot RAA-CRISPR/Cas12a Combined With Fe-Iron Flocculation Technology

Cyprinid herpesvirus 2 (CyHV-2) poses a substantial global threat to goldfish (Carassius auratus) and crucian carp (Carassius carassius). Despite the development of several sensitive molecular diagnostic techniques, there is an ongoing demand for alternative visualisation platforms to streamline the workflow, enhance safety profiles, and improve accessibility for end-users. In this study, we have integrated recombinase-aided amplification (RAA) technology with the CRISPR/Cas12a system to establish a rapid diagnostic system for CyHV-2, termed one-pot RAA-CRISPR/Cas12a. This method enables the results of detection within 60 min. The RAA-CRISPR/Cas12a platform is capable of detecting as few as 10 copies of CyHV-2 per reaction cycle without exhibiting cross-reactivity with other pathogens. The positive detection rate in clinical samples exceeds that of conventional PCR approaches, underscoring its high precision. Furthermore, the method could be used in conjunction with iron flocculation for the concentration and detection of viruses within aquaculture settings. This approach minimises the dissection of aquatic organisms, thereby maximising animal welfare and bolstering detection efficiency. Collectively, our findings validate the RAA-CRISPR/Cas12a method as a robust, specific, confirmatory, user-friendly and promising approach for on-site diagnosis of CyHV-2.

A loop-mediated isothermal amplification assay for the rapid and quantitative tracking of fecal contamination sources in water

Fecal contamination in water poses a serious threat to public health and the ecological environment. Numerous qPCR-based methods have been used to identify the source of fecal contamination, but this method relies on expensive equipment, well-established laboratory conditions, and experienced personnel, significantly reducing the timeliness of identifying contamination sources. Here, we developed a loop-mediated isothermal amplification (LAMP) assay for tracking the sources of fecal contamination to rapid identifying and quantifying humans, ruminants, pigs, and poultry fecal contamination. The results demonstrated that LAMP assay enabled us to easily and quickly (<30 min) detect associated gene of the host gut microbes for tracking of fecal contamination sources, exhibiting a same detection level of 100 gene copies/μL as lab-based qPCR. Compared to LAMP molecular markers of other bacterial genera and bacteriophages, the LAMP molecular markers of Bacteroidales showed a higher sensitivity and detection concentration. The majority of the non-target species (96.9%) showed little effect on the LAMP marker genes of the target species. Moreover, the LAMP assay was used to identify a multiple fecal contamination and spatial distribution characteristics in the Liuxi River basin. The detection frequency and abundance of human-associated marker genes were the highest, followed by pig-associated marker gene; the mean concentration of human- and pig-associated marker gene in tributaries were higher than that in the mainstem. This LAMP assay could be used to easily and quickly identify the sources of fecal contamination and contribute in the control and treatment of fecal contamination in water.

Nanobiodevices and quantum life science for future healthcare

Maintaining healthy life in old age (healthy aging) is an important social challenge. An effective approach to realizing healthy aging involves providing personalized healthcare through disease prevention, early diagnostics, and optimal treatments. Nanobiodevices and quantum life sciences have tremendous potential to revolutionize current techniques for disease prevention, diagnostics, and treatment via the efficient analyses of biomolecules, bioparticles, pathogens, and cells. In this review, we outline our research on nanobiodevices and quantum life sciences for future healthcare, including cancer diagnostics, pathogen detection, in vivo imaging-guided therapy, and intracellular sensing for stem cell quality checks.

Up-to-date nucleic acid assays for diagnosing respiratory infection

Nucleic acid assays have been widely used as rapid tests for diagnosing respiratory infections during and after the coronavirus disease 2019 (COVID-19) pandemic. An ideal point-of-care diagnostic must be affordable, sensitive, specific, user-friendly, rapid/robust, equipment-free and deliverable (ASSURED), and in addition to improvements to conventional methods based on polymerase chain reaction (PCR), point-of-care testing aiming for "REASSURED" are emerging through integration with microfluidic technology. Compared to conventional immunoassays, nucleic acid assays, especially rapid nucleic acid assays as point-of-care testing, contribute to improvements in various clinical outcomes, such as diagnostic yield, turnaround time, length of hospital stay, disease treatment, and infection control management. Rapid and diverse development of new nucleic acid-based molecular diagnostic technologies, such as those based on the CRISPR/Cas system or biosensor nucleic acid assays, is expected to become increasingly diverse in the future as point-of-care testing. In addition, laboratory-based DNA sequencing technology has been used to perform microbiome analyses over a wide area and is expected to shed light on the pathological mechanisms of various respiratory infectious diseases. One example of the benefits of nucleic acid amplification analysis methods is their ability to reveal the true nature of the bacterial flora in pneumonia lesions. This has been demonstrated based on the results of 16S ribosomal RNA gene sequencing analyses using bronchoalveolar lavage fluid directly obtained from pneumonia lesions in patients with pneumonia.

Loop-Mediated Isothermal Amplification (LAMP) for the Diagnosis of Sexually Transmitted Infections: A Review

Sexually transmitted infections (STIs) remain a significant public health concern. Given the asymptomatic nature of many STIs, diagnostic testing is critical for determining the appropriate treatment, enabling effective tracing and reducing the risk of further transmission. Nucleic acid amplification tests (NAATs) are the most sensitive and the most widely used in well-resourced settings. The majority of available NAATs are based on polymerase chain reaction (PCR), which requires highly trained personnel and costly equipment, making it impractical for resource-limited settings. Loop-mediated isothermal amplification (LAMP) has emerged as a simple, rapid, sensitive and low-cost alternative for pathogen detection, particularly well-suited for point-of-care tests (POCT). In this review, we evaluate LAMP assays reported in the literature for the detection of pathogens linked to the high incidence STIs prioritised by the World Health Organization (WHO) for POCT in 2023. These include Neisseria gonorrhoeae, Chlamydia trachomatis, Trichomonas vaginalis, T. pallidum subspecies pallidum, as well as other common STIs such as herpes simplex virus, hepatitis B virus and human immunodeficiency virus (HIV). For each LAMP assay, we identified and summarised the key elements such as the type and number of tested clinical specimens, chosen target gene, detection system, reference test and clinical outcomes. We highlight the advantages and limitations of these assays and discuss the gaps that should be addressed to improve their applicability for POCT.

Highly efficient loop cleavage for human papillomavirus detection with a novel thermophilic Argonaute from Thermus brockianus

Argonaute proteins (Agos), endowed with the capacity to cleave DNA or RNA under the guidance of small nucleic acid guides, have emerged as versatile biotechnological tools. This study endeavored to characterize a novel thermophilic Argonaute protein from Thermus brockianus (TbAgo), revealing its proficiency as a DNA-guided DNA endonuclease. Demonstrating high catalytic efficiency and precision at 65 °C, TbAgo possessed compatibility with loop-mediated isothermal amplification (LAMP) method, whose optimal temperature is also around 65 °C. Therefore, an innovative isothermal nucleic acid detection platform named AMEND (Argonaute-mediated loop cleavage for nucleic acid detection) was developed by integrating LAMP with TbAgo's targeted cleavage. This novel detection strategy was used to detect human papillomavirus (HPV) 16 and 18 DNA simultaneously with the limit of detection (LoD) of 1 aM within 30 min. Furthermore, a two-step microfluidic chip was designed to streamline the above HPV DNA detection workflow with high sensitivity of HPV 16 (1 aM) and 18 (10 aM) within 30 min. The present work not only characterized a novel Argonaute protein with the highest cleavage efficiency among the literature, but also paved the way to coordinate and streamline the two sequential reactions (isothermal DNA amplification and Ago mediated cleavage) at the same optimal temperature for high-efficiency DNA detection.

ViPER: A visual bipolar electrochemical biosensor based on isothermal addition of a universal tag for detection of SARS-CoV-2

Emergence of recent pandemics/endemics e.g. COVID-19 and Dengue fever, demonstrated the necessity of development of strategies for swift adaptation of present biosensor for detection of the new emerging pathogens. However, development of a biosensor for a new target is time- and labor-consuming. In this study, we aimed to integrate the primer exchange reaction (PER), an isothermal technique that extends an initiator DNA with a user-defined single-stranded DNA tail, with bipolar electrochemistry. This integration led to the development of a universal biosensor, termed ViPER. We demonstrated the utility of the developed system to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic RNA as a model. The genomic RNA was reverse transcribed to a short cDNA and was tailed with a universal tag, consequently, the tagged cDNA was applied to an electrochemiluminescence integrated bipolar electrochemical biosensor (BPE-ECL). ECL signals were recorded using a digital camera and analyzed by ImageJ. The platform demonstrated a linear response over a wide dynamic range of 10-7-10-17 M for the target nucleic acid with a detection limit of 2.31 × 10-17 M for synthetic targets. The biosensor could also successfully discriminate between biological RNA samples from infected and non-infected individuals. This study introduces the potential of DNA-based visual biosensors for detecting single-stranded RNAs in low-equipped environments, and it holds promises for further development of an ultrasensitive method for various human RNA-based viral pathogens. Moreover, we can design a platform with a predetermined DNA probe sequence for a vast variety of different targets, simply by changing the PER input.

Development of a loop-mediated isothermal amplification assay for the rapid detection of Alongshan virus

Alongshan virus (ALSV) is a recently discovered tick-borne zoonotic virus. Currently, there is no rapid and accurate clinical method for ALSV detection. This study aimed to develop a loop-mediated isothermal amplification (LAMP) assay for precise ALSV infection detection. Specific primers were designed based on the S1 segment of the ALSV NE-TH4 strain's genome (GenBank accession no. ON408067.1). The reaction time, temperature and concentration of the neutral red staining solution in the LAMP assay were optimized. Thorough evaluations of specificity, sensitivity and repeatability led to the development of a visually interpretable LAMP assay. The optimal amplification time was 50 min. The minimum detection limit for cDNA was as low as 0.005 pg μl-1, and sensitivity for standards was 1.68×103 copies per μl, surpassing that of PCR and real-time PCR. No cross-reactivity was observed with Jingmen tick virus, Bole tick virus 4 and Beiji nairovirus. These results indicate that the LAMP assay is more sensitive and accurate than PCR and real-time PCR. The developed LAMP assay allows for on-site detection, reduces testing costs and provides rapid and accurate results. Thus, it lays a solid foundation for the prevention and control of emerging tick-borne ALSV.