Rapid On-Site Detection of the Bursaphelenchus xylophilus Using Recombinase Polymerase Amplification Combined With Lateral Flow Dipstick That Eliminates Interference From Primer-Dependent Artifacts

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.

RH-RPA: A Rapid and Highly Sensitive Assay for Nucleic Acid Detection Based on RNase HII Combined with Recombinase Polymerase Amplification

Currently, RPA-exo and RPA-nfo are the primary methods for RPA/RT-RPA probe assays, both of which have been widely applied to the detection of various targets. However, RPA-nfo exhibits lower sensitivity compared with the exo probe method, while RPA-exo lacks the capability for equipment-free visualization inherent to RPA-nfo. Both of the approaches mentioned above limit the broader application of RPA/RT-RPA probe assays. To address those limitations, we have developed a novel recombinase polymerase amplification (RPA) combined with an E. coli RNase HII assay (RH-RPA). This approach supports both fluorescence signal detection and lateral-flow strip readouts. Due to the high efficiency and specificity of E. coli RNase HII in recognizing and cleaving targets, this method serves as a rapid and accurate molecular diagnostic platform. Under the fluorescence detection mode, RH-RPA achieves a limit of detection as low as 10 copies per reaction for both DNA and RNA within 20 min. Additionally, the lateral-flow strip mode enables the detection of as few as 5 copies per reaction of nucleic acids within 20 min. In clinical sample analysis, the RT RH-RPA demonstrated 100% accuracy in detecting the influenza A virus, underscoring its reliability in practical diagnostics. These findings highlight the stable specificity, rapid performance, high sensitivity, and cost-effectiveness of the RH-RPA methods, showcasing their potential as promising tools for point-of-care nucleic acid detection.

Establishment of a Rapid Detection Technique Based on RPA-LFD and RPA-CRISPR/Cas12a on Phytophthora pini

Phytophthora pini, a globally dispersed plant pathogen, poses a significant threat to natural ecosystems and cultivated horticultural crops. Early and precise detection of P. pini is essential for effective disease management. This study focused on developing specific, rapid, and sensitive molecular diagnostic techniques to identify the pathogenic oomycete P. pini. We employed recombinase polymerase amplification with lateral flow device (RPA-LFD) and RPA combined with CRISPR/Cas12a. The RPA-LFD method can identify P. pini at concentrations as low as 10 pg/μL in 30 min, while the RPA-CRISPR/Cas12a approach can detect the pathogen at 1 pg/μL in approximately 50 min. These methods are highly effective in identifying disease caused by P. pini and provide a basis for future field detection, which may reduce the economic losses associated with this devastating disease.

On-site genetic diagnosis for the invasive pest Hylurgus ligniperda (Fabricius) and its possible application

BACKGROUND

Forests in nearly all regions worldwide are affected by invasions of non-native bark beetles. Hylurgus ligniperda (Fabricius) is a globally invasive bark beetle that stealthily jeopardizes pine health and spreads worldwide insidiously. The worldwide occurrence of Hylurgus ligniperda challenges trade in pine logs or wooden materials. Early identification of Hylurgus ligniperda is crucial in implementing appropriate pest management strategies.

RESULTS

This study established a simple, efficient, and accurate method for identifying Hylurgus ligniperda based on recombinase polymerase amplification and the lateral flow dipstick (RPA-LFD). The method can distinguish Hylurgus ligniperda from other species and has a sensitivity threshold of 10 fg/μL. Subsequently, field application tests were conducted using RPA-LFD assays, the first field application case in forestry entomology. The field test results showed that RPA-LFD combined with crude DNA extraction could accurately identify Hylurgus ligniperda (except elytra). The influence of environmental factors (temperature, humidity, and wind) was also investigated. The results showed that only wind speed (P = 0.003) was significantly correlated with the color rendering of the LFD and negatively correlated with the color and density of the LFD detection line.

CONCLUSION

A rapid field-based identification method applied helps the elimination of barriers to the lagging identification of invasive pests. Implementing RPA-LFD aims to provide a reliable and efficient tool for rapidly identifying invasive insects, enabling timely intervention and effective management strategies. © 2025 Society of Chemical Industry.

Rapid and Accurate Detection of Chrysomya megacephala (Diptera: Calliphoridae) Using Recombinase Polymerase Amplification Combined with Lateral Flow Dipstick

Estimating the postmortem interval (PMI) is critical in the field of forensic science, and necrophagous insects play a significant role in this process. Chrysomya megacephala (Fabricius) (Diptera: Calliphoridae) is a common necrophagous insect species, making its rapid and accurate identification essential. However, commonly used molecular biology methods, such as DNA barcode, still have some limitations in identifying necrophagous insects as they are often complex, time-consuming, and reliant on laboratory instruments. Therefore, in this study, we have developed an innovative detection system for the rapid and accurate identification of C. megacephala based on the Cytochrome b gene using recombinase polymerase amplification (RPA) and lateral flow dipstick (LFD) in combination. The developed RPA-LFD detection system achieved complete amplification in just 15 min at 37 °C with good sensitivity and specificity. Only 7.8 × 10-4 ng or more of target DNA fragments were required, and a positive detection rate of 100% was achieved in 18 C. megacephala samples from actual cases. In addition, the ability of the developed RPA-LFD detection system in combination with rapid DNA extraction methods to enable on-site detection was preliminarily explored. The results suggested that when the RPA-LFD detection system was combined with the grinding ddH2O extraction method (a rapid DNA extraction method), the process from species acquisition to visualization of detection results could be completed in less than 20 min. In conclusion, this innovative RPA-LFD detection system outperforms commonly used molecular biology methods for C. megacephala identification in terms of speed, sensitivity and convenience, making it suitable for direct application at crime scenes, promising to provide important assistance in estimating PMI and expanding the impact of forensic entomological evidence.

Detection Methods for Pine Wilt Disease: A Comprehensive Review

Pine wilt disease (PWD), caused by the nematode Bursaphelenchus xylophilus, is a highly destructive forest disease that necessitates rapid and precise identification for effective management and control. This study evaluates various detection methods for PWD, including morphological diagnosis, molecular techniques, and remote sensing. While traditional methods are economical, they are limited by their inability to detect subtle or early changes and require considerable time and expertise. To overcome these challenges, this study emphasizes advanced molecular approaches such as real-time polymerase chain reaction (RT-PCR), droplet digital PCR (ddPCR), and loop-mediated isothermal amplification (LAMP) coupled with CRISPR/Cas12a, which offer fast and accurate pathogen detection. Additionally, DNA barcoding and microarrays facilitate species identification, and proteomics can provide insights into infection-specific protein signatures. The study also highlights remote sensing technologies, including satellite imagery and unmanned aerial vehicle (UAV)-based hyperspectral analysis, for their capability to monitor PWD by detecting asymptomatic diseases through changes in the spectral signatures of trees. Future research should focus on combining traditional and innovative techniques, refining visual inspection processes, developing rapid and portable diagnostic tools for field application, and exploring the potential of volatile organic compound analysis and machine learning algorithms for early disease detection. Integrating diverse methods and adopting innovative technologies are crucial to effectively control this lethal forest disease.

Establishment of a Sensitive and Reliable Droplet Digital PCR Assay for the Detection of Bursaphelenchus xylophilus

Pine wilt disease (PWD), which poses a significant risk to pine plantations across the globe, is caused by the pathogenic agent Bursaphelenchus xylophilus, also referred to as the pine wood nematode (PWN). A droplet digital PCR (ddPCR) assay was developed for the quick identification of the PWN in order to improve detection sensitivity. The research findings indicate that the ddPCR assay demonstrated significantly higher analysis sensitivity and detection sensitivity in comparison to traditional quantitative PCR (qPCR). However, it had a more limited dynamic range. High specificity was shown by both the ddPCR and qPCR techniques in the diagnosis of the PWN. Assessments of reproducibility revealed that ddPCR had lower coefficients of variation at every template concentration. Inhibition tests showed that ddPCR was less susceptible to inhibitors. There was a strong linear association between standard template measurements obtained using ddPCR and qPCR (Pearson correlation = 0.9317; p < 0.001). Likewise, there was strong agreement (Pearson correlation = 0.9348; p < 0.001) between ddPCR and qPCR measurements in the evaluation of pine wood samples. Additionally, wood samples from symptomatic (100% versus 86.67%) and asymptomatic (31.43% versus 2.9%) pine trees were diagnosed with greater detection rates using ddPCR. This study's conclusions highlight the advantages of the ddPCR assay over qPCR for the quantitative detection of the PWN. This method has a lot of potential for ecological research on PWD and use in quarantines.

Nanomaterials for Plant Disease Diagnosis and Treatment: A Review

Currently, the excessive use of pesticides has generated environmental pollution and harmful effects on human health. The controlled release of active ingredients through the use of nanomaterials (NMs) appears to reduce human exposure and ecosystem alteration. Although the use of NMs can offer an alternative to traditional methods of disease diagnosis and control, it is necessary to review the current approach to the application of these NMs. This review describes the most recent and significant advances in using NMs for diagnosing and treating plant diseases (bacteria, phytopathogenic fungi, viruses, and phytopathogenic nematodes) in cultivated plants. Most studies have focused on reducing, delaying, or eliminating bacteria, fungi, viruses, and nematodes in plants. Both metallic (including metal oxides) and organic nanoparticles (NPs) and composites are widely used in diagnosing and controlling plant diseases due to their biocompatibility and ease of synthesis. Few studies have been carried out with regard to carbon-based NPs due to their toxicity, so future studies should address the development of detection tools, ecological and economic impacts, and human health. The synergistic effect of NMs as fertilizers and pesticides opens new areas of knowledge on the mechanisms of action (plant-pathogen-NMs interaction), the interaction of NMs with nutrients, the effects on plant metabolism, and the traceability of NMs to implement sustainable approaches. More studies are needed involving in vivo models under international regulations to ensure their safety. There is still controversy in the release of NMs into the environment because they could threaten the stability and functioning of biological systems, so research in this area needs to be improved.

Point-of-Care Diagnostic System for Viable Salmonella Species via Improved Propidium Monoazide and Recombinase Polymerase Amplification Based Nucleic Acid Lateral Flow

Salmonella species are prominent foodborne microbial pathogens transmitted through contaminated food or water and pose a significant threat to human health. Accurate and rapid point-of-care (POC) diagnosis is gaining attention in effectively preventing outbreaks of foodborne disease. However, the presence of dead bacteria can interfere with an accurate diagnosis, necessitating the development of methods for the rapid, simple, and efficient detection of viable bacteria only. Herein, we used an improved propidium monoazide (PMAxx) to develop a nucleic acid lateral flow (NALF) assay based on recombinase polymerase amplification (RPA) to differentiate viable Salmonella Typhimurium. We selected an RPA primer set targeting the invA gene and designed a probe for NALF. RPA-based NALF was optimized for temperature (30-43 °C), time (1-25 min), and endonuclease IV concentration (0.025-0.15 unit/µL). PMAxx successfully eliminated false-positive results from dead S. Typhimurium, enabling the accurate detection of viable S. Typhimurium with a detection limit of 1.11 × 102 CFU/mL in pure culture. The developed method was evaluated with spiked raw chicken breast and milk with analysis completed within 25 min at 39 °C. This study has potential as a tool for the POC diagnostics of viable foodborne pathogens with high specificity, sensitivity, rapidity, and cost-effectiveness.

Mitochondrial genome provides species-specific targets for the rapid detection of early invasive populations of Hylurgus ligniperda in China

BACKGROUND

Hylurgus ligniperda, a major international forestry quarantine pest, was recently found to have invaded and posed a serious threat to the Pinus forests of the Jiaodong Peninsula in China. Continuous monitoring and vigilance of the early population is imperative, and rapid molecular detection technology is urgently needed. We focused on developing a single-gene-based species-specific PCR (SS-PCR) method.

RESULTS

We sequenced and assembled the mitochondrial genome of H. ligniperda to identify suitable target genes. We identified three closely related species for detecting the specificity of SS-PCR through phylogenetic analysis based on 13 protein-coding genes (PCGs). Subsequently, we analyzed the evolution of 13 PCGs and selected four mitochondrial genes to represent slow-evolving gene (COI) and faster-evolving genes (e.g. ND2, ND4, and ND5), respectively. We developed four species-specific primers targeting COI, ND2, ND4, and ND5 to rapidly identify H. ligniperda. The results showed that the four species-specific primers exhibited excellent specificity and sensitivity in the PCR assays, with consistent performance across a broader range of species. This method demonstrates the ability to identify beetles promptly, even during their larval stage. The entire detection process can be completed within 2-3 h.

CONCLUSIONS

This method is suitable for large-scale species detection in laboratory settings. Moreover, the selection of target genes in the SS-PCR method is not affected by the evolutionary rate. SS-PCR can be widely implemented at port and forestry workstations, significantly enhancing early management strategies and quarantine measures against H. ligniperda. This approach will help prevent the spread of the pest and effectively preserve the resources of Chinese pine forests.

CRISPR-Cas Detection Coupled with Isothermal Amplification of Bursaphelenchus xylophilus

The pine wood nematode (PWN), Bursaphelenchus xylophilus, causes significant damage to pine trees and, thus, poses a serious threat to pine forests worldwide, particularly in China, Korea, and Japan. A fast, affordable, and ultrasensitive detection of B. xylophilus is urgently needed for disease diagnosis. Recently, clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostics have reshaped molecular diagnosis, with high speed, precision, specificity, strength, efficiency, and versatility. Herein, we established two isothermal diagnostics methods based on CRISPR-based platforms (CRISPR/Cas12a and CRISPR/Cas13a) for B. xylophilus-specific detection via fluorescence or lateral-flow strip readout. The guide RNA and CRISPR RNA were designed to target the 5S ribosomal DNA intergenic spacer sequences region of B. xylophilus. Recombinase-aided amplification was used for preamplification whose reaction condition was 37°C for 15 min. The sensitivity of CRISPR/Cas12a could reach 94 copies/µl of plasmid DNA, or 2.37 copies/µl of purified genomic DNA (gDNA) within 45 min at 37°C, while the sensitivity of CRISPR/Cas13a was 1,000 times higher than that of CRISPR/Cas12a of plasmid DNA in 15 min or 100 times higher of purified gDNA at the minimum reaction time of 4 min via fluorescence measurement. The CRISPR/Cas12a assay enabled the detection of 0.01 PWNs per 100 mg of pine wood, 10 times higher than that of the CRISPR/Cas13a assay. This work enriches molecular detection approaches for B. xylophilus and provides huge potential for ultrasensitive and rapid methods to detect B. xylophilus in pine wood, facilitating point-of-sample diagnostic processing for pine wilt disease management.

Bursaphelenchus xylophilus detection and analysis system based on CRISPR - Cas12

Pine wilt disease is caused by the pine wood nematode (Bursaphelenchus xylophilus) and leads to wilting and death of pines. It is one of the most damaging diseases of pines worldwide. Therefore, accurate and rapid detection methods are of great importance for the control of B. xylophilus. Traditional detection methods have some problems, such as being time-consuming and requiring expensive instruments. In this study, the loop-mediated isothermal amplification (LAMP) and clustered regularly interspaced short palindromic repeats (CRISPR) were used to establish a set of intelligent detection and analysis system for B. xylophilus, called LAMP-CRISPR/Cas12a analysis, which integrated field sampling, rapid detection and intelligent control analysis. The process can be completed within 1 hour, from sample pretreatment and detection to data analysis. Compared with the single LAMP method, the LAMP-CRISPR/Cas12a assay uses species-specific fluorescence cleavage to detect target amplicons. This process confirms the amplicon identity, thereby avoiding false-positive results from non-specific amplicons, and the large amounts of irrelevant background DNA do not interfere with the reaction. The LAMP-CRISPR/Cas12a assay was applied to 46 pine wood samples and the samples carrying B. xylophilus nematodes were successfully identified. To meet the needs of different environments, we designed three methods to interpret the data: 1) naked eye interpretation; 2) lateral flow biosensor assay; and 3) integrated molecular analysis system to standardize and intellectualize the detection process. Application of the B. xylophilus detection and analysis system will reduce the professional and technical requirements for the operating environment and operators and help to ensure the accuracy of the detection results, which is important in grass-root B. xylophilus detection institutions.

Microfluidic chip and isothermal amplification technologies for the detection of pathogenic nucleic acid

The frequency of outbreaks of newly emerging infectious diseases has increased in recent years. The coronavirus disease 2019 (COVID-19) outbreak in late 2019 has caused a global pandemic, seriously endangering human health and social stability. Rapid detection of infectious disease pathogens is a key prerequisite for the early screening of cases and the reduction in transmission risk. Fluorescence quantitative polymerase chain reaction (qPCR) is currently the most commonly used pathogen detection method, but this method has high requirements in terms of operating staff, instrumentation, venues, and so forth. As a result, its application in the settings such as poorly conditioned communities and grassroots has been limited, and the detection needs of the first-line field cannot be met. The development of point-of-care testing (POCT) technology is of great practical significance for preventing and controlling infectious diseases. Isothermal amplification technology has advantages such as mild reaction conditions and low instrument dependence. It has a promising prospect in the development of POCT, combined with the advantages of high integration and portability of microfluidic chip technology. This study summarized the principles of several representative isothermal amplification techniques, as well as their advantages and disadvantages. Particularly, it reviewed the research progress on microfluidic chip-based recombinase polymerase isothermal amplification technology and highlighted future prospects.

Rapid detection of Phytophthora cinnamomi based on a new target gene Pcinn13739

Phytophthora cinnamomi causes crown and root wilting in more than 5,000 plant species and represents a significant threat to the health of natural ecosystems and horticultural crops. The early and accurate detection of P. cinnamomi is a fundamental step in disease prevention and appropriate management. In this study, based on public genomic sequence data and bioinformatic analysis of several Phytophthora, Phytopythium, and Pythium species, we have identified a new target gene, Pcinn13739; this allowed us to establish a recombinase polymerase amplification–lateral flow dipstick (RPA-LFD) assay for the detection of P. cinnamomi. Pcinn13739-RPA-LFD assay was highly specific to P. cinnamomi. Test results for 12 isolates of P. cinnamomi were positive, but negative for 50 isolates of 25 kinds of Phytophthora species, 13 isolates of 10 kinds of Phytopythium and Pythium species, 32 isolates of 26 kinds of fungi species, and 11 isolates of two kinds of Bursaphelenchus species. By detecting as little as 10 pg.µl−1 of genomic DNA from P. cinnamomi in a 50-µl reaction, the RPA-LFD assay was 100 times more sensitive than conventional PCR assays. By using RPA-LFD assay, P. cinnamomi was also detected on artificially inoculated fruit from Malus pumila, the leaves of Rhododendron pulchrum, the roots of sterile Lupinus polyphyllus, and the artificially inoculated soil. Results in this study indicated that this sensitive, specific, and rapid RPA-LFD assay has potentially significant applications to diagnosing P. cinnamomi, especially under time- and resource-limited conditions.