Brief review of monitoring methods for loop-mediated isothermal amplification (LAMP)

Direct or DNA Extraction-Free Amplification and Quantification of Foodborne Pathogens

The use of direct nucleic acid amplification of pathogens from food matrices has the potential to reduce time to results over DNA extraction-based approaches as well as traditional culture-based approaches. Here we describe protocols for assay design and experiments for direct amplification of foodborne pathogens in food sample matrices using loop-mediated isothermal amplification (LAMP) and polymerase chain reaction (PCR). The examples provided include the detection of Escherichia coli in milk samples and Salmonella in pork meat samples. This protocol includes relevant reagents and methods including obtaining target sequences, assay design, sample processing, and amplification. These methods, though used for specific example matrices, could be applied to many other foodborne pathogens and sample types.

Rapid real-time quantitative colorimetric LAMP methodology for field detection of Verticillium dahliae in crude olive-plant samples

BACKGROUND

Verticilium dahliae is the most important wilt pathogen of olive trees with a broad host range causing devastating diseases currently without any effective chemical control. Traditional detection methodologies are based on symptoms-observation or lab-detection using time consuming culturing or molecular techniques. Therefore, there is an increasing need for portable tools that can detect rapidly V. dahliae in the field.

RESULTS

In this work, we report the development of a novel method for the rapid, reliable and on-site detection of V. dahliae using a newly designed isothermal LAMP assay and crude extracts of olive wood. For the detection of the fungus, LAMP primers were designed targeting the internal transcribed spacer (ITS) region of the rRNA gene. The above assay was combined with a purpose-built prototype portable device which allowed real time quantitative colorimetric detection of V. dahliae in 35 min. The limit of detection of our assay was found to be 0.8 fg/μl reaction and the specificity 100% as indicated by zero cross-reactivity to common pathogens found in olive trees. Moreover, detection of V. dahliae in purified DNA gave a sensitivity of 100% (Ct < 30) and 80% (Ct > 30) while the detection of the fungus in unpurified crude wood extracts showed a sensitivity of 80% when multisampling was implemented. The superiority of the LAMP methodology regarding robustness and sensitivity was demonstrated when only LAMP was able to detect V. dahliae in crude samples from naturally infected trees with very low infection levels, while nested PCR and SYBR qPCR failed to detect the pathogen in an unpurified form.

CONCLUSIONS

This study describes the development of a new real time LAMP assay, targeting the ITS region of the rRNA gene of V. dahliae in olive trees combined with a 3D-printed portable device for field testing using a tablet. The assay is characterized by high sensitivity and specificity as well as ability to operate using directly crude samples such as woody tissue or petioles. The reported methodology is setting the basis for the development of an on-site detection methodology for V. dahliae in olive trees, but also for other plant pathogens.

Development of a loop-mediated isothermal amplification (LAMP) assay for rapid and visual detection of Anguillid herpesvirus 1

China has the largest aquaculture eel production in the world. High-density cultivation pattern often results in an outbreak of epidemic diseases. Since the 1990s, eel "mucus sloughing and hemorrhagic septicemia disease" was often broke out in China, and brought huge economic losses to eel breeders. Anguillid herpesvirus 1 (AngHV) was detected and isolated from the diseased eel, and proved to be the pathogen of the disease. In this study, a loop-mediated isothermal amplification (LAMP) assay was developed for rapid, sensitive, and specific detection of AngHV. A set of six primers targeting the ORF51 gene of AngHV was designed, which could effectively detect purified AngHV virions, AngHV-infected cells, or eel tissue samples. The suitable reaction temperature is 63℃, and the reaction time is 40 min. There was no cross-reaction with eel and other fish viruses, including Infectious pancreatic necrosis virus (IPNV), Marine birnavirus (MABV), Rana grylio virus (RGV), Cyprinid herpesvirus 3 (CyHV-3), and Eel iridovirus (EIV). The lower detection limit of the AngHV LAMP assay is 10 copies of AngHV genome DNA, which is at least 100 times more sensitive than conventional PCR in detecting AngHV. The assay could effectively detect AngHV from collected samples with typical clinical symptoms of AngHV infection. It suggested that the LAMP assay could be used in specific detection of AngHV and has great potential for early diagnosis of AngHV infection in the farm.

Innovative PNA-LB mediated allele-specific LAMP for KRAS mutation profiling on a compact lab-on-a-disc device

Tailored healthcare, an approach focused on individual patients, requires integrating emerging interdisciplinary technologies to develop accurate and user-friendly diagnostic tools. KRAS mutations, prevalent in various common cancers, are crucial determinants in selecting patients for novel KRAS inhibitor therapies. This study presents a novel state-of-the-art Lab-on-a-Disc system utilizing peptide nucleic acids-loop backward (PNA-LB) mediated allele-specific loop-mediated isothermal amplification (LAMP) for detecting the frequent G12D KRAS mutation, signifying its superiority over alternative mutation detection approaches. The designed Lab-on-a-Disc system demonstrated exceptional preclinical and technical precision, accuracy, and versatility. By applying varying cutoff values to PNA- LB LAMP reactions, the assay's sensitivity and specificity were increased by 80 % and 90 %, respectively. The device's key advantages include a robust microfluidic Lab-on-a-Disc design, precise rotary control, and a cutting-edge induction heating module. These features enable multiplexing of LAMP reactions with high reproducibility and repeatability, with CV% values less than 3.5 % and 5.5 %, respectively. The device offers several methods for accurate endpoint result detection, including naked-eye observation, RGB image analysis using Python code, and time of fluorescence (Tf) values. Preclinical specificity and sensitivity, assessed using different cutoffs for Eva-Green fluorescence Tf values and pH-sensitive dyes, demonstrated comparable performance to the best standard methods. Overall, this study represents a significant step towards tailoring treatment strategies for cancer patients through precise and efficient mutation detection technologies.

Molecular Detection of Respiratory Tract Viruses in Chickens at the Point of Need by Loop-Mediated Isothermal Amplification (LAMP)

Accurate and timely molecular diagnosis of respiratory diseases in chickens is essential for implementing effective control measures, preventing the spread of diseases within poultry flocks, minimizing economic loss, and guarding food security. Traditional molecular diagnostic methods like polymerase chain reaction (PCR) require expensive equipment and trained personnel, limiting their use to centralized labs with a significant delay between sample collection and results. Loop-mediated isothermal amplification (LAMP) of nucleic acids offers an attractive alternative for detecting respiratory viruses in broiler chickens with sensitivity comparable to that of PCR. LAMP's main advantages over PCR are its constant incubation temperature (∼65 °C), high amplification efficiency, and contaminant tolerance, which reduce equipment complexity, cost, and power consumption and enable instrument-free tests. This review highlights effective LAMP methods and variants that have been developed for detecting respiratory viruses in chickens at the point of need.

Colorimetric strategies applicable for loop-mediated isothermal amplification

In recent years, loop-mediated isothermal amplification (LAMP) has gained popularity for detecting various pathogen-specific genes due to its superior sensitivity and specificity compared to conventional polymerase chain reaction (PCR). The simplicity and flexibility of naked-eye detection of the amplicon make LAMP an ideal rapid and straightforward diagnostic tool, especially in resource-limited laboratories. Colorimetric detection is one of the simplest and most straightforward among all detection methods. This review will explore various colorimetric dyes used in LAMP techniques, examining their reaction mechanisms, advantages, limitations and latest applications.

Visual Loop-Mediated Isothermal Amplification (LAMP) Assay for Rapid On-Site Detection of Escherichia coli O157: H7 in Milk Products

(1) Background: Rapid on-site testing is an effective method for the detection of Escherichia coli O157: H7(E. coli O157: H7) in food ingredients and the environment. (2) Methods: In this study, we developed colorimetric loop-mediated isothermal amplification (LAMP) and immunochromatographic test strips (ICTs) for the rapid and visual detection of E. coli O157: H7. This study designed new specific LAMP primers for E. coli O157: H7 virulence island genes. After the LAMP amplification, the double-stranded DNA target sequence labeled with digoxin and fluorescein isothiocyanate (FITC) at both ends was bound to the anti-digoxin antibody on the gold nanoparticles. Subsequently, it was further bound to the anti-FITC antibody at the T line of the ICTs, forming a positive test result. Hydroxynaphthyl blue dye was directly added to the LAMP amplification product. A blue color indicated positive results, while a purple color indicated negative results. (3) Results: Two visualization methods showed high specificity for the target strains. The visualization tests had sensitivities of 5.7 CFU mL-1, and the detection limit of the Escherichia coli O157: H7 in artificially contaminated milk samples was 5.7 × 102 CFU mL-1, which was consistent with the results of the standard method (LAMP-electrophoresis method) used in commercial inspection. (4) Conclusions: Both methods could be useful in remote and under-resourced areas.

One-pot electrochemical detection of foodborne pathogen based on in situ nucleic acid amplification and wash-free assay

A signal amplification electrochemical biosensor chip was developed to integrate loop-mediated isothermal amplification (LAMP) based on in situ nucleic acid amplification and methyl blue (MB) serving as the hybridization redox indicator for sensitive and selective foodborne pathogen detection without a washing step. The electrochemical biosensor chip was designed by a screen-printed carbon electrode modified with gold nanoparticles (Au NPs) and covered with polydimethylsiloxane membrane to form a microcell. The primers of the target were immobilized on the Au NPs by covalent attachment for in situ amplification. The electroactive MB was used as the electrochemical signal reporter and embedded into the double-stranded DNA (dsDNA) amplicons generated by LAMP. Differential pulse voltammetry was introduced to survey the dsDNA hybridization with MB, which differentiates the specifically electrode-unbound and -bound labels without a washing step. Pyrene as the back-filling agent can further improve response signaling by reducing non-specific adsorption. This method is operationally simple, specific, and effective. The biosensor showed a detection linear range of 102-107 CFU mL-1 with the limit of detection of 17.7 CFU mL-1 within 40 min. This method showed promise for on-site testing of foodborne pathogens and could be integrated into an all-in-one device.

High-throughput identification of meat ingredients in adulterated foods based on centrifugal integrated purification-CRISPR array

Rapid, accurate, and sensitive analytical methods for the detection of food fraud are now an urgent requirement in the global food industry to ensure food quality. In response to this demand, a centrifugal integrated purification-CRISPR array for meat adulteration (CIPAM) was established. In detail, CIPAM system combines microneedles for DNA extraction and RAA-CRISPR/Cas12a integrated into a centrifugal microfluidic chip for the detection of meat adulteration. The RAA-CRISPR/Cas12a reaction reagents were pre-embedded into the different reaction chambers on the microfluidic chip to achieve the streamline of operations, markedly simplifying the detection process. The whole reaction was completed within 30 min with a detection limit of 0.1 % (w/w) in pig, chicken, duck, and lamb products. Referring to the results of the standard method, CIPAM system achieved 100 % accuracy. The automatic multiplex detection process implemented in the developed CIPAM system met the needs of food regulatory authorities.

A microfluidic-based quantitative analysis system for the multiplexed genetic diagnosis of human viral infections using colorimetric loop-mediated isothermal amplification

In this study, a microfluidic-based system utilizing colorimetric loop-mediated isothermal amplification (LAMP) is introduced for the quantitative analysis of nucleic acid targets. This system offers a user-friendly and cost-effective platform for the multiplexed genetic diagnosis of various infectious diseases across multiple samples. It includes time-lapse imaging equipment for capturing images of the microfluidic device during the LAMP assay and a hue-based quantitative analysis software to analyze the LAMP reaction, streamlining diagnostic procedures. An electric pipette was used to simplify the loading of samples and LAMP reagents into the device, allowing easy operation even by untrained individuals. The hue-based analysis software employs efficient image processing and post-processing techniques to calculate DNA amplification curves based on color changes in multiple reaction chambers. This software automates several tasks, such as identifying reaction chamber areas from time-lapse images, quantifying color information within each chamber, correcting baselines of DNA amplification curves, fitting experimental data to theoretical curves, and determining the threshold time for each curve. To validate the developed system, conventional off-chip LAMP assays were conducted with a 25 μL reaction mixture in 0.2 mL polymerase chain reaction (PCR) tubes using a real-time turbidimeter. The results indicated that the threshold time obtained using the colorimetric LAMP assay in the developed system is comparable to that obtained with real-time turbidity measurements in PCR tubes, demonstrating the system's capability for quantitative analysis of target nucleic acids, including those from human herpesviruses.

Online monitoring system for qualitative and quantitative analysis of bioaerosols by combined ATP bioluminescence assay with loop-mediated isothermal amplification

Rapid detection of airborne pathogens is crucial in preventing respiratory infections and allergies. However, technologies aiming to real-time analysis of microorganisms in air remain limited due to the sparse and complex nature of bioaerosols. Here, we introduced an online bioaerosol monitoring system (OBMS) comprised of integrated units including a rotatable stainless-steel sintered filter-based sampler, a lysis unit for extracting adenosine triphosphate (ATP), and a single photon detector-based fluorescence unit. Through optimization of the ATP bioluminescence method and establishment of standard curves between relative luminescence units (RLUs) and ATP as well as microbial concentration, we achieved simultaneous detection of bioaerosols' concentration and activity. Testing OBMS with four bacterial and two fungal aerosols at a sampling flow rate of 10 to 50 L/min revealed an outstanding collection efficiency of 95 % at 30 L/min. A single OBMS measurement takes only 8 min (sampling: 5 min; lysis and detection: 3 min) with detection limits of 3 Pcs/ms photons (2.9 × 103 and 292 CFU/m3 for Staphylococcus aureus and Candida albicans aerosol). In both laboratory and field tests, OBMS detected higher concentrations of bioaerosol compared to the traditional Andersen impactor and liquid biosampler. When combined OBMS with loop-mediated isothermal amplification (LAMP), the bioaerosol can be qualitative and quantitative analyzed within 40 min without the cumbersome procedures of sample pretreatment and DNA extraction. These results offer a high compressive and humidity resistance membrane filtration sampler and validate the potential of OBMS for online measurement of bioaerosol concentration and composition.

Laboratory and field validation of the recombinase polymerase amplification assay targeting the Schistosoma mansoni mitochondrial minisatellite region (SmMIT-RPA) for snail xenomonitoring for schistosomiasis

Improvements in diagnostics for schistosomiasis in both humans and snail hosts are priorities to be able to reach the World Health Organization (WHO) goal of eliminating the disease as a public health problem by 2030. In this context, molecular isothermal amplification tests, such as Recombinase Polymerase Amplification (RPA), are promising for use in endemic areas at the point-of-need for their accuracy, robustness, simplicity, and time-effectiveness. The developed recombinase polymerase amplification assay targeting the Schistosoma mansoni mitochondrial minisatellite region (SmMIT-RPA) was used to detect S. mansoni DNA from both laboratory and field Biomphalaria snails. Laboratory snails were experimentally infected and used at one, seven, and 28 days post-exposure (dpe) to 10 S. mansoni miracidia to provide samples in the early pre-patent infection stage. Field samples of Biomphalaria spp. were collected from the Mucuri Valley and Jequitinhonha Valley regions in the state of Minas Gerais, Brazil, which are endemic for S. mansoni. The sensitivity and specificity of the SmMIT-RPA assay were analysed and compared with existing loop-mediated isothermal amplification (LAMP), PCR-based methods, parasitological examination of the snails, and nucleotide sequencing. The SmMIT-RPA assay was able to detect S. mansoni DNA in the experimentally infected Biomphalaria glabrata as early as one dpe to 10 miracidia. It also detected S. mansoni infections (55.5% prevalence) in the field samples with the highest accuracy (100% sensitivity and specificity) compared with the other molecular tests used as the reference. Results from this study indicate that the SmMIT-RPA assay is a good alternative test to be used for snail xenomonitoring of S. mansoni due to its high sensitivity, accuracy, and the possibility of detecting early pre-patent infection. Its simplicity and portability also make it a suitable methodology in low-resource settings.

Retrospective study and implementation of a low-cost LAMP-turbidimetric assay for screening α0-thalassemia (SEA deletion): preventing and controlling Hb Bart's hydrops fetalis syndrome in Thailand

Homozygous α0-thalassemia (SEA deletion) or Hb Bart's hydrops fetalis syndrome is a significant public health issue in Thailand and Southeast Asia. A prevention and control program has been implemented in this region. This study focuses on retrospective laboratory data collected between January 2021 and April 2023 at a single center. Additionally, we developed a low-cost LAMP-turbidimetric assay to propose in the screening strategy. A total of 3,623 samples underwent screening tests (MCV, MCH, and DCIP), including 1,658 couple screenings (84.25%) and 310 single pregnant screenings (15.75%). Negative screenings, which did not require further investigation, were found in 75.51% for couple screenings and 46.58% for single pregnant screenings. At hemoglobin (Hb) analysis identified 129 couples which had fetuses at risk of severe thalassemia, whereas molecular analysis during the retrospective period revealed 210 samples with different genotypes. These remaining samples were validated using the low-cost LAMP-turbidimetric assay to detect α0-thalassemia (SEA deletion). The developed LAMP turbidimetric assay demonstrated a sensitivity and specificity of 100% (36/36 × 100) and 97.7% (170/174 × 100), respectively, when compared with gap-PCR. Furthermore, we propose a strategy involving the addition of the low-cost LAMP-turbidimetric assay before performing the gold standard. This strategy represents a cost-saving of USD 2,608 based on 210 samples that required DNA analysis. Finally, the developed LAMP turbidimetric assays offer advantages such as reduced time, workload, cost savings, no need for highly developed instruments, and a straightforward interpreting process. Therefore, implementation of LAMP assays into routine settings would be improve the efficiency of prevention and control program for severe thalassemia disease in this region.

Rapid Detection of Colletotrichum siamense from Infected Tea Plants Using Filter-Disc DNA Extraction and Loop-Mediated Isothermal Amplification

The pathogen Colletotrichum siamense causes tea anthracnose, resulting in economic losses to the Chinese tea industry. To effectively diagnose this pathogen in the field, we developed a loop-mediated isothermal amplification (LAMP) method using highly specific primers with a sensitivity of 1 pg/μl designed for amplifying the CAL gene, which was 10 times higher than that of conventional PCR. Additionally, to improve the method for obtaining DNA samples required for on-site diagnosis, we used the filter-disc DNA extraction method, which does not require special instruments and can be completed in a few minutes, and found that it effectively meets the requirements for the LAMP reaction. Finally, we combined LAMP with a filter-disc DNA extraction method (FDE-LAMP) to diagnose different degrees of disease in inoculated samples and 20 samples from the field. The results showed that the procedure had sufficient sensitivity for pathogen detection. Therefore, the FDE-LAMP procedure could greatly contribute to managing and preventing tea anthracnose in the field.

Two independent LAMP assays for rapid identification of the serpentine leafminer, Liriomyza huidobrensis (Blanchard, 1926) (Diptera: Agromyzidae) in Australia

Liriomyza huidobrensis is a leafminer fly and significant horticultural pest. It is a quarantine listed species in many countries and is now present as an established pest in Australia. Liriomyza huidobrensis uses a broad range of host plants and has potential for spread into various horticultural systems and regions of Australia. Rapid in-field identification of the pest is critically needed to assist efforts to manage this pest. Morphological identification of the pest is effectively limited to specialist examinations of adult males. Generally, molecular methods such as qPCR and DNA barcoding for identification of Liriomyza species require costly laboratory-based hardware. Herein, we developed two independent and rapid LAMP assays targeted to independently inherited mitochondrial and nuclear genes. Both assays are highly sensitive and specific to L. huidobrensis. Positive signals can be detected within 10 min on laboratory and portable real-time amplification fluorometers. Further, we adapted these assays for use with colorimetric master mixes, to allow fluorometer free in-field diagnostics of L. huidobrensis. Our LAMP assays can be used for stand-alone testing of query specimens and are likely to be essential tools used for rapid identification and monitoring of L. huidobrensis.

A paper-embedded thermoplastic microdevice integrating additive-enhanced allele-specific amplification and silver nanoparticle-based colorimetric detection for point-of-care testing

This study introduces a thermoplastic microdevice integrated with additive-enhanced allele-specific amplification and hydrazine-induced silver nanoparticle-based detection of single nucleotide polymorphism (SNP) and opportunistic pathogens. For point-of-care testing of SNP, an allele-specific loop-mediated isothermal amplification reaction using nucleotide-mismatched primers and molecular additives was evaluated to discriminate single-nucleotide differences in the samples. The microdevice consists of purification and reaction units that enable DNA purification, amplification, and detection in a sequential manner. The purification unit enables the silica-based preparation of samples using an embedded glass fiber membrane. Hydrazine-induced silver nanoparticle formation was employed for endpoint colorimetric detection of amplicons within three min at room temperature. The versatile applicability of the microdevice was demonstrated by the successful identification of SNPs related to sickle cell anemia, genetically-induced hair loss, and Enterococcus faecium. The microdevice exhibited a detection limit of 103 copies per μL of SNP targets in serum and 102 CFU mL-1 of Enterococcus faecium in tap water within 70 min. The proposed microdevice is a promising and versatile platform for point-of-care nucleic acid testing of different samples in low-resource settings.

Establishment of two visual interpretation methods of DIV1 LAMP amplification products

Viral diseases have become a significant impediment to the sustainable development of the global shrimp aquaculture industry. Decapod iridescent virus 1 (DIV1) is an emerging shrimp virus that has affected shrimp in China recent years. Rapid detection of DIV1 could improve enhance the effectiveness of prevention, control and treatment in the absence of good prevention and control measures. This study established loop-mediated isothermal amplification (LAMP) along with two visual interpretation methods, LAMP-dye and LAMP-LFD, to detect DIV1. The newly developed method would not cause cross-reactions with other shrimp pathogens such as white spot syndrome virus (WSSV), infectious hypodermal and hematopoietic necrosis virus (IHHNV), Enterocytozoon hepatopenaei (EHP), and Vibrio parahaemolyticus acute hepatopancreatic necrosis disease (VpAHPND). The detection limit of DIV1 LAMP was as low as 103 copies of DIV1 per reaction, with a reaction time of less than 40 min. The diagnostic sensitivity and diagnostic specificity of this method were determined to be 88% and 100%, respectively, when compared with the conventional PCR. Both of the LAMP-dye and LAMP-LFD methods are cost-effective and do not require expensive amplification equipment. They can be combined with LAMP and other temperature amplification methods for rapid on-site detection, effectively prevent aerosol contamination, and which are convenient and suitable for field testing or preliminary infection rish prediction experiments to predict the risk of infection.

Rapid and Visual Detection of Actinidia Chlorotic Ringspot-Associated Virus Using One-Step Reverse-Transcription Recombinase Polymerase Amplification Combined with Lateral Flow Dipstick Assay

Actinidia chlorotic ringspot-associated virus (AcCRaV) occurs widely in major kiwifruit producing areas of China and is often accompanied by coinfecting viruses, affecting the growth, yield, and quality of kiwifruit. Therefore, a rapid and sensitive detection method is crucial for diagnosing and developing effective AcCRaV management strategies. In this study, a one-step reverse-transcription recombinase polymerase amplification combined with a lateral flow dipstick (RT-RPA-LFD) assay was developed for rapid detection of AcCRaV. Specific primers and a probe were designed based on the conserved region of the coat protein gene sequence of AcCRaV. The one-step RT-RPA reaction can be performed at 35 and 40°C within 10 to 30 min, and the amplification results can be read directly on the LFD within 5 min. The detection limit of the one-step RT-RPA-LFD assay was 10-8 ng (about 20 viral copies), which was equal with one-step RT-qPCR and 100 times more sensitive than one-step RT-PCR. Moreover, the one-step RT-RPA-LFD assay was successfully applied to detect AcCRaV from crude extracts, and the entire detection process can be completed within 40 min. These results indicate that the RT-RPA-LFD assay is a simple, rapid, and sensitive strategy that can be used for accurate diagnosis of AcCRaV-infected kiwifruit plants in the field. To our knowledge, this is the first study applying the one-step RT-RPA-LFD assay to detect a kiwifruit virus.

Loop-Mediated Isothermal Amplification-Integrated CRISPR Methods for Infectious Disease Diagnosis at Point of Care

Infectious diseases continue to pose an imminent threat to global public health, leading to high numbers of deaths every year and disproportionately impacting developing countries where access to healthcare is limited. Biological, environmental, and social phenomena, including climate change, globalization, increased population density, and social inequity, contribute to the emergence of novel communicable diseases. Rapid and accurate diagnoses of infectious diseases are essential to preventing the transmission of infectious diseases. Although some commonly used diagnostic technologies provide highly sensitive and specific measurements, limitations including the requirement for complex equipment/infrastructure and refrigeration, the need for trained personnel, long sample processing times, and high cost remain unresolved. To ensure global access to affordable diagnostic methods, loop-mediated isothermal amplification (LAMP) integrated clustered regularly interspaced short palindromic repeat (CRISPR) based pathogen detection has emerged as a promising technology. Here, LAMP-integrated CRISPR-based nucleic acid detection methods are discussed in point-of-care (PoC) pathogen detection platforms, and current limitations and future directions are also identified.

Maximising Affordability of Real-Time Colorimetric LAMP Assays

Molecular diagnostics have become indispensable in healthcare, agriculture, and environmental monitoring. This diagnostic form can offer rapid and precise identification of pathogens and biomarkers. However, traditional laboratory-based molecular testing methods can be expensive and require specialised training, limiting their accessibility in resource-limited settings and on-site applications. To overcome these challenges, this study proposes an innovative approach to reducing costs and complexity in portable colorimetric loop-mediated isothermal amplification (LAMP) devices. The research evaluates different resistive heating systems to create an energy-efficient, cost-effective, and compact device to heat a polydimethylsiloxane (PDMS) block for precise temperature control during LAMP reactions. By combining this novel heating system with an off-the-shelf red-green-blue (RGB) sensor to detect and quantify colour changes, the integrated system can accurately detect Leifsonia xyli subsp. xyli, the bacteria responsible for ratoon stunting disease (RSD) in sugarcane. The experimental validation of this system demonstrates its ability to detect the target pathogen in real time, making it an important development for low cost, portable, and easy-to-use molecular diagnostics in healthcare, agriculture, and environmental monitoring applications.

Diverse methods of reducing and confirming false-positive results of loop-mediated isothermal amplification assays: A review

Loop-mediated isothermal amplification (LAMP), a rapid and sensitive isothermal nucleic acid amplification method, is a promising alternative to other molecular amplification techniques due to its superior specificity and sensitivity. However, due to primer dimerization, LAMP results in nonspecific and nontemplate amplification. And during the amplification confirmation process, there is carry-over contamination. These factors can result in false-positive results that overestimate the amount of DNA, preventing accurate detection. This review outlined several techniques for reducing false-positive LAMP results before amplification and confirming false-positive results after amplification. Before the amplification step, DNA polymerase activity can be decreased with organic additives such as dimethyl sulfoxide, betaine, and pullulan to prevent nonspecific amplification. The enzyme uracil-DNA-glycosylase (UDG) can eliminate false-positive results caused by carry-over contamination, and the hot-start effect with gold nanoparticles can reduce nonspecific amplification. When confirming false-positive results using clustered regularly interspaced short palindromic repeats, guide RNA accurately detects LAMP amplification, allowing differentiation from nonspecific amplification. By confirming amplification, the colorimetric change in the deoxyribozyme (DNAzyme) formed by the reaction of the G-quadruplex sequence of the LAMP amplicon and hemin can distinguish false-positive results. Lateral flow immunoassay can distinguish false-positive results by accurately recognizing hybridized probes to LAMP amplicons.

CRISPR/Cas12a and primer-assisted rolling circle amplification integrated ultra-sensitive dual-signal sensing platform for EGFR 19 detection

Herein, we integrated CRISPR/Cas12a with primer-assisted rolling circle amplification (PARCA) to specifically detect EGFR 19 from the genome. We fused the method into fluorescent and electrochemical detection systems forming a stable and sensitive dual-signal sensing platform. The fluorescent detection system stably detected EGFR 19 in a linear range from 500 fM to 10 nM with an ultra-low background signal. The electrochemical detection system possessed a detection limit as low as 42 aM due to the introduction of nanomaterial UIO-66-NH2. The dual-signal sensing platform showed superior performance in complex serum samples and real cell genomes and provided a flexible and dynamic approach for the ultra-sensitive detection of EGFR 19.

Additive manufacturing leveraged microfluidic setup for sample to answer colorimetric detection of pathogens

Colorimetric readout for the detection of infectious diseases is gaining traction at the point of care/need owing to its ease of analysis and interpretation, and integration potential with highly specific loop-mediated amplification (LAMP) assays. However, coupling colorimetric readout with LAMP is rife with challenges including, rapidity, inter-user variability, colorimetric signal quantification, and user involvement in sequential steps of the LAMP assay, hindering its application. To address these challenges, for the first time, we propose a remotely smartphone-operated automated setup consisting of (i) an additively manufactured microfluidic cartridge, (ii) a portable reflected-light imaging setup with controlled epi-illumination (PRICE) module, and (iii) a control and data analysis module. The microfluidic cartridge facilitates sample collection, lysis, mixing of amplification reagents stored on-chip, and subsequent isothermal heating for initiation of amplification in a novel way by employing tunable elastomeric chambers and auxiliary components (heaters and linear actuators). PRICE offers a new imaging setup that captures the colorimetric change of the amplification media over a plasmonic nanostructured substrate in a controlled and noise-free environment for rapid minute-scale nucleic acid detection. The control and data analysis module employs microprocessors to automate cartridge operation in tandem with the imaging module. The different device components were characterized individually and finally, as a proof of concept, SARS-CoV-2 wild-type RNA was detected with a turnaround time of 13 minutes, showing the device's clinical feasibility. The suggested automated device can be adopted in future iterations for other detection and molecular assays that require sequential fluid handling steps.

Current and Future Advances in the Detection and Surveillance of Biosecurity-Relevant Equine Bacterial Diseases Using Loop-Mediated Isothermal Amplification (LAMP)

Horses play an important role throughout the world, whether for work, culture, or leisure, providing an ever-growing significant contribution to the economy. The increase in importation and movement of horses, both nationally and internationally, has inevitably allowed for the global equine industry to grow. Subsequently, however, the potential for transmission of fatal equine bacterial diseases has also escalated, and devasting outbreaks continue to occur. To prevent such events, disease surveillance and diagnosis must be heightened throughout the industry. Current common, or "gold-standard" techniques, have shown to be inadequate at times, thus requiring newer technology to impede outbreaks. Loop-mediated isothermal amplification (LAMP) has proven to be a reliable, rapid, and accessible tool in both diagnostics and surveillance. This review will discuss equine bacterial diseases of biosecurity relevance and their current diagnostic approaches, as well as their respective LAMP assay developments. Additionally, we will provide insight regarding newer technology and advancements associated with this technique and their potential use for the outlined diseases.

Analytical and diagnostic performance characteristics of reverse-transcriptase loop-mediated isothermal amplification assays for dengue virus serotypes 1-4: A scoping review to inform potential use in portable molecular diagnostic devices

Dengue is a mosquito-borne disease caused by dengue virus (DENV) serotypes 1-4 which affects 100-400 million adults and children each year. Reverse-transcriptase (RT) quantitative polymerase chain reaction (qPCR) assays are the current gold-standard in diagnosis and serotyping of infections, but their use in low-middle income countries (LMICs) has been limited by laboratory infrastructure requirements. Loop-mediated isothermal amplification (LAMP) assays do not require thermocycling equipment and therefore could potentially be deployed outside laboratories and/or miniaturised. This scoping literature review aimed to describe the analytical and diagnostic performance characteristics of previously developed serotype-specific dengue RT-LAMP assays and evaluate potential for use in portable molecular diagnostic devices. A literature search in Medline was conducted. Studies were included if they were listed before 4th May 2022 (no prior time limit set) and described the development of any serotype-specific DENV RT-LAMP assay ('original assays') or described the further evaluation, adaption or implementation of these assays. Technical features, analytical and diagnostic performance characteristics were collected for each assay. Eight original assays were identified. These were heterogenous in design and reporting. Assays' lower limit of detection (LLOD) and linear range of quantification were comparable to RT-qPCR (with lowest reported values 2.2x101 and 1.98x102 copies/ml, respectively, for studies which quantified target RNA copies) and analytical specificity was high. When evaluated, diagnostic performance was also high, though reference diagnostic criteria varied widely, prohibiting comparison between assays. Fourteen studies using previously described assays were identified, including those where reagents were lyophilised or 'printed' into microfluidic channels and where several novel detection methods were used. Serotype-specific DENV RT-LAMP assays are high-performing and have potential to be used in portable molecular diagnostic devices if they can be integrated with sample extraction and detection methods. Standardised reporting of assay validation and diagnostic accuracy studies would be beneficial.

A real-time monitoring platform of colorimetric LAMP for developing rapid visual detection kits of SARS-CoV-2

Visual detection of nucleic acids is important to diagnose the serious acute infectious diseases such as coronavirus disease 2019 (COVID-19). During this pandemic, reliable visual detection kits have been in high demand for screening and prevention of the virus. While developing these visual detection kits, a real-time monitoring platform is usually applied to study the amplification and detection processes of nucleic acids and optimize the detecting conditions. Herein, we developed a real-time monitoring platform of colorimetric loop-mediated isothermal amplification (LAMP) to investigate the amplification and detection processes of nucleic acids. Using this platform, we could obtain the real-time amplification curves, and optimize the reaction temperature, color change, and detection time. Based on the optimized conditions, a visual detection kit for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was successfully developed with a sensitivity of 102 copies µL−1 in 12 min. This real-time monitoring platform has advantages of simple construction, steady performance, high sensitivity, and outstanding anti-pollution capability, and could replace the traditional colorimetric methods by photographing and reading values. This platform would accelerate the development of visual detection kits for colorimetric LAMP, help to explore the amplification and transcription of nucleic acids, and provide support for the prevention of emerging biological threats.

Accurate and ultrasensitive detection for PEDV based on photoelectrochemical sensing coupling loop-mediated isothermal amplification

Porcine epidemic diarrhea (PED) is a serious disease requiring a simple and accurate detection method. Accordingly, this study developed a novel, ultrasensitive photoelectrochemical (PEC) sensing platform using the loop-mediated isothermal amplification (LAMP) technique (LAMP-PEC). An amino (-NH₂)-modified LAMP product is obtained by amplification of the PED virus gene with specially designed primers. The generated NH₂-modified LAMP product is assembled on the surface of an electrode by forming imine linkages between aldehyde and amino groups based on the Schiff base reaction. A stable photocurrent is provided by a CdIn₂S₄ photoactive material, which possesses high photoelectric conversion efficiency. Amplified DNA assembled on the electrode surface increases steric hindrance and hinders electrons from moving from the electrode to electron acceptors, which decreases the photocurrent. This strategy can detect PEDV with a low detection limit of 0.3 fg μL^-1 and a wide linear range of 1 × 10^-3-1 × 10² pg/μL. The sensing platform has excellent specificity and sensitivity and can be used for the quantitative detection of many other pathogens with the assistance of LAMP.

Loop-mediated isothermal amplification (LAMP)/Cas12a assay for detection of Ralstonia solanacearum in tomato

Introduction: Bacterial wilt (BW) caused by the aerobic, Gram-negative pathogenic species Ralstonia solanacearum (RS) is a major disease impacting commercial agriculture worldwide. Asian phylotype I of RS is the cause of tomato bacterial wilt, which has caused severe economic losses in southern China for many years. An urgent priority in control of bacterial wilt is development of rapid, sensitive, effective methods for detection of RS. Methods: We describe here a novel RS detection assay based on combination of loop-mediated isothermal amplification (LAMP) and CRISPR/Cas12a. crRNA1, with high trans-cleavage activity targeting hrpB gene, was selected out of four candidate crRNAs. Two visual detection techniques, involving naked-eye observation of fluorescence and lateral flow strips, were tested and displayed high sensitivity and strong specificity. Results and Discussion: The LAMP/Cas12a assay accurately detected RS phylotype Ⅰ in 14 test strains, and showed low detection limit (2.0 × 10⁰ copies). RS in tomato stem tissue and soil samples from two field sites with suspected BW infection was identified accurately, suggesting potential application of LAMP/Cas12a assay as point-of-care test (POCT). The overall detection process took less than 2 h and did not require professional lab equipment. Our findings, taken together, indicate that LAMP/Cas12a assay can be developed as an effective, inexpensive technique for field detection and monitoring of RS.

A rapid and closed-tube method based on the dual-color fluorescence loop-mediated isothermal amplification for visual detection of Atlantic salmon (Salmo salar)

Loop-mediated isothermal amplification (LAMP) visual detection based on hydroxyl naphthol blue (HNB) and SYTO 9 is often confounded by the narrow color variation window and the requirement of empirical preset of cutoff intensity value. To improve the suitability for naked-eye inspection, the present work proposed a strategy based on the fluorescence property of SYTO 9 and HNB to enlarge the contrast and a novel dual-color fluorescence LAMP (dfLAMP) assay was developed for visual detection of Atlantic salmon. Specifically, HNB of 26.25 μM, blended with SYTO 9 of 0.75-1.5 μM, was added in the mixture before amplification, producing light green fluorescence for both positive and negative samples. After amplification, green or yellow-green fluorescence was observed for positive samples, while only orange-red fluorescence emitted for negative ones, enabling an easy and rapid distinguish. The optimized dfLAMP assay has proved its specificity and can detect as little as 1 fg Atlantic salmon DNA.

Enzyme-Assisted Nucleic Acid Amplification in Molecular Diagnosis: A Review

Infectious diseases and tumors have become the biggest medical challenges in the 21st century. They are driven by multiple factors such as population growth, aging, climate change, genetic predispositions and more. Nucleic acid amplification technologies (NAATs) are used for rapid and accurate diagnostic testing, providing critical information in order to facilitate better follow-up treatment and prognosis. NAATs are widely used due their high sensitivity, specificity, rapid amplification and detection. It should be noted that different NAATs can be selected according to different environments and research fields; for example, isothermal amplification with a simple operation can be preferred in developing countries or resource-poor areas. In the field of translational medicine, CRISPR has shown great prospects. The core component of NAAT lies in the activity of different enzymes. As the most critical material of nucleic acid amplification, the key role of the enzyme is self-evident, playing the upmost important role in molecular diagnosis. In this review, several common enzymes used in NAATs are compared and described in detail. Furthermore, we summarize both the advances and common issues of NAATs in clinical application.

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.

Development of Recombinase Polymerase Amplification Combined with Lateral Flow Dipstick Assay To Detect Hemolysin Gene of Vibrio vulnificus in Oysters

ABSTRACT

Vibrio vulnificus inhabits estuarine waters around the world and can cause severe infections in people who eat contaminated raw or undercooked oysters. Although current detection methods are sensitive and specific, there are continuous demands for the development of rapid and accurate methods without a trained operator and equipment in the field conditions. Herein, we developed a simple and rapid method by detecting the hemolysin (vvh) gene of V. vulnificus by using recombinase polymerase amplification (RPA) combined with a lateral flow dipstick (LFD). The RPA-LFD could detect 100 fg of DNA (P < 0.05) and 20 CFU of V. vulnificus per reaction within 30 min (P < 0.01) and showed the result with incubation temperature ranges from 30 to 45°C (P < 0.001). The test was specific only to V. vulnificus and was not responsive to 10 other closely related Vibrio species and 18 foodborne pathogenic bacteria. Compared with PCR, quantitative PCR, and colony hybridization assays by using naturally contaminated oyster samples, our RPA-LFD showed the same detection ability as quantitative PCR assay. Therefore, the current RPA-LFD would be a valuable tool to detect V. vulnificus in oysters, especially in field conditions.

HIGHLIGHTS

Multiplexed Detection of Pathogens Using Solid-Phase Loop-Mediated Isothermal Amplification on a Supercritical Angle Fluorescence Array for Point-of-Care Applications

Adaptations of new generation molecular techniques for multiplexed detection of pathogens are gaining interest in the field of point-of-care (POC) industry and onsite testing. Loop-mediated isothermal amplification (LAMP), an advanced molecular amplification technique, has proven promising due to its unique features that suits ideal for POC applications. However, application of LAMP for multiplexed detection of pathogens remains challenging because of the difficulty in the identification of specific LAMP amplicons that does not have a well-definite molecular size. In this study, we developed a solid-phase loop-mediated isothermal amplification (SP-LAMP) technique to address the challenge. Integration of LAMP with the supercritical angle fluorescence (SAF) micro-optic structures as a solid support (SS) in an array format enabled spatial separation of LAMP amplicons in a multiplexed configuration. Important parameters such as length of the SS primers, length of the primer-binding region, the effect of surface density of immobilized SS primers, and cross-reactivity among the primers of different targets were iteratively tested and optimized. With the combination of SP-LAMP and SAF techniques, it was possible to detect multiple pathogens that include Salmonella spp, Campylobater spp., Campylobacter coli, Campylobacter jejuni, avian influenza virus (AIV), and pan avian internal control (IC) under singleplex conditions. The multiplexing capacity of the SP-LAMP was demonstrated using AIV and IC with promising results. The success of SP-LAMP has opened a promising direction toward the development of a multiplex POC system for rapid detection of multiple pathogens.

Rapid detection of hepatitis C virus using recombinase polymerase amplification

Over 71 million people are infected with hepatitis C virus (HCV) worldwide, and approximately 400,000 global deaths result from complications of untreated chronic HCV. Pan-genomic direct-acting antivirals (DAAs) have recently become widely available and feature high cure rates in less than 12 weeks of treatment. The rollout of DAAs is reliant on diagnostic tests for HCV RNA to identify eligible patients with viremic HCV infections. Current PCR-based HCV RNA assays are restricted to well-resourced central laboratories, and there remains a prevailing clinical need for expanded access to decentralized HCV RNA testing to provide rapid chronic HCV diagnosis and linkage to DAAs in outpatient clinics. This paper reports a rapid, highly accurate, and minimally instrumented assay for HCV RNA detection using reverse transcription recombinase polymerase amplification (RT-RPA). The assay detects all HCV genotypes with a limit of detection of 25 copies per reaction for genotype 1, the most prevalent in the United States and worldwide. The clinical sensitivity and specificity of the RT-RPA assay were both 100% when evaluated using 78 diverse clinical serum specimens. The accuracy, short runtime, and low heating demands of RT-RPA may enable implementation in a point-of-care HCV test to expand global access to effective treatment via rapid chronic HCV diagnosis.

Visual LAMP method for the detection of Vibrio vulnificus in aquatic products and environmental water

Background

A visual, rapid, simple method was developed based on a loop-mediated isothermal amplification (LAMP) assay to detect Vibrio vulnificus in aquatic products and aquaculture waters.

Results

Genomic DNA was extracted from Vibrio vulnificus using the boiling method, and optimized primers were used to detect the gyrB gene using a visual LAMP method. The sensitivity of the assay was 10 fg/μL, and the obtained results were stable and reliable. Out of 655 aquatic product samples and 558 aquaculture water samples, the positive rates of Vibrio vulnificus detection were 9.01% and 8.60%, respectively, which are markedly higher than those of the traditional culture identification methods.

Conclusion

The relatively simple technical requirements, low equipment cost, and rapid detection make the visual LAMP method for the detection of Vibrio vulnificus a convenient choice for field detection in the aquaculture industry.

Untargeted metabolomics and proteomics approach using liquid chromatography-Orbitrap high resolution mass spectrometry to detect pork adulteration in Pangasius hypopthalmus meat

Pangasius hypopthalmus is well known as a good source of protein. However, Pangasius hypopthalmus meat (PHM) can be adulterated with pork for economic concern, thus, analytical methods for authentication are required. Untargeted metabolomics and proteomics using liquid chromatography-high resolution mass spectrometry (LC-HRMS) and chemometrics of principal component analysis (PCA) and partial least square-discriminant analysis (PLS-DA) was successfully used to differentiate authentic and adulterated PHM with the good of fitness (R > 0.95) and good of predictivity (Q > 0.5). Metabolites of PC(o-18:0/18:2(9Z,12Z)) was found to be a potential marker for pork whereas DMPC (dimyristoylphosphatidylcholine) was a potential marker for PHM. Meanwhile, pork peptide marker of myoglobin (HPGDFGADAQGAMSK) and β-hemoglobin (FFESFGDLSNADAVMGNPK) could be identified. Both metabolomics and proteomics using LC-HRMS could detect pork at the lowest concentration level (0.5% w/w). In conclusion, untargeted metabolomics and proteomics using LC-HRMS in combination with chemometrics could be used as powerful methods to detect pork adulteration in fish meat.

Visual detection of rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar) simultaneously by duplex loop-mediated isothermal amplification

Loop-mediated isothermal amplification (LAMP) is often confounded by the non-specific amplification arising from primer dimers, off-target priming, and other artifacts. Precipitation of the DNA produced during LAMP with the use of specific fluorescently labeled probe has proved the effectiveness in specific detection. Herein, two fluorophores (ROX and FAM) were attached to the primers S-LB-6 and R-FIP for Atlantic salmon and rainbow trout, respectively, which are self-quenched in unbound state and become de-quenched after binding to the dumbbell-shaped DNA specifically. The DNA precipitation and appearance of small sediment took 10 s of centrifugation at 1000 g, by adding polyethylenimine (PEI) 600. Each target species was specifically amplified with the predicted color of PEI-DNA sediment, namely red for Atlantic salmon, green for rainbow trout, and pale yellow for mixed species. The optimized duplex LAMP system has proved its specificity and can detect as little as 1 ng DNA in visual detection.

Asymmetric stem-loop–mediated isothermal amplification of nucleic acids for DNA diagnostic assays by simple modification of canonical PCR primers

Nucleic acid–based assays have been adopted as mainstream tools for clinical diagnostics, food safety, and environment monitoring with the merits of accuracy, rapidity, and sensitivity. Loop-mediated isothermal amplification (LAMP) is a well-established method to rapidly identify nucleic acids and has gained recognition and been developed for clinical applications in resource-limited areas. However, the needs for specifically designed primer sets and non-specific amplification hinder the development of LAMP-based nucleic acid tests. Here, a promoted method, termed asymmetric stem-loop–mediated isothermal amplification (ASLAMP) by simple modification of canonical PCR primers, was developed to attempt to overcome those drawbacks. The two primers in the ASLAMP reaction can be easily obtained by adding a stem-loop sequence part to one PCR primer at 5′-ends to get the folding primer (FP), then adding the same primer to the counter canonical PCR primer at 5′-ends to get the turn-back primer (TP). The ASLAMP method was demonstrated in detecting the H1N1 gene fragment with merits of simple primer design, short target sequence, and high amplification efficiency. In addition, the ASLAMP method showed similar efficacy compared with LAMP targeting at the same H1N1 gene sequence. Furthermore, Shigella detection monitored by real-time fluorescence and endpoint colorimetric approaches were taken as examples for evaluation of the practical application of the ASLAMP method, both offered 100% sensitivity and specificity. In conclusion, the novel ASLAMP method with simplicity of primer design, low requirement of equipment, efficiency, and rapidity has exhibited its great prospect for establishment of DNA isothermal amplification in point of care application.

A LAMP Assay for the Detection of Thecodiplosis japonensis, an Alien Gall Midge Species Pest of Pine Trees

Simple Summary

Thecodiplosis japonensis is considered the most harmful pest to pines in South Korea. T. japonensis is a native species of Japan. Recently, T. japonensis was discovered in China and has caused serious damage to local pine trees. Due to the small size and little morphological difference with its related species, it is difficult to accurately identify T. japonensis by morphological methods. Accurate and efficient molecular identification methods are urgently needed to detect this invasive gall midge pest, yet there was no molecular identification method for T. japonensis. In this study, we developed a LAMP assay to detect T. japonensis based on the COI gene sequence. The LAMP assay could detect as little as 300 fg of gDNA. Using colorimetric amplification and a crude gDNA extraction method, the total procedure could be processed in 75 min. The method established in the study can be easily used in both laboratory and field conditions, enabling rapid molecular identification of T. japonensis.

Abstract

Pine needle gall midge (T. japonensis), native to Japan, has become a serious invasive pest in South Korea and, more recently in 2006, in China. It was first discovered in Qingdao, Shandong Province, and has caused serious damage to local Pinus thunbergii. The insect’s small size makes morphological-based identification difficult; therefore, molecular detection techniques are urgently needed for monitoring and preventing its further spread. At present, there is no simple and accurate field molecular identification tool. To solve this problem, a LAMP-based molecular diagnosis technology of T. japonensis was developed. Four LAMP primers were designed to specifically amplify T. japonensis DNA. Positive LAMP reactions usually produce amplification in one hour. The optimal incubation conditions for LAMP detection were determined with 4 LAMP primers for 60 min at 61 °C. The LAMP detection range of gDNA concentrations is wide, with a minimum detectable gDNA concentration of 300 fg. A non-destructive DNA-releasing procedure, HotSHOT “HS6”, which could extract “crude DNA” for LAMP assay in 10 min, was used for larval and adult samples. Therefore, we established a LAMP-based rapid molecular identification method that can be applied in the monitoring and management of T. japonensis.

RT-LAMP assay combining multi-fluorescent probes for SARS-CoV-2 RNA detection and variant differentiation

Simple and accurate testing tools for SARS-CoV-2 viral RNA detection are essential for the prevention of the spread of the virus and timely governmental actions. Herein, we present a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the simultaneous detection of ORF1ab and N gene fragments of SARS-CoV-2 in one pot. Using two primer sets and two molecular beacon (MB) probes respectively labelled with different fluorophore, positive results were obtained with a limit of detection of 20 and 2 copies/μL for ORF1ab and N gene fragments, respectively. Moreover, the RT-LAMP based assay was applied to detect single-site differences in S genes using two one-step displacement (OSD) probes targeting wild-type and mutant (P681R mutation was chosen as model) genes. Through that, the wild type strain and P681R mutant variant were well distinguished from each other, and a preliminary observation was also made on other mutations at this site such as P681H. The proposed method has high sensitivity for quantification and high specificity for mutation differentiation. In addition, it does not require accurate sophisticated thermal cycler instrumentation and can be used in clinical settings in resource-limited regions.

Toward a next-generation diagnostic tool: A review on emerging isothermal nucleic acid amplification techniques for the detection of SARS-CoV-2 and other infectious viruses

As the COVID-19 pandemic continues to affect human health across the globe rapid, simple, point-of-care (POC) diagnosis of infectious viruses such as SARS-CoV-2 remains challenging. Polymerase chain reaction (PCR)-based diagnosis has risen to meet these demands and despite its high-throughput and accuracy, it has failed to gain traction in the rapid, low-cost, point-of-test settings. In contrast, different emerging isothermal amplification-based detection methods show promise in the rapid point-of-test market. In this comprehensive study of the literature, several promising isothermal amplification methods for the detection of SARS-CoV-2 are critically reviewed that can also be applied to other infectious viruses detection. Starting with a brief discussion on the SARS-CoV-2 structure, its genomic features, and the epidemiology of the current pandemic, this review focuses on different emerging isothermal methods and their advancement. The potential of isothermal amplification combined with the revolutionary CRISPR/Cas system for a more powerful detection tool is also critically reviewed. Additionally, the commercial success of several isothermal methods in the pandemic are highlighted. Different variants of SARS-CoV-2 and their implication on isothermal amplifications are also discussed. Furthermore, three most crucial aspects in achieving a simple, fast, and multiplexable platform are addressed.

Simple, sensitive, and cost-effective detection of wAlbB Wolbachia in Aedes mosquitoes, using loop mediated isothermal amplification combined with the electrochemical biosensing method

Background

Wolbachia is an endosymbiont bacterium generally found in about 40% of insects, including mosquitoes, but it is absent in Aedes aegypti which is an important vector of several arboviral diseases. The evidence that Wolbachia trans-infected Ae. aegypti mosquitoes lost their vectorial competence and became less capable of transmitting arboviruses to human hosts highlights the potential of using Wolbachia-based approaches for prevention and control of arboviral diseases. Recently, release of Wolbachia trans-infected Ae. aegypti has been deployed widely in many countries for the control of mosquito-borne viral diseases. Field surveillance and monitoring of Wolbachia presence in released mosquitoes is important for the success of these control programs. So far, a number of studies have reported the development of loop mediated isothermal amplification (LAMP) assays to detect Wolbachia in mosquitoes, but the methods still have some specificity and cost issues.

Methodology/Principal findings

We describe here the development of a LAMP assay combined with the DNA strand displacement-based electrochemical sensor (BIOSENSOR) method to detect wAlbB Wolbachia in trans-infected Ae. aegypti. Our developed LAMP primers used a low-cost dye detecting system and 4 oligo nucleotide primers which can reduce the cost of analysis while the specificity is comparable to the previous methods. The detection capacity of our LAMP technique was 1.4 nM and the detection limit reduced to 2.2 fM when combined with the BIOSENSOR. Our study demonstrates that a BIOSENSOR can also be applied as a stand-alone method for detecting Wolbachia; and it showed high sensitivity when used with the crude DNA extracts of macerated mosquito samples without DNA purification.

Conclusions/Significance

Our results suggest that both LAMP and BIOSENSOR, either used in combination or stand-alone, are robust and sensitive. The methods have good potential for routine detection of Wolbachia in mosquitoes during field surveillance and monitoring of Wolbachia-based release programs, especially in countries with limited resources.

Mosquito-borne diseases such as dengue, chikungunya, zika, and yellow fever are transmitted to humans mainly by the bites of Aedes aegypti mosquitoes. Controlling the vectors of these diseases relies mostly on the use of insecticides. However, the efficiency has been reduced through the development of insecticide resistance in mosquitoes. Wolbachia is an endosymbiotic bacterium that is naturally found in 40% of insects, including mosquitoes. The bacterium can protect its insect hosts from viral infections and can also cause sterility in insect host populations, therefore, providing an opportunity to use it for human disease control. Application of a Wolbachia trans-infected mosquitoes needs simple, rapid and sensitive methods for detecting the bacteria in released mosquitoes. In this paper, we develop the methods of LAMP and BIOSENSORS for detecting wAlbB Wolbachia in mosquitoes. Our positive LAMP reaction can be visualized by color change from violet to blue at a sensitivity of ≥ 10 pg of genomic DNA. When used in combination with the BIOSENSOR method, the sensitivity increases a millionfold without losing specificity. Our study suggests that both developed methods, either used in combination or stand-alone, are efficient and cost-effective, hence, they could be applied for routine surveys of Wolbachia in mosquito control programs that use Wolbachia-based approaches.

Detection of Haemophilus influenzae by loop-mediated isothermal amplification coupled with nanoparticle-based lateral flow biosensor assay

Background

Haemophilus influenzae was the most aggressive pathogen and formed a major cause of bacterial meningitis and pneumonia in young children and infants, which need medical emergency requiring immediate diagnosis and treatment. However, From isolation to identification of H. influenzae, the traditional diagnose strategy was time-consuming and expensive. Therefore, the establishment of a convenient, highly sensitive, and stable detection system is urgent and critical.

Results

In this study, we used a combined method to detect H. influenzae. Six specific primers were designed on the basis of outer membrane protein P6 gene sequence of H. influenzae. The reaction condition such as the optimum temperature was 65℃, and the optimum reaction time was 30 min, respectively. Through the loop-mediated isothermal amplification (LAMP) in combination with nanoparticle-based lateral flow biosensor (LFB), the sensitivity of LAMP-LFB showed 100 fg was the lowest genomic DNA templates concentration in the pure cultures. Meanwhile, the specificity of H. influenzae-LAMP-LFB assay showed the exclusive positive results, which were detected in H. influenzae templates. In 55 clinical sputum samples, 22 samples were positive with LAMP-LFB method, which was in accordance with the traditional culture and Polymerase Chain Reaction (PCR) method. The accuracy in diagnosing H. influenzae with LAMP-LFB could reach 100%, compared to culture and PCR method, indicating the LAMP-LFB had more advantages in target pathogen detection.

Conclusions

Taken together, LAMP-LFB could be used as an effective diagnostic approach for H. influenzae in the conditions of basic and clinical labs, which would allow clinicians to make better informed decisions regarding patient treatment without delay.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02547-5.