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Abstract The rocketing number of COVID-19 cases highlighted the critical role that diagnostic tests play in medical and public health decision-making to contain and mitigate the SARS-CoV-2 pandemic. This study reports the evaluation and implementation of different tests for the molecular detection of SARS-CoV-2 in the central region of Argentina. We evaluated 3 real time RT-PCR kits (GeneFinder COVID-19 Plus RealAmp Kit, DisCoVery SARS-CoV-2 RT-PCR Detection Kit and WGene SARS-CoV-2 RT Detection), 2 nucleic acid extraction methods [MagaBio plus Virus DNA/RNA Purification Kit II (BioFlux), 35-min vs. 9-min, a pre-analytical reagent (FlashPrep®) and 2 isothermal amplification tests (Neokit Plus and ELA CHEMSTRIP®). The order according to the best performance of the 3 real-time RT-PCR kits evaluated was: DisCoVery > GeneFinderTM> WGene. The 2 RNA extraction methods showed similar good results: MagaBio plus Virus RNA Purification Kit II (BioFlux) 9-min was selected due to its faster performance. FlashPrep® reagent showed excellent results to perform direct RNA detection. Isothermal amplification assays showed acceptable sensitivity and specificity values (>80%), except in samples with Ct> 30. Our data show optimal real time RT-PCR kits and alternative molecular methods for SARS-CoV-2 diagnostic. These alternative assays proved to be aceptable.
Resumen La explosión de casos de COVID-19 resaltó el papel fundamental que desempeñan las pruebas de diagnóstico en la toma de decisiones médicas y de salud pública para contener y mitigar la pandemia de SARS-CoV-2. Este estudio reporta la evaluación y la implementación de diferentes test para la detección molecular de SARS-CoV-2 en la región central de Argentina. Evaluamos tres kits de RT-PCR en tiempo real (GeneFinder COVID-19 Plus RealAmp Kit, DisCoVery SARS-CoV-2 RT-PCR Detection Kit y WGene SARS-CoV-2 RT Detection), dos métodos de extracción de ácidos nucleicos (MagaBio plus Virus DNA/RNA Purification Kit II [BioFlux, 35-min vs. 9-min), un reactivo pre-analítico (FlashPrep®) y dos test de amplificación isotérmica (Neokit Plus and ELA CHEMSTRIP®). El orden de rendimiento de los tres kits de RT-PCR en tiempo real evaluados fue el siguiente: DisCoVery GeneFinder™ WGene. Los dos métodos de extracción de RNA mostraron buenos y similares resultados; se seleccionó MagaBio plus Virus RNA Purification Kit II (BioFlux) 9-min debido a su rápido tiempo de procesamiento. El reactivo FlashPrep® mostró excelentes resultados para realizar detección directa de RNA. Los ensayos de amplificación isotérmica mostraron valores de sensibilidad y de especificidad aceptables (80%), excepto en muestras con Ct 30. Nuestros resultados muestran kits de RT-PCR en tiempo real óptimos, como así también métodos moleculares alternativos para el diagnóstico de SARS-CoV-2 que resultan aceptables para su uso en contextos adversos, de descentralización y en diferentes escenarios epidemiológicos, para la detección rápida y precisa del SARS-CoV-2.
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Background: Malaria is a major health issue in tropical and subtropical areas. Out of all subtypes, Plasmodium falciparum (Pf) is the most dangerous form accounting for high mortality and morbidity. It is transmitted by infected female anopheles mosquitoes and infected blood transfusions. Aims and Objectives: The aim of the study is to establish correct diagnosis by direct microscopy, Immunochromatographic test (ICT), and molecular studies. Materials and Methods: This prospective study was conducted in the PG Department of Microbiology, SCB Medical College, Cuttack. Thick blood smears were drawn and then stained with Leishman’s stain to visualize falciparum rings. DNA was extracted from infected blood samples by phenol chloroform method with some modification as described by Sambrook and Russel for molecular analysis. Results: In the present study, 150 cases of malaria were analyzed. The male: female ratio was 1.7:1 and age ranged from 0 to 56 years. The Plasmodium vivax positivity was compared with thin smear to 21 (84%) in ICT, 100% both polymerase chain reaction (PCR) and loop mediated isothermal amplification assay (LAMP) assays followed by the Pf positivity as 76 (92.7%) in ICT, 82 (100%) both PCR and LAMP assays, respectively. The results obtained were statistically significant with P < 0.001. The PCR and LAMP showed 100% response to specificity and positive predictive value. Conclusion: The present study established the role of molecular tests such as PCR and LAMP are highly specific for diagnosis of Plasmodium species whereas they are more or less similar in sensitivity as compared to other diagnostic methods such as ICT and microscopy.
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The neglected tropical disease mycetoma can become extremely devastating, and can be caused both by fungi and bacteria; these are popularly known as eumycetoma and actinomycetoma respectively. The classical triad of the disease is subcutaneous swelling, multiple discharging sinuses and the presence of macroscopic granules. The present study aims to highlight the existing diagnostic modalities and the need to incorporate newer and more advanced laboratory techniques like pan fungal/pan bacterial 16S rRNA gene polymerase chain reaction (PCR) and sequencing, Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), rolling circle amplification (RCA), loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA). It is important for the medical team to be aware of the various diagnostic options (both existing and future), so that diagnosis of such a debilitating disease is never missed, both by clinicians and microbiologists/pathologists. The newer diagnostic methods discussed in this article will help in rapid, accurate diagnosis thus facilitating early treatment initiation, and decreasing the overall morbidity of the disease. In the Indian context, newer technologies need to be made available more widely. Making clinicians aware and promoting research and development in mycetoma diagnostics is the need of the hour.
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Background & objectives: Timely intervention is needed to minimize the economic losses of vector-borne bovine anaplasmosis which can be possible by the isothermal amplification assay. Methods: Anaplasma marginale in the cattle of south Gujarat, India was detected in the PCR and LAMP by amplifying the fragment of msp5 gene. The PCR product was digested with EcoRI, and sequenced to confirm its pathogen specific detection. Results: Species specific PCR observed a band of 457 bp of msp5 DNA following 1% agarose gel electrophoresis. Positive LAMP reaction turned into yellow colour while negative sample depicted original pink colour. A detection limit of PCR and LAMP was up to 10-6 and 10-8 of the original genomic DNA of A. marginale, respectively. A single cut site of EcoRI was observed in the PCR product. Current msp5 DNA sequences of A. marginale (MW538962 and MW538961) showed 100% homology with the published sequences. Monophyletic lineage type relationship was observed with high bootstrap proportion among the msp5 DNA sequences of A. marginale in the phylogram. Prevalence rate of A. marginale was significantly higher (p<0.05) in the PCR [43/280 (15.36%)] and LAMP [62/280 (22.14%)] than the microscopic technique [17/280 (6.07%)]. Diagnostic sensitivity, specificity, positive and negative predictive values at 95% CI for LAMP assay with respect to PCR were 93.02%, 90.72%, 64.52% and 98.62%, respectively. Interpretation & conclusion: Thus LAMP can be a practical alternative to the PCR for the diagnosis of A. marginale infection in the cattle even in field condition
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@#Abstract: Objective To establish a method for detecting sdaB virulence gene of Streptococcus pyogenes with loop mediated isothermal amplification (LAMP). Methods According to the conserved sequence of Streptococcus pyogenes sdaB gene published in GenBank (GenBank: 69901515), LAMP primers were designed with Primer Explorer V5.0 software. Main components of LAMP reaction system were optimized including of fluorescent dye, MgSO4, betaine, deoxyribonucleosidetriphosphate (dNTP), and Bst DNA polymerase, with the concentration of MgSO4 from 0 mmol/L to 12 mmol/L, betaine from 0 mol/L to 2.4 mol/L, dNTP from 0.2 µmol/L to 2 µmol/L, forward inner primer (FIP) and backward inner primer (BIP) from 0.2 µmol/L to 2 µmol/L respetively, forward outer primer (F3) and backward outer primer (B3) from 0.2 µmol/L to 0.4 µmol/L, Bst DNA polymerase from 0.16 U/µL to 0.96 U/µL, fluorescent dye from 0.2 µmol/L to 2 µmol/L. With the optimized system, the methodological specificity and the minimum detection limit were evaluated on the ABI7500 real-time fluorescent quantitative PCR analyzer, and 13 standard strains including Group A Streptococcus, Group B Streptococcus, Group C Streptococcus, Group G Streptococcus, Streptococcus pneumoniae, Streptococcus viridis, Enterococcus faecalis, Enterococcus faecium, Neisseria gonorrhoeae, Lactobacillus acidophilus, Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa were detected. Finally, 103 clinical samples were tested. Results The optimized reaction system contained 25 µL reaction mixture, including 0.8 µL of 25 µmol/L fluorescent dye, 1 µL of 100 mmol/L MgSO4, 6 µL of 5 mol/L betaine, 1.4 µL of 25 mmol/L dNTP, 2 µL of 20 µmol/L FIP and BIP, 0.5 µL of 20 µmol/L F3 and B3, 1 µL of 8 U/µL Bst DNA polymerase, and 2 µL of template. After adding deionized water, the mixture was incubated at 63°C for 45 min to complete the reaction. The limit of detection (LOD) was 500 pg/µL. All 12 non-S. pyogenes strains tested were negative. Compared with the culture method, the clinical sensitivity and specificity were 100.0% (16/16) and 96.6% (84/87), respectively, for 103 clinical samples. Conclusions This LAMP assay is reliable for the detection of Streptococcus pyogenes in clinic and is suitable for field detection with good specificity and sensitivity, as well as simply operation.
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@#Abstract: Objective To establish a sensitive and specific nucleic acid detection method for Schistosoma japonicum based on loop-mediated isothermal amplification (LAMP) and clustered regularly interspaced short palindromic repeats (CRISPR) technology. Methods The LAMP primers, gRNA and ssDNA probe that target Schistosoma japonicum SjR2 genes were designed according to the principles of LAMP and CRISPR. The LAMP-CRISPR reaction system was established and optimized. The sensitivity and specificity of the method were evaluated against the ten-fold serial dilutions of plasmid containing SjR2 target sequences, as well as genomic DNA at different stages of Schistosoma japonicum and other parasites, including Fasciola hepatica, Schistosoma mansoni, Taenia saginata, Clonorchis sinensis, Ascaris lumbricoides, Necator americanus, Paragonimus westermani, and Echinococcus granulosus. Additionally, 15 schistosome-infected snail and 30 uninfected samples were tested by LAMP-CRISPR and LAMP methods, respectively, to evaluate the potential of this method for screening for infected snails. Results The developed LAMP-CRISPR method was able to specifically amplify and detect the SjR2 gene of S. japonicum. The optimal reaction temperature was 37 ℃, and the optimal reaction concentrations were both 40 nmol/L for gRNA and Cas12a protein. No cross-reaction was observed with genomic DNA from other parasites such as F. hepatica. The detection limit of the method was 10 copies/μL when testing 10-fold dilutions of recombinant plasmids as a template. Furthermore, the LAMP-CRISPR method was able to accurately detect genomic DNA from S. japonicum at various stages of development, including eggs, cercariae, schistosomula, juvenile worms, and adult worms. The results of testing 45 snail samples showed no significant difference between the LAMP-CRISPR and LAMP methods for detecting infected snails (χ2=0.05, P>0.05). The sensitivity and specificity of the LAMP-CRISPR method were 100.00% (15/15) and 96.67% (29/30), respectively, compared to the gold standard, while the sensitivity and specificity of the LAMP method were 100.00% (15/15) and 93.33% (28/30), respectively. Conclusions This established LAMP-CRISPR detection method presented good sensitivity, specificity and reliability, making it a promising tool for rapid detection and risk monitoring of S. japonicum.
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@#Abstract: Objective To evaluate the value and significance of rifampicin-resistant real-time fluorescence quantitative nucleic acid amplification detection technology (GeneXpert MTB/RIF) in the diagnosis of pulmonary tuberculosis. Methods The clinical data of 228 patients with suspected pulmonary tuberculosis, who admitted to Hebei Chest Hospital from January 2018 to December 2019, were analyzed retrospectively. The sputum was collected for GeneXpert MTB/RIF, sandwich cup liquid-based bacterial acid-fast staining smear microscopy (referred to as “sandwich cup method”) and Loop-Mediated isothermal amplification (referred to as “LAMP method”) and the results were statistically analyzed by SPSS 17.0 software. Results Among the 228 patients with suspected cases, 200 cases were clinically diagnosed as pulmonary tuberculosis and 28 were non-tuberculosis. The positive detection rate of GeneXpert MTB/RIF (81.0%, 162/200) was significantly higher than that of sandwich cup method (62.5%, 125/200) and LAMP method (72.5%,145/200) (χ2=16.885, 4.049, P<0.05). Taking clinical diagnosis as gold standard, the sensitivity of GeneXpert MTB/RIF (80.00%,160/200) was significantly higher than that of sandwich cup method (60.00%, 120/200) and LAMP method (70.50%, 141/200) (χ2=19.048, 4.846, P<0.05). The diagnostic consistency of GeneXpert MTB/RIF (K=0.73) was higher than that of sandwich cup method (K=0.39) and LAMP method (K=0.56). Conclusions The GeneXpert MTB/RIF detection method is rapid and simple, and can diagnose pulmonary tuberculosis rapidly and simultaneously detect rifampicin resistance of Mycobacterium tuberculosis with high sensitivity. It has high clinical value for early diagnosis of pulmonary tuberculosis and guidance of treatment in general and specialized hospitals.
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@#Abstract： Objective To analyze the value and influencing factors of cross-primer isothermal amplification technology(CPA) in clinical screening and diagnosis of tuberculosis (TB). Methods We collected 543 inpatients in the Second Affiliated Hospital of Hainan Medical College from January 1, 2018 to December 31, 2021, including 179 patients with tuberculosis, 187 patients with pneumonia and 177 patients with other diseases. The patients' sputum, alveolar lavage fluid, pleural effusion and midstream urine were detected by CPA, smear microscopy, culture method and gene detection. The value of CPA detection in the diagnosis of tuberculosis and its influencing factors were evaluated. Statistical analysis was performed using SPSS 26.0. Results The total positive rate of CPA was 14.4% (78/543), and the positive rate of sputum samples accounted for 29.1% (39/134). Among the 78 cases of CPA positive patients, the tuberculosis group accounted for 69.2% (54/78), followed by pneumonia group 21.8% (17/78), and other diseases group accounted for 9.0% (7/78). Taking CPA test as the reference method, the "sensitivity" of smear microscopy was lower than that of genetic testing and culture, while the "specificity" was higher than that of culture and gene testing, and the "missed diagnosis rate" of smear microscopy was higher than that of genetic testing and culture. CPA test positive was related to gender, ESR and pneumonia. There is a good agreement between CPA test and culture method and gene test (Kappa>0.9), and a moderate agreement between CPA test and smear microscopy (Kappa=0.616). Conclusions Sputum specimen is the best choice for CPA detection, while the value of pleural effusion detection is relatively limited. Sputum, alveolar lavage fluid and midcourse urine can be used as clinical specimens for screening and diagnosis of "tuberculosis group and other disease group", while sputum can be used for screening and diagnosis of "tuberculosis group and pneumonia group". Gender, ESR and pneumonia are the influencing factors of CPA positive patients. Therefore, CPA testing is worthy of clinical promotion, but more clinical research data are needed.
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Abstract Introduction: Most successful cases of COVID-19 pandemic mitigation and handling have relied on extensive reverse-transcription quantitative polymerase chain reaction (RT-qPCR). However, many emerging economies have struggled with current molecular testing demands due to economic, technical and technological constraints. Objective: To define a potential diagnostic protocol to increase testing capacity in current and post-pandemic conditions. Methods: We reviewed the literature, patents and commercial applications, for alternatives. Results: We found a good potential in saliva samples, viral inactivation and quick RNA extraction by heating; the use of an isothermal technology such as loop mediated isothermal amplification (LAMP) and naked eye test-result visualization by in-tube colorimetry or turbidity. Conclusions: Saliva samples with quick RNA extraction by heating and colorimetric LAMP are promising options for countries with economic and infrastructure limitations.
Resumen Introducción: La mayoría de los casos exitosos de mitigación y manejo de la pandemia de COVID-19 se han dado mediante pruebas basadas en la reacción en cadena de la polimerasa cuantitativa (RT-qPCR por sus siglas en inglés). Sin embargo, muchas economías emergentes han tenido problemas con las demandas actuales de pruebas moleculares debido a limitaciones económicas, técnicas y tecnológicas. Objetivo: Definir un protocolo de diagnóstico potencial para aumentar la capacidad de prueba en las condiciones actuales y posteriores a la pandemia. Métodos: Revisamos la literatura, las patentes y las aplicaciones comerciales, en busca de alternativas. Resultados: Encontramos un buen potencial en muestras de saliva, inactivación viral y extracción rápida de ARN por calentamiento; el uso de una tecnología isotérmica como la amplificación isotérmica mediada por horquillas (LAMP, por sus siglas en inglés) y la visualización del resultado de la prueba a simple vista mediante colorimetría o turbidez en el tubo. Conclusiones: Las muestras de saliva con extracción rápida de ARN por calentamiento y LAMP colorimétrico son opciones prometedoras para países con limitaciones económicas y de infraestructura.
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Humans , Molecular Diagnostic Techniques/methods , COVID-19 Serological Testing , COVID-19ABSTRACT
RESUMEN Objetivo. Desarrollar y evaluar un método de bajo costo basado en celulosa para la purificación rápida y amplificación directa de ADN de Bordetella pertussis de hisopados nasofaríngeos. Materiales y métodos. Se prepararon discos de celulosa y se evaluaron diferentes parámetros (buffers de lisis/lavado, número de discos y elución de ADN). El método se acopló a una amplificación directa por PCR en tiempo real (qPCR) y se estimó el rendimiento utilizando hisopados nasofaríngeos que fueron positivos (n=100) y negativos (n=50) para ADN B. pertussis por qPCR, comparado con el método basado en columnas de sílice. Se calculó el grado de concordancia, sensibilidad, especificidad, valor predictivo positivo (VPP) y valor predictivo negativo (VPN). Se evaluó la factibilidad del método rápido para ser acoplado a un ensayo colorimétrico de amplificación isotérmica mediada por lazo (LAMP). Resultados. El método rápido con un disco de celulosa y buffer de lisis y lavado conteniendo PVP-40 y Tween 20, respectivamente, mostró una mayor capacidad para purificar ADN amplificable de B. pertussis. El método tuvo una sensibilidad de 89,0% (IC95%, 80,2%-94,9%) y una especificidad de 98,5% (IC95%, 92,1%-100,0%), con un buen grado de concordancia (Kappa=0,867; IC95% 0,788 - 0,946), respecto al método referencial. Los VPP y VPN fueron 98,6% (IC95%, 92,7,2%-100,0%) y 88,2% (IC95%, 78,7%-94,4%), respectivamente. Se evidenció una amplificación exitosa por LAMP, y se obtuvieron resultados comparables con el método por columnas de sílice. Conclusión. El método desarrollado es simple, de bajo costo y libre de equipos para la obtención rápida (60 segundos) de ADN en el punto de atención, y puede ser implementado en diversas técnicas moleculares orientados al diagnóstico oportuno y al estudio epidemiológico de tos ferina.
ABSTRACT Objective. To develop and evaluate a low-cost cellulose-based method for rapid purification and direct amplification of Bordetella pertussis DNA from nasopharyngeal swabs. Materials and methods. We prepared cellulose discs and evaluated different parameters (lysis/wash buffers, number of discs and DNA elution). The method was coupled to a direct real-time PCR (qPCR) amplification and the performance was estimated using nasopharyngeal swabs that were positive (n=100) and negative (n=50) for B. pertussis DNA by qPCR, compared to the silica column-based method. We calculated sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) and the degree of agreement. The feasibility of the rapid method to be coupled to a loop-mediated isothermal amplification colorimetric assay (LAMP) was evaluated. Results. The rapid method, with a cellulose disk and lysis and wash buffer containing PVP-40 and Tween 20, respectively, showed a greater capacity to purify amplifiable DNA from B. pertussis. The method had a sensitivity of 89.0% (95%CI: 80.2%-94.9%) and a specificity of 98.5% (95%CI: 92.1%-100.0%), with a good degree of agreement (Kappa=0.867; 95%CI: 0.788 - 0.946), compared to the reference method. The PPV and NPV were 98.6% (95%CI: 92.7.2%-100.0%) and 88.2% (95%CI: 78.7%-94.4%), respectively. Successful amplification by LAMP was evident, and comparable results were obtained with the silica column method. Conclusion. The developed method is simple, low-cost and equipment-free for rapid (60 seconds) DNA collection at the point of care, and can be implemented in various molecular techniques aimed at the timely diagnosis and epidemiological study of pertussis.
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Humans , Bordetella pertussis/genetics , DNA, Bacterial/isolation & purification , Cellulose , Real-Time Polymerase Chain Reaction , Whooping Cough/diagnosis , Nasopharynx/microbiology , Sensitivity and Specificity , Molecular Diagnostic TechniquesABSTRACT
Background & objectives: The pandemic of SARS-COV-2 began in Wuhan, China in December 2019 and has caused more than 101 million cases worldwide. Diagnostic technologies possessing sensitivity and specificity equivalent to real-time reverse-transcriptase polymerase chain reaction (rRT-PCR) assays are needed to ramp up testing capacity in most countries. Newer platforms need to be technically less demanding, require minimum equipment and reduce turn-around time for reporting results. The objective of this study was to exploit loop-mediated isothermal amplification (LAMP) for the detection of SARS-CoV-2 and evaluate its performance by comparison with rRT-PCR. Methods: Reverse-transcription LAMP (RT-LAMP) assay primers were designed to detect envelop (E) and nucleocapsid (N) genes of SARS-CoV-2. Positive control RNA was prepared by in vitro transcription of E and N genes clones. RT-LAMP amplification reactions were incubated at 65°C for 30 min. Results were recorded visually. RT-LAMP results were evaluated by comparing the results obtained with a commercial rRT-PCR kit. Results: The RT-LAMP assay for E and N genes was carried out in separate tubes. RT-LAMP detected about 40 copies of SARS-CoV-2 RNA per reaction. A total of 253 throat swabs were tested using the RT-LAMP assay. The overall diagnostic sensitivity and specificity of the LAMP assay were 98.46 and 100 per cent, respectively, as compared to the rRT-PCR. Interpretation & conclusions: SARS-CoV-2 RT-LAMP assay was designed, standardized and evaluated. The assay showed diagnostic sensitivity and specificity equivalent to rRT-PCR assays. The assay will be useful to increase testing capacity for the detection of SARS-CoV-2 in the country.
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Diagnosis of malaria is a prominent challenge due to the endemic nature of infection. Malaria poses a great threat to global public health. The disease can be diagnosed by several techniques out of which microscopy is a known gold standard. High sensitivity of molecular techniques is making them more reliable and popular as tools for diagnosis of malaria. However, new methods are required which can fulfill the criteria of being Point of Care Test (POCT) as defined by WHO. Loop-mediated isothermal amplification (LAMP) technique amplifies DNA in an isothermal condition, and surpasses the disadvantages of conventional molecular techniques such as polymerase chain reaction. Multiplex LAMP, a modification of LAMP may emerge as a new POC for malaria diagnosis. This review deals with the use of LAMP and multiplex LAMP in diagnosis of malaria and its prospective use as point of care techniques.
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Polymerase chain reaction (PCR) is the gold standard for nucleic acid amplification in molecular diagnostics. The PCR includes multiple reaction stages (denaturation, annealing, and extension), and a complicated thermalcycler is required to repetitively provide different temperatures for different stages for 30-40 cycles within at least 1-2 hours. Due to the complicated devices and the long amplification time, it is difficult to adopt conventional PCR in point-of-care testing (POCT). Comparing to conventional PCR, isothermal amplification is able to provide a much faster and more convenient nucleic acid detection because of highly efficient amplification at a constant reaction temperature provided by a simple heating device. When isothermal amplification is combined with microfluidics, a more competent platform for POCT can be established. For example, various diagnosis devices based on isothermal amplification have been used to rapidly and conveniently detect SARS-CoV-2 viruses. This review summarized the recent development and applications of the microfluidics-based isothermal amplification. First, different typical isothermal amplification methods and related detection methods have been introduced. Subsequently, different types of microfluidic systems with isothermal amplification were discussed based on their characteristics, for example, functionality, system structure, flow control, and operation principles. Furthermore, detection of pathogens (e.g. SARS-CoV-2 viruses) based on isothermal amplification was introduced. Finally, the combination of isothermal amplification with other new technologies, e.g. CRISPR, has been introduced as well.
Subject(s)
Humans , COVID-19/diagnosis , Microfluidics , Nucleic Acid Amplification Techniques , Polymerase Chain Reaction , SARS-CoV-2/geneticsABSTRACT
@#Abstract: At present, nucleic acid detection technology based on the PCR principle is commonly used to detect malaria parasites, the existing Plasmodium detection methods mainly include microscopy, antigen immunoassay, and nucleic acid detection,but due to the long detection time, high personnel and equipment requirements, and other shortcomings, its popularization, and application at the grassroots level are limited. What challenges previous Plasmodium detection methods are the lack of experienced professionals and advanced equipment at the grassroots as well as the requirement of rapid detection of large samples under extreme conditions. The isothermal amplification technology developed in recent years has potential application prospects due to its simplicity, rapidity, high sensitivity, and high specificity. This article attempts to review the principles, characteristics, and prospects of various isothermal amplification technologies, and on this basis, focuses on the introduction of recombinase polymerase amplification (RPA) and recombinase⁃aided isothermal amplification (RAA) assay technologies and proposes the use of such recombinant enzyme amplification technologies to achieve rapid and accurate diagnosis of common Plasmodium species possibility and imagination.
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@#Abstract: The loop-mediated isothermal amplification (LAMP) technique is a technique for the specific and efficient amplification of target fragments at a constant temperature using two pairs of specially designed primers and a strand displacement activity DNA polymerase. LAMP technique is a simple, rapid, specific, sensitive and cost-effective nucleic acid amplification method, and therefore has a promising future in the field rapid detection of Mycobacterium tuberculosis and grassroots applications. In this review, the basic principles and characteristics of the LAMP technique, the main molecular markers for the diagnosis of tuberculosis, and the use of different molecular markers and various types of novel techniques in the diagnosis of pulmonary tuberculosis, extrapulmonary tuberculosis, and drug-resistant tuberculosis were described. The LAMP technique has been widely used in the diagnosis of tuberculosis with high sensitivity and specificity, but the technique still has some shortcomings. This paper reviews the progress of its application in tuberculosis in recent years and provides an outlook on its development, with a view to providing a rational research direction for rapid diagnosis of tuberculosis in a resource-limited environment.
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With the advantage of being capable of detecting multiple targets at the same time, high throughput and cost-effective, multiplex nucleic acid detection technologies meet the need of large-scale nucleic acid screening and quantification. Multiplex polymerase chain reaction has been applied to detect pathogen, methylated DNA, mutated gene, and single nucleotide polymorphism typing. Isothermal amplification technologies, such as loop-mediated isothermal amplification and recombinase polymerase amplification are promising in the field of point-of-care testing. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein (Cas)-based multiplex nucleic acid detection technologies have become a hotspot due to their high sensitivity and specificity. Metagenomics sequencing plays a leading role in the detection of emerging pathogens and their gene mutation monitoring as well as tumor research. In this review, the advancements and future of multiplex acid detection technologies in clinical application are discussed.
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Recombinase polymerase amplification (RPA) is a novel technology for nucleic acid isothermal amplification. It can achieve the rapid amplification and detection of a target gene under 37-42 ℃. This amplification method is highly sensitive, more specific and less instrument-dependent than other existing methods, and it can also integrate multiple detection modes. Therefore, it is especially suitable for applying in low-resource settings and conducting point-of-care tests. Starting from the reaction principles and the experimental design of RPA, this article pointed out some key points when using RPA in a clinical setting. The current development and related problems of RPA were concluded and the various future uses of this method were also prospected.
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With the development of the concept of precision medicine, under the background of the new coronavirus pneumonia epidemic, the clinical diagnosis and treatment of infectious diseases has received more and more attention. The experimental diagnosis technology with molecular biology as the core is used as important means for the clinical laboratory diagnosis of infectious diseases. This lcind of technology is paid special attention. In recent years, advances in nanomaterials, applied chemistry, photophysics, and biosensing technologies have also ushered in revolutionary and creative developments in molecular diagnostic technology. This article reviews the application and development of the latest molecular diagnostic technologies, such as next-generation quantitative PCR technology and gene sequencing technology, isothermal amplification technology, biochip and biosensor technology in the clinical diagnosis of infectious diseases.
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Objective:To explore the value of detecting pneumocystis carini(PC)rapidly in immunocompromised patients by loop mediated isothermal amplification(LAMP).Methods:Respiratory tract specimens of immunocompromised children suspected of pneumocystis carinii pneumonia(PCP) at Shanghai Children′s Medical Center, School of Medicine, Shanghai Jiao Tong University were collected from May 2020 to May 2021.PCR and LAMP methods were used to detect PC.Firstly, LAMP primers of PC were synthetized according to the conserved region of PC gene, and the LAMP reaction system and reaction conditions were optimized to evaluate the sensitivity and specificity.Then, the results of pathogens were compared with those of PCR detection.Results:The established LAMP detection technology for PC had high specificity and super sensitivity.The detection results could be obtained within 1 hour.In 12 clinical samples, 10 cases were positive and 2 cases were negative, the coincidence rate of LAMP and PCR technique was 100%.Conclusion:LAMP can detect PC more rapidly and sensitively than PCR, and it can provide a good support for clinical rapid diagnosis of PCP.
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Objective:To explore the value of detecting pneumocystis carini(PC)rapidly in immunocompromised patients by loop mediated isothermal amplification(LAMP).Methods:Respiratory tract specimens of immunocompromised children suspected of pneumocystis carinii pneumonia(PCP) at Shanghai Children′s Medical Center, School of Medicine, Shanghai Jiao Tong University were collected from May 2020 to May 2021.PCR and LAMP methods were used to detect PC.Firstly, LAMP primers of PC were synthetized according to the conserved region of PC gene, and the LAMP reaction system and reaction conditions were optimized to evaluate the sensitivity and specificity.Then, the results of pathogens were compared with those of PCR detection.Results:The established LAMP detection technology for PC had high specificity and super sensitivity.The detection results could be obtained within 1 hour.In 12 clinical samples, 10 cases were positive and 2 cases were negative, the coincidence rate of LAMP and PCR technique was 100%.Conclusion:LAMP can detect PC more rapidly and sensitively than PCR, and it can provide a good support for clinical rapid diagnosis of PCP.