scholarly journals A rapid, highly sensitive and open-access SARS-CoV-2 detection assay for laboratory and home testing

2020 ◽  
Author(s):  
Max J. Kellner ◽  
James J. Ross ◽  
Jakob Schnabl ◽  
Marcus P.S. Dekens ◽  
Robert Heinen ◽  
...  
Keyword(s):  
Lamp Assay ◽  
Rna Isolation ◽  
Major Step ◽  
Home Testing ◽  
Detection Assay ◽  
Highly Sensitive ◽  
Hydroxynaphthol Blue ◽  
Increased Sensitivity ◽  
Alternative Detection ◽  
Carry Over

AbstractGlobal efforts to combat the Covid-19 pandemic caused by the beta coronavirus SARS-CoV-2 are currently based on RT-qPCR-based diagnostic tests. However, their high cost, moderate throughput and reliance on sophisticated equipment limit widespread implementation. Loop-mediated isothermal amplification after reverse transcription (RT-LAMP) is an alternative detection method that has the potential to overcome these limitations. Here we present a rapid, robust, highly sensitive and versatile RT-LAMP based SARS-CoV-2 detection assay. Our forty-minute procedure bypasses a dedicated RNA isolation step, is insensitive to carry-over contamination, and uses a hydroxynaphthol blue (HNB)-based colorimetric readout, which allows robust SARS-CoV-2 detection from various sample types. Based on this assay we have substantially increased sensitivity and scalability by a simple nucleic acid enrichment step (bead-LAMP), established a pipette-free version for home testing (HomeDip-LAMP), and developed a version with open source enzymes that could be produced in any molecular biology setting. Our advanced, universally applicable RT-LAMP assay is a major step towards population-scale SARS-CoV-2 testing.

scholarly journals Loop-mediated isothermal amplification (LAMP) for rapid detection of L. monocytogenes in meat

10.5219/1165 ◽  
2019 ◽  
Vol 13 (1) ◽  
pp. 800-805
Author(s):  
Yuliya Yushina ◽  
Anzhelika Makhova ◽  
Elena Zayko ◽  
Dagmara Bataeva
Keyword(s):  
Foodborne Pathogens ◽  
Meat Products ◽  
Lamp Assay ◽  
Isothermal Amplification ◽  
Meat Industry ◽  
Safety Testing ◽  
Loop Mediated Isothermal Amplification ◽  
Specificity And Sensitivity ◽  
Detection Assay ◽  
Highly Sensitive

There is a continued need to develop improved rapid methods for detection of foodborne pathogens. Rapid and sensitive methods for enumeration of Listeria monocytogenes are important for microbiological food safety testing purpose. The aim of this project was to evaluate a commercial loop-mediated isothermal amplification (LAMP) based system with bioluminescence, named as 3M™ Molecular Detection Assay (MDA), was validated for the detection of L. monocytogenes in food products with a standard GOST 32031-2012 method as reference. The results of this study revealed that a commercial LAMP-based method performed equally effective compared with method, showing from 94% to 100% specificity and sensitivity, respectively. The LAMP-based method was shown to be rapid and reliable detection technique for L. monocytogenes present at low numbers (10 CFU.g-1) on raw meat and meat products and can be applicable in meat industry. Thus, compared with the microbiological method based GOST 32031-2012, the LAMP assay is a relatively rapid and highly sensitive method for detecting L. monocytogenes and will facilitate the surveillance for contamination of L. monocytogenes in food. The 3M MDS result and culture-based detection (GOST 32031-2012) did not differ significantly (p >0.05) regarding the number of positive samples.

scholarly journals LAMP-based foldable microdevice platform for the rapid detection of Magnaporthe oryzae and Sarocladium oryzae in rice seed

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
M. K. Prasannakumar ◽  
P. Buela Parivallal ◽  
Devanna Pramesh ◽  
H. B. Mahesh ◽  
Edwin Raj
Keyword(s):  
Magnaporthe Oryzae ◽  
Plant Pathogens ◽  
Point Of Care ◽  
Lamp Assay ◽  
Rice Seed ◽  
Highly Sensitive ◽  
Polymerase Chain ◽  
Rice Seeds ◽  
Template Dna ◽  
Assay Conditions

AbstractRice blast (caused by Magnaporthe oryzae) and sheath rot diseases (caused by Sarocladium oryzae) are the most predominant seed-borne pathogens of rice. The detection of both pathogens in rice seed is essential to avoid production losses. In the present study, a microdevice platform was designed, which works on the principles of loop-mediated isothermal amplification (LAMP) to detect M. oryzae and S. oryzae in rice seeds. Initially, a LAMP, polymerase chain reaction (PCR), quantitative PCR (qPCR), and helicase dependent amplification (HDA) assays were developed with primers, specifically targeting M. oryzae and S. oryzae genome. The LAMP assay was highly efficient and could detect the presence of M. oryzae and S. oryzae genome at a concentration down to 100 fg within 20 min at 60 °C. Further, the sensitivity of the LAMP, HDA, PCR, and qPCR assays were compared wherein; the LAMP assay was highly sensitive up to 100 fg of template DNA. Using the optimized LAMP assay conditions, a portable foldable microdevice platform was developed to detect M. oryzae and S. oryzae in rice seeds. The foldable microdevice assay was similar to that of conventional LAMP assay with respect to its sensitivity (up to 100 fg), rapidity (30 min), and specificity. This platform could serve as a prototype for developing on-field diagnostic kits to be used at the point of care centers for the rapid diagnosis of M. oryzae and S. oryzae in rice seeds. This is the first study to report a LAMP-based foldable microdevice platform to detect any plant pathogens.

Application strategies of peptide nucleic acids toward electrochemical nucleic acid sensors

The Analyst ◽  
2021 ◽  
Author(s):  
Qingteng Lai ◽  
Wei Chen ◽  
Yanke Zhang ◽  
Zheng-Chun Liu
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Peptide Nucleic Acids ◽  
Dna Probes ◽  
Highly Sensitive ◽  
Increased Sensitivity ◽  
Acid Sensors

Peptide nucleic acids (PNAs) have attracted tremendous interest in the fabrication of highly sensitive electrochemical nucleic acid biosensor due to their higher stability and increased sensitivity than common DNA probes....

scholarly journals Development and Clinical Evaluation of Loop-Mediated Isothermal Amplification (LAMP) Assay for the Diagnosis of Human Visceral Leishmaniasis in Brazil

2019 ◽  
Vol 2019 ◽  
pp. 1-7 ◽  
Author(s):  
Daniel Moreira de Avelar ◽  
Débora Moreira Carvalho ◽  
Ana Rabello
Keyword(s):  
Visceral Leishmaniasis ◽  
Lamp Assay ◽  
Isothermal Amplification ◽  
Health Concern ◽  
Serological Tests ◽  
Blood Samples ◽  
Loop Mediated Isothermal Amplification ◽  
Human Visceral Leishmaniasis ◽  
Highly Sensitive ◽  
Sensitivity Specificity

Visceral leishmaniasis (VL) is considered a major public health concern in Brazil and several regions of the world. A recent advance in the diagnosis of infectious diseases was the development of loop-mediated isothermal amplification (LAMP). The aim of this study was to develop and evaluate a new LAMP assay for detection of K26 antigen-coding gene of L. donovani complex. A total of 219 blood samples of immunocompetent patients, including 114 VL cases and 105 non-VL cases, were analyzed for the diagnosis of VL in the present study. Diagnostic accuracy was calculated against a combination of parasitological and/or serological tests as a reference standard. The results were compared to those of kDNA Leishmania-PCR. The detection limit for the K26-Lamp assay was 1fg L. infantum purified DNA and 100 parasites/mL within 60 min of amplification time with visual detection for turbidity. The assay was specific for L. donovani complex. Sensitivity, specificity, and accuracy were 98.2%, 98.1%, and 98.2%, respectively, for K26-LAMP and 100%, 100%, and 100%, respectively, for kDNA Leishmania-PCR. Excellent agreement was observed between K26-LAMP and kDNA Leishmania-PCR assays (K = 0.96). A highly sensitive and specific LAMP assay targeting K26 antigen-coding gene of L. donovani complex was developed for diagnosis in peripheral blood samples of VL patients.

Rapid Detection of Listeria in Ice Cream in 13 Hours Using the Roka Listeria Detection Assay

2018 ◽  
Vol 101 (6) ◽  
pp. 1806-1812
Author(s):  
Elba Veronica Arias-Rios ◽  
Kristina Tenney ◽  
Tam Mai ◽  
Sam Anderson ◽  
Ruth Marie Cantera ◽  
...  
Keyword(s):  
Early Detection ◽  
New Media ◽  
Rapid Detection ◽  
Method Comparison ◽  
Reference Method ◽  
Ice Cream ◽  
Detection Methods ◽  
Media Formulation ◽  
Detection Assay ◽  
Highly Sensitive

Abstract Background: Listeria contamination is a major concern in the ice cream industry; therefore, early and accurate detection is vital. Current detection methods require about a 24 h enrichment period for detection. Objective: Enhance the early detection of Listeria in ice cream using the highly sensitive isothermal ribosomal RNA-based Roka/Atlas Listeria Detection Assay. Methods: The R2 Medium was developed for Listeria enrichment by Molecular Epidemiology, Inc. (Seattle, WA). Comparative growth curve studies were performed on the new R2 Medium for Listeria and the currently validated media for the Roka Listeria Detection Assay. Subsequently, a method comparison between the Roka Listeria Detection Assay and the U.S. Food and Drug Administration’s (FDA) Bacteriological Analytical Manual (BAM) Chapter 10 reference method on ice cream was carried out. Results: The R2 Medium supports the growth of L. monocytogenes better than Buffered Listeria Enrichment Broth, Demi-Fraser broth, and Modified University of Vermont Broth, as indicated by the faster growth rate of the organism. When used as an enrichment medium in a method comparison study of ice cream, the results showed that R2 Medium–enriched samples tested with the Roka Listeria Detection Assay gave an equivalent performance compared with the 24 h FDA-BAM reference method at 10 and 18 h post-enrichment for Listeria. Conclusions: The results from this study indicate that the new R2 Medium and the highly sensitive Roka Listeria Detection Assay allowed for the rapid detection of Listeria species in ice cream in 13 h. Highlights: The Roka Listeria Detection Assay, in conjunction with a new media formulation (R2 Medium), allowed for the early detection of Listeria in ice cream and may be applied in other food matrixes and environmental samples.

scholarly journals 3D Study Of Magnetic Fields In NGC 6946

2014 ◽  
Vol 10 (S309) ◽  
pp. 351-351
Author(s):  
Anna Williams ◽  
George Heald ◽  
Eric Wilcots ◽  
Ellen Zweibel
Keyword(s):  
Magnetic Fields ◽  
3D Structure ◽  
Model Fitting ◽  
Radio Continuum ◽  
Polarization Spectrum ◽  
Ngc 6946 ◽  
New Radio ◽  
Highly Sensitive ◽  
The Galaxy ◽  
Increased Sensitivity

AbstractRecent advancements in both radio observatories and computing have opened a new regime of 3D observations. Not only do these instruments measure emission lines and radio continuum over much larger bandpasses, but they also simultaneously observe the polarized emission over the same large bandpasses with increased sensitivity. This “polarization spectrum" can be used to recover information about the 3D structure of magnetic fields in the universe. Our combined 3-20~cm observations of NGC 6946 taken with the Westerbork Synthesis Radio Telescope provide highly sensitive diagnostics of the internal depolarization across the galaxy. We use model fitting to determine likely mechanisms for depolarization in different regions of the galaxy, and glean information about the coherent and turbulent magnetic fields in NGC 6946. We produce Faraday dispersion maps that illustrate how we can probe different depths into the galaxy at different wavelengths and display new features of the line of sight magnetic field. This work is just a sample of the new 3D studies that are possible with upgraded and new radio instruments like the VLA, ATCA, and SKA.

scholarly journals An enhanced isothermal amplification assay for viral detection

2020 ◽  
Author(s):  
Jason Qian ◽  
Sarah A. Boswell ◽  
Christopher Chidley ◽  
Zhi-xiang Lu ◽  
Mary E. Pettit ◽  
...  
Keyword(s):  
Rna Isolation ◽  
Isothermal Amplification ◽  
Molecular Diagnostic ◽  
Nucleic Acid Detection ◽  
Sample Collection ◽  
Amplification Method ◽  
Current State ◽  
Highly Sensitive ◽  
Amplification Assay ◽  
Molecular Diagnostic Test

AbstractRapid, inexpensive, robust diagnostics are essential to control the spread of infectious diseases. Current state of the art diagnostics are highly sensitive and specific, but slow, and require expensive equipment. We developed a molecular diagnostic test for SARS-CoV-2, FIND (Fast Isothermal Nucleic acid Detection), based on an enhanced isothermal recombinase polymerase amplification reaction. FIND has a detection limit on patient samples close to that of RT-qPCR, requires minimal instrumentation, and is highly scalable and cheap. It can be performed in high throughput, does not cross-react with other common coronaviruses, avoids bottlenecks caused by the current worldwide shortage of RNA isolation kits, and takes ~45 minutes from sample collection to results. FIND can be adapted to future novel viruses in days once sequence is available.One sentence summarySensitive, specific, rapid, scalable, enhanced isothermal amplification method for detecting SARS-CoV-2 from patient samples.

scholarly journals Development of a dual-gene loop-mediated isothermal amplification (LAMP) detection assay for SARS-CoV-2: A preliminary study

2020 ◽  
Author(s):  
Azeem Mehmood Butt ◽  
Shafiqa Siddique ◽  
Xiaoping An ◽  
Yigang Tong
Keyword(s):  
Point Of Care ◽  
Lamp Assay ◽  
Cross Reactivity ◽  
Isothermal Amplification ◽  
Nasopharyngeal Swab ◽  
Loop Mediated Isothermal Amplification ◽  
Qualitative Detection ◽  
Detection Assay ◽  
Testing Protocols ◽  
Positive Results

AbstractSevere acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2) has emerged as a rapidly spreading global pathogen stressing the need for development of rapid testing protocols ever than before. The aim of present study was to develop a SARS-CoV-2 detection protocol which can be performed within minimal resources and timeframe. For this purpose, we implemented the reverse transcription loop-mediated isothermal amplification (RT-LAMP) methodology for the qualitative detection of SARS-CoV-2 RNA. In order to improve the detection capability, the RT-LAMP assay was developed to simultaneously amplify two viral genes: ORF1a and N. A total of 45 SARS-CoV-2 associated coronavirus disease 2019 (COVID-19) and 25 non-COVID-19 cases were enrolled. Viral RNA was extracted from the nasopharyngeal swab samples and analyzed simultaneously using PCR and RT-LAMP protocols. Overall, our SARS-CoV-2 dual gene RT-LAMP assay was found to be 95% accurate in detecting positive cases and showed no cross-reactivity or false-positive results in non-COVID-19 samples. Further evaluation on larger and multi-centric cohorts is currently underway to establish the diagnostic accuracy and subsequent implementation into clinical practice and at point-of-care settings.

scholarly journals Xpert MTB/RIF Ultra is highly sensitive for the diagnosis of tuberculosis lymphadenitis in an HIV-endemic setting

2021 ◽  
Author(s):  
Stephanie Minnies ◽  
Byron W.P. Reeve ◽  
Loren Rockman ◽  
Georgina Nyawo ◽  
Charissa C. Naidoo ◽  
...  
Keyword(s):  
Clinical Investigation ◽  
False Negative ◽  
Needle Aspiration ◽  
World Health ◽  
Number Of Patients ◽  
Highly Sensitive ◽  
Specimen Processing ◽  
Increased Sensitivity ◽  
Health Organization ◽  
Low Sensitivity

Background: Tuberculosis lymphadenitis (TBL) is the most common extrapulmonary TB (EPTB) manifestation. Xpert MTB/RIF Ultra (Ultra) is a World Health Organization-endorsed diagnostic test, but performance data for TBL, including on non-invasive specimens, are limited. Methods: Fine needle aspiration biopsies (FNABs) from outpatients (≥18 years) with presumptive TBL (n=135) underwent: 1) routine Xpert (later Ultra once programmatically available), 2) a MGIT 960 culture (if Xpert- or Ultra-negative, or rifampicin-resistant), and 3) study Ultra. Concentrated paired urine underwent Ultra. Primary analyses used a microbiological reference standard (MRS). Results: In a head-to-head comparison (n=92) of FNAB study Ultra and Xpert, Ultra had increased sensitivity [91% (95% confidence interval 79, 98) vs. 72% (57, 84); p=0.016] and decreased specificity [76% (61, 87) vs. 93% (82, 99); p=0.020], and detected patients not on treatment. HIV nor alternative reference standards affected sensitivity and specificity. In patients with both routine and study Ultras, the latter detected more cases [+20% (0, 42); p=0.034] and, further indicative of potential laboratory-based room-for-improvement (e.g., specimen processing optimisation), false-negative study Ultras were more inhibited than true-positives. Study Ultra false-positives had less mycobacterial DNA than true-positives [trace-positive proportions 59% (13/22) vs. 12% (5/51); p<0.001]. “Trace” exclusion or recategorization removed potential benefits offered over Xpert. Urine Ultra had low sensitivity [18% (7, 35)]. Conclusions: Ultra on FNABs is highly sensitive and detects more TBL than Xpert. Patients with FNAB Ultra-positive “trace” results, most of whom will be culture-negative, may require additional clinical investigation. Urine Ultra could reduce the number of patients needing invasive sampling.

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