scholarly journals RT-LAMP has high accuracy for detecting SARS-CoV-2 in saliva and naso/oropharyngeal swabs from asymptomatic and symptomatic individuals

2021 ◽  
Author(s):  
Stephen P Kidd ◽  
Dan Burns ◽  
Bryony Armson ◽  
Andrew D Beggs ◽  
Emma L. A Howson ◽  
...  
Keyword(s):  
Preparation Method ◽  
Rna Extraction ◽  
Improved Method ◽  
Diagnostic Specificity ◽  
Sample Preparation Method ◽  
Viral Loads ◽  
Healthcare Settings ◽  
Frequent Interval ◽  
Oropharyngeal Swab ◽  
Asymptomatic Individuals

Previous studies have described RT-LAMP methodology for the rapid detection of SARS-CoV-2 in nasopharyngeal/oropharyngeal swab and saliva samples. Here we describe the validation of an improved simple sample preparation method for Direct SARS-CoV-2 RT-LAMP, removing the need for RNA extraction, using 559 swabs and 86,760 saliva samples from asymptomatic and symptomatic individuals across multiple healthcare settings. Using this improved method we report a diagnostic sensitivity (DSe) of 70.35% (95% CI 63.48-76.60%) on swabs and 84.62% (79.50-88.88%) on saliva, with diagnostic specificity (DSp) 100% (98.98-100.00%) on swabs and 100% (99.72-100.00%) on saliva when compared to RT-qPCR. Analysing samples with RT-qPCR ORF1ab CT values of <25 and <33 (high and medium-high viral loads, respectively), we found DSe of 100% (96.34-100%) and 77.78% (70.99-83.62%) for swabs, and 99.01% (94.61-99.97%) and 87.32% (80.71-92.31%) for saliva. We also describe RNA RT-LAMP (on extracted RNA) performed on 12,619 swabs and 12,521 saliva samples to provide updated performance data with DSe and DSp of 95.98% (92.74-98.06%) and 99.99% (99.95-100%) for swabs, and 80.65% (73.54-86.54%) and 99.99% (99.95-100%) for saliva, respectively. We also report on daily samples collected from one individual from symptom onset where both Direct and RNA RT-LAMP detected SARS-CoV-2 in saliva collected on all six days where symptoms were recorded, with RNA RT-LAMP detecting SARS-CoV-2 for an additional further day. The findings from these studies demonstrate that RT-LAMP testing of swabs and saliva is potentially applicable to a variety of use-cases, including frequent, interval-based testing of saliva from asymptomatic individuals via Direct RT-LAMP that may be missed using symptomatic testing alone.

scholarly journals Preliminary optimisation of a simplified sample preparation method to permit direct detection of SARS-CoV-2 within saliva samples using reverse-transcription loop-mediated isothermal amplification (RT-LAMP)

2020 ◽  
Author(s):  
Emma Howson ◽  
Stephen Kidd ◽  
Jason Sawyer ◽  
Claire Cassar ◽  
David Cross ◽  
...  
Keyword(s):  
Sample Preparation ◽  
Reverse Transcription ◽  
Preparation Method ◽  
Direct Detection ◽  
Saliva Sample ◽  
Rna Extraction ◽  
Isothermal Amplification ◽  
Molecular Testing ◽  
Sample Preparation Method ◽  
Loop Mediated Isothermal Amplification

We describe the optimization of a simplified sample preparation method which permits rapid and direct detection of SARS-CoV-2 RNA within saliva using reverse-transcription loop-mediated isothermal amplification (RT-LAMP). Treatment of saliva samples prior to RT-LAMP by dilution 1:1 in MucolyseTM, followed by dilution (within the range of 1 in 5 to 1 in 40) in 10% (w/v) Chelex 100 Resin and a 98oC heat step for 2 minutes enabled detection of SARS-CoV-2 RNA in all positive saliva samples tested, with no amplification detected in pooled negative saliva. The time to positivity for which SARS-CoV-2 RNA was detected in these positive saliva samples was proportional to the real-time reverse-transcriptase PCR cycle threshold (CT), with SARS-CoV-2 RNA detected in as little as 05:43 (CT 21.08), 07:59 (CT 24.47) and 08:35 (CT 25.27) minutes, respectively. The highest CT where direct RT-LAMP detected SARS-CoV-2 RNA was 31.39 corresponding to a 1 in 40 dilution of a positive saliva sample (1:1 in MucolyseTM) with a starting CT of 25.27. When RT-LAMP was performed on pools of SARS-CoV-2 negative saliva samples spiked with whole inactivated SARS-CoV-2 virus, RNA was detected at dilutions spanning 1 in 5 to 1 in 160 representing CTs spanning 22.49-26.43. Here we describe a simple but critical rapid sample preparation method which can be used up front of RT-LAMP to permit direct detection of SARS-CoV-2 within saliva samples. Saliva is a sample which can be collected non-invasively without the use of highly skilled staff and critically can be obtained from both healthcare and home settings. Critically, this approach overcomes both the requirement and validation of different swabs and the global bottleneck in obtaining RNA extraction robots and reagents to enable molecular testing by PCR. Such testing opens the possibility of public health approaches for effective intervention to control the COVID-19 pandemic through regular SARS-CoV-2 testing at a population scale, combined with isolation and contact tracing for positive cases.

To Eliminate Curtain Effect of FIB TEM Samples by a Combination of Sample Dicing and Backside Milling

2014 ◽  
Author(s):  
Jian-Shing Luo ◽  
Hsiu Ting Lee
Keyword(s):  
Sample Preparation ◽  
Focused Ion Beam ◽  
Preparation Method ◽  
Low Cost ◽  
Ion Beam ◽  
Sample Preparation Method ◽  
Site Specific ◽  
Dual Beam ◽  
Transmission Electron

Abstract Several methods are used to invert samples 180 deg in a dual beam focused ion beam (FIB) system for backside milling by a specific in-situ lift out system or stages. However, most of those methods occupied too much time on FIB systems or requires a specific in-situ lift out system. This paper provides a novel transmission electron microscopy (TEM) sample preparation method to eliminate the curtain effect completely by a combination of backside milling and sample dicing with low cost and less FIB time. The procedures of the TEM pre-thinned sample preparation method using a combination of sample dicing and backside milling are described step by step. From the analysis results, the method has applied successfully to eliminate the curtain effect of dual beam FIB TEM samples for both random and site specific addresses.

Site-Specific Low Angle Plasma FIB Milling for Cross-Sectional Electrical Characterization

2019 ◽  
Author(s):  
Chuan Zhang ◽  
Jane Y. Li ◽  
John Aguada ◽  
Howard Marks
Keyword(s):  
Cross Section ◽  
Focused Ion Beam ◽  
Electrical Characteristic ◽  
Preparation Method ◽  
Ion Beam ◽  
Grazing Angle ◽  
Electrical Characterization ◽  
Sample Preparation Method ◽  
Cross Sectional ◽  
Site Specific

Abstract This paper introduces a novel sample preparation method using plasma focused ion-beam (pFIB) milling at low grazing angle. Efficient and high precision preparation of site-specific cross-sectional samples with minimal alternation of device parameters can be achieved with this method. It offers the capability of acquiring a range of electrical characteristic signals from specific sites on the cross-section of devices, including imaging of junctions, Fins in the FinFETs and electrical probing of interconnect metal traces.

Cross-Section Sample Preparation Method for Imaging Dopant Related Anomalies Using Scanning Probe Microscopy Techniques

2014 ◽  
Author(s):  
Swaminathan Subramanian ◽  
Khiem Ly ◽  
Tony Chrastecky
Keyword(s):  
Sample Preparation ◽  
Failure Analysis ◽  
Cross Section ◽  
Scanning Probe Microscopy ◽  
Preparation Method ◽  
Fault Isolation ◽  
Scanning Probe ◽  
Sample Preparation Method ◽  
Probe Microscopy ◽  
Section Sample

Abstract Visualization of dopant related anomalies in integrated circuits is extremely challenging. Cleaving of the die may not be possible in practical failure analysis situations that require extensive electrical fault isolation, where the failing die can be submitted of scanning probe microscopy analysis in various states such as partially depackaged die, backside thinned die, and so on. In advanced technologies, the circuit orientation in the wafer may not align with preferred crystallographic direction for cleaving the silicon or other substrates. In order to overcome these issues, a focused ion beam lift-out based approach for site-specific cross-section sample preparation is developed in this work. A directional mechanical polishing procedure to produce smooth damage-free surface for junction profiling is also implemented. Two failure analysis applications of the sample preparation method to visualize junction anomalies using scanning microwave microscopy are also discussed.

scholarly journals Application of the Dehydration Homogeneous Liquid–Liquid Extraction (DHLLE) Sample Preparation Method for Fingerprinting of Honey Volatiles

Molecules ◽  
2021 ◽  
Vol 26 (8) ◽  
pp. 2277
Author(s):  
Piotr M. Kuś ◽  
Igor Jerković
Keyword(s):  
Carboxylic Acid ◽  
Sample Preparation ◽  
Preparation Method ◽  
Liquid Extraction ◽  
Sample Preparation Method ◽  
Phenyllactic Acid ◽  
Homogeneous Liquid ◽  
Liquid Liquid Extraction ◽  
Wide Range ◽  
Chemical Groups

Recently, we proposed a new sample preparation method involving reduced solvent and sample usage, based on dehydration homogeneous liquid–liquid extraction (DHLLE) for the screening of volatiles and semi-volatiles from honey. In the present research, the method was applied to a wide range of honeys (21 different representative unifloral samples) to determine its suitability for detecting characteristic honey compounds from different chemical classes. GC-FID/MS disclosed 130 compounds from different structural and chemical groups. The DHLLE method allowed the extraction and identification of a wide range of previously reported specific and nonspecific marker compounds belonging to different chemical groups (including monoterpenes, norisoprenoids, benzene derivatives, or nitrogen compounds). For example, DHLLE allowed the detection of cornflower honey chemical markers: 3-oxo-retro-α-ionols, 3,4-dihydro-3-oxoedulan, phenyllactic acid; coffee honey markers: theobromine and caffeine; linden honey markers: 4-isopropenylcyclohexa-1,3-diene-1-carboxylic acid and 4-(2-hydroxy-2-propanyl)cyclohexa-1,3-diene-1-carboxylic acid, as well as furan derivatives from buckwheat honey. The obtained results were comparable with the previously reported data on markers of various honey varieties. Considering the application of much lower volumes of very common reagents, DHLLE may provide economical and ecological advantages as an alternative sample preparation method for routine purposes.

scholarly journals Micro Salting-Out Assisted Matrix Solid-Phase Dispersion: A Simple and Fast Sample Preparation Method for the Analysis of Bisphenol Contaminants in Bee Pollen

Molecules ◽  
2021 ◽  
Vol 26 (8) ◽  
pp. 2350
Author(s):  
Jianing Zhang ◽  
Fengjie Yu ◽  
Yunmin Tao ◽  
Chunping Du ◽  
Wenchao Yang ◽  
...  
Keyword(s):  
Sample Preparation ◽  
Preparation Method ◽  
Solid Phase ◽  
Sample Preparation Method ◽  
Salting Out ◽  
Bee Pollen ◽  
Matrix Solid Phase Dispersion ◽  
Phase Dispersion ◽  
New Strategy ◽  
Semi Solid

In the present work, a novel sample preparation method, micro salting-out assisted matrix solid-phase dispersion (μ-SOA-MSPD), was developed for the determination of bisphenol A (BPA) and bisphenol B (BPB) contaminants in bee pollen. The proposed method was designed to combine two classical sample preparation methodologies, matrix solid-phase dispersion (MSPD) and homogenous liquid-liquid extraction (HLLE), to simplify and speed-up the preparation process. Parameters of μ-SOA-MSPD were systematically investigated, and results indicated the significant effect of salt and ACN-H2O extractant on the signal response of analytes. In addition, excellent clean-up ability in removing matrix components was observed when primary secondary amine (PSA) sorbent was introduced into the blending operation. The developed method was fully validated, and the limits of detection for BPA and BPB were 20 μg/kg and 30 μg/kg, respectively. Average recoveries and precisions were ranged from 83.03% to 94.64% and 1.76% to 5.45%, respectively. This is the first report on the analysis of bisphenol contaminants in bee pollen sample, and also on the combination of MSPD and HLLE. The present method might provide a new strategy for simple and fast sample preparation of solid and semi-solid samples.

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