scholarly journals The Effect of Pooling on the Detection of the Nucleocapsid Protein of SARS-CoV-2 with Rapid Antigen Tests

Diagnostics ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1290
Author(s):  
Tim Berking ◽  
Sabrina Lorenz ◽  
Alexander Ulrich ◽  
Joachim Greiner ◽  
Eric Kervio ◽  
...  
Keyword(s):  
Nucleocapsid Protein ◽  
Large Scale ◽  
Signal To Noise Ratio ◽  
Point Of Care ◽  
Pilot Project ◽  
Individual Case ◽  
Positive Control ◽  
Control Line ◽  
Antigen Tests ◽  
Set Up

The COVID-19 pandemic puts significant stress on the viral testing capabilities of many countries. Rapid point-of-care (PoC) antigen tests are valuable tools but implementing frequent large scale testing is costly. We have developed an inexpensive device for pooling swabs, extracting specimens, and detecting viral antigens with a commercial lateral flow test for the nucleocapsid protein of SARS-CoV-2 as antigen. The holder of the device can be produced locally through 3D printing. The extraction and the elution can be performed with the entire set-up encapsulated in a transparent bag, minimizing the risk of infection for the operator. With 0.35 mL extraction buffer and six swabs, including a positive control swab, 43 ± 6% (n = 8) of the signal for an individual extraction of a positive control standard was obtained. Image analysis still showed a signal-to-noise ratio of approximately 2:1 at 32-fold dilution of the extract from a single positive control swab. The relative signal from the test line versus the control line was found to scale linearly upon dilution (R2 = 0.98), indicating that other pooling regimes are conceivable. A pilot project involving 14 participants and 18 pooled tests in a laboratory course at our university did not give any false positives, and an individual case study confirmed the ability to detect a SARS-CoV-2 infection with five-fold or six-fold pooling, including one swab from a PCR-confirmed COVID patient. These findings suggest that pooling can make frequent testing more affordable for schools, universities, and similar institutions, without decreasing sensitivity to an unacceptable level.

scholarly journals Reducing the Cost of Rapid Antigen Tests through Swab Pooling and Extraction in a Device

2021 ◽  
Author(s):  
Tim Berking ◽  
Sabrina G. Lorenz ◽  
Alexander Ulrich ◽  
Joachim Greiner ◽  
Clemens Richert
Keyword(s):  
Large Scale ◽  
Signal To Noise Ratio ◽  
Point Of Care ◽  
Positive Control ◽  
Extraction Buffer ◽  
Large Scale Testing ◽  
Antigen Tests ◽  
Set Up ◽  
Cost Of Materials ◽  
The Cost

AbstractThe COVID-19 pandemic places a significant stress on the viral testing capabilities of many countries. The value of rapid point-of-care (PoC) antigen tests is becoming increasingly clear, but implementing frequent large scale testing is costly. We have developed an inexpensive device for pooling swabs, extracting specimens, and detecting viral antigens with a commercial lateral flow assay detecting the nucleocapsid protein of SARS-CoV-2 as antigen. The holder of the device can be produced locally through 3D printing. The extraction and the elution can be performed with the entire set-up encapsulated in a transparent bag, minimizing the risk of infection for the operator. With 6 swabs holding approx. 0.1 mL specimen each and 0.35 mL extraction buffer, 43±6 % (n= 8) of the signal for an individual extraction of a positive control standard was obtained. Image analysis still showed a signal-to-noise ratio of ≥ 7 upon further eight-fold dilution. Our current total cost of materials is below $ 2 per tested person or 20% of our cost for an individual PoC test. These findings suggest that pooling can make frequent testing more affordable for schools, universities and other institutions, without decreasing sensitivity to an unacceptable level. Further validation of the method is required.

scholarly journals mslp: a comprehensive pipeline in predicting cancer mutations specific synthetic lethal partners

2021 ◽  
Author(s):  
Chunxuan Shao
Keyword(s):  
Cell Viability ◽  
Cell Lines ◽  
Large Scale ◽  
Signal To Noise Ratio ◽  
Model Organisms ◽  
Lethal Gene ◽  
Synthetic Lethal ◽  
Cancer Mutations ◽  
Set Up ◽  
Context Specific

Background: Mutation specific synthetic lethal partners (SLPs) offer significant insights in identifying novel targets and designing personalized treatments in cancer studies. Large scale genetic screens in cell lines and model organisms provide crucial resources for mining SLPs, yet those experiments are expensive and might be difficult to set up. Various computational methods have been proposed to predict the potential SLPs from different perspectives. However, those efforts are hampered by the low signal-to-noise ratio in simple correlation based approaches, or incomplete reliable training sets in supervised approaches. Results: Here we present mslp, a comprehensive pipeline to identify potential SLPs via integrating genomic and transcriptomic datasets from both patient tumours and cancer cell lines. Leveraging cutting-edges algorithms, we identify a broad spectrum of primary SLPs for mutations presented in patient tumours. Further, for mutations detected in cell lines, we develop the idea of consensus SLPs which are also identified as screen hits, and show consistency impact on cell viability. Applied in real datasets, we successfully identified known synthetic lethal gene pairs. Remarkably, genetic screen results suggested that consensus SLPs have a significant impact on cell viability compared to common hits. Conclusions: Mslp is a powerful and flexible pipeline to identify potential SLPs in a cancer context-specific manner, which might aid in drug developments and precise medicines in cancer treatments. The pipeline is implemented in R and freely available in github.

scholarly journals The sensitivity of SARS-CoV-2 antigen tests in the view of large-scale testing

2020 ◽  
Author(s):  
Pavel Drevinek ◽  
Jakub Hurych ◽  
Zdenek Kepka ◽  
Ales Briksi ◽  
Michal Kulich ◽  
...  
Keyword(s):  
Large Scale ◽  
Point Of Care ◽  
Rapid Test ◽  
Antigen Test ◽  
Repeated Testing ◽  
Diagnostic Pcr ◽  
Large Scale Testing ◽  
Oropharyngeal Swab ◽  
Antigen Tests ◽  
Low Sensitivity

AbstractObjectivesAntigen tests have recently emerged as an interesting alternative to SARS-CoV-2 diagnostic PCR, thought to be valuable especially for the screening of bigger communities. To check appropriateness of the antigen based testing, we determined sensitivity of two point-of-care antigen tests when applied to a cohort of COVID-19 symptomatic, COVID-19 asymptomatic and healthy persons.MethodsWe examined nasopharyngeal swabs with antigen test 1 (Panbio Covid-19 Ag Rapid Test, Abbott) and antigen test 2 (Standard F Covid-19 Ag FIA, SD Biosensor). An additional nasopharyngeal and oropharyngeal swab of the same individual was checked with PCR (Allplex SARS-nCoV-2, Seegene). Within a 4-day period in October 2020, we collected specimens from 591 subjects. Of them, 290 had COVID-19 associated symptoms.ResultsWhile PCR positivity was detected in 223 cases, antigen test 1 and antigen test 2 were found positive in 148 (sensitivity 0.664, 95% CI 0.599 - 0.722) and 141 (sensitivity 0.623, 95% CI 0.558 - 0.684) patients, respectively. When only symptomatic patients were analysed, sensitivity increased to 0.738 (95% CI 0.667 - 0.799) for the antigen test 1 and to 0.685 (95% CI 0.611 - 0.750) for the antigen test 2. The substantial drop in sensitivity to 12.9% (95% CI 0.067 - 0.234) was observed for samples with the PCR threshold cycle above > 30.ConclusionsLow sensitivity of antigen tests leads to the considerable risk of false negativity. It is advisable to implement repeated testing with high enough frequency if the antigen test is used as a frontline screening tool.

scholarly journals Neutralising SARS-CoV-2 RBD-specific antibodies persist for at least six months independently of symptoms in adults

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Angelika Wagner ◽  
Angela Guzek ◽  
Johanna Ruff ◽  
Joanna Jasinska ◽  
Ute Scheikl ◽  
...  
Keyword(s):  
Nucleocapsid Protein ◽  
Large Scale ◽  
Kappa Coefficient ◽  
Receptor Binding Domain ◽  
Neutralising Antibodies ◽  
Specific Antibodies ◽  
Time Points ◽  
Large Scale Testing ◽  
Iga Antibodies ◽  
Set Up

Abstract Background In spring 2020, at the beginning of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Europe, we set up an assay system for large-scale testing of virus-specific and neutralising antibodies including their longevity. Methods We analysed the sera of 1655 adult employees for SARS-CoV-2-specific antibodies using the S1 subunit of the spike protein of SARS-CoV-2. Sera containing S1-reactive antibodies were further evaluated for receptor-binding domain (RBD)- and nucleocapsid protein (NCP)-specific antibodies in relation to the neutralisation test (NT) results at three time points over six months. Results We detect immunoglobulin G (IgG) and/or IgA antibodies reactive to the S1 protein in 10.15% (n = 168) of the participants. In total, 0.97% (n = 16) are positive for S1-IgG, 0.91% (n = 15) were S1-IgG- borderline and 8.28% (n = 137) exhibit only S1-IgA antibodies. Of the 168 S1-reactive sera, 8.33% (n = 14) have detectable RBD-specific antibodies and 6.55% (n = 11) NCP-specific antibodies. The latter correlates with NTs (kappa coefficient = 0.8660) but start to decline after 3 months. RBD-specific antibodies correlate most closely with the NT (kappa = 0.9448) and only these antibodies are stable for up to six months. All participants with virus-neutralising antibodies report symptoms, of which anosmia and/or dysgeusia correlate most closely with the detection of virus-neutralising antibodies. Conclusions RBD-specific antibodies are most reliably detected post-infection, independent of the number/severity of symptoms, and correlate with neutralising antibodies at least for six months. They thus qualify best for large-scale seroepidemiological evaluation of both antibody reactivity and virus neutralisation.

scholarly journals Development and Efficacy of Lateral Flow Point-of-Care Testing Devices for Rapid and Mass COVID-19 Diagnosis by the Detections of SARS-CoV-2 Antigen and Anti-SARS-CoV-2 Antibodies

Diagnostics ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 1760
Author(s):  
Wen-Yeh Hsieh ◽  
Cheng-Han Lin ◽  
Tzu-Ching Lin ◽  
Chao-Hsu Lin ◽  
Hui-Fang Chang ◽  
...  
Keyword(s):  
Large Scale ◽  
Point Of Care ◽  
Standard Procedure ◽  
Surface Enhanced Raman Spectroscopy ◽  
Lateral Flow ◽  
Control Measures ◽  
Nucleic Acid Amplification ◽  
Antibody Detection ◽  
Infection Prevention And Control ◽  
Antigen Tests

The COVID-19 pandemic is an ongoing global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2020–2021. COVID-19 is becoming one of the most fatal pandemics in history and brings a huge challenge to the global healthcare system. Opportune detection, confinement, and early treatment of infected cases present the first step in combating COVID-19. Diagnosis via viral nucleic acid amplification tests (NAATs) is frequently employed and considered the standard procedure. However, with an increasing urge for point-of-care tests, rapid and cheaper immunoassays are widely utilized, such as lateral flow immunoassay (LFIA), which can be used for rapid, early, and large-scale detection of SARS-CoV-2 infection. In this narrative review, the principle and technique of LFIA applied in COVID-19 antigen and antibody detection are introduced. The diagnostic sensitivity and specificity of the commercial LFIA tests are outlined and compared. Generally, LFIA antigen tests for SARS-CoV-2 are less sensitive than viral NAATs, the “gold standard” for clinical COVID-19 diagnosis. However, antigen tests can be used for rapid and mass testing in high-risk congregate housing to quickly identify people with COVID-19, implementing infection prevention and control measures, thus preventing transmission. LFIA anti-SARS-CoV-2 antibody tests, IgM and/or IgG, known as serology tests, are used for identification if a person has previously been exposed to the virus or vaccine immunization. Notably, advanced techniques, such as LFT-based CRISPR-Cas9 and surface-enhanced Raman spectroscopy (SERS), have added new dimensions to the COVID-19 diagnosis and are also discussed in this review.

scholarly journals Considerations for Assessment and Deployment of Rapid Antigen Tests for Diagnosis of COVID-19

2021 ◽  
Author(s):  
Nira R Pollock ◽  
Francesca Lee ◽  
Christine C Ginocchio ◽  
Joseph D Yao ◽  
Romney M Humphries
Keyword(s):  
Test Performance ◽  
Large Scale ◽  
Point Of Care ◽  
Diagnostic Testing ◽  
Molecular Testing ◽  
Successful Implementation ◽  
Protein Antigens ◽  
Operational Characteristics ◽  
Scale Population ◽  
Antigen Tests

Abstract Diagnostic testing is a critical tool to mitigate the SARS-CoV-2 pandemic, but molecular testing capacity remains limited. Rapid diagnostic tests (RDTs) that detect SARS-CoV-2 protein antigens (Ag) offer the potential to substantially expand testing capacity and to allow frequent, large scale population screening. Testing is simple, rapid (results generally available within 15 minutes), and applicable for diagnosis at point of care. However, implementation of Ag RDTs requires a detailed understanding of test performance and operational characteristics in each testing scenario and population being evaluated. Successful implementation of Ag RDTs on a large scale should combine testing with technical oversight and with clinical and public health infrastructure, and will require production at levels much higher than presently possible. In this commentary, we provide detailed considerations for Ag RDT assessment and use cases to encourage and enable broader manufacturing and deployment.

Platelet Anti-Aggregating Activity and Tolerance of Clopidogrel in Atherosclerotic Patients

1996 ◽  
Vol 76 (06) ◽  
pp. 0939-0943 ◽  
Author(s):  
B Boneu ◽  
G Destelle ◽  
Keyword(s):  
Platelet Aggregation ◽  
Large Scale ◽  
Bleeding Time ◽  
Antithrombotic Activity ◽  
Ambulatory Patients ◽  
Patients At Risk ◽  
Set Up ◽  
Ischemic Events ◽  
Large Scale Clinical Trial ◽  
Selection Of

SummaryThe anti-aggregating activity of five rising doses of clopidogrel has been compared to that of ticlopidine in atherosclerotic patients. The aim of this study was to determine the dose of clopidogrel which should be tested in a large scale clinical trial of secondary prevention of ischemic events in patients suffering from vascular manifestations of atherosclerosis [CAPRIE (Clopidogrel vs Aspirin in Patients at Risk of Ischemic Events) trial]. A multicenter study involving 9 haematological laboratories and 29 clinical centers was set up. One hundred and fifty ambulatory patients were randomized into one of the seven following groups: clopidogrel at doses of 10, 25, 50,75 or 100 mg OD, ticlopidine 250 mg BID or placebo. ADP and collagen-induced platelet aggregation tests were performed before starting treatment and after 7 and 28 days. Bleeding time was performed on days 0 and 28. Patients were seen on days 0, 7 and 28 to check the clinical and biological tolerability of the treatment. Clopidogrel exerted a dose-related inhibition of ADP-induced platelet aggregation and bleeding time prolongation. In the presence of ADP (5 \lM) this inhibition ranged between 29% and 44% in comparison to pretreatment values. The bleeding times were prolonged by 1.5 to 1.7 times. These effects were non significantly different from those produced by ticlopidine. The clinical tolerability was good or fair in 97.5% of the patients. No haematological adverse events were recorded. These results allowed the selection of 75 mg once a day to evaluate and compare the antithrombotic activity of clopidogrel to that of aspirin in the CAPRIE trial.

Antibody Screening Results for Anti-Nucleocapsid Antibodies Towards the Development of a SARS-CoV-2 Nucleocapsid Protein Antigen Detecting Lateral Flow Assay

2021 ◽  
Author(s):  
David Cate ◽  
Helen Hsieh ◽  
Veronika Glukhova ◽  
Joshua D Bishop ◽  
H Gleda Hermansky ◽  
...  
Keyword(s):  
Nucleocapsid Protein ◽  
Point Of Care ◽  
Lateral Flow ◽  
Screening Methods ◽  
Antibody Screening ◽  
Liquid Handling ◽  
Large Numbers ◽  
Accurate Performance ◽  
Further Development ◽  
Assay Conditions

<p></p><p>The global COVID-19 pandemic has created an urgent demand for large numbers of inexpensive, accurate, rapid, point-of-care diagnostic tests. Analyte-based assays are suitably inexpensive and can be rapidly mass-produced, but for sufficiently accurate performance they require highly optimized antibodies and assay conditions. We used an automated liquid handling system, customized to handle arrays of lateral flow immunoassay (LFA) tests in a high-throughput screen, to identify anti-nucleocapsid antibodies that will perform optimally in an LFA. We tested 1021 anti-nucleocapsid antibody pairs as LFA capture and detection reagents with the goal of highlighting pairs that have the greatest affinity for unique epitopes of the nucleocapsid protein of SARS-CoV-2 within the LFA format. In contrast to traditional antibody screening methods (e.g., ELISA, bio-layer interferometry), the method described here integrates real-time reaction kinetics with transport in, and immobilization directly onto, nitrocellulose. We have identified several candidate antibody pairs that are suitable for further development of an LFA for SARS-CoV-2.</p><p></p>

MODELING THE SOUTH ATLANTIC OCEAN FROM MEDIUM TO HIGH RESOLUTION

2014 ◽  
Vol 31 (2) ◽  
Author(s):  
Mariela Gabioux ◽  
Vladimir Santos da Costa ◽  
Joao Marcos Azevedo Correia de Souza ◽  
Bruna Faria de Oliveira ◽  
Afonso De Moraes Paiva
Keyword(s):  
High Resolution ◽  
Atlantic Ocean ◽  
Large Scale ◽  
South Atlantic ◽  
Surface Relaxation ◽  
The South ◽  
Small Surface ◽  
Basic Model ◽  
Basic Set ◽  
Set Up

Results of the basic model configuration of the REMO project, a Brazilian approach towards operational oceanography, are discussed. This configuration consists basically of a high-resolution eddy-resolving, 1/12 degree model for the Metarea V, nested in a medium-resolution eddy-permitting, 1/4 degree model of the Atlantic Ocean. These simulations performed with HYCOM model, aim for: a) creating a basic set-up for implementation of assimilation techniques leading to ocean prediction; b) the development of hydrodynamics bases for environmental studies; c) providing boundary conditions for regional domains with increased resolution. The 1/4 degree simulation was able to simulate realistic equatorial and south Atlantic large scale circulation, both the wind-driven and the thermohaline components. The high resolution simulation was able to generate mesoscale and represent well the variability pattern within the Metarea V domain. The BC mean transport values were well represented in the southwestern region (between Vitória-Trinidade sea mount and 29S), in contrast to higher latitudes (higher than 30S) where it was slightly underestimated. Important issues for the simulation of the South Atlantic with high resolution are discussed, like the ideal place for boundaries, improvements in the bathymetric representation and the control of bias SST, by the introducing of a small surface relaxation. In order to make a preliminary assessment of the model behavior when submitted to data assimilation, the Cooper & Haines (1996) method was used to extrapolate SSH anomalies fields to deeper layers every 7 days, with encouraging results.

scholarly journals Vibration characteristics of triple-gear-rotor system in compressed air energy storage under variable torque load

2021 ◽  
Vol 104 (1) ◽  
pp. 003685042098705
Author(s):  
Xinran Wang ◽  
Yangli Zhu ◽  
Wen Li ◽  
Dongxu Hu ◽  
Xuehui Zhang ◽  
...  
Keyword(s):  
Large Scale ◽  
Three Dimensional ◽  
Element Model ◽  
Rotor System ◽  
Dynamic Responses ◽  
System Response ◽  
Rotating Speed ◽  
Torque Load ◽  
Set Up ◽  
Two Stages

This paper focuses on the effects of the off-design operation of CAES on the dynamic characteristics of the triple-gear-rotor system. A finite element model of the system is set up with unbalanced excitations, torque load excitations, and backlash which lead to variations of tooth contact status. An experiment is carried out to verify the accuracy of the mathematical model. The results show that when the system is subjected to large-scale torque load lifting at a high rotating speed, it has two stages of relatively strong periodicity when the torque load is light, and of chaotic when the torque load is heavy, with the transition between the two states being relatively quick and violent. The analysis of the three-dimensional acceleration spectrum and the meshing force shows that the variation in the meshing state and the fluctuation of the meshing force is the basic reasons for the variation in the system response with the torque load. In addition, the three rotors in the triple-gear-rotor system studied show a strong similarity in the meshing states and meshing force fluctuations, which result in the similarity in the dynamic responses of the three rotors.

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