scholarly journals High performances of a novel antigen detection test on nasopharyngeal specimens for SARS-CoV-2 infection diagnosis: a prospective study

2020 ◽  
Author(s):  
Laura Courtellemont ◽  
jerome Guinard ◽  
Clemence Guillaume ◽  
Susanna Giache ◽  
Vincent Rzepecki ◽  
...  
Keyword(s):  
Prospective Study ◽  
Large Scale ◽  
Quantitative Polymerase Chain Reaction ◽  
Real Life ◽  
Rapid Test ◽  
Threshold Value ◽  
Public Health Issue ◽  
Nasopharyngeal Swab ◽  
Specificity And Sensitivity ◽  
Asymptomatic Patients

Introduction The SARS-CoV-2 pandemic has become a major public health issue worldwide. Developing and evaluating rapid and easy-to-perform diagnostic tests is an absolute priority. The current prospective study was designed to assess diagnostic performances of an antigen-based rapid detection test (COVID-VIRO) in a real-life setting. Methods Two nasopharyngeal specimens of symptomatic or asymptomatic adult patients hospitalized in the Infectious Diseases Department or voluntarily accessing the COVID-19 Screening Department of the Regional Hospital of Orleans, France, were concurrently collected. COVID VIRO diagnostic specificity and sensitivity were assessed in comparison to real-time reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) results. A subgroup of patients underwent an additional oropharyngeal and/or a saliva swab for rapid testing. Results 121 patients already having a confirmed infection and 127 patients having no evidence of recent or ongoing infection were enrolled, for a total of 248 couple of nasopharyngeal swab specimens. Overall COVID-VIRO sensitivity was 96.7% (IC: 93.5%-99.9%). In asymptomatic patients, patients having symptoms for more than 4 days and those having a RT-qPCR Cycle threshold value >32, sensitivity was of 100%, 95.8% and 96.9% respectively. The concordance between RT-qPCR and COVID VIRO rapid test was 100% for the 127 patients with no SARS-CoV-2 infection. Conclusion COVID-VIRO test had 100% specificity and above 95% sensitivity, better than WHO recommendations (specificity ≥97-100%, sensitivity ≥80%). These rapid tests are particularly interesting for large-scale screening in Emergency Department, low resource settings and airports.

scholarly journals Evaluation of performance of two SARS-CoV-2 Rapid whole-blood finger-stick IgM-IgG Combined Antibody Tests

2020 ◽  
Author(s):  
Thierry Prazuck ◽  
Mathilda Colin ◽  
Susanna Giachè ◽  
Camélia Gubavu ◽  
Aymeric Seve ◽  
...  
Keyword(s):  
Whole Blood ◽  
Real Life ◽  
Rapid Test ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Life Study ◽  
Negative Results ◽  
Specificity And Sensitivity ◽  
Capillary Blood Sample ◽  
Finger Stick

AbstractBackgroundThe SARS-CoV-2 virus is responsible for the infectious respiratory disease called COVID-19 (COronaVIrus Disease). In response to the growing COVID-19 pandemic, Rapid Diagnostic Tests (RDTs) have been developed to detect specific antibodies, IgG and IgM, to SARS-CoV-2 virus in human whole blood. We conducted a real-life study to evaluate the performance of two RDTs, COVID-PRESTO® and COVID-DUO®, compared to the gold standard, RT-PCR.MethodsRT-PCR testing of SARS-Cov-2 was performed from nasopharyngeal swab specimens collected in adult patients visiting the infectious disease department at the hospital (Orléans, France). Fingertip whole blood samples taken at different time points after onset of the disease were tested with RDTs. The specificity and sensitivity of the rapid test kits compared to test of reference (RT-PCR) were calculated.ResultsAmong 381 patients with symptoms of COVID-19 who went to the hospital for a diagnostic, 143 patients were RT-PCR negative. Results of test with RDTs were all negative for these patients, indicating a specificity of 100% for both RDTs.In the RT-PCR positive subgroup (n=238), 133 patients were tested with COVID-PRESTO® and 129 patients were tested with COVID-DUO® (24 patients tested with both). The further the onset of symptoms was from the date of collection, the greater the sensitivity. The sensitivity of COVID-PRESTO® test ranged from 10.00% for patients having experienced their 1st symptoms from 0 to 5 days ago to 100% in patients where symptoms had occurred more than 15 days before the date of tests. For COVID-DUO® test, the sensitivity ranged from 35.71% [0-5 days] to 100% (> 15 days).ConclusionCOVID-PRESTO® and DUO® RDTs turned out to be very specific (none false positive) and to be sensitive enough after 15 days from onset of symptom. These easy to use IgG/IgM combined test kits are the first ones allowing a screening with capillary blood sample, by typing from a finger prick. These rapid tests are particularly interesting for screening in low resource settings.

scholarly journals SARS-CoV-2 in peritoneal swabs from asymptomatic patients undergoing emergency abdominal surgery

2021 ◽  
Vol 2021 (4) ◽  
Author(s):  
Jasim AlAradi ◽  
Rawan A Rahman AlHarmi ◽  
Mariam AlKooheji ◽  
Sayed Ali Almahari ◽  
Mohamed Abdulla Isa ◽  
...  
Keyword(s):  
Peritoneal Fluid ◽  
Case Series ◽  
Rapid Test ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Protective Measures ◽  
The Public ◽  
Asymptomatic Patients ◽  
Number Of Patients ◽  
Viral Transfer

Abstract This is a case series of five patients with acute abdomen requiring surgery who tested positive for coronavirus disease 2019 (COVID-19) and were asymptomatic, with the purpose of detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in peritoneal fluid. Nasopharyngeal swab was done as a prerequisite for admission or prior to admission as part of random testing. Two methods of viral testing were employed: Xpert® Xpress SARS-CoV-2 (rapid test) and real-time reverse transcription polymerase chain reaction (RT-PCR). Either or both tests were done, with the former performed for patients requiring surgery immediately. Surgery was performed within 24–36 h from admission. Peritoneal fluid swabs were obtained for the detection of SARS-CoV-2 using RT-PCR test. Swabs were immediately placed in viral transfer media and delivered to the public health laboratory in an ice bag. SARS-CoV-2 was not detected in peritoneal swabs. Due to the limited number of patients, further studies are required; yet, protective measures should still be taken by surgeons when dealing with COVID-19 cases.

scholarly journals SARS-CoV-2 show no infectivity at later stages in a prolonged COVID-19 patient despite positivity in RNA testing

2021 ◽  
Author(s):  
Xiu-Feng Wan ◽  
Cynthia Y Tang ◽  
Detlef Ritter ◽  
Yang Wang ◽  
Tao Li ◽  
...  
Keyword(s):  
Large Scale ◽  
Disease Onset ◽  
Nasopharyngeal Swab ◽  
Rt Pcr ◽  
Virus Growth ◽  
Chain Reactions ◽  
Polymerase Chain Reactions ◽  
Asymptomatic Patients ◽  
Hospitalization Period ◽  
Polymerase Chain

Inpatient COVID-19 cases present enormous costs to patients and health systems. Many hospitalized patients may still test COVID-19 positive, even after resolution of symptoms. Thus, a pressing concern for clinicians is the safety of discharging these asymptomatic patients if they have any remaining infectivity. This case report explores the viral viability in a patient with persistent COVID-19 over the course of a two-month hospitalization. Positive nasopharyngeal swab samples, analyzed by quantitative reverse transcription polymerase chain reactions (qRT-PCR), were collected and isolated in the laboratory, and infectious doses were analyzed throughout the hospitalization period. The patient experienced waning symptoms by hospital day 40 and had no viable virus growth in the laboratory by hospital day 41, suggesting no risk of infectivity, despite positive RT-PCR results, which prolonged his hospital stay. Notably, this case showed infectivity for at least 24 days from disease onset, which is longer than the discontinuation of transmission-based precautions recommendation by CDC. Thus, our findings suggest that the timeline for discontinuing transmission-based precautions may need to be extended for patients with prolonged illness. Additional large-scale studies are needed to draw definitive conclusions on the appropriate clinical management for these patients.

scholarly journals Performance of antigen testing for diagnosis of COVID-19: a direct comparison of a lateral flow device to nucleic acid amplification based tests

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Maria Kahn ◽  
Lukas Schuierer ◽  
Christina Bartenschlager ◽  
Stephan Zellmer ◽  
Ramona Frey ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Real Life ◽  
Lateral Flow ◽  
Nucleic Acid Amplification ◽  
University Hospital ◽  
Nasopharyngeal Swab ◽  
Screening Programs ◽  
Asymptomatic Patients ◽  
Antigen Tests ◽  
Antigen Testing

Abstract Objectives The gold standard for diagnosing an infection with SARS-CoV-2 is detection of viral RNA by nucleic acid amplification techniques. Test capacities, however, are limited. Therefore, numerous easy-to-use rapid antigen tests based on lateral flow technology have been developed. Manufacturer-reported performance data seem convincing, but real-world data are missing. Methods We retrospectively analysed all prospectively collected antigen tests results performed between 23.06.2020 and 26.11.2020, generated by non-laboratory personnel at the point-of-care from oro- or nasopharyngeal swab samples at the University Hospital Augsburg and compared them to concomitantly (within 24 h.) generated results from molecular tests. Results For a total of 3630 antigen tests, 3110 NAAT results were available. Overall, sensitivity, specificity, NPV and PPV of antigen testing were 59.4%, 99.0%, 98.7% and 64.8%, respectively. Sensitivity and PPV were lower in asymptomatic patients (47.6% and 44.4%, respectively) and only slightly higher in patients with clinical symptoms (66.7% and 85.0%, respectively). Some samples with very low Ct-values (minimum Ct 13) were not detected by antigen testing. 31 false positive results occurred. ROC curve analysis showed that reducing the COI cut-off from 1, as suggested by the manufacturer, to 0.9 is optimal, albeit with an AUC of only 0.66. Conclusion In real life, performance of lateral-flow-based antigen tests are well below the manufacturer's specifications, irrespective of patient’s symptoms. Their use for detection of individual patients infected with SARS-CoV2 should be discouraged. This does not preclude their usefulness in large-scale screening programs to reduce transmission events on a population-wide scale.

Konkurrenz zwischen Stieleiche und Buche auf Lothar-Sturmflächen | Competition between pedunculate oak and European beech on Lothar windthrow areas

2009 ◽  
Vol 160 (5) ◽  
pp. 114-123 ◽  
Author(s):  
Daniel Otto ◽  
Sven Wagner ◽  
Peter Brang
Keyword(s):  
Large Scale ◽  
Early Stage ◽  
Tree Height ◽  
European Beech ◽  
Threshold Value ◽  
Test Methods ◽  
Permanent Plots ◽  
Pedunculate Oak ◽  
Competitive Pressure ◽  
Competition Index

The competitive pressure of naturally regenerated European beech (Fagus sylvatica) saplings on planted pedunculate oak (Quercus robur) was investigated on two 1.8 ha permanent plots near Habsburg and Murten (Switzerland). The plots were established with the aim to test methods of artificial oak regeneration after large-scale windthrow. On both plots, 80 oaks exposed to varying levels of competitive pressure from at most 10 neighbouring beech trees were selected. The height of each oak as well as stem and branch diameters were measured. The competitive pressure was assessed using Schütz's competition index, which is based on relative tree height, crown overlap and distance from competing neighbours. Oak trees growing without or with only slight competition from beech were equally tall, while oaks exposed to moderate to strong competition were smaller. A threshold value for the competition index was found above which oak height decreased strongly. The stem and branch diameters of the oaks started to decrease even if the competition from beech was slight, and decreased much further with more competition. The oak stems started to become more slender even with only slight competition from beech. On the moderately acid beech sites studied here, beech grow taller faster than oak. Thus where beech is competing with oak and the aim is to maintain the oak, competitive pressure on the oak must be reduced at an early stage. The degree of the intervention should, however, take the individual competitive interaction into account, with more intervention if the competition is strong.

Methods for the Quantification of Salivary Cortisol and of a-amylase in Biosensors and Portable Devices

2018 ◽  
Vol 68 (12) ◽  
pp. 2857-2859
Author(s):  
Cristina Mihaela Ghiciuc ◽  
Andreea Silvana Szalontay ◽  
Luminita Radulescu ◽  
Sebastian Cozma ◽  
Catalina Elena Lupusoru ◽  
...  
Keyword(s):  
Real Time ◽  
Medical Practice ◽  
Salivary Cortisol ◽  
Clinical Studies ◽  
Large Scale ◽  
Psychological Research ◽  
Portable Devices ◽  
Salivary Amylase ◽  
Specificity And Sensitivity

There is an increasing interest in the analysis of salivary biomarkers for medical practice. The objective of this article was to identify the specificity and sensitivity of quantification methods used in biosensors or portable devices for the determination of salivary cortisol and salivary a-amylase. There are no biosensors and portable devices for salivary amylase and cortisol that are used on a large scale in clinical studies. These devices would be useful in assessing more real-time psychological research in the future.

scholarly journals Neural methods for effective, efficient, and exposure-aware information retrieval

2021 ◽  
Vol 55 (1) ◽  
pp. 1-2
Author(s):  
Bhaskar Mitra
Keyword(s):  
Information Retrieval ◽  
Language Processing ◽  
Large Scale ◽  
Web Search ◽  
Real Life ◽  
Inverted Index ◽  
Information Need ◽  
Product Model ◽  
Performance Improvements ◽  
Deep Model

Neural networks with deep architectures have demonstrated significant performance improvements in computer vision, speech recognition, and natural language processing. The challenges in information retrieval (IR), however, are different from these other application areas. A common form of IR involves ranking of documents---or short passages---in response to keyword-based queries. Effective IR systems must deal with query-document vocabulary mismatch problem, by modeling relationships between different query and document terms and how they indicate relevance. Models should also consider lexical matches when the query contains rare terms---such as a person's name or a product model number---not seen during training, and to avoid retrieving semantically related but irrelevant results. In many real-life IR tasks, the retrieval involves extremely large collections---such as the document index of a commercial Web search engine---containing billions of documents. Efficient IR methods should take advantage of specialized IR data structures, such as inverted index, to efficiently retrieve from large collections. Given an information need, the IR system also mediates how much exposure an information artifact receives by deciding whether it should be displayed, and where it should be positioned, among other results. Exposure-aware IR systems may optimize for additional objectives, besides relevance, such as parity of exposure for retrieved items and content publishers. In this thesis, we present novel neural architectures and methods motivated by the specific needs and challenges of IR tasks. We ground our contributions with a detailed survey of the growing body of neural IR literature [Mitra and Craswell, 2018]. Our key contribution towards improving the effectiveness of deep ranking models is developing the Duet principle [Mitra et al., 2017] which emphasizes the importance of incorporating evidence based on both patterns of exact term matches and similarities between learned latent representations of query and document. To efficiently retrieve from large collections, we develop a framework to incorporate query term independence [Mitra et al., 2019] into any arbitrary deep model that enables large-scale precomputation and the use of inverted index for fast retrieval. In the context of stochastic ranking, we further develop optimization strategies for exposure-based objectives [Diaz et al., 2020]. Finally, this dissertation also summarizes our contributions towards benchmarking neural IR models in the presence of large training datasets [Craswell et al., 2019] and explores the application of neural methods to other IR tasks, such as query auto-completion.

scholarly journals Retinal microvascular signs in COVID-19

2021 ◽  
pp. bjophthalmol-2020-318236
Author(s):  
Ralene Sim ◽  
Gemmy Cheung ◽  
Daniel Ting ◽  
Edmund Wong ◽  
Tien Yin Wong ◽  
...  
Keyword(s):  
Medical History ◽  
Vital Signs ◽  
Plexiform Layer ◽  
Nasopharyngeal Swab ◽  
Inner Plexiform Layer ◽  
Cross Sectional ◽  
Imaging Device ◽  
Asymptomatic Patients ◽  
Significant Difference ◽  
Retinal Microvascular Signs

Background/aimsTo explore if retinal findings are associated with COVID-19 infection.MethodsIn this prospective cross-sectional study, we recruited participants positive for COVID-19 by nasopharyngeal swab, with no medical history. Subjects underwent retinal imaging with an automated imaging device (3D OCT-1 Maestro, Topcon, Tokyo, Japan) to obtain colour fundus photographs (CFP) and optical coherence tomographic (OCT) scans of the macula. Data on personal biodata, medical history and vital signs were collected from electronic medical records.Results108 patients were recruited. Mean age was 36.0±5.4 years. 41 (38.0%) had symptoms of acute respiratory infection (ARI) at presentation. Of 216 eyes, 25 (11.6%) had retinal signs—eight (3.7%) with microhaemorrhages, six (2.8%) with retinal vascular tortuosity and two (0.93%) with cotton wool spots (CWS). 11 eyes (5.1%) had hyper-reflective plaques in the ganglion cell-inner plexiform layer layer on OCT, of which two also had retinal signs visible on CFP (CWS and microhaemorrhage, respectively). There was no significant difference in the prevalence of retinal signs in symptomatic versus asymptomatic patients (12 (15.0%) vs 13 (9.6%), p=0.227). Patients with retinal signs were significantly more likely to have transiently elevated blood pressure than those without (p=0.03).ConclusionOne in nine had retinal microvascular signs on ocular imaging. These signs were observed even in asymptomatic patients with normal vital signs. These retinal microvascular signs may be related to underlying cardiovascular and thrombotic alternations associated with COVID-19 infection.

scholarly journals Multi-GPU approach to global induction of classification trees for large-scale data mining

2021 ◽  
Author(s):  
Krzysztof Jurczuk ◽  
Marcin Czajkowski ◽  
Marek Kretowski
Keyword(s):  
Data Mining ◽  
Large Scale ◽  
Real Life ◽  
Population Based ◽  
Tree Structure ◽  
Global Approach ◽  
Data Parallel ◽  
Large Scale Data ◽  
The Impact ◽  
Scale Data

AbstractThis paper concerns the evolutionary induction of decision trees (DT) for large-scale data. Such a global approach is one of the alternatives to the top-down inducers. It searches for the tree structure and tests simultaneously and thus gives improvements in the prediction and size of resulting classifiers in many situations. However, it is the population-based and iterative approach that can be too computationally demanding to apply for big data mining directly. The paper demonstrates that this barrier can be overcome by smart distributed/parallel processing. Moreover, we ask the question whether the global approach can truly compete with the greedy systems for large-scale data. For this purpose, we propose a novel multi-GPU approach. It incorporates the knowledge of global DT induction and evolutionary algorithm parallelization together with efficient utilization of memory and computing GPU’s resources. The searches for the tree structure and tests are performed simultaneously on a CPU, while the fitness calculations are delegated to GPUs. Data-parallel decomposition strategy and CUDA framework are applied. Experimental validation is performed on both artificial and real-life datasets. In both cases, the obtained acceleration is very satisfactory. The solution is able to process even billions of instances in a few hours on a single workstation equipped with 4 GPUs. The impact of data characteristics (size and dimension) on convergence and speedup of the evolutionary search is also shown. When the number of GPUs grows, nearly linear scalability is observed what suggests that data size boundaries for evolutionary DT mining are fading.

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