Browse
Submit Data
Databases
API
Help

Dataset Information

22 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Rapid COVID-19 antigenic tests: Usefulness of a modified method for diagnosis.

ABSTRACT: The current reliable recommended test for coronavirus disease 2019 (COVID-19) diagnosis is quantitative reverse-transcription polymerase chain reaction (RT-qPCR). Rapid antigen test devices could be useful as they are less expensive, faster without the need of specialized laboratories to perform the test. We report the performances of two rapid immunochromatographic antigen testing devices compared with RT-qPCR for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection in nasopharyngeal samples. We carried out a lateral-flow tests study on 401 nasopharyngeal swab samples from nonduplicated suspected COVID-19 subjects. An equal volume of universal transport medium tubes-containing samples (dilution ratio = 1:15) were added to the manufacturer's extraction buffer solution (dilution ratio = 1:2) and analyzed on BioSpeedia COVID19Speed-Antigen Test and on Abbott Panbio™ COVID-19 Ag Rapid Test, devices. Qualitative results were compared to those obtained by the RT-qPCR (Allplex™ SARS-CoV-2 Assay Seegene). Based on our data, the overall sensitivity for BioSpeedia and Panbio devices was estimated at 65.5% and 75.0%, respectively. The sensitivity was greater for cycle threshold values less than 25 achieving 90.4 and 96.8 for BioSpeedia and Panbio devices, respectively. A perfect specificity of 100.0% was observed for both devices.

SUBMITTER: Soleimani R

PROVIDER: S-EPMC8242554 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Comparative evaluation of Panbio and SD Biosensor antigen rapid diagnostic tests for COVID-19 diagnosis.

Project description:The aim of our study was to evaluate the diagnostic performance of two antigen rapid diagnostic tests (Ag-RDTs) to diagnose severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We evaluated Panbio and SD-Biosensor Ag-RDTs. We employed 186 polymerase chain reaction (PCR) negative samples to evaluate the specificity and 170 PCR positive samples to assess the sensitivity. We evaluated their sensitivity according to Cycle threshold (C t ) values and days post onset of symptoms (d.p.o.). Tests were compared using the McNemar's test. Agreement was evaluated using the kappa score. Specificity was 100% for Panbio and 97.3% for SD-Biosensor. Sensitivity for samples with C t ≤ 20 was 100% for both assays and for samples with C t = 20-25 was 93.0% (Panbio) and 95.3% (SD-Biosensor) (p = 1.000). Sensitivity decreased for samples wit C t = 25-30 (Panbio: 41.3%, SD-Biosensor: 52.2%, p = 0.125) and samples with C t ≥ 30 (Panbio: 5.0%, SD-Biosensor: 17.5%, p = 0.063). Sensitivity within seven d.p.o. was 87.7% for Panbio and 90.4% for SD-Biosensor and notably decreased after seven d.p.o. Agreement with PCR was excellent for high viral load samples (C t ≤ 25): Panbio, 98.9%, kappa = 0.974; SD-Biosensor, 97.4%, kappa = 0.940. Agreement between Ag-RDTs was excellent (94.9%, kappa = 0.882). Panbio and SD-Biosensor Ag-RDTs showed excellent agreement and diagnostic performance results for samples with high viral loads (C t ≤ 25) or samples within seven d.p.o.

| S-EPMC8242635 | biostudies-literature

Performance of Rapid Antigen Tests for COVID-19 Diagnosis: A Systematic Review and Meta-Analysis.

Project description:The identification of viral RNA using reverse transcription quantitative polymerase chain reaction (RT-qPCR) is the gold standard for identifying an infection caused by SARS-CoV-2. The limitations of RT-qPCR such as requirement of expensive instruments, trained staff and laboratory facilities led to development of rapid antigen tests (RATs). The performance of RATs has been widely evaluated and found to be varied in different settings. The present systematic review aims to evaluate the pooled sensitivity and specificity of the commercially available RATs. This review was registered on PROSPERO (registration number: CRD42021278105). Literature search was performed through PubMed, Embase and Cochrane COVID-19 Study Register to search studies published up to 26 August 2021. The overall pooled sensitivity and specificity of RATs and subgroup analyses were calculated. Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS-2) was used to assess the risk of bias in each study. The overall pooled sensitivity and specificity of RATs were 70% (95% CI: 69-71) and 98% (95% CI: 98-98), respectively. In subgroup analyses, nasal swabs showed the highest sensitivity of 83% (95% CI: 80-86) followed by nasopharyngeal swabs 71% (95% CI: 70-72), throat swabs 69% (95% CI: 63-75) and saliva 68% (95% CI: 59-77). Samples from symptomatic patients showed a higher sensitivity of 82% (95% CI: 82-82) as compared to asymptomatic patients at 68% (95% CI: 65-71), while a cycle threshold (Ct) value ≤25 showed a higher sensitivity of 96% (95% CI: 95-97) as compared to higher Ct value. Although the sensitivity of RATs needs to be enhanced, it may still be a viable option in places where laboratory facilities are lacking for diagnostic purposes in the early phase of disease.

| S-EPMC8774565 | biostudies-literature

COVID-19 diagnosis by routine blood tests using machine learning.

Project description:Physicians taking care of patients with COVID-19 have described different changes in routine blood parameters. However, these changes hinder them from performing COVID-19 diagnoses. We constructed a machine learning model for COVID-19 diagnosis that was based and cross-validated on the routine blood tests of 5333 patients with various bacterial and viral infections, and 160 COVID-19-positive patients. We selected the operational ROC point at a sensitivity of 81.9% and a specificity of 97.9%. The cross-validated AUC was 0.97. The five most useful routine blood parameters for COVID-19 diagnosis according to the feature importance scoring of the XGBoost algorithm were: MCHC, eosinophil count, albumin, INR, and prothrombin activity percentage. t-SNE visualization showed that the blood parameters of the patients with a severe COVID-19 course are more like the parameters of a bacterial than a viral infection. The reported diagnostic accuracy is at least comparable and probably complementary to RT-PCR and chest CT studies. Patients with fever, cough, myalgia, and other symptoms can now have initial routine blood tests assessed by our diagnostic tool. All patients with a positive COVID-19 prediction would then undergo standard RT-PCR studies to confirm the diagnosis. We believe that our results represent a significant contribution to improvements in COVID-19 diagnosis.

| S-EPMC8144373 | biostudies-literature

Scaling up COVID-19 rapid antigen tests: promises and challenges.

Project description:WHO recommends a minimum of 80% sensitivity and 97% specificity for antigen-detection rapid diagnostic tests (Ag-RDTs), which can be used for patients with symptoms consistent with COVID-19. However, after the acute phase when viral load decreases, use of Ag-RDTs might lead to high rates of false negatives, suggesting that the tests should be replaced by a combination of molecular and serological tests. When the likelihood of having COVID-19 is low, such as for asymptomatic individuals in low prevalence settings, for travel, return to schools, workplaces, and mass gatherings, Ag-RDTs with high negative predictive values can be used with confidence to rule out infection. For those who test positive in low prevalence settings, the high false positive rate means that mitigation strategies, such as molecular testing to confirm positive results, are needed. Ag-RDTs, when used appropriately, are promising tools for scaling up testing and ensuring that patient management and public health measures can be implemented without delay.

| S-EPMC7906660 | biostudies-literature

Fluorescence polarization system for rapid COVID-19 diagnosis.

Project description:Prompt diagnosis, patient isolation, and contact tracing are key measures to contain the coronavirus disease 2019 (COVID-19). Molecular tests are the current gold standard for COVID-19 detection, but are carried out at central laboratories, delaying treatment and control decisions. Here we describe a portable assay system for rapid, onsite COVID-19 diagnosis. Termed CODA (CRISPR Optical Detection of Anisotropy), the method combined isothermal nucleic acid amplification, activation of CRISPR/Cas12a, and signal generation in a single assay, eliminating extra manual steps. Importantly, signal detection was based on the ratiometric measurement of fluorescent anisotropy, which allowed CODA to achieve a high signal-to-noise ratio. For point-of-care operation, we built a compact, standalone CODA device integrating optoelectronics, an embedded heater, and a microcontroller for data processing. The developed system completed SARS-CoV-2 RNA detection within 20 min of sample loading; the limit of detection reached 3 copy/μL. When applied to clinical samples (10 confirmed COVID-19 patients; 10 controls), the rapid CODA test accurately classified COVID-19 status, in concordance with gold-standard clinical diagnostics.

| S-EPMC7846465 | biostudies-literature

A retrospective analysis of COVID-19 diagnosis results obtained by rapid antigen tests and RT-PCR: Implications for disease management.

Project description:There is a need for understanding and establishment of the most appropriate testing algorithm for COVID-19 diagnosis in asymptomatic high-risk groups. Here, we present a retrospective analysis of RT-PCR results obtained from 412 cases tested negative for coronavirus disease 2019 (COVID-19) by rapid antigen testing method. Among 178 (43.2%) asymptomatic individuals, 44.9% of the high risk contacts, 12.2% of police custody individuals, 22.22% of the pregnant women and 33.33% of individuals hospitalised for preoperative or other medical conditions showed RT-PCR positivity. Our results suggest a need for focussed and intensive (multi-modality) testing in groups at high risk for SARS-CoV-2 infection.

| S-EPMC8143916 | biostudies-literature

Public health-focused use of COVID-19 rapid antigen and PCR tests.

Project description:During the Covid-19 pandemic, accurate PCR tests were augmented by the cheap, rapid, and logistically convenient, yet less sensitive antigen tests. In Israel, a testing policy shift was implemented due to limited availability of PCR tests during the Omicron surge. Thus, both PCR and antigen tests were used, as this was the only alternative for mass testing and surveillance at the time. Yet, evidence-based surveillance requires a robust understanding of the expected consequences of changing the testing policy. Using 41,065 paired tests performed by trained staff between January and April 2022 in Israel, we estimate how the sensitivity of antigen tests changes as a function of Ct value and other key covariates. The results reveal a logarithmic relationship between antigen detection probability and viral load, as quantified by Ct-values of the PCR tests. Further analysis shows a statistically significant association with an odds ratio of approximately 0.76 with each unit of Ct-value. The analysis suggests that in spite of their compromised sensitivity, antigen tests are a natural solution for routine use, while PCR tests should be considered in situations where a false negative result could have serious consequences. These findings are the foundations of policies that will utilize the strengths of the different tests, and achieve enhanced hybrid surveillance.

| S-EPMC10792091 | biostudies-literature

A Bayesian method for synthesizing multiple diagnostic outcomes of COVID-19 tests.

Project description:The novel coronavirus disease 2019 (COVID-19) has spread worldwide and threatened human life. Diagnosis is crucial to contain the spread of SARS-CoV-2 infections and save lives. Diagnostic tests for COVID-19 have varying sensitivity and specificity, and the false-negative results would have substantial consequences to patient treatment and pandemic control. To detect all suspected infections, multiple testing is widely used. However, it may be challenging to build an assertion when the testing results are inconsistent. Considering the situation where there is more than one diagnostic outcome for each subject, we proposed a Bayesian probabilistic framework based on the sensitivity and specificity of each diagnostic method to synthesize a posterior probability of being infected by SARS-CoV-2. We demonstrated that the synthesized posterior outcome outperformed each individual testing outcome. A user-friendly web application was developed to implement our analytic framework with free access via http://www2.ccrb.cuhk.edu.hk/statgene/COVID_19/. The web application enables the real-time display of the integrated outcome incorporating two or more tests and calculated based on Bayesian posterior probability. A simulation-based assessment demonstrated higher accuracy and precision of the Bayesian probabilistic model compared with a single-test outcome. The online tool developed in this study can assist physicians in making clinical evaluations by effectively integrating multiple COVID-19 tests.

| S-EPMC8441124 | biostudies-literature

Rapid diagnosis of COVID-19 using disposal paper capacitive sensor

Project description:Accurate and rapid detection and isolation become indispensable to restrict the spread of COVID-19. Since the start of COVID-19 pandemic in December 2019, many indisposal diagnostic tools are being developed incessantly. Out of all presently used tools, the gold standard rRT- PCR tool having very high sensitivity and specificity is a time consuming complicated molecular technique having requirements of special expensive equipment. Here, the main focus of this work is to develop rapid disposal paper capacitance sensor having simple and easy detection. We discovered a strong interaction between limonin and Spike-glycoprotein of SARS-COV-2 in comparison to its interaction with other similar viruses such as HCOV-OC43, HCOV-NL63, HCOV-HKU1, Influenza B and A viruses. The antibody free capacitive sensor having comb electrode structure was fabricated on whatman paper with drop coating of limonin (extracted using green method from pomelo seeds) and calibrated with known swab samples. The Blind test with unknown swab samples shows high sensitivity of 91.5% and high specificity of 88.37%. Requiring low sample volume and detection time and using biodegradable materials in the sensor fabrication assure the potential application as a point of care disposal diagnostic tool. Graphical abstract Image 1

| S-EPMC10243487 | biostudies-literature

Clinical usefulness of tomographic standards for COVID-19 pneumonia diagnosis: Experience from a Brazilian reference center.

Project description:BackgroundCOVID-19 is a new disease and the most common complication is pneumonia. The Radiological Society of North America (RSNA) proposed an expert consensus for imaging classification for COVID-19 pneumonia.ObjectiveTo evaluate sensitivity, specificity, accuracy, and reproducibility of chest CT standards in the beginning of the Brazilian COVID-19 outbreak.MethodsCross-sectional study performed from March 1st to April 14th, 2020. Patients with suspected COVID-19 pneumonia submitted to RT-PCR test and chest computed tomography (CT) were included. Two thoracic radiologists blinded for RT-PCR and clinical and laboratory results classified every patient scan according to the RSNA expert consensus. A third thoracic radiologist also evaluated in case of discordance, and consensus was reached among the three radiologists. A typical appearance was considered a positive chest CT for COVID-19 pneumonia. Sensitivity, specificity, positive and negative predictive values were calculated. Cohen's kappa coefficient was used to evaluate intra- and inter-rater agreements.ResultsA total of 159 patients were included (mean age 57.9 ± 18.0 years; 88 [55.3%] males): 86 (54.1%) COVID-19 and 73 (45.9%) non-COVID-19 patients. Eighty (50.3%) patients had a positive CT for COVID-19 pneumonia. Sensitivity and specificity of typical appearance were 88.3% (95%CI, 79.9-93.5) and 94.5% (95%CI, 86.7-97.8), respectively. Intra- and inter-rater agreement were assessed (Cohen's kappa = 0.924, P = 0.06; Cohen's kappa=0.772, P = 0.05, respectively).ConclusionChest CT categorical classification of COVID-19 findings is reproducible and demonstrates high level of agreement with clinical and RT-PCR diagnosis of COVID-19. In RT-PCR scarcity scenarios or in equivocal cases, it may be useful for attending physicians in the evaluation of suspected COVID-19 pneumonia patients attended at the emergency unit.

| S-EPMC7603997 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data