Non-SARS-CoV-2 respiratory viral detection and whole genome sequencing from COVID-19 rapid antigen test devices
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PROVIDER: PRJEB67729 | ENA |
REPOSITORIES: ENA
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Project description:ObjectivesThere is limited information on the performance of rapid antigen detection (RAD) tests to identify SARS-CoV-2-infected asymptomatic individuals. In this field study, we evaluated the Panbio™ COVID-19 Ag Rapid Test Device (Abbott Diagnostics, Jena, Germany) for this purpose.MethodsA total of 634 individuals (355 female; median age, 37 years; range, 9-87) were enrolled. Two nasopharyngeal swabs were collected from household (n = 338) and non-household contacts (n = 296) of COVID-19 cases. RAD testing was carried out at the point of care. The RT-PCR test used was the TaqPath COVID-19 Combo Kit (Thermo Fisher Scientific, MA, USA).ResultsHousehold contacts were tested at a median of 2 days (range, 1-7) after diagnosis of the index case, whereas non-household contacts (n = 296) were tested at a median of 6 days (range, 1-7) after exposure. In total, 79 individuals (12.4%) tested positive by RT-PCR, of whom 38 (48.1%) yielded positive RAD results. The overall sensitivity and specificity of the RAD test was 48.1% (95% CI 37.4-58.9) and 100% (95% CI 99.3-100), respectively. Sensitivity was higher in household (50.8%; 95% CI 38.9-62.5) than in non-household (35.7%; 95% CI 16.3-61.2%) contacts. Individuals testing positive by RAD test were more likely (p < 0.001) to become symptomatic than their negative counterparts.DiscussionThe Panbio test displays low sensitivity in asymptomatic close contacts of COVID-19 patients, particularly in non-household contacts. Nonetheless, establishing the optimal timing for upper respiratory tract collection in this group seems imperative to pinpoint test sensitivity.
| S-EPMC7833843 | biostudies-literature
Project description:Live, attenuated vaccines generate humoral and cellular immune memory, increasing the duration of protective immune memory. We previously found that antigens derived from vaccination or viral infection persist beyond infection clearance via acquisition and retention (“archiving”) in lymphatic endothelial cells (LECs). Archived antigen maintains an effector-like pool of antigen-specific memory T cells, enhancing clearance of subsequent infections. Technical limitations of fluorescent labeling have precluded a complete picture of antigen archiving across cell types in lymph tissue. We developed a “molecular tracking device” to follow the distribution, acquisition, and retention of antigen in the lymph node. We immunized mice with an antigen conjugated to a nuclease-resistant DNA tag and used single-cell mRNA sequencing to quantify its abundance across major cell types in the lymph node two weeks later, validating its acquisition by migratory dendritic cells and durable retention by LECs and unexpected stromal cell types. Variable antigen levels in LECs enabled the identification and validation of caveolar endocytosis as a mechanism of antigen acquisition. Molecular tracking devices enable new approaches to study dynamic tis-sue dissemination at cellular resolution in vivo. We developed a 'molecular tracking device' to follow the distribution, acquisition, and retention of antigen across cell types in the lymph node. We immunized mice with an antigen conjugated to a nuclease-resistant DNA tag and used single-cell mRNA sequencing to quantify its abundance in immune and stromal cell types two weeks later, validating its retention by LECs and transfer to migratory dendritic cells and defining new reservoirs of archived antigen in stromal cells. Molecular tracking devices broadly enable new approaches to study molecular dissemination and retention in live animals.
2021-04-12 | GSE150719 | GEO
Project description: Not available
| S-EPMC8111145 | biostudies-literature
Project description:OBJECTIVES:In the context of the coronavirus disease 2019 (COVID-19) pandemic, the development and validation of rapid and easy-to-perform diagnostic methods are of high priority. This study was performed to evaluate a novel rapid antigen detection test (RDT) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in respiratory samples. METHODS:The fluorescence immunochromatographic SARS-CoV-2 antigen test (Bioeasy Biotechnology Co., Shenzhen, China) was evaluated using universal transport medium with nasopharyngeal (NP) and oropharyngeal (OP) swabs from suspected COVID-19 cases. Diagnostic accuracy was determined in comparison to SARS-CoV-2 real-time (RT)-PCR. RESULTS:A total of 127 samples were included; 82 were RT-PCR-positive. The median patient age was 38 years, 53.5% were male, and 93.7% were from the first week after symptom onset. Overall sensitivity and specificity were 93.9% (95% confidence interval 86.5-97.4%) and 100% (95% confidence interval 92.1-100%), respectively, with a diagnostic accuracy of 96.1% and Kappa coefficient of 0.9. Sensitivity was significantly higher in samples with high viral loads. CONCLUSIONS:The RDT evaluated in this study showed a high sensitivity and specificity in samples mainly obtained during the first week of symptoms and with high viral loads, despite the use of a non-validated sample material. The assay has the potential to become an important tool for early diagnosis of SARS-CoV-2, particularly in situations with limited access to molecular methods.
| S-EPMC7263236 | biostudies-literature
Project description:Chikungunya fever is a mosquito-borne disease of key public health importance in tropical and subtropical countries. Although severe joint pain is the most distinguishing feature of chikungunya fever, diagnosis remains difficult because the symptoms of chikungunya fever are shared by many pathogens, including dengue fever. The present study aimed to develop a new immunochromatographic diagnosis test for the detection of chikungunya virus antigen in serum. Mice were immunized with isolates from patients with Thai chikungunya fever, East/Central/South African genotype, to produce mouse monoclonal antibodies against chikungunya virus. Using these monoclonal antibodies, a new diagnostic test was developed and evaluated for the detection of chikungunya virus. The newly developed diagnostic test reacted with not only the East/Central/South African genotype but also with the Asian and West African genotypes of chikungunya virus. Testing of sera from patients suspected to have chikungunya fever in Thailand (n = 50), Laos (n = 54), Indonesia (n = 2), and Senegal (n = 6) revealed sensitivity, specificity, and real-time PCR (RT-PCR) agreement values of 89.4%, 94.4%, and 91.1%, respectively. In our study using serial samples, a new diagnostic test showed high agreement with the RT-PCR within the first 5 days after onset. A rapid diagnostic test was developed using mouse monoclonal antibodies that react with chikungunya virus envelope proteins. The diagnostic accuracy of our test is clinically acceptable for chikungunya fever in the acute phase.
| S-EPMC4298496 | biostudies-literature
Project description:Rapid Acceleration of Diagnostics - Radical (RADx-rad): A Rapid Saliva Antigen Test for SARs-CoV-2 Detection
| PRJNA778273 | ENA
Project description:Rapid Acceleration of Diagnostics - Radical (RADx-rad): A Rapid Saliva Antigen Test for SARs-CoV-2 Detection
| PRJNA778274 | ENA
Project description:We evaluated the Panbio™ COVID-19 Ag Rapid Test Device as a point-of-care diagnostic tool for COVID-19 in 357 patients at a pediatric emergency department. Thirty-four patients tested positive by reverse transcription polymerase chain reaction, of which 24 were positive by the antigen assay. The sensitivity and specificity of the assay were 70.5% and 100%, respectively.
| S-EPMC8426967 | biostudies-literature
Project description:Molecular tests are the gold standard to diagnose severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection but are associated with a diagnostic delay, while antigen detection tests can generate results within 20 min even outside a laboratory. In order to evaluate the accuracy and reliability of the FAST COVID-19 SARS-CoV-2 Antigen Rapid Test Kit (Ag-RDT), two respiratory swabs were collected simultaneously from 501 patients, with mild or no coronavirus disease 2019 (COVID-19)-related symptoms, and analyzed with both the Reverse Transcriptase-quantitative Polymerase Chain Reaction (RT-qPCR) and the FAST COVID-19 SARS-CoV-2 Antigen Rapid Test. Results were then compared to determine clinical performance in a screening setting. We measured a precision of 97.41% (95% CI 92.42-99.15%) and a recall of 98.26% (95% CI 93.88-99.25%), with a specificity of 99.22% (95% CI 97.74-99.74%), a negative predictive value of 99.48% (95% CI 97.98-99.87%), and an overall accuracy of 99.00% (95% CI 97.69-99.68%). Concordance was described by a Kappa coefficient of 0.971 (95% CI 0.947-0.996). Considering short lead times, low cost, and opportunities for decentralized testing, the Ag-RDT test can enhance the efforts to control SARS-CoV-2 spread in several settings.
| S-EPMC8947527 | biostudies-literature
Project description:Current methods used for diagnosis of acute infection of pathogens rely on detection of nucleic acids, antigens, or certain classes of antibodies such as IgM. Here we report a virus enzyme assay as an alternative to these methods for detection of acute viral infection. In this method, we used a luciferin derivative as the substrate for detection of the enzyme activity of influenza viral neuraminidase as a means for diagnosis of influenza. The resulting commercial test, the qFLU Dx Test, uses a different supply chain that does not compete with those for the current tests. The assay reagents were formulated as a master mix that accommodated both the neuraminidase and luciferase reactions, thereby enabling rapid and prolonged production of stable light signal in the presence of influenza virus in the sample. The assay was evaluated using depository throat swab specimens. As expected, the assay exhibited similar detection rates for all influenza types and subtypes except for A(H7N9), which exhibited lower detection rate due to lower viral titer in the specimens. When throat swab specimens were diluted with the sample buffer of the test kit and tested with the qFLU Dx Test. The sensitivity and specificity were 82.41% (95% confidence interval: 79.66-85.84%) and 95.39% (95% confidence interval: 94.32-96.46%), respectively, for these diluted specimens in comparison to a real-time polymerase chain reaction assay. The uniqueness of the qFLU Dx Test as an enzymatic assay makes it highly complementary with currently available methods.
| S-EPMC8752744 | biostudies-literature