A retrospective analysis of COVID-19 diagnosis results obtained by rapid antigen tests and RT-PCR: Implications for disease management.
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ABSTRACT:
SUBMITTER: Munne K
PROVIDER: S-EPMC8143916 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Background Rapid antigen (RA) tests are being increasingly employed to detect SARS-CoV-2 infections in quarantine and surveillance. Prior research has focused on RT-PCR testing, a single RA test, or generic diagnostic characteristics of RA tests in assessing testing strategies. Methods We have conducted a comparative analysis of the post-quarantine transmission, the effective reproduction number during serial testing, and the false-positive rates for 18 RA tests with emergency use authorization from The United States Food and Drug Administration and an RT-PCR test. To quantify the extent of transmission, we developed an analytical mathematical framework informed by COVID-19 infectiousness, test specificity, and temporal diagnostic sensitivity data. Results We demonstrate that the relative effectiveness of RA tests and RT-PCR testing in reducing post-quarantine transmission depends on the quarantine duration and the turnaround time of testing results. For quarantines of two days or shorter, conducting a RA test on exit from quarantine reduces onward transmission more than a single RT-PCR test (with a 24-h delay) conducted upon exit. Applied to a complementary approach of performing serial testing at a specified frequency paired with isolation of positives, we have shown that RA tests outperform RT-PCR with a 24-h delay. The results from our modeling framework are consistent with quarantine and serial testing data collected from a remote industry setting. Conclusions These RA test-specific results are an important component of the tool set for policy decision-making, and demonstrate that judicious selection of an appropriate RA test can supply a viable alternative to RT-PCR in efforts to control the spread of disease. Plain language summary Previous research on SARS-CoV-2 infection has determined optimal timing for testing in quarantine and the utility of different frequencies of testing for infection surveillance using RT-PCR and generalized rapid antigen tests. However, these strategies can depend on the specific rapid antigen test used. By examining 18 rapid antigen tests, we demonstrate that a single rapid antigen test performs better than RT-PCR when quarantines are two days or less in duration. In the context of infection surveillance, the ability of a rapid antigen test to provide results quickly counteracts its lower sensitivity with potentially more false positives. Our findings indicate that rapid antigen tests can be a suitable alternative to RT-PCR for application in quarantine and infection surveillance. Wells et al. use mathematical modeling to compare quarantine duration, testing frequency, and false-positive rate for 18 rapid antigen (RA) and RT-PCR tests. They show that the relative effectiveness of RA and RT-PCR tests in reducing post-quarantine transmission depends on the quarantine duration, the timing of their use in the infection time course, and the turnaround time of test results.
| S-EPMC9271059 | biostudies-literature
Project description:Background To prevent spread to patients and co-workers, health care workers (HCWs) infected with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) should quickly be identified. Although real time polymerase chain reaction (RT-PCR) is the gold standard, this test takes several hours, during which a HCW is unable to work. Antigen (Ag) tests may be an efficacious means of screening HCWs since they are easy to perform and provide fast results. Methods In this study, 48,010 paired results of Ag-testing and RT-PCR, performed on HCWs between January 2021 and April 2022, were evaluated to determine the diagnostic accuracy of SARS-CoV-2 Ag-tests in diagnosing potentially infectious individuals. This analysis was performed with cycling threshold values (Ct-values) ≤30 and ≤25 as cut-offs. Results Respectively 3.1% (n = 1507) and 0.3% (n = 140) of Ag-tests were positive or indeterminate, and thus indicative for SARS-CoV-2 infection. In total, 2479 (5.2%) RT-PCRs were positive, of which 1529 (61.7%) had a Ct-value ≤25 and 402 (16.2%) a Ct-value between 26 and 30. At Ct-value ≤30 as a cut-off, sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of Ag-tests were 79.0%, 99.8%, 93.8% and 99.1%, respectively. At Ct-value ≤25, sensitivity further improved to 92.0%, by which the NPV increased to 99.7%. Conclusions To prevent transmission from HCWs to patients and co-workers, while maintaining workforce capacity, Ag-tests are a valuable addition to RT-PCR tests, as they have a quick turnaround time and excellent sensitivity for identifying individuals with high potential for transmission.
| S-EPMC9652101 | biostudies-literature
Project description:BackgroundSARS-CoV-2 molecular diagnostics is facing material shortages and long turnaround times due to exponential increase of testing demand.ObjectiveWe evaluated the analytic performance and handling of four rapid Antigen Point of Care Tests (AgPOCTs) I-IV (Distributors: (I) Roche, (II) Abbott, (III) MEDsan and (IV) Siemens).Methods100 RT-PCR negative and 84 RT-PCR positive oropharyngeal swabs were prospectively collected and used to determine performance and accuracy of these AgPOCTs. Handling was evaluated by 10 healthcare workers/users through a questionnaire.ResultsThe median duration from symptom onset to sampling was 6 days (IQR 2-12 days). The overall respective sensitivity were 49.4 % (CI95 %: 38.9-59.9), 44.6 % (CI95 %: 34.3-55.3), 45.8 % (CI95 %: 35.5-56.5) and 54.9 % (CI95 %: 43.4-65.9) for tests I, II, III and IV, respectively. In the high viral load subgroup (containing >106 copies of SARS-CoV-2 /swab, n = 26), AgPOCTs reached sensitivities of 92.3 % or more (range 92.3 %-100 %). Specificity was 100 % for tests I, II (CI95 %: 96.3-100 for both tests) and IV (CI95 %: 96.3-100) and 97 % (CI95 %: 91.5-98.9) for test III. Regarding handling, test I obtained the overall highest scores, while test II was considered to have the most convenient components. Of note, users considered all assays, with the exception of test I, to pose a significant risk for contamination by drips or spills.DiscussionBesides some differences in sensitivity and handling, all four AgPOCTs showed acceptable performance in high viral load samples. However, due to the significantly lower sensitivity compared to RT-qPCR, a careful consideration of pro and cons of AgPOCT has to be taken into account before clinical implementation.
| S-EPMC7927591 | biostudies-literature
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
Project description:BackgroundThe Coronavirus disease 2019 (COVID-19) pandemic continues to spread across the world. Hence, there is an urgent need for rapid, simple, and accurate tests to diagnose severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Performance characteristics of the rapid SARS-CoV-2 antigen detection test should be evaluated and compared with the gold standard real-time reverse transcription-polymerase chain reaction (RT-PCR) test for diagnosis of COVID-19 cases.MethodsThe rapid SARS-CoV-2 antigen detection test, Standard™ Q COVID-19 Ag kit (SD Biosensor®, Republic of Korea), was compared with the real-time RT-PCR test, Allplex™ 2019-nCoV Assay (Seegene®, Korea) for detection of SARS-CoV-2 in respiratory specimens. Four hundred fifty-four respiratory samples (mainly nasopharyngeal and throat swabs) were obtained from COVID-19 suspected cases and contact individuals, including pre-operative patients at Siriraj Hospital, Bangkok, Thailand during March-May 2020.ResultsOf 454 respiratory samples, 60 (13.2%) were positive, and 394 (86.8%) were negative for SARS-CoV-2 RNA by real-time RT-PCR assay. The duration from onset to laboratory test in COVID-19 suspected cases and contact individuals ranged from 0 to 14 days with a median of 3 days. The rapid SARS-CoV-2 antigen detection test's sensitivity and specificity were 98.33% (95% CI, 91.06-99.96%) and 98.73% (95% CI, 97.06-99.59%), respectively. One false negative test result was from a sample with a high real-time RT-PCR cycle threshold (Ct), while five false positive test results were from specimens of pre-operative patients.ConclusionsThe rapid assay for SARS-CoV-2 antigen detection showed comparable sensitivity and specificity with the real-time RT-PCR assay. Thus, there is a potential use of this rapid and simple SARS-CoV-2 antigen detection test as a screening assay.
| S-EPMC7665091 | biostudies-literature
Project description: Not available
| S-EPMC9305720 | biostudies-literature
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
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
Project description:Infection of mouse bone marrow Flts3L-derived dendritic cells (FL-DCs) with chimeric human T cell leukemia virus type 1 (HTLV-1) results in the upregulation as well as selective downregulation of various DC-specific genes.
2010-10-28 | GSE24959 | GEO
Project description:BackgroundThe SARS-CoV-2 pandemic has resulted in massive testing by Rapid Antigen Tests (RAT) without solid independent data regarding clinical performance being available. Thus, decision on purchase of a specific RAT may rely on manufacturer-provided data and limited peer-reviewed data.MethodsThis study consists of two parts. In the retrospective analytical part, 33 RAT from 25 manufacturers were compared to RT-PCR on 100 negative and 204 positive deep oropharyngeal cavity samples divided into four groups based on RT-PCR Cq levels. In the prospective clinical part, nearly 200 individuals positive for SARS-CoV-2 and nearly 200 individuals negative for SARS-CoV-2 by routine RT-PCR testing were retested within 72 h for each of 44 included RAT from 26 manufacturers applying RT-PCR as the reference method.ResultsThe overall analytical sensitivity differed significantly between the 33 included RAT; from 2.5% (95% CI 0.5-4.8) to 42% (95% CI 35-49). All RAT presented analytical specificities of 100%. Likewise, the overall clinical sensitivity varied significantly between the 44 included RAT; from 2.5% (95% CI 0.5-4.8) to 94% (95% CI 91-97). All RAT presented clinical specificities between 98 and 100%.ConclusionThe study presents analytical as well as clinical performance data for 44 commercially available RAT compared to the same RT-PCR test. The study enables identification of individual RAT that has significantly higher sensitivity than other included RAT and may aid decision makers in selecting between the included RAT.FundingThe study was funded by a participant fee for each test and the Danish Regions.
| S-EPMC9173826 | biostudies-literature