Evaluation of Rapid Antigen Tests Using Nasal Samples to Diagnose SARS-CoV-2 in Symptomatic Patients

IntroductionThe best way to mitigate an outbreak besides mass vaccination is via early detection and isolation of infected cases. As such, a rapid, cost-effective test for the early detection of COVID-19 is required.MethodsThe study included 4,183 mildly symptomatic patients. A nasal and nasopharyngeal sample obtained from each patient was analyzed to determine the diagnostic ability of the rapid antigen detection test (RADT, nasal swab) in comparison with the current gold-standard (RT-PCR, nasopharyngeal swab).ResultsThe calculated sensitivity and specificity of the RADT was 82.1 and 99.1%, respectively. Kappa's coefficient of agreement between the RADT and RT-PCR was 0.859 (p < 0.001). Stratified analysis showed that the sensitivity of the RADT improved significantly when lowering the cut-off RT-PCR Ct value to 24.ConclusionOur study's results support the potential use of nasal swab RADT as a screening tool in mildly symptomatic patients, especially in patients with higher viral loads.

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Reducing COVID-19 quarantine with SARS-CoV-2 testing: a simulation study

BMJ Open ◽

10.1136/bmjopen-2021-050473 ◽

2021 ◽

Vol 11 (7) ◽

pp. e050473

Author(s):

Bo Peng ◽

Wen Zhou ◽

Rowland W Pettit ◽

Patrick Yu ◽

Peter G Matos ◽

...

Keyword(s):

Optimal Strategies ◽

Cost Effective ◽

Transmission Risk ◽

Sensitivity Analyses ◽

Rt Pcr ◽

Viral Loads ◽

Reverse Transcription Pcr ◽

Highly Sensitive ◽

Antigen Tests ◽

The Impact

ObjectiveTo evaluate the effectiveness of SARS-CoV-2 testing on shortening the duration of quarantines for COVID-19 and to identify the most effective choices of testing schedules.DesignWe performed extensive simulations to evaluate the performance of quarantine strategies when one or more SARS-CoV-2 tests were administered during the quarantine. Simulations were based on statistical models for the transmissibility and viral loads of SARS-CoV-2 infections and the sensitivities of available testing methods. Sensitivity analyses were performed to evaluate the impact of perturbations in model assumptions on the outcomes of optimal strategies.ResultsWe found that SARS-CoV-2 testing can effectively reduce the length of a quarantine without compromising safety. A single reverse transcription-PCR (RT-PCR) test performed before the end of quarantine can reduce quarantine duration to 10 days. Two tests can reduce the duration to 8 days, and three highly sensitive RT-PCR tests can justify a 6-day quarantine. More strategic testing schedules and longer quarantines are needed if tests are administered with less-sensitive RT-PCR tests or antigen tests. Shorter quarantines can be used for applications that tolerate a residual postquarantine transmission risk comparable to a 10-day quarantine.ConclusionsTesting could substantially reduce the length of isolation, reducing the physical and mental stress caused by lengthy quarantines. With increasing capacity and lowered costs of SARS-CoV-2 tests, test-assisted quarantines could be safer and more cost-effective than 14-day quarantines and warrant more widespread use.

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An assessment of a rapid SARS-CoV-2 antigen test in Bangladesh

10.1101/2021.10.05.21264551 ◽

2021 ◽

Author(s):

Zannat Kawser ◽

Mohabbat Hossain ◽

Sara Suliman ◽

Shahin Lockman ◽

Jesse Gitaka ◽

...

Keyword(s):

False Positive ◽

Rapid Test ◽

Field Evaluation ◽

Ease Of Use ◽

Large Field ◽

Antigen Test ◽

Rt Pcr ◽

Rapid Antigen Detection Test ◽

Antigen Tests ◽

Asymptomatic Individuals

Early detection of SARS-CoV-2 infection is crucial to prevent the spread of the virus. In this study, we evaluated the performance of a commercial rapid antigen detection test, BD Veritor, and compared this (and another rapid test, Standard Q) against a gold-standard of nasopharyngeal (NP) swab tested by reverse transcription-polymerase chain reaction (RT-PCR) in prospectively recruited adults in Dhaka, Bangladesh. We compared the sensitivity and specificity of the two rapid antigen tests against RT-PCR results in 130 symptomatic and 130 asymptomatic adults. In addition, we evaluated the suitability and ease-of-use of the BD Veritor test in a subsample of study participants (n=42) and implementers (n=5). The sensitivity of the BD Veritor rapid antigen 66 test was 70% in symptomatic (95% confidence interval [CI]: 51-85%) and 87% (95% CI: 69-96%) in asymptomatic individuals with positive SARSCoV-2 RT-PCR, for overall sensitivity of 78% (95% CI: 66-88%). The sensitivity of the Standard Q rapid antigen test was 63% (95% CI: 44-69 80%) in symptomatic and 73% (95% CI: 54-87%) in asymptomatic individuals. One false positive in BD Veritor test (specificity 99.5) and no false positive in Standard Q tests were observed (specificity 100%). The BD Veritor rapid antigen test was 78% sensitive when compared with RT-PCR irrespective of the cycle threshold (Ct) levels in this evaluation in Bangladesh. The implementation evaluation data showed good acceptability in the field settings. This warrants large field evaluation as well as use of the rapid antigen test for quick assessment of SARS-CoV-2 for containment of epidemics in the country.

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Evaluation of rapid SARS-CoV-2 antigen tests, AFIAS COVID-19 Ag and ichroma COVID-19 Ag, with serial nasopharyngeal specimens from COVID-19 patients

PLoS ONE ◽

10.1371/journal.pone.0249972 ◽

2021 ◽

Vol 16 (4) ◽

pp. e0249972

Author(s):

Oh Joo Kweon ◽

Yong Kwan Lim ◽

Hye Ryoun Kim ◽

Yoojeong Choi ◽

Min-Chul Kim ◽

...

Keyword(s):

Early Detection ◽

Point Of Care ◽

Molecular Testing ◽

Test Results ◽

Molecular Test ◽

Viral Loads ◽

Molecular Tests ◽

Antigen Tests ◽

Diagnostic Sensitivity And Specificity ◽

Negative Controls

We evaluated the diagnostic accuracy of two newly developed, point-of-care, rapid antigen tests (RATs) for detecting SARS-CoV-2, the AFIAS COVID-19 Ag and the ichromaTM COVID-19 Ag, and investigated antigen kinetics. A total of 200 serially collected nasopharyngeal (NP) specimens from 38 COVID-19 patients and 122 specimens from negative controls were analyzed. Diagnostic sensitivity and specificity were assessed in comparison to molecular test results and subdivided according to targeted genes (E, RdRP, and N) and days post-symptom onset (PSO). For the kinetics evaluation, cut-off-indices from serial NP specimens were used according to the number of days PSO. Both RATs showed sensitivity of 91.3‒100% for specimens with cycle threshold (Ct) < 25. The specificity of AFIAS was 98.7‒98.9% and that of ichromaTM was 100.0%. The kappa values of AFIAS and ichromaTM for the molecular testing of specimens with Ct < 25 (RdRP) were 0.97 and 1.00, respectively. The sensitivity of AFIAS and ichromaTM for all genes was lower for specimens collected at 8‒14 PSO than for those collected before 7-days PSO. The kinetics profiles showed that antigen levels gradually decreased from ≤ 7-days PSO to > 22-days PSO. Both RATs showed excellent specificity and acceptable sensitivity for NP specimens with higher viral loads and for specimens collected within 7-days PSO. Hence, they have the potential to become useful tools for the early detection of SARS-CoV-2. However, because of concerns about false negativity, RATs should be used in conjunction with molecular tests.

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Optimal test-assisted quarantine strategies for COVID-19

10.1101/2020.11.06.20222398 ◽

2020 ◽

Author(s):

Bo Peng ◽

Wen Zhou ◽

Rowland W. Pettit ◽

Patrick Yu ◽

Peter G. Matos ◽

...

Keyword(s):

Herd Immunity ◽

Optimal Strategies ◽

Cost Effective ◽

Sensitivity Analyses ◽

Rt Pcr ◽

Optimal Test ◽

Viral Loads ◽

Lost Productivity ◽

The Impact ◽

Pcr Test

AbstractBackgroundUntil herd immunity occurs for COVID-19, quarantine will remain a pillar for disease mitigation. A 14-day quarantine, although widely recommended for self-quarantine after potential infections and mandated by many government agencies can be physically and mentally stressful for those under quarantine and leads to lost productivity. Testing during quarantine is currently implemented by businesses and governments as a promising method to shorten the duration of quarantine. However, to our knowledge, no study has been performed to evaluate the performance of test-assisted quarantines or to identify the most effective choices of testing schedule.MethodsBased on statistical models for the transmissibility and viral loads of SARS-CoV-2 infections and the sensitivities of available SARS-CoV-2 testing methods, we performed extensive simulations to evaluate the performance of quarantine strategies with one or more tests administered during quarantine. Sensitivity analyses were performed to evaluate the impact of perturbations in model assumptions on the determination of optimal strategies.FindingsWe found that SARS-CoV-2 testing can effectively reduce the length of quarantine without compromising personal or public safety. Whereas a single RT-PCR test performed before the end of quarantine can reduce the duration of quarantine to 10 days, two tests can further reduce the duration to 8-days and three tests with a highly sensitive RT-PCR test can justify a 6-day quarantine. More strategic testing schedules and one more day of quarantine are needed if tests are administrated with a less sensitive but more cost-effective antigen test.InterpretationTesting during quarantine could substantially reduce the length of isolation, reducing the physical and mental stress caused by long quarantines. With increasing capacity and lowered costs of SARS-CoV-2 tests, testing-assisted quarantines could be safer and more cost-effective than 14-day quarantines and warrant more widespread use.

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Evaluation of RNA extraction free method for detection of SARS-COV-2 in salivary samples for mass screening for COVID-19

10.1101/2021.03.15.21253570 ◽

2021 ◽

Author(s):

Sally A. Mahmoud ◽

Esra Ibrahim ◽

Subhashini Ganesan ◽

Bhagyashree Thakre ◽

Juliet G Teddy ◽

...

Keyword(s):

Sensitivity And Specificity ◽

Gold Standard ◽

Rna Extraction ◽

High Sensitivity ◽

High Specificity ◽

Cost Effective ◽

Kappa Coefficient ◽

Nasopharyngeal Swab ◽

Rt Pcr ◽

Good Percentage

AbstractIn this current COVID - 19 pandemic, there is a dire need for cost effective and less time-consuming alternatives for SARS-COV-2 testing. The RNA extraction free method for detecting SARS-COV-2 in saliva is a promising option, this study found that it has high sensitivity (85.34%), specificity (95.04%) and was comparable to the gold standard nasopharyngeal swab. The method showed good percentage of agreement (kappa coefficient) 0.797 between salivary and NPS samples. However, there are variations in the sensitivity and specificity based on the RT-PCR kit used. The Thermo Fischer-Applied biosystems showed high sensitivity, PPV and NPV but also showed higher percentage of invalid reports. Whereas the BGI kit showed high specificity, better agreement (kappa coefficient) between the results of saliva and NPS samples and higher correlation between the Ct values of saliva and NPS samples. Thus, the RNA extraction free method for salivary sample serves as an effective alternative for SARS-CoV 2-testing.

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A scalable saliva-based, extraction-free rt-lamp protocol for sars-cov-2 diagnosis

10.1101/2020.10.27.20220541 ◽

2020 ◽

Author(s):

Paula Asprino ◽

Fabiana Bettoni ◽

Anamaria Camargo ◽

Diego Coelho ◽

Guilherme Coppini ◽

...

Keyword(s):

Rna Extraction ◽

Cost Effective ◽

Turnaround Time ◽

Curve Analysis ◽

Nasopharyngeal Swab ◽

Screening Methods ◽

Rt Pcr ◽

Effective Screening ◽

Point Curve ◽

Average Turnaround Time

I.ABSTRACTScalable, cost-effective screening methods are an essential tool to control SARS-CoV-2 spread. We have developed a straight saliva-based, RNA extraction-free, RT-LAMP test that is comparable to current nasopharyngeal swab RT-PCR tests in both sensitivity and specificity. Using a 2-step readout of fluorescence and melting-point curve analysis, the test is scalable to more than 30,000 tests per day with average turnaround time of less than 3 hours. The test was validated using samples from 244 symptomatic patients, and showed sensitivity of 78.9% (vs. 85.5% for nasopharyngeal swabs RT-PCR) and specificity of 100% (vs. 100% for nasopharyngeal swabs RT-PCR). Our method is therefore accurate, robust, time and cost effective and therefore can be used for screening of SARS-CoV-2.

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ImplemeNting SARS-CoV-2 Rapid antigen testing in the Emergency wArd of a Swiss univErsity hospital: the INCREASE study

10.1101/2021.02.10.21250915 ◽

2021 ◽

Author(s):

Giorgia Caruana ◽

Antony Croxatto ◽

Eleftheria Kampouri ◽

Antonios Kritikos ◽

Onya Opota ◽

...

Keyword(s):

University Hospital ◽

Lower Sensitivity ◽

Clinical Settings ◽

Rt Pcr ◽

Emergency Ward ◽

Viral Loads ◽

Molecular Tests ◽

One Step ◽

Antigen Tests ◽

Second Wave

BackgroundWhile facing a second wave in SARS-CoV-2 pandemic, in November 2020 the Swiss Federal Office of Public Health (FOPH) authorized the use of rapid antigen tests (RATs) in addition to the gold-standard reverse transcription-polymerase chain reaction (RT-PCR).MethodsWe implemented the use of RAT in the emergency ward of our university hospital for rapid patients’ triaging and compared performances of four different antigen tests. All results were compared to SARS-CoV-2 specific RT-PCR (reference standard).ResultsTriaging patients using RAT in association with RT-PCR allowed us to isolate promptly positive patients and to save resources, in a context of rapid RT-PCR reagents shortage. Among 532 patients with valid results, overall sensitivities were 48.3% for One Step Exdia and 41.2% for Standard Q®, Panbio−and BD Veritor. All four antigen tests exhibited specificity above 99%. Sensitivity increased up to 74.6%, 66.2%, 66.2% and 64.8% for One Step Exdia, Standard Q, Panbio, and BD Veritor respectively, when considering viral loads above 105copies/ml, up to 100%, 97.8%, 96.6% and 95.6% for viral loads above 106 copies/ml and 100% (for all tests) when considering viral loads above 107 copies/ml. Sensitivity was significantly higher for patients presenting with symptoms onset within 4 days (74.3%, 69.2%, 69.2% and 64%, respectively) versus patients with evolution of symptoms for more than 4 days (36.8%, 21.1%, 21.1% and 23.7%, respectively). Sensitivities of all RAT assays were of only 33% among hospitalized patients without COVID-19 symptoms.ConclusionRAT might represent a useful epidemiological resource in selected clinical settings as a complementary tool to the molecular tests for rapid patients triaging, but the lower sensitivity compared to RT-PCR, especially in late presenters and subjects without COVID-19 symptoms, must be taken into account in order to correctly use RAT for triaging.

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Sensitive detection and quantification of SARS-CoV-2 in saliva

10.1101/2020.12.04.20241059 ◽

2020 ◽

Author(s):

Mustafa Fatih Abasiyanik ◽

Blake Flood ◽

Jing Lin ◽

Sefika Ozcan ◽

Sherin J Rouhani ◽

...

Keyword(s):

Nasal Swab ◽

Digital Pcr ◽

Rt Pcr ◽

Community Screening ◽

Viral Loads ◽

Reverse Transcription Pcr ◽

Testing Facility ◽

Wide Range ◽

Nasal Swabs ◽

Higher Sensitivity

AbstractSaliva has significant advantages as a test medium for detection of SARS-CoV-2 infection in patients, such as ease of collection, minimal requirement of supplies and trained personnel, and safety. Comprehensive validation in a large cohort of prospectively collected specimens with unknown SARS-CoV-2 status should be performed to evaluate the potential and limitations of saliva-based testing. We developed a saliva-based testing pipeline for detection of SARS-CoV-2 nucleic acids using real-time reverse transcription PCR (RT-PCR) and droplet digital PCR (ddPCR) readouts, and measured samples from 137 outpatients tested at a curbside testing facility and 29 inpatients hospitalized for COVID-19. These measurements were compared to the nasal swab results for each patient performed by a certified microbiology laboratory. We found that our saliva testing positively detects 100% (RT-PCR) and 93.75% (ddPCR) of curbside patients that were identified as SARS-CoV-2 positive by the Emergency Use Authorization (EUA) certified nasal swab testing assay. Quantification of viral loads by ddPCR revealed an extremely wide range, with 1 million-fold difference between individual patients. Our results demonstrate for both community screening and hospital settings that saliva testing reliability is on par with that of the nasal swabs in detecting infected cases, and has potential for higher sensitivity when combined with ddPCR in detecting low-abundance viral loads that evade traditional testing methods.

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Time scale performance of rapid antigen testing for SARS-COV-2: evaluation of ten rapid antigen assays

10.1101/2021.05.27.21257868 ◽

2021 ◽

Author(s):

Zakarya Abusrewil ◽

Inas M Alhudiri ◽

Hamza Kaal ◽

Salah Edin El Meshri ◽

Fawzi O Ebrahim ◽

...

Keyword(s):

Sensitivity And Specificity ◽

Symptom Onset ◽

False Negative ◽

Rapid Test ◽

High Sensitivity ◽

Molecular Diagnostic ◽

Nasopharyngeal Swab ◽

Viral Loads ◽

Biotechnology Research ◽

Antigen Tests

Background: There is a great demand for more rapid tests for SARS-COV-2 detection to reduce waiting time, boost public health strategies for combating disease, decrease costs, and prevent overwhelming laboratory capacities. This study was conducted to assess the performance of 10 antigen-based rapid assays for the detection of SARS-CoV-2 in nasopharyngeal swab specimens. Methods: We analyzed 231 nasopharyngeal samples collected from October 2020-December 2020, from suspected COVID-19 cases and contacts of positive cases at Biotechnology Research Center laboratories, Tripoli, Libya. The performance of 10 COVID-19 Ag rapid test devices (Fluorecare, ESPLINE, RapiGen, Abbott Panbio, Flowflex, Acon, Assut Europe, Orient Gene, CerTest, Bioperfectus, AMP) for the detection of SARS-CoV-2 antigen was compared to RT-qPCR. Results: Among the 108 positive samples detected by RT-qPCR, the COVID-19 antigen (Ag) tests detected 83, giving a sensitivity of 76.85% (95% CI, 67.75- 84.43). 161 patients were symptomatic. The median cycle threshold was 25. The mean duration from symptom onset was 6.6 plus/minus 4.3 days. Sensitivity and specificity during the first 6 days of symptoms and in samples with high viral loads ct<25, was 96.4%. No false positives were detected by any of the Ag tests utilized in this study. False negative samples had a median Ct of 34 and average duration of onset of symptoms of 11.3 days (range=5-20). Conclusions: Rapid antigen test diagnosis has high sensitivity and specificity in early disease when patients present less than 7 days of symptom onset. Patients are encouraged to test as soon as they get COVID-19 related symptoms within 1 week and to seek medical advice within 24 hrs. if they develop disturbed smell/taste. The use of rapid antigen tests is important for controlling COVID-19 pandemic and reducing burden on molecular diagnostic laboratories.

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Is the glass half full? Extraction-free RT-LAMP to detect SARS-CoV-2 is less sensitive but highly specific compared to standard RT-PCR in 101 samples

10.1101/2020.12.07.20239558 ◽

2020 ◽

Author(s):

John J. Schellenberg ◽

Margaret Ormond ◽

Yoav Keynan

Keyword(s):

Point Of Care ◽

N Gene ◽

Nasopharyngeal Swab ◽

Lower Sensitivity ◽

Rt Pcr ◽

Public And Private ◽

Viral Loads ◽

Negative Results ◽

Viral Transport Medium ◽

Point Of Care Tests

AbstractThe current scale of public and private testing cannot be expected to meet the emerging need for higher levels of community-level and repeated screening of asymptomatic Canadians for SARS-CoV-2. Rapid point-of-care techniques are increasingly being deployed to fill the gap in screening levels required to identify undiagnosed individuals with high viral loads. However, rapid, point-of-care tests often have lower sensitivity in practice. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) for SARS-CoV-2 has proven sensitive and specific and provides visual results in minutes. Using a commercially available kit for RT-LAMP and primer set targetting nucleocapsid (N) gene, we tested a blinded set of 101 archived nasopharyngeal (NP) swab samples with known RT-PCR results. RT-LAMP reactions were incubated at 65°C for 30 minutes, using heat-inactivated nasopharyngeal swab sample in viral transport medium, diluted tenfold in water, as input. RT-LAMP agreed with all RT-PCR defined negatives (N=51), and all positives with Ct less than 20 (N=24), 65% of positives with Ct between 20-30 (N=17), and no positives with Ct greater than 30 (N=9). RT-LAMP requires fewer and different core components, so may not compete directly with the mainline testing workflow, preserving precious central laboratory resources and gold standard tests for those with the greatest need. Careful messaging must be provided when using less-sensitive tests, so that people are not falsely reassured by negative results – “glass half empty” – in exchange for reliable detection of those with high levels of virus within an hour, using <$10 worth of chemicals – “glass half full”.

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