Genomic surveillance empowers agile responses to SARS-CoV-2 by enabling scientists and public health analysts to issue recommendations aimed at slowing transmission, prioritizing contact tracing, and building a robust genomic sequencing surveillance strategy. Since the start of the pandemic, real time RT-PCR diagnostic testing from upper respiratory specimens, such as nasopharyngeal (NP) swabs, has been the standard.
Moreover, respiratory samples in viral transport media are the ideal specimen for SARS-CoV-2 whole-genome sequencing (WGS). In early 2021, many clinicians transitioned to antigen-based SARS-CoV-2 detection tests, which use anterior nasal swabs for SARS-CoV-2 antigen detection. Despite this shift in testing methods, the need for whole-genome sequence surveillance remains. Thus, we developed a workflow for whole-genome sequencing with antigen test-derived swabs as an input rather than nasopharyngeal swabs. In this study, we use excess clinical specimens processed using the BinaxNOW COVID-19 Ag Card. We demonstrate that whole-genome sequencing from antigen tests is feasible and yields similar results from Rapid antigen test procedure RT-PCR-based assays utilizing a swab in viral transport media.
Diagnostic accuracy of a rapid diagnostic test for the early detection of COVID-19
- This study was undertaken to evaluate the diagnostic performance of the BinaxNOW COVID-19 Ag Card rapid antigen assay (Abbott; Chicago, IL, USA) in the detection of COVID-19 infection compared to the reference standard of PCR testing.
- We evaluated the BinaxNOW COVID-19 Ag Card rapid antigen assay relative to a standard reference PCR test. We tested 3810 nasal swabs from symptomatic and asymptomatic adults undergoing surveillance COVID-19 testing at Howard University using one swab for each nostril. One swab was tested using the rapid antigen assay and the other using the PCR test.
- The sensitivity of the BinaxNOW COVID-19 Ag Card rapid antigen assay was 91.84% (95% confidence interval (CI): 80.40-97.73%) and the specificity was 99.95% (95% CI: 99.81-99.99%). The range of Ct values for the N gene was 10.74-34.90 (M = 26.88, SD=4.86). Fourteen (28.6%) samples had an N gene Ct value > 30. The average N gene Ct value for rapid test negative (i.e. false negative) samples was 31.92.
- The sensitivity of the test in our symptomatic and asymptomatic cohort was lower than the manufacturer’s reported sensitivity in a symptomatic cohort (97.1%). Despite their relatively lower sensitivity (especially in asymptomatic individuals), rapid tests have undeniable benefits (i.e., ease of use and rapid results) that make them a helpful tool in the control of the SARS-CoV-2 pandemic. Given the diagnostic accuracy of these tests as evidenced by this study, rapid tests can be thoughtfully employed in situations where swift results are critical.
Clinical evaluation of the Diagnostic Analyzer for Selective Hybridization (DASH): a point-of-care PCR test for rapid detection of SARS-CoV-2 infection
- Rapid and accurate testing for SARS-CoV-2 is an essential tool in the medical and public health response to the COVID-19 pandemic. An ideal test for COVID-19 would combine the sensitivity of laboratory-based PCR combined with the speed and ease of use of point-of-care (POC) or home-based rapid antigen testing.
- To evaluate the performance of the Diagnostic Analyzer for Selective Hybridization (DASH) SARS-CoV-2 POC PCR (sample insertion to result time of 16 minutes), we conducted a cross-sectional study of adults with and without symptoms of COVID-19 at four clinical sites. We collected two bilateral anterior nasal swabs from each participant and information on COVID-19 symptoms, vaccination, and exposure. One swab was tested with the DASH SARS-CoV-2 POC PCR and the second in a central laboratory using Cepheid Xpert Xpress SARS-CoV-2 PCR. We assessed test concordance and calculated sensitivity, specificity, negative and positive predictive values using Xpert as the “gold standard.”
- We enrolled 315 and analyzed 313 participants with median age 42 years; 65% were female, 62% symptomatic, 75% had received ≥2 doses of mRNA COVID-19 vaccine, and 16% currently COVID-19 positive. There were concordant results for 307 tests indicating an overall agreement for DASH of 0.98 [95% CI 0.96, 0.99] compared to Xpert. DASH performed at 0.96 [95% CI 0.86, 1.00] sensitivity and 0.98 [95% CI 0.96, 1.00] specificity, with a positive predictive value of 0.85 [95% CI 0.73, 0.96] and negative predictive value of 0.996 [95% CI 0.99, 1.00]. The six discordant tests between DASH and Xpert all had high Ct values (>30) on the respective positive assay. DASH and Xpert Ct values were highly correlated (R=0.89 [95% CI 0.81, 0.94]).
- DASH POC SARS-CoV-2 PCR was accurate, easy to use, and provided fast results in real-life clinical settings with an overall performance similar to an EUA-approved laboratory-based PCR. Its compact design and ease of use are optimal for a variety of healthcare, and potentially community settings, including areas with lack of access to central laboratory-based PCR testing.
- DASH is an accurate, easy to use, and fast point-of-care test with applications for diagnosis and screening of SARS-CoV-2 infection.
Sensitivity and Specificity of SARS-CoV-2 Rapid Antigen Detection Tests Using Oral, Anterior Nasal, and Nasopharyngeal Swabs: a Diagnostic Accuracy Study
- The objective of our study was to evaluate the sensitivity and specificity of rapid antigen detection tests versus those of reverse transcriptase PCR (RT-PCR) using oral, anterior nasal, and nasopharyngeal swabs.
- The underlying prospective, diagnostic case-control-type accuracy study included 87 hospitalized and nonhospitalized participants in a positive and a negative sample cohort between 16 March and 14 May 2021 in two hospitals in Vienna.
- SARS-CoV-2 infection status was confirmed by RT-PCR. Participants self-performed one oral and one anterior nasal swab for the rapid antigen test, immediately followed by two nasopharyngeal swabs for the rapid antigen test and RT-PCR by the investigator.
- Test results were read after 15 min, and participants completed a questionnaire in the meantime. Test parameters were calculated based on the evaluation of 87 participants. The overall sensitivity of rapid antigen detection tests versus that of RT-PCR with oral, anterior nasal, and nasopharyngeal samples was 18.18% (95% confidence interval [CI] 8.19% to 32.71%), 63.04% (95% CI 47.55% to 76.79%), and 73.33% (95% CI 58.06% to 85.4%), respectively.
- All sampling methods had a test specificity of 100% regardless of the cycle threshold (CT) value. Rapid antigen detection tests using self-collected anterior nasal swabs proved to be as sensitive as and more tolerable than professionally collected nasopharyngeal swabs for CT values up to 30 determined by RT-PCR. This finding illustrates the reliability of tests obtained by adequate self-collected anterior nasal specimen. Sensitivity was dependent upon the CT value for each sampling method. While the main advantage of rapid antigen detection tests is the immediate availability of results, PCR should be preferred in crucial settings wherever possible.
- Rapid antigen detection devices for SARS-CoV-2 represent a valuable tool for monitoring the spread of infection. However, the reliability of the tests depends largely on the test performance and the respective sampling method. Nasopharyngeal swabs mark the gold standard for sample collection in suspected respiratory tract infections but are unsuitable for widespread application, as they must be performed by medically trained personnel.
SARS-CoV-2 Rapid Antigen Test Nasal |
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| 9901-NCOV-03G | Roche Diagnostics | 25 Tests/Kit |
Panbio™ COVID-19 Ag Rapid Test Device (Nasal) |
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| 41FK11 | Abbott | 25 Tests/Kit |
Accu-Tell COVID-19 IgG/IgM Rapid Test |
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| GEN-B352-20tests | Accu test | 20 tests |
Accu-Tell COVID-19 IgG/IgM Rapid Test |
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| GEN-B352-40tests | Accu test | 40 tests |
NOVATest Antigen Rapid Test Kit (For Single Use) (NOVA Test) |
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| nCov-500-01 | Atlas Link Technology | 1T |
CEA (Cancer antigen) ELISA test |
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| 9 | Biobase | 96T/Box |
CA50 (Cancer antigen) ELISA test |
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| 10 | Biobase | 96T/Box |
CA199 (Cancer antigen) ELISA test |
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| 13 | Biobase | 96T/Box |
CA153 (Cancer antigen) ELISA test |
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| 12 | Biobase | 96T/Box |
CA125 (Cancer antigen) ELISA test |
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| 11 | Biobase | 96T/Box |
2019-nCoV IgG/IgM Rapid Test Cassette (Whole Blood/Serum/Plasma) |
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| GEN-402-25tests | All test | 25 tests |
Toc Vial Test (Purgin Method) 3-30Mg/L 25 Test/Box |
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| WAT3672 | Scientific Laboratory Supplies | EACH |
NOVATest Antigen Rapid Kit (NOVA Test) |
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| nCov-500 | Atlas Link Technology | 20 Tests |
PSA (Prostate-specific antigen) ELISA test |
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| 8 | Biobase | 96T/Box |
SARS-CoV-2 Antigen Rapid Test Kit |
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| CoV2Ag-1 | UnScience | 1T |
SARS-CoV-2 Antigen Rapid Test Kit |
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| CoV2Ag-25 | UnScience | 25T/kit |
HBeAg hepatitis B E antigen ELISA test |
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| 79 | Biobase | 96T/Box |
HEV-Ag hepatitis E antigen ELISA test |
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| 94 | Biobase | 96T/Box |
HBsAg hepatitis B surface antigen ELISA test |
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| 77 | Biobase | 96T/Box |
TruStrip RDT Anthrax Protective antigen 83 (PA83) Rapid Test cards, 25/pk |
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| 800-100-RDT-25 | Alpha Diagnostics | 1 pk |
Human Streptococcus Pneumoniae (SP) Antigen Rapid Test Kit |
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| abx092096-20tests | Abbexa | 20 tests |
Avian Influenza Virus Antigen Rapid Test Kit (Colloidal gold) |
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| abx092015-40tests | Abbexa | 40 tests |
Coronavirus (SARS-Cov-2) Antigen Rapid Test Device (Saliva) |
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| IOV87952 | INVBIO | 20T/kit |
Newcastle Disease Virus Antigen Rapid Test Kit (Colloidal gold) |
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| abx092016-40tests | Abbexa | 40 tests |
Human Chlamydia Trachomatis Antigen Rapid Test Kit (Colloidal gold) |
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| abx092049-20tests | Abbexa | 20 tests |
Avian Influenza H5 Virus Antigen Rapid Test Kit (Colloidal gold) |
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| abx092014-40tests | Abbexa | 40 tests |
Avian Influenza H7 Virus Antigen Rapid Test Kit (Colloidal gold) |
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| abx092017-40tests | Abbexa | 40 tests |
Recombinant human RHD antigen |
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| P1958 | FN Test | 100ug |
Rat Cd44(CD44 antigen) ELISA Kit |
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| ER0342 | FN Test | 96T |
Rat CA125(Carbohydrate Antigen 125) ELISA Kit |
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| ER0788 | FN Test | 96T |
Mouse CA125(Carbohydrate Antigen 125) ELISA Kit |
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| EM0887 | FN Test | 96T |
Rat Alcam(CD166 antigen) ELISA Kit |
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| ER0216 | FN Test | 96T |
Human CD48(CD48 antigen) ELISA Kit |
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| EH4332 | FN Test | 96T |
Mouse CD44( CD44 antigen) ELISA Kit |
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| EM0433 | FN Test | 96T |
Human CD44(CD44 antigen) ELISA Kit |
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| EH0654 | FN Test | 96T |
Human CD81(CD81 antigen) ELISA Kit |
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| EH7221 | FN Test | 96T |
Recombinant human Lymphocyte antigen 6K |
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| P2272 | FN Test | 100ug |
Human CD109(CD109 antigen) ELISA Kit |
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| EH1701 | FN Test | 96T |
Human CD177(CD177 antigen) ELISA Kit |
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| EH1752 | FN Test | 96T |
Mouse Alcam(CD166 antigen) ELISA Kit |
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| EM0324 | FN Test | 96T |
Human ALCAM(CD166 antigen) ELISA Kit |
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| EH0001 | FN Test | 96T |
Human CD276(CD276 antigen) ELISA Kit |
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| EH0634 | FN Test | 96T |
Human CA-125(Carbohydrate Antigen 125) ELISA Kit |
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| EH0361 | FN Test | 96T |
HBV-NRAg hepatitis B virus nucleic acid related antigen ELISA test |
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| 84 | Biobase | 96T/Box |
Human MKI67(Antigen KI-67) ELISA Kit |
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| EH0684 | FN Test | 96T |
25 mm Test Tube Foam Rack |
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| MIX1116 | Scientific Laboratory Supplies | EACH |
Human CD5L(CD5 antigen-like) ELISA Kit |
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| EH2229 | FN Test | 96T |
Mouse CD5l( CD5 antigen-like) ELISA Kit |
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| EM0762 | FN Test | 96T |
Human CD52(CAMPATH-1 antigen) ELISA Kit |
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| EH1286 | FN Test | 96T |
Human CEA(Carcinoembryonic Antigen) ELISA Kit |
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| EH0090 | FN Test | 96T |
Recombinant human B-lymphocyte antigen CD19 |
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| P1837 | FN Test | 100ug |
Recombinant human B-lymphocyte antigen CD20 |
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| P2398 | FN Test | 100ug |
Human LY75(Lymphocyte antigen 75) ELISA Kit |
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| EH0299 | FN Test | 96T |
Rat PSA(Prostate Specific Antigen) ELISA Kit |
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| ER1293 | FN Test | 96T |
Rat TPA(Tissue Polypeptide Antigen) ELISA Kit |
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| ER1398 | FN Test | 96T |
Mouse Ly6c1( Lymphocyte antigen 6C1) ELISA Kit |
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| EM0555 | FN Test | 96T |
Human CA50(Carbohydrate Antigen 50) ELISA Kit |
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| EH1396 | FN Test | 96T |
Recombinant human Antigen peptide transporter 1 |
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| P1680 | FN Test | 100ug |
Mouse PSA(Prostate Specific Antigen) ELISA Kit |
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| EM1314 | FN Test | 96T |
Mouse TPA(Tissue Polypeptide Antigen) ELISA Kit |
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| EM1633 | FN Test | 96T |
Human TPA(Tissue Polypeptide Antigen) ELISA Kit |
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| EH3901 | FN Test | 96T |
Recombinant human Melanoma-associated antigen 3 |
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| P1547 | FN Test | 100ug |
Recombinant human Melanoma-associated antigen 2 |
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| P1622 | FN Test | 100ug |
Human HLA-A(Leukocyte Antigen A) ELISA Kit |
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| EH3227 | FN Test | 96T |
Rat Tp53(Cellular tumor antigen p53) ELISA Kit |
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| ER0394 | FN Test | 96T |
Human GPA33(Cell surface A33 antigen) ELISA Kit |
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| EH1535 | FN Test | 96T |
Human PSCA(Prostate stem cell antigen) ELISA Kit |
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| EH2380 | FN Test | 96T |
Human SSA(Sjogren syndrome antigen A) ELISA Kit |
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| EH4256 | FN Test | 96T |
Human CYFRA21-1(Cytokeratin Fragment Antigen 21-1) ELISA Kit |
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| EH0364 | FN Test | 96T |
Human LCA/CD45(Leukocyte Common Antigen) ELISA Kit |
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| EH3290 | FN Test | 96T |
Human SPAG5(sperm associated antigen 5) ELISA Kit |
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| EH4134 | FN Test | 96T |
Human MS4A1(B-lymphocyte antigen CD20) ELISA Kit |
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| EH14877 | FN Test | 96T |
Human CD69(Early activation antigen CD69) ELISA Kit |
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| EH1314 | FN Test | 96T |
Human CD2(T-cell surface antigen CD2) ELISA Kit |
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| EH0466 | FN Test | 96T |
Human SPAG1(Sperm-associated antigen 1) ELISA Kit |
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| EH2525 | FN Test | 96T |
Human fPSA(Free Prostate Specific Antigen) ELISA Kit |
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| EH3082 | FN Test | 96T |
Recombinant human T-lymphocyte activation antigen CD80 |
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| P2350 | FN Test | 100ug |
Rat PCNA(Proliferating Cell Nuclear Antigen) ELISA Kit |
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| ER1234 | FN Test | 96T |
Human CD72(B-cell differentiation antigen) ELISA Kit |
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| EH4178 | FN Test | 96T |
Human HBeAg(hepatitis B virus E Antigen) ELISA Kit |
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| EH4105 | FN Test | 96T |
Test product |
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| testttt | National Diagnostics | 0 |
Human PCNA(Proliferating Cell Nuclear Antigen) ELISA Kit |
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| EH3523 | FN Test | 96T |
Mouse Pcna(Proliferating cell nuclear antigen) ELISA Kit |
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| EM0416 | FN Test | 96T |
Human MAGEC1(Melanoma-associated antigen C1) ELISA Kit |
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| EH1115 | FN Test | 96T |
Human MAGEA3(Melanoma-associated antigen 3) ELISA Kit |
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| EH9915 | FN Test | 96T |
Human TES(Testin) ELISA Kit |
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| EH1738 | FN Test | 96T |
Human EPCA2(Early Prostate Cancer Antigen 2) ELISA Kit |
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| EH1781 | FN Test | 96T |
Mouse CD209a(CD209 antigen-like protein A) ELISA Kit |
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| EM0786 | FN Test | 96T |
COD Test Kit 25 to 1500mg/L |
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| WAT4314 | Scientific Laboratory Supplies | PK25 |
Mouse CD14(Monocyte differentiation antigen CD14) ELISA Kit |
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| EM0039 | FN Test | 96T |
Human HbsAg(hepatitis B virus Surface Antigen) ELISA Kit |
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| EH4002 | FN Test | 96T |
NOVATest IgG/IgM Antibody Rapid Test Kit (NOVA Test) |
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| UNCOV-40 | Atlas Link Technology | 40 Tests |
Human CD80(T-lymphocyte activation antigen CD80) ELISA Kit |
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| EH0088 | FN Test | 96T |
Human CD86(T-lymphocyte activation antigen CD86) ELISA Kit |
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| EH0659 | FN Test | 96T |
Human proPSA(precursor of Prostate Specific Antigen) ELISA Kit |
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| EH3659 | FN Test | 96T |
Human CD34(Hematopoietic progenitor cell antigen CD34) ELISA Kit |
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| EH2020 | FN Test | 96T |
Human SLC3A2(4F2 cell-surface antigen heavy chain) ELISA Kit |
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| EH2042 | FN Test | 96T |
Human CD58(Lymphocyte function-associated antigen 3) ELISA Kit |
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| EH1082 | FN Test | 96T |
Recombinant human Lymphocyte antigen 6 complex locus protein G6d |
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| P1817 | FN Test | 100ug |
Human MNDA(Myeloid cell nuclear differentiation antigen) ELISA Kit |
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| EH1924 | FN Test | 96T |
With the underlying study, the head-to-head test performance and the usability of self-collected samples for SARS-CoV-2 detection using rapid antigen detection devices were evaluated. The results confirm similar sensitivity of self-collected anterior nasal swabs to that of professionally collected nasopharyngeal swabs for patients with a CT of < 30 determined by RT-PCR.