Diagnostic Performance of an Antigen Test with RT-PCR for the Detection of SARS-CoV-2 in a Hospital Setting — Los Angeles County, California, June–August 2020

Prompt and accurate detection of SARS-CoV-2, the virus that causes COVID-19, has been important during public health responses for containing the spread of COVID-19, including in hospital settings (1–3). In vitro diagnostic nucleic acid amplification tests (NAAT), such as real-time reverse transcription–polymerase chain reaction (RT-PCR) can be expensive, have relatively long turnaround times, and require experienced laboratory personnel.* Antigen detection tests can be rapidly and more easily performed and are less expensive. The performance^† of antigen detection tests, compared with that of NAATs, is an area of interest for the rapid diagnosis of SARS-CoV-2 infection. The Quidel Sofia 2 SARS Antigen Fluorescent Immunoassay (FIA) (Quidel Corporation) received Food and Drug Administration Emergency Use Authorization for use in symptomatic patients within 5 days of symptom onset (4). The reported test positive percentage agreement^§ between this test and an RT-PCR test result is 96.7% (95% confidence interval [CI] = 83.3%–99.4%), and the negative percentage agreement is 100.0% (95% CI = 97.9%–100.0%) in symptomatic patients.^¶ However, performance in asymptomatic persons in a university setting has shown lower sensitivity (5); assessment of performance in a clinical setting is ongoing. Data collected during June 30–August 31, 2020, were analyzed to compare antigen test performance with that of RT-PCR in a hospital setting. Among 1,732 paired samples from asymptomatic patients, the antigen test sensitivity was 60.5%, and specificity was 99.5% when compared with RT-PCR. Among 307 symptomatic persons, sensitivity and specificity were 72.1% and 98.7%, respectively. Health care providers must remain aware of the lower sensitivity of this test among asymptomatic and symptomatic persons and consider confirmatory NAAT testing in high-prevalence settings because a false-negative result might lead to failures in infection control and prevention practices and cause delays in diagnosis, isolation, and treatment.

During a period of high community COVID-19 prevalence,** the Los Angeles County Department of Public Health collaborated with hospital A, a tertiary medical center serving a large urban population in central Los Angeles, to evaluate the performance of the Quidel Sofia 2 SARS Antigen FIA (antigen test) compared with that of the Fulgent COVID-19 RT-PCR (Fulgent Genetics) (RT-PCR test) for screening of all patients admitted to the hospital through the ED during June 30–August 31. Admitting orders included requests for both tests to enable prompt inpatient cohorting. Each admitted patient had two simultaneously collected samples for SARS-CoV2 testing by ED nursing staff members: an anterior nasal swab successively swabbing both nostrils with one swab and a nasopharyngeal swab. Nasopharyngeal swab specimens were processed and sent by courier to a Clinical Laboratory Improvement Amendments–certified laboratory for RT-PCR testing. Results were available 24–48 hours after specimen collection. Test cycle threshold (Ct) values for N1 and N2 nucleocapsid viral gene targets were reported. N1 and N2 targets with Ct values <40 were used to define a positive RT-PCR result, per manufacturer instructions.^†† Because differences between N1 and N2 targets were negligible, for this analysis, N1 target Ct values were used. The anterior nasal swab specimens were processed for antigen testing using calibrated Sofia 2 analyzers in the ED.

The RT-PCR test was used as the standard. Results were considered concordant if they were positive for both tests or negative for both, and discordant if one was positive and the other was negative. Persons were categorized as having COVID-19–compatible symptoms if they had a temperature ≥100.4°F (38°C) at triage, or reported respiratory distress, shortness of breath, cough, flu-like symptoms, nausea, vomiting, diarrhea, or headache. Signs and symptoms (ED chief complaints and vital signs) were categorized into those more commonly reported by COVID-19 patients (6) (i.e., fever, respiratory distress or shortness of breath, and cough) and those less commonly reported (i.e., flu-like symptoms, nausea or vomiting, diarrhea, and headache). Symptoms were retrospectively ascertained through medical record abstraction using the ED triage assessment. Hospital service codes and vital signs were evaluated for patients without an ED chief complaint. Patients who went to a non-ED location (e.g., labor and delivery), might not have an ED chief complaint and were classified as asymptomatic for this analysis. Additional information regarding symptoms was obtained from the hospital’s electronic medical records system for patients with discordant antigen and RT-PCR test results.

Data were managed and analyzed using SAS software (version 9.4; SAS Institute). Sensitivity, specificity, negative predictive value, and positive predictive value were calculated for antigen testing and compared with those of RT-PCR. N1 Ct values for antigen-positive and antigen-negative symptomatic and asymptomatic groups were compared using t-tests; p-values <0.05 were considered statistically significant. Signs and symptoms, demographic characteristics, and underlying medical conditions for the group of patients with discordant results were compared using chi-square or Fisher’s exact tests. Odds ratios were calculated for each of the more common or less common symptoms and overall. This investigation was reviewed by the Los Angeles County Institutional Review Board and CDC and was conducted consistent with applicable federal law and CDC policy.^§§

During June 30–August 31, hospital A tested 2,039 patients admitted through the ED with paired antigen and RT-PCR tests. Median patient age was 56 years (range = 16–107 years); 1,126 (55%) were female, and 913 (45%) were male. The mean test turnaround time for RT-PCR was 28.2 hours. Overall, 307 (15%) patients had COVID-19–compatible symptoms (Table 1). Among the 307 symptomatic patients, 120 (39%) had a positive test result by either test, including 52 (17%) by antigen and 68 (22%) by RT-PCR. Positive test result by both the antigen and the RT-PCR tests were reported for 49 (16%) patients. Mean N1 Ct values were significantly lower among patients with a positive antigen result (mean Ct = 21.3) than among patients with a negative antigen result (mean Ct = 28.5; p<0.001).

Among the 1,732 asymptomatic patients, 139 (8%) had a positive test result by either test (58 [3%] by antigen and 81 [5%] by RT-PCR). Mean N1 Ct values did not differ significantly between samples from patients who were symptomatic (mean Ct = 23.5) and those who were asymptomatic (mean Ct = 23.9). Among asymptomatic and symptomatic patients, the specificity of the antigen test was 99.5% and 98.7%, respectively, and the sensitivity was 60.5% and 72.1%, respectively. The diagnostic performance between the two groups did not differ significantly, with the exception of negative predictive value (p<0.001). Sensitivity of the discordant antigen test results from patients who were symptomatic and asymptomatic was assessed across a range of Ct values. Antigen test sensitivity increased in symptomatic and asymptomatic persons as N1 Ct values decreased (sensitivity 75% for Ct ≤30 and sensitivity 90.7% for Ct ≤25).

RT-PCR–positive and antigen-positive test results were compared with patients’ signs and symptoms at the time of admission. Symptoms associated with a positive RT-PCR test result included fever, respiratory distress or shortness of breath, cough, and flu-like symptoms (Table 2). Shortness of breath was the most commonly reported symptom among persons with a positive RT-PCR test result (28%) and among both discordant groups (RT-PCR–positive/antigen-negative = 39%; RT-PCR–negative/antigen-positive = five of 12 patients) (Table 3). No COVID-19–compatible symptoms occurred in 27 (53%) patients with RT-PCR positive/antigen-negative test results and six of 12 patients with RT-PCR negative/antigen-positive test results. Some patients with RT-PCR–positive/antigen-negative test results had underlying medical conditions recorded in medical records (10% reporting having diabetes and 18% having hypertension) and were at higher risk for severe COVID-19–associated illness.^¶¶

Acknowledgments

Jaime Reyes, CHA Hollywood Presbyterian Medical Center; Sarah Guerry, Paul Simon, Los Angeles County Department of Public Health, California.

Corresponding author: Auguste Brihn, abrihn@ph.lacounty.gov.

¹Epidemic Intelligence Service, CDC; ²Los Angeles County Department of Public Health, California; ³CHA Hollywood Presbyterian Medical Center, California.

References

1. Tang YW, Schmitz JE, Persing DH, Stratton CW. Laboratory diagnosis of COVID-19: current issues and challenges. J Clin Microbiol 2020;58:e00512–20. https://doi.org/10.1128/JCM.00512-20 PMID:32245835
2. Fauci AS, Lane HC, Redfield RR. Covid-19—navigating the uncharted. N Engl J Med 2020;382:1268–9. https://doi.org/10.1056/NEJMe2002387 PMID:32109011
3. Del Rio C, Malani PN. COVID-19—new insights on a rapidly changing epidemic. JAMA 2020;323:1339–40. https://doi.org/10.1001/jama.2020.3072 PMID:32108857
4. Food and Drug Administration. In vitro diagnostics EUAs. Silver Spring, MD: US Department of Health and Human Services, Food and Drug Administration; 2020. https://www.fda.gov/medical-devices/coronavirus-disease-2019-covid-19-emergency-use-authorizations-medical-devices/in-vitro-diagnostics-euas
5. Pray IW, Ford L, Cole D, et al. ; CDC COVID-19 Surge Laboratory Group. Performance of an antigen-based test for asymptomatic and symptomatic SARS-CoV-2 testing at two university campuses—Wisconsin, September–October 2020. MMWR Morb Mortal Wkly Rep 2021;69:1642–7. https://doi.org/10.15585/mmwr.mm695152a3 PMID:33382679
6. Guan WJ, Ni ZY, Hu Y, et al. ; China Medical Treatment Expert Group for Covid-19. Clinical characteristics of coronavirus disease 2019 in China. N Engl J Med 2020;382:1708–20. https://doi.org/10.1056/NEJMoa2002032 PMID:32109013

Abbreviations: CI = confidence interval; RT-PCR = reverse transcription–polymerase chain reaction.
* Quidel Sofia 2 SARS Antigen Fluorescent Immunoassay test characteristics (sensitivity, specificity, positive predictive value, and negative predictive value) were based on comparison with the Fulgent COVID-19 RT-PCR test.
^† Chi-square and Fisher’s exact p-value comparing symptomatic patients with asymptomatic patients.
^§ At hospital A, the Quidel Sofia 2 SARS Antigen Fluorescent Immunoassay was used for qualitative detection of nucleocapsid protein from SARS-CoV-2.

Abbreviations: CI = confidence interval; OR = odds ratio; RT-PCR = reverse transcription–polymerase chain reaction.
* 372 patients (11 RT-PCR–positive and 361 RT-PCR–negative) with missing emergency department chief complaint data were excluded.
^† Among patients with and without symptoms.
^§ Case was defined as symptomatic if patient had a chief complaint of more common or less common COVID-19–compatible signs and symptoms.

Abbreviation: RT-PCR = reverse transcription–polymerase chain reaction.
* False negative = antigen-negative and RT-PCR–positive; false positive = antigen-positive and RT-PCR–negative.
^† 2,039 patients admitted through the emergency department were tested with paired SARS-CoV-2 antigen and RT-PCR tests.
^§ The Fulgent COVID-19 by RT-PCR test, a real-time RT-PCR test intended for the qualitative detection of nucleic acid from SARS-CoV-2 in upper and lower respiratory specimens, was used.
^¶ The Quidel Sofia 2 SARS Antigen Fluorescent Immunoassay was used for qualitative detection of the SARS-CoV-2 nucleocapsid protein.
** No symptoms identified through individual medical chart abstraction.
^†† Ethnicity data were not collected for this analysis.