Comparison of SARS-CoV-2 Reverse Transcriptase Polymerase Chain Reaction and BinaxNOW Rapid Antigen Tests at a Community Site During an Omicron Surge : A Cross-Sectional Study

Abstract

Background: SARS-CoV-2 rapid antigen tests are an important public health tool.

Objective: To evaluate field performance of the BinaxNOW rapid antigen test (Abbott) compared with reverse transcriptase polymerase chain reaction (RT-PCR) for detecting infection with the Omicron variant of SARS-CoV-2.

Design: Cross-sectional surveillance study.

Setting: Free, walk-up, outdoor, urban community testing and vaccine site led by Unidos en Salud, serving a predominantly Latinx community highly impacted by COVID-19.

Participants: Persons seeking COVID-19 testing in January 2022.

Measurements: Simultaneous BinaxNOW and RT-PCR from nasal, cheek, and throat swabs, including cycle threshold (Ct) measures; a lower Ct value is a surrogate for higher amounts of virus.

Results: Among 731 persons tested with nasal swabs, there were 296 (40.5%) positive results on RT-PCR; 98.9% were the Omicron variant. BinaxNOW detected 95.2% (95% CI, 91% to 98%) of persons who tested positive on RT-PCR with a Ct value below 30, 82.1% (CI, 77% to 87%) of those who tested positive on RT-PCR with a Ct value below 35, and 65.2% (CI, 60% to 71%) of all who were positive on RT-PCR. Among 75 persons with simultaneous nasal and cheek swabs, BinaxNOW using a cheek swab failed to detect 91% (20 of 22) of specimens that were positive on BinaxNOW with a nasal swab. Among persons with simultaneous nasal and throat swabs who were positive on RT-PCR with a Ct value below 30, 42 of 49 (85.7%) were detected by nasal BinaxNOW, 23 of 49 (46.9%) by throat BinaxNOW, and 44 of 49 (89.8%) by either.

Limitation: Participants were a cross-sectional sample from a community-based sentinel surveillance site, precluding study of viral or symptom dynamics.

Conclusion: BinaxNOW detected persons with high SARS-CoV-2 levels during the Omicron surge, enabling rapid responses to positive test results. Cheek or throat swabs should not replace nasal swabs. As currently recommended, high-risk persons with an initial negative BinaxNOW result should have repeated testing.

Primary funding source: University of California, San Francisco.

Visual Abstract.. SARS-CoV-2 RT-PCR Versus BinaxNOW Rapid Antigen Test During Omicron Surge.

This study compares the performance of the BinaxNOW rapid antigen test versus reverse transcriptase polymerase chain reaction for community-based detection of infection with the Omicron variant of SARS-CoV-2 in San Francisco, California, during January 2022.

Figure 1.. RT-PCR Ct values and BinaxNOW rapid antigen test results among all participants with positive RT-PCR results tested on 3 and 4 January 2022 (A) and stratified according to COVID-19 symptoms (B and C).

Average viral Ct values of all persons with positive RT-PCR and/or BinaxNOW results (n = 296) are plotted in ascending order of Ct value. Each point represents 1 person. Blue circles represent persons whose samples were positive on both BinaxNOW and RT-PCR. Orange diamonds represent persons with positive results on RT-PCR but negative results on BinaxNOW. Ct = cycle threshold; RT-PCR = reverse transcriptase polymerase chain reaction.

Figure 2.. SARS-CoV-2 Ct values by symptom status, days since symptom onset, and vaccination status among persons with positive RT-PCR results tested on 3 and 4 January 2022.

The figure shows RT-PCR Ct values and BinaxNOW rapid antigen test results among symptomatic and asymptomatic participants (A) and stratified by days since symptom onset among symptomatic participants (B) and by vaccination status (completed primary mRNA vaccine series plus booster, completed primary mRNA vaccine series without booster, incomplete mRNA primary vaccine series, no vaccine, and unknown vaccination status or self-reported receipt of non-mRNA vaccine) (C). Each point represents 1 person. Blue circles represent persons whose samples were positive on both BinaxNOW and RT-PCR. Orange diamonds represent persons with positive results on RT-PCR but negative results on BinaxNOW. Box plots show the first quartile, median, and third quartile in the shaded regions. Ct = cycle threshold; RT-PCR = reverse transcriptase polymerase chain reaction.