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Direct Comparison of SARS-CoV-2 Nasal RT- PCR and Rapid Antigen Test (BinaxNOW(TM)) at a Community Testing Site During an Omicron Surge

By John Schrom, Carina Marquez, Genay Pilarowski, Grace Wang, Anthea Mitchell, Robert Puccinelli, Doug Black, Susana Rojas, Salustiano Ribeiro, Jacqueline Martinez, Diane Jones, Robert Nakamura, Vivek Jain, Maya Petersen, Joe DeRisi, Diane Havlir

Posted 10 Jan 2022
medRxiv DOI: 10.1101/2022.01.08.22268954

In 731 persons seeking COVID-19 testing at a walk-up San Francisco community site in January 2022, simultaneous nasal rapid antigen testing (BinaxNOW(TM)) and RT-PCR testing was performed. There were 296 (40.5%) positive tests by RT-PCR; 98.5% of a random sample (N=67) were the omicron variant. Sensitivity of a single antigen test was 95.2% (95% CI 92-98%); 82.1% (95% CI 77-87%) and 65.2% (95% CI 60-71%) for Ct threshold of < 30, < 35 and no threshold, respectively. We also compared BinaxNOW(TM) to RT-PCR from oral cheek swabs to nasal swabs (N=75); oral cheek specimen was significantly less sensitive than nasal swab. A single BinaxNOW(TM) oral cheek rapid antigen test failed to detect 91% (20 of 22) of specimens that were BinaxNOW(TM) positive from the standard nasal sampling. In a separate direct comparison of BinaxNOW(TM) between specimens collected from nasal or throat (tonsillar) swab (N=115), sensitivity was 97.7% for nasal and 48.8% for throat swabs that were PCR-positive on nasal swab with a Ct threshold < 30. Among persons with either a nasal or throat RT-PCR positive swab with Ct<30, BinaxNOW(TM) sensitivity was 85.7% for nasal and 89.8% for nasal plus throat swabs. BinaxNOW continues to be a very useful diagnostic during the omicron surge; oral (throat or cheek swab) should not replace nasal swabs due to significantly reduced sensitivity compared to nasal. As currently recommended, repeat testing should be done for high-risk persons with an initial negative antigen test result.

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