Comparison of two nucleic acid amplification tests (NAATs) and two antigen tests for detection of SARS-CoV-2 from upper respiratory specimens

Abstract

There are numerous tests available for acute diagnosis of SARS-CoV-2, the virus that causes the disease COVID-19. These tests fall into two main groups: nucleic acid amplification tests (NAATs) and antigen-based assays. We evaluated the clinical performance of two rapid antigen assays (BD Veritor System for Rapid Detection of SARS CoV-2 and Abbott BinaxNOW COVID-19 Ag Card) and one NAAT (Hologic Aptima SARS CoV-2 Assay) by comparing them with the initial test of record, the Roche cobas SARS-CoV-2 assay; the antigen tests were also compared to Aptima. We tested remnant frozen specimens from patients suspected of SARS-CoV-2 infections (either due to symptoms or exposure) on the comparator platforms to evaluate assay performance across a wide range of positive results, including cobas cycle threshold (Ct) values ranging between 12 and 35. We tested 250 previous positive and 50 previous negative specimens and found 95.6% positive percent agreement (PPA) with the Aptima assay. The few discrepancies between the NAATs occurred only when Ct values were >32. Agreement was much lower for the rapid antigen tests, with 45.2%/47.3% PPA for the Veritor and 47.0%/47.0% PPA for the Binax compared to cobas/Aptima. Discrepancies occurred when cobas Ct values were >20 for Veritor and >25 for Binax. The negative percent agreement (NPA) was 100% for all assay comparisons. These data indicate similar performance between the cobas and Aptima NAATs but demonstrate that antigen-based assays may be insufficient to diagnose SARS-CoV-2 infection when lower levels of the virus are shed.

Keywords: Antigen testing; Automation; COVID-19; Nucleic acid amplification test; SARS-CoV-2.

Fig. 1

Scatter plot demonstrating the cobas Ct1 values of specimens that test positive or negative on the Aptima, Veritor, and Binax assays. The y-axis shows the Ct1 values and the x-axis shows positive and negative results for each assay. Positive Aptima results are shown in dark blue, Veritor results in orange, and Binax results in purple. Negative Aptima results are shown in cyan, Veritor results in yellow, and Binax results in magenta. Positivity rates based on Ct1 results are demonstrated in the table below. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)