Impaired detection of omicron by SARS-CoV-2 rapid antigen tests

Abstract

Since autumn 2020, rapid antigen tests (RATs) have been implemented in several countries as an important pillar of the national testing strategy to rapidly screen for infections on site during the SARS-CoV-2 pandemic. The current surge in infection rates around the globe is driven by the variant of concern (VoC) omicron (B.1.1.529). Here, we evaluated the performance of nine SARS-CoV-2 RATs in a single-centre laboratory study. We examined a total of 115 SARS-CoV-2 PCR-negative and 166 SARS-CoV-2 PCR-positive respiratory swab samples (101 omicron, 65 delta (B.1.617.2)) collected from October 2021 until January 2022 as well as cell culture-expanded clinical isolates of both VoCs. In an assessment of the analytical sensitivity in clinical specimen, the 50% limit of detection (LoD50) ranged from 1.77 × 10⁶ to 7.03 × 10⁷ RNA copies subjected to the RAT for omicron compared to 1.32 × 10⁵ to 2.05 × 10⁶ for delta. To score positive in these point-of-care tests, up to 10-fold (LoD50) or 101-fold (LoD95) higher virus loads were required for omicron- compared to delta-containing samples. The rates of true positive test results for omicron samples in the highest virus load category (Ct values < 25) ranged between 31.4 and 77.8%, while they dropped to 0-8.3% for samples with intermediate Ct values (25-30). Of note, testing of expanded virus stocks suggested a comparable RAT sensitivity of both VoCs, questioning the predictive value of this type of in vitro-studies for clinical performance. Given their importance for national test strategies in the current omicron wave, awareness must be increased for the reduced detection rate of omicron infections by RATs and a short list of suitable RATs that fulfill the minimal requirements of performance should be rapidly disclosed.

Keywords: Diagnostic test; Lateral flow; Nucleocapsid protein; SARS-CoV-2 rapid antigen test; Sensitivity; Specificity; VoC.

Fig. 1

Schematic overview of the nasal swab sampling and testing procedure. Step 1: viral particles are collected with the provided collecting device (swab) from the anterior part of the nasal cavity. In general, the test sensitivity is influenced by the amount of nucleocapsid antigen collected with the swab from nasal mucosa and secretions. Step 2: antigen-containing sample material is eluted from the swab into an extraction buffer. The sensitivity of the assay can be affected by the efficiency of the physical elution of the antigen from the collection device. Step 3: extracted nucleocapsid antigen is applied onto the rapid antigen test cassette. In this step, manufacturer-specific recommendations for the volume of antigen-containing buffer that are applied to the test cassette (known as “input ratio”) exist. The amount of “RNA copies subjected to assay” investigated in this study refers to an input equivalent at step 1

Fig. 2

SARS-CoV-2 viral load distribution of respiratory samples included in the study containing either delta or omicron. a, c Shown is the log10 viral load (Geq/ml) distribution of all 65 delta (a) and all 101 omicron (c) sorted by ascending magnitude from left to right. Each dot indicates one patient and the sample ID is indicated. b, d Histogram of the viral load distribution in specimen containing delta (b) or omicron (d) categorized into the indicated ranges of log10 viral load. Each bar depicts the number of samples in the respective viral load range. e The horizontal line in the box plots shows the median of the samples shown in a and c, bound between upper and lower quartiles, and whiskers between minimum and maximum are indicated. n.s. = not significant by Wilcoxon rank sum test with continuity correction and by two-sample Kolmogorov–Smirnov test

Fig. 3

Limit of detection analyses of respiratory samples positive for either delta (top panels) or omicron (bottom panels) by RT-qPCR for nine SARS-CoV-2 RATs. a test #1–5, b test #6–9. The log10 RNA copies subjected to the test of quantified samples on the x axis were plotted against a positive (+ 1) or negative (0) test outcome on the y axis. For readability of the figure, slight normal jitter was added to the y values. Blue (delta) and red (omicron) curves, respectively, show logistic regressions of the viral load on the test outcome; vertical dashed lines indicate log10 RNA copies subjected to the test at which 50% (LoD50) and 95% (LoD95), respectively, of the samples are expected positive based on the regression results. Significant differences for LoD50: test 2, 3, 4 and 7. Significant difference for LoD95: test 7