Performance of rapid antigen tests to detect SARS-CoV-2 variant diversity and correlation with viral culture positivity: implication for diagnostic development and future public health strategies

Abstract

Antigen-based rapid diagnostic tests (Ag-RDTs) provide timely results, are simple to use, and are less expensive than molecular assays. Recent studies suggest that antigen-based testing aligns with virus culture-based results (a proxy of contagiousness at the peak viral phase of illness); however, the performance of Ag-RDTs for newer SARS-CoV-2 variants is unclear. In this study, we (i) assessed the performance of Ag-RDTs and diagnostic antibodies to detect a range of SARS-CoV-2 variants and (ii) determined whether Ag-RDT results correlated with culture positivity. We noted only minor differences in the limit of detection by variant for all assays, and we demonstrated consistent antibody affinity to the N protein among the different variants. We observed moderate to high sensitivity (46.8%-83.9%) for Ag-RDTs when compared to PCR positivity (100%), and all variants were assessed on each assay. Ag-RDT sensitivity and PCR Ct showed an inverse correlation with the detection of viable virus. Collectively, our results demonstrate that commercially available Ag-RDTs offer variable sensitivity compared to PCR, show similar diagnostic validity across variants, and may predict the risk of transmissibility. These findings may be used to support more tailored SARS-CoV-2 isolation strategies, particularly if other studies clarify the direct association between Ag-RDT positivity and transmission risk. The apparent trade-off between sensitivity in the detection of any PCR-positive infection and concordance with infectious virus positivity may also inform new RDT diagnostic development strategies for SARS-CoV-2 and other epidemic respiratory pathogens.

Importance: Despite the availability of vaccines, COVID-19 continues to be a major health concern, and antigen-based rapid diagnostic tests (Ag-RDTs) are commonly used as point-of-care or at-home diagnostic tests. In this study, we evaluated the performance of two commercially available Ag-RDTs and a research Ag-RDT to detect multiple SARS-CoV-2 variants using upper respiratory tract swab samples from clinical COVID-19 cases. Furthermore, we determined whether Ag-RDT results correlated with culture positivity, a potential proxy of viral transmissibility. Our results have important implications to inform future testing and response strategies during periods of high COVID-19 transmission with new variants.

Keywords: SARS-CoV-2; antigen-based rapid diagnostic tests; viral culture positivity.

Fig 1

Overview of the study design. In this study, we (i) assessed the performance of Ag-RDTs and diagnostic antibodies to detect a range of SARS-CoV-2 variants and (ii) determined whether Ag-RDT results correlated with culture positivity.

Fig 2

Binding of representative diagnostic antibodies to recombinant N variants. The binding kinetics (K_D, pM) of a human mAb (circle), a mouse mAb (square), and a rabbit polyclonal antibody (triangle) to recombinant N with various mutations representative of SARS-CoV-2 variants.

Fig 3

The relationship between clinical swab SARS-CoV-2 PCR Ct value and viral culture positivity. (A) The distribution of culture-positive (circles; n = 26) and culture-negative (squares; n = 36) samples with their corresponding Ct values. A Mann–Whitney U test of the Ct values was significant (P < 0.0001). (B) Correlation and regression analyses of Ct values vs viral titer (PFU/mL) for positive culture samples (n = 26). Spearman rho correlation coefficient with 95% confidence intervals and P-value are shown.

Fig 4

Sensitivity of Ag-RDTs in detecting PCR-positive samples in relation to culture positivity. (A) The PCR-positive samples were tested using three Ag-RDTs. For each Ag-RDT test, the tables show the number of positive and negative results and how many of each were culture-positive or culture-negative. (B) A bar graph of the three Ag-RDTs comparing the percentage of Ag-RDT-positive samples divided by the total samples per assay (gray), the percentage of Ag-RDT-positive and culture-positive samples divided by the culture-positive samples (black), and the percentage of Ag-RDT-positive samples and culture-negative samples divided by the culture-negative samples (white). The P-values for the differences across the three assays were determined by the chi-squared test. Ag-RDT-positive samples divided by the total samples per assay (gray): Abbott vs Sofia, P = 0.0034 (**); Abbott vs C2Sense, P < 0.0001 (****); Sofia vs C2Sense, P = 0.1277. Ag-RDT-positive and culture-positive divided by the culture-positive samples (black): Abbott vs Sofia, P = 0.2715; Abbott vs C2Sense, P = 0.0422 (*); Sofia vs C2Sense (P = 0.2980). Ag-RDT-positive samples and culture-negative samples divided by the culture-negative samples (white): Abbott vs Sofia, P = 0.0020 (**); Abbott vs C2Sense, P < 0.0001 (****); Sofia vs C2Sense, P = 0.2063.

Fig 5

The relationship between Ct value and a positive Ag-RDT. (A) Ct values for positive and negative Ag-RDT results for Abbott, Sofia, and C2Sense assays and SARS-CoV-2 viral culture results. The P-values for the differences across the assays were determined by Tukey’s multiple comparisons test. (B) Percentage of Ag-RDT-positive samples with Ct values less than or equal to the Ct values shown on the x-axis for Abbott (black squares), Sofia (gray triangles), and C2Sense (light-gray inverted triangles) Ag-RDTs. Among these, 20 specimens had a Ct ≤ 20, 38 had a Ct ≤ 25, 51 had a Ct ≤ 30, and 62 specimens had a Ct ≤ 41. The P-values for the differences across the three assays were determined by the Chi-squared test.