The Rapid Antigen Detection Test for SARS-CoV-2 Underestimates the Identification of COVID-19 Positive Cases and Compromises the Diagnosis of the SARS-CoV-2 (K417N/T, E484K, and N501Y) Variants

Abstract

Timely detection of severe acute respiratory syndrome due to coronavirus 2 (SARS-CoV-2) by reverse transcription quantitative polymerase chain reaction (RT-qPCR) has been the gold- strategy for identifying positive cases during the current pandemic. However, faster and less expensive methodologies are also applied for the massive diagnosis of COVID-19. In this way, the rapid antigen test (RAT) is widely used. However, it is necessary to evaluate its detection efficiency considering the current pandemic context with the circulation of new viral variants. In this study, we evaluated the sensitivity and specificity of RAT (SD BIOSENSOR, South Korea), widely used for testing and SARS-CoV-2 diagnosis in Santiago of Chile. The RAT showed a 90% (amplification range of 20 ≤ Cq <25) and 10% (amplification range of 25 ≤ Cq <30) of positive SARS-CoV-2 cases identified previously by RT-qPCR. Importantly, a 0% detection was obtained for samples within a Cq value>30. In SARS-CoV-2 variant detection, RAT had a 42.8% detection sensitivity in samples with RT-qPCR amplification range 20 ≤ Cq <25 containing the single nucleotide polymorphisms (SNP) K417N/T, N501Y and E484K, associated with beta or gamma SARS-CoV-2 variants. This study alerts for the special attention that must be paid for the use of RAT at a massive diagnosis level, especially in the current scenario of appearance of several new SARS-CoV-2 variants which could generate false negatives and the compromise of possible viral outbreaks.

Clinical Performance of Rapid and Point-of-Care Antigen Tests for SARS-CoV-2 Variants of Concern: A Living Systematic Review and Meta-Analysis

“…However, there were several studies evaluating the sensitivity of RATs for variants without specificity because the sensitivity is an important variable considering RATs as screening tests rather than confirming assays. Therefore, we searched manually and reviewed an additional seven studies with sensitivities for variants [ 21 , 22 , 49 , 50 , 51 , 52 , 53 ], which were not included in the formal meta-analysis. Five out of seven studies dealt with the Delta and Omicron variants.…”

A Reagent and Virus Benchmarking Panel for a Uniform Analytical Performance Assessment of N Antigen–Based Diagnostic Tests for COVID-19

“…Understanding the reactivity against inactivated virus and recombinant protein is valuable, as these can be readily expressed, noninfectious sources of N antigen for emerging virus strains for which there may be a concern for sequence-dependent false negativity. [21][22][23][24] The 90% probability of detection, a proxy for LOD, for the clinical specimen pool ranged from 20 pg/mL to 100 pg/mL across the four tests. While the 90% probability of detection limit model is not a standardized method, it allows a continuous detection response function to be fit to standardized panels, rather than requiring custom dilutions for each test.…”

Combined Diagnosis of SARS-CoV-2: Rapid Antigen Detection as an Adjunct to Nucleic Acid Detection

“… 51 In the detection of nonvariant SARS-CoV-2, RAD showed a sensitivity of 90% (20 ≤ Ct < 25) and 10% (25 ≤ Ct < 30); In Beta or Gamma-associated SARS-CoV-2 variants, RAD has a detection sensitivity of 42.8% in samples with 20 ≤ Ct < 25. 52 The marked decrease in sensitivity in SARS-CoV-2 variants suggests that special care must be taken when using RAD at the large-scale diagnostic level, especially in the current context of the emergence of several new SARS-CoV-2 variants that may produce false-negatives. The use of either RAD or RT-PCR alone increases false-negatives in the detection of SARS-CoV-2 variants, and the use of both RAD and nucleic acid diagnostics for SARS-CoV-2 can rapidly correct false-negative results and control and prevent COVID-19 outbreaks.…”