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.
Highlights
The 2019 coronavirus disease (COVID-19) is a current pandemic respiratory disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [1]
We compare the efficacy of the results of 55 nasopharyngeal swab samples (NPSs) obtained by the rapid antigen test for SARS-CoV-2 (SD Biosensor, South Korea), a chromatographic assay using a monoclonal antibody against the nucleocapsid (N) protein of the SARS-CoV-2 virus, and the standard reverse transcription quantitative PCR (RT-qPCR) detection method
We observed differences in the detection of positive COVID-19 cases for the different ranges of amplification assessed. We determined that this antigen test loses sensitivity for detecting SARS-CoV-2 variants carrying the K417N/T, E484K and N501Y single nucleotide polymorphisms (SNPs)
Summary
The 2019 coronavirus disease (COVID-19) is a current pandemic respiratory disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) [1]. The technique’s principle consists of a rapid chromatographic immunoassay for the qualitative detection of specific SARS-CoV-2 antigens from nasopharyngeal swab samples (NPSs) [4]. This strategy has begun to be used in several countries, and its effectiveness compared to the standard RT-qPCR method has been the target of study and analysis [5]. Its effectiveness has been verified in various studies showing differences between manufacturers, currently, there are no studies on the effectiveness of the antigenic tests used in Chile, nor on their performance for detecting the outbreak of new SARS-CoV-2 variants. We determined that this antigen test loses sensitivity for detecting SARS-CoV-2 variants carrying the K417N/T, E484K and N501Y single nucleotide polymorphisms (SNPs)
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