Detecting novel SARS-CoV-2 variants via rapid RT-PCR assays medrxivpreprint UW SARSCoV2 COVID19 Variant RTPCR Assay
By Dr. Priyom Bose, Ph.D.Feb 6 2023Reviewed by Aimee Molineux Accurate and rapid diagnosis of severe acute respiratory syndrome coronavirus 2 infection has been instrumental in mitigating viral spread during the coronavirus disease 2019 pandemic. One of the first diagnostic tools developed was the reverse transcriptase-polymerase chain reaction tests for detecting SARS-CoV-2. The emergence of SARS-CoV-2 variants of concern has adversely affected testing performance.
The Xpert® Xpress SARS-CoV-2 assay conformed with the Centers for Disease Control and Prevention RT-PCR test and the Cobas® SARS-CoV-2 assay . It was seen to be more sensitive than the Abbott ID Now SARS-CoV-2 Assay. However, since its development, several SARS-CoV-2 VOCs have emerged, which have affected the performance of diagnostic PCR assays, owing to mutations in primer binding sites. This is problematic as it could lead to false negative results.
The samples were collected in Seattle between March 2021 and December 2021. All VOC samples were determined positive for SARS-CoV-2 by the Brotman Baty Institute’s Advanced Technology Lab . They were then sequenced using the Illumina COVIDSeq Kit. The last step was the identification of the variants using the Pangolin Web App.
The novel SARS-CoV-2 variants have augmented the speed of the spread of COVID-19 through different mechanisms, including avoiding detection by RT-PCR. As an example, the Omicron variant has a large number of S-gene mutations, which leads to significant S-gene target failure. The current study showed that Xpert® Xpress could precisely detect SARS-CoV-2 variants despite a large number of mutations in the viral genome.
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