PCR-Based SARS-CoV-2 Assay Quickly Detects All Known COVID-19 Variants

A rapid test that detects all known COVID-19 variants, including the highly transmissible Omicron variant, is up for approval for clinical testing, and could guide treatment as well as identify high-risk patients.

The test, which has been developed by researchers at Rutgers New Jersey Medical School (Newark, NJ, USA) and can be performed at laboratories experienced in COVID-19 testing, can quickly detect clinical samples that contain the SARS-CoV-2 virus with signature mutations for each known variant of concern - namely, the Alpha, Beta/Gamma, Delta and Omicron variants. The test uses special probes called “sloppy molecular beacons” that perform particularly well at detecting mutations in organisms that mutate frequently. These probes work even if other mutations unexpectedly develop near a mutation of interest. A study demonstrated that their approach is 100% sensitive and specific for identifying the correct variant when tested on clinical samples. The test can be used in a variety of instruments and assay formats.

The researchers are now working to obtain rapid approval to use the new test on patients, where it could help determine the correct type of antibody therapy and potentially help identify patients at high risk for severe COVID-19. To bolster the world’s public health fight against COVID-19, the team is releasing all of the information needed to create and run the test as well as supporting information.

“Our approach is unusually flexible in being able to detect unanticipated mutations,” said David Alland, director of the Rutgers New Jersey Medical School Public Health Research Institute and the Center for COVID-19 Response and Pandemic Preparedness. “We had recently improved an older version of the assay, so that it could detect the Delta variant, but when Omicron appeared, we suspected that it would be able to specifically identify this variant as well, and we are happy to find that our testing shows that we were correct.”

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Rutgers New Jersey Medical School