Test uses ‘sloppy beacons’ to detect SARS-CoV-2 variants

A new rapid test detects all known COVID-19 variants, including the highly transmissible Omicron variant, researchers report.

The test, which can be performed at laboratories experienced in COVID-19 testing, quickly detects 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.

Researchers say the study demonstrates that the 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.

“Our approach is unusually flexible in being able to detect unanticipated mutations,” says David Alland, director of the Rutgers New Jersey Medical School Public Health Research Institute and the Center for COVID-19 Response and Pandemic Preparedness within the Rutgers Biomedical and Health Sciences Institute for Infectious and Inflammatory Diseases.

“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.”

The Rutgers Genomics Center Clinical Lab Team, which includes Patricia Soteropoulos, Deanna Streck, and James Dermody, are now working to obtain rapid approval from the New Jersey Department of Health 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.

The study, all of the information needed to create and run the test, and supporting information are published in the preprint journal MedRxiv, which publishes research not yet peer reviewed.

Source: Rutgers University

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