New PCR test can identify coronavirus variants

A new type of PCR test can quickly tell which variant of the coronavirus is causing infection, helping doctors choose the most effective antibody treatments, researchers said.

Most current PCR tests can check broadly for the presence of the virus but cannot identify specific variants. The new test uses special “probes” – fluorescently labeled molecules – called “sloppy molecular beacons” that glow in different colors when they attach themselves to DNA or RNA in the virus. When the sample from the patient is heated, the probes fall off their DNA or RNA targets and their color disappears.

They fall off at different temperatures depending on the DNA or RNA sequence they were bound to. Because the variants each have some unique sequences, they can be identified based on the pattern of color changes at each temperature, explained Dr. David Alland of Rutgers New Jersey Medical School.

“We have already performed a clinical study which showed that the assay was 100% sensitive and 100% specific for identifying variants of concern including Delta and Omicron,” Alland said.

“We are asking the N.J. Dept of Health to clear our test” so that New Jersey labs can use it, he added. A typical hospital molecular laboratory would be able to perform it, his team reported on Friday on medRxiv ahead of peer review.