Do Current COVID-19 Tests Still Detect Omicron?

While no cases of the new coronavirus variant, Omicron, have been reported in the U.S. yet, it’s only a matter of time. In fact, Dr. Anthony Fauci, chief medical advisor on COVID-19 to President Biden, says it’s likely the virus is already in the country, given how much travel is occurring between countries as pandemic restrictions have started to lift in recent months.

Existing tests could tell whether someone is infected even if it was a variant. Experts in testing say both yes and no. The majority of tests used by commercial and public health labs can detect SARS-CoV-2, but they can’t confirm which version of the virus is present. That’s because the tests intentionally target parts of the virus that don’t change much. Variants are designated based on differences in mutations—in Omicron’s case, especially those in spike protein, a part of the virus that changes frequently to bypass drugs and immune cells, and thus are difficult to test for. So the majority of the tests available will show if a person is carrying the virus—but there’s no way to tell whether that virus is Omicron.
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To do this, your doctor must send your sample to the lab to be sequenced genetically.

There is one commercial test, from Thermo Fisher Scientific, that can perform the two-fer: both detect the presence of the virus and give testers an inkling that what they’re dealing with might be the Omicron variant. The company’s test targets three different parts of SARS-CoV-2: two relatively stable regions, and the more variable spike protein. Omicron is expected to show positive matches in two of the more stable areas, similar to the Alpha variant’s, and a mismatch in the spike protein part.

The Delta variant, which is now responsible for nearly 99% of new cases around the world, does not share this omission, and produces a three-for-three match on all three regions targeted by Thermo Fisher’s PCR test. That means, given Delta’s dominance, if a sample produces all three matches, it’s likely Delta; if it results in only two positive matches, it’s likely to be Omicron. To confirm, researchers can then send those samples in for sequencing to definitively look for Omicron’s genetic profile.

“This happens to be good fortune that this pattern can flag the presence of Omicron,” says Mark Stevenson, executive vice president and chief operating officer at Thermo Fisher. “It’s a good early warning system.” Clients using the company’s test in South Africa alerted Thermo Fisher last Wednesday that they were seeing those unusual patterns, even before the country’s health officials announced the spurt of new cases. Stevenson anticipates that public health laboratories in Europe and America will now use the Omicron test to search for new cases.

Qiagen, which is a multinational testing company, makes assays both for diagnostic and research testing. They immediately compared the test to Omicron samples uploaded by health specialists into the public GISAID Database. “We’ve seen no drop in performance in our products,” says Dr. Davide Manissero, chief medical officer at Qiagen.

The same thing happened when the research team from diagnostic testing company BD conducted tests on its COVID-19 test using Omicron sequences of GISAID. “We are confident that our rapid antigen and PCR tests for COVID-19 will detect the novel variant,” Dave Hickey, president of BD Life Sciences, said in a statement.

You can also use the over-the-counter tests at pharmacies to get results quickly. The at-home tests cannot be used to determine if someone has been infected by the Omicron virus variant. However, they can detect if anyone is infected.


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