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.
Even if the variant were here, could existing tests tell if someone were infected by it? Testing experts say 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.
For that, a doctor would have to send your sample to a lab that can then sequence genetically to look for the genetic signatures unique to Omicron.
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. It turns out that Omicron will show positive matches on the two more stable regions, a pattern similar to the one from the Alpha variant, but will show a mismatch on the spike protein portion.
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 expects public health labs in Europe and the U.S. are now also using the test to look for the first cases of the Omicron variant.
At Qiagen, a global testing company that makes assays for both diagnostic testing and research purposes, the team immediately evaluated their test against the samples of genetic sequences of Omicron uploaded by public health experts into the public GISAID database. “We’ve seen no drop in performance in our products,” says Dr. Davide Manissero, chief medical officer at Qiagen.
Similarly, the research team at diagnostic testing company BD ran tests of its COVID-19 assays using the Omicron sequences in 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.
If you prefer to rely on the at-home tests available over-the-counter at pharmacies that can provide results in a few minutes, those are also still useful, at least for letting you know if you might be positive. Like most PCR tests, the at-home kits cannot determine if someone is infected with the Omicron variant specifically, but they will turn positive for anyone infected with any version of the virus.
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