There is no case of the new coronaviruses variant, Omicron, reported in the U.S. yet it is only a matter of time. Dr. Anthony Fauci, chief medical advisor on COVID 19 to President Biden, says it's likely that the virus is already in the country, given how much travel is taking place between countries as the restrictions on the pandemic have started to lift in recent months.
If the variant were here, could existing tests tell if someone had been infected? 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 is because the tests intentionally target parts of the virus that don't change much. Variants are designated based on differences in mutations - particularly 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. The majority of the tests available will show if a person is carrying the virus, but there is no way to tell if that virus is Omicron.
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 a commercial test from Thermo Fisher Scientific that can perform the two-fer: detect the presence of the virus and give testers an indication that what they are 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 that if a sample produces all three matches, it is likely Delta; if it results only in two positive matches, it is likely that it will be Omicron. Researchers can then send samples in for sequencing to look for Omicron's genetic profile.
Mark Stevenson, executive vice president and chief operating officer at Thermo Fisher, says that this pattern can flag the presence of Omicron. It is a good early warning system. Clients using the company's test in South Africa alerted Thermo Fisher last Wednesday that they were seeing unusual patterns, even before the country's health officials announced the spurt of new cases. Stevenson expects that public health labs in Europe and the U.S. are using the test to look for the first cases of the Omicron variant.
The team immediately evaluated the results against the samples of Omicron uploaded by public health experts into the public GISAID database, as well as by Qiagen, a global testing company that makes assays for both diagnostic testing and research purposes. "We have seen no drop in performance in our products," says Davide Manissero, chief medical officer at Qiagen.
The research team at diagnostic testing company BD ran tests of its COVID 19 assays using the Omicron sequences in GISAID. Dave Hickey, president of BD Life Sciences, said in a statement that they are confident that our rapid antigen and PCR tests for COVID 19 will detect the novel variant.
If you prefer to rely on the at- home tests available over-the-counter at pharmacies that can give results in a few minutes, those are also useful, at least for letting you know if you might be positive. Like most PCR tests, at-home kits can't determine if someone is infected with the Omicron variant, but they will turn positive for anyone infected with any version of the virus.