Omicron variant: How do health care officials know which variant a person has?

With news of a second case of the omicron variant of the COVID-19 virus in the United States, some are wondering how doctors determine if a person has the original novel coronavirus or if they are suffering from one of several variants of the illness.

Here’s a look at how health care officials determine what version of the virus a person is suffering from.

Most tests do not tell you what variant you have

Most tests available in the United States test for SARS-CoV-2, the COVID-19 virus, but they do not confirm which variant a person may have.

The tests target certain aspects of the novel coronavirus that don’t change. Those aspects make up the original — or alpha — verstion of the virus.

A variant of the original virus is, by definition, something different than the original version. Something in the virus has changed.

Again, current tests are not looking for any changes, only the original features of the virus. So, while the test shows that the COVID-19 virus is present, it is not able to pinpoint which version of the virus it is.

To find out which variant it may be, the test sample must be sent to a lab that can genetically sequence it to look for mutations that are specific to a certain variant.

For instance, the omicron variant has many mutations to the spike protein part of the virus -- the little spikes you see on an illustration of the virus.

What test is a person given?

The test used when a person first goes to a health care facility with COVID-19 symptoms is known as a polymerase chain reaction (PCR) test.

The PCR test is a common one. It copies small segments of genetic material and amplifies them so they can be analyzed.

According to National Human Genome Research Institute, “COVID-19 testing uses a modified version of PCR called quantitative polymerase chain reaction (qPCR). This method adds fluorescent dyes to the PCR process to measure the amount of genetic material in a sample.”

What researchers look for is genetic material that does not match the original strain of the virus. If found, that means that the person from which the sample came is suffering from a different version or variant of the original virus.

A new test found omicron

According to Reuters, a commercial test from Thermo Fisher Scientific can both detect the presence of the virus and give testers an idea as to what variant it may be if it is not the original virus.

Time reports that “the company’s test targets three different parts of SARS-CoV-2: two relatively stable regions, and the more variable spike protein.”

The omicron variant 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.

That is how the tester knows it is likely the omicron variant.

The most common version of the virus is the delta variant, which is responsible for nearly 99% of new cases around the world.

The test for the delta variant does not show the mismatch on the spike protein, but matches all three regions, letting the tester know it is likely the delta variant.

“This happens to be good fortune that this pattern can flag the presence of omicron,” Mark Stevenson, executive vice president and chief operating officer at Thermo Fisher told Time. “It’s a good early warning system.”

Stevenson said the company was alerted by health care workers in South Africa of unusual test results, leading health officials to realize that there was another variant circulating there.