Can a rapid test tell me if I have Omicron? Experts on testing for the new variant

It has now been more than a month since the Omicron variant was first reported to the World Health Organization.

Since then, case counts of Omicron have exploded around the world, including in Canada. According to data compiled by CTVNews.ca, more than 8,000 cases of Omicron have already been reported across the country.

But for each new variant of concern that arises, with it may also come questions about how exactly researchers know what to look for, and whether or not current tests are able to identify a new variant.

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Nucleic acid-based testing, also known as molecular testing, is the main type of test used in Canada to diagnose COVID-19, according to the Public Health Agency of Canada. Of all the molecular tests, the polymerase chain reaction (PCR) is the most common.

Dr. Marek Smieja is an infectious diseases physician and professor at McMaster University in Hamilton. He explained that PCR tests typically focus on two to three targets, or parts of the COVID-19 genome, that are analyzed to determine which variant it is. One part that’s of particular concern is the S-gene.

“A commonly used [procedure] will detect parts of the S-gene, the spike protein,” he told CTVNews.ca in a phone interview on Wednesday. “That's always been of interest because the spike protein is probably the main protein that binds to human receptors and interacts with our immune system.”

When conducting a test, there’s an expectation that all the targets will see positive results, indicating they exist in roughly similar amounts, said Dr. Dan Gregson, an associate professor at the University of Calgary's Cumming School of Medicine. But with the Omicron variant, he said, similar to what’s been observed with the Alpha variant, the S-gene can’t be detected.

“There's a mutation in the spike region that causes it not to flag positive,” he said in a phone interview with CTVNews.ca on Wednesday. “You lose the spike – this is called a spike gene target failure.”

Smieja described this as “an early clue that this is a different virus.” The Delta variant for example, which accounts for the most COVID-19 cases detected in Canada so far, possesses an S-gene. While the Omicron and Alpha variants both share this trait, Smieja explained that because the latter has almost completely disappeared, most instances of this S-gene target failure involve the Omicron variant.

It was after scientists in South Africa observed this dropout that they performed what’s called whole genome sequencing, which looks at the full genetic makeup of viral samples, said Smieja. This led to the discovery of the Omicron variant with its large number of mutations – more than 30 on the spike protein alone.

“It looked like something different, and it certainly has shown up to be much more transmissible,” he said. “It’s still an open question whether it's a milder disease or not, we're still learning that.”

HOW TO CONFIRM WHETHER OR NOT YOU HAVE OMICRON

Whole genome sequencing is the best way to truly confirm whether a person has the Omicron strain of COVID-19, said Smiieja. It involves analyzing the full set of genetic instructions from a viral sample, a total of at least 29,000 base pairs, he explained. This makes it much more complicated and time-consuming than a PCR test, for example, and can take up to a matter of days to process.

“Rather than doing one PCR, [it’s similar to] doing about 90 PCRs, and then we're getting the actual sequence of the product,” he said. “We put this all together so that we actually see the entire genetic code of that one virus.”

Not only is this tedious, but it’s also expensive, Smieja said. As a result, it’s often not done for every single positive COVID-19 case reported, but rather a sampling, he said. In Ontario, there are five main labs that provide whole genome sequencing, Smieja said, and they only look at a percentage of the province’s positive cases to determine how many are associated with each variant.

“They're not going to do that for every positive [case], that's too much work,” he said.

But even with just a percentage of positive cases to analyze, scientists have noticed the variant’s alarmingly rapid rate of spreading within the province, said Smieja.

“We're seeing in most of our labs over 90 per cent of new infections of COVID are now Omicron,” he said. “In two weeks, it’s gone from very, very rare to overwhelmingly the most common [variant].”

In Alberta, Omicron has already become the dominant strain of COVID-19. The province’s chief medical officer of health, Dr. Deena Hinshaw, has said that anyone who continues to test positive should now assume they have Omicron. In this scenario, keeping track of different strains becomes less of a problem, said Gregson.

“If all the cookies in the box are chocolate chip, you don't have to taste them all to know that they’re all chocolate chip,” he said.

DO RAPID ANTIGEN TESTS REVEAL A VARIANT?

All existing COVID-19 variants can be detected by rapid antigen tests commonly used in Canada, said Smieja, even Omicron.

These tests, however, only provide results on whether or not someone has COVID-19. They are not able to tell whether someone has specifically been infected with the Omicron variant. This is because these tests target the N-gene product, or the nucleocapsid protein, as opposed to the spike protein, explained Gregson.

“It's not going to pick up these variants of concern, which are primarily in the spike region,” he said. “You could theoretically have a variant of concern that has a mutation in the N-gene that affects your antigen detection kits, but that's not what we've seen so far.”

Still, they can be easily delivered to a large number of people and provide quick test results. But Smieja insisted they are not a replacement for the PCR test.

“PCR always can detect much smaller amounts of virus [and] remains the gold standard for ill people, for people with suspected COVID who get admitted to hospital, and in general, any symptomatic person,” he said.