Why your COVID test may not reveal what strain you have

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(NEXSTAR) – Amidst the holidays, many Americans have been rushing to get a COVID-19 test. The demand has been so great that lines stretching for blocks have been seen around the country and retailers have imposed shopping limits on available at-home tests.

Yet the sudden rush of testing may not be enough to combat the virus and its variants, primarily delta and omicron. The omicron variant, the fifth to be labeled a variant of concern by the World Health Organization, has proven to be more transmissible and causing more cases than we’ve seen before, according to Dr. Jim Conway, medical director with the immunization program at UW Health in Wisconsin.

“It’s really kind of taxing the testing system,” he tells Nexstar. In Wisconsin, there are dozens of sites to get tested, which can mean test totals reach into the tens of thousands in any given week. Dr. Conway explains that five labs within the state can test somewhere between 800 and 1,000 specimens in a week for variants, known as sequencing, which is “really only sort of doing the tip of the iceberg.”

According to the Wisconsin State Lab of Hygiene, over 70% of the positive sequences are reported as omicron. ?However, only about 5% of the state’s cases are sequenced.

“We have to suspect that there’s multiple strains circulating at any given time that we honestly don’t know what strains people have,” he said.

If you aren’t waiting in line for a test at sites throughout the country, you may be on the hunt for an at-home test. Those tests, typically antigen tests, may not be picking up which variant you have, either.

Dr. Kelly Oakeson, Utah Public Health Laboratory chief scientist of bioinformatics and next generation sequencing, explains that antigen tests can be difficult to sequence for variant information.

“So with those antigen tests, you take the nasal swab and you put it in some fluid, some solution that basically breaks apart the virus and then allows for that antigen, or that part of the virus that’s detected, to travel up that filter paper,” Dr. Oakeson tells Nexstar. “When you do that, you’re also really damaging the nucleic acid, the RNA, that we would need for sequencing. So it’s doable, but it’s really, really hard. You’ve got to basically get the rapid antigen test to the lab really quickly so we can do the RNA extraction almost immediately. So it’s possible but ridiculously hard.”

He continues, noting studies have found the antigen tests work as well as PCR tests at detecting the virus itself if you are showing symptoms. This is because there is enough virus for the test to detect it. If you’re asymptomatic, though, Dr. Oakeson says the PCR tests are more sensitive and able to pick up smaller amounts of the virus than antigen tests.

Regardless of whether you’re able to get an antigen test or a PCR test, Dr. Conway says testing availability is crucial to fight the virus. Knowing whether your runny nose is COVID or just a cold can help you be more cautious around others, he explains.

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