SALT LAKE CITY (ABC4) – Health officials said the delta variant has changed the fight against the Coronavirus as it causes more than two times as many infections than previous strains. However, the question of how experts track variants is being raised after one woman who tested positive for the virus claims no one could tell her if she had the variant or not.
Linda Crismer tested positive for COVID-19 in July. However, a month later she still doesn’t know if she had the delta variant or not.
“How do they keep saying everybody has the delta variant when nobody can test and say you’re positive for the delta variant?” Crismer says.
After Crismer contacted several doctors, health departments and testing sites and still wasn’t able to find out if she had the delta variant or not, she started to question how the variants are reported.
“For people that don’t believe that this whole scenario is real…they believe that the testing is not accurate, they believe the disease isn’t as bad as we’re told it is…not being able to say that you have the delta variant or not confirms their theories,” Crismer says.
However Dr. Kelly Oakeson, Chief Scientist with Next-Generation Sequencing & Bioinformatics says there is a simple explain for why people aren’t being told one way or the other.
“We can’t by law tell the patient they have delta because there’s not an FDA approved test,” Dr. Oakeson said.
The Delta variant can only be detected with a PCR test – a swab of your nose. But that is just the start of it.
“The process of detecting variants is a bit more complex than just a PCR test; it is a process call whole-genome sequencing (WGS),” Dr. Oakeson said.
The Utah Public Health Laboratory does the majority of the sequencing on PCR samples in Utah to figure out which variants are circulating.
He explains after a PCR test, scientists are able to extract the viral genetic material from the same sample the swab test receives. Typically, they are able to use the leftover material not used to conduct the PCR test.
“Once we have the genetic material, we use some rather complex molecular biology to determine the sequence of the SARS-CoV-2 viral genome in that sample,” Oakeson outlines. “In other words, we determine the sequence of A, C, T, G of the virus.”
When they have the sequence of the virus, scientists are able to look for specific mutations that “tell us what variant of concern we have,” Oakeson says. This process is the same regardless of the variant of the virus.
However, until that sequencing is approved, Utahans like Crismer won’t know if they have the delta variant or not.
“We are working on getting it under what’s called Laboratory Developed Test so we can report it back out to patients. But right now, because of that regulatory burden, we just aren’t able to report it back out as a clinical diagnostic test,” Oakeson says.
Not every COVID-19 test is sequenced. According to Oakeson, only samples collected by a PCR test can be sequenced – rapid antigen tests do not leave any type of sample that can be sequenced. That’s why he encourages any Utahans who test positive with a rapid antigen test to get a PCR test too.
“You are going and helping the greater good. The more we know how the virus is evolving, the more we know what’s circulating in Utah, the better we can help protect the health of Utahans,” Oakeson said.
Oakeson’s team currently has a goal to sequence 75% of all the positive PCR tests.
“We have a really good sample of what is circulating in Utah, so with that, we’re confident that we’re catching the majority of what’s out there,” Oakeson states.
Oakeson says it is taking his team an average of 10 days from PCR sample collection to whole-genome sequencing variant result.
He tells ABC4 News his lab is in the final stages of getting approval in place for the sequencing and hopefully within the next several weeks his team can start telling people what their sequencing result is. That way they will know if they have the delta variant or not.