How do scientists find COVID-19 variants?

How do you know if you have the delta variant?

Like the coronavirus itself, 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. Kelly Oakeson, Chief Scientist with Next-Generation Sequencing & Bioinformatics, tells Oakeson and his colleagues are working with the Utah Department of Health to conduct these tests. 

He explains after a PCR test, scientists are able to extract the viral genetic material from the same sample the swap 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. 

“Right now, it is taking my team an average of 10 days from PCR sample collection to whole-genome sequencing variant result.”

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. Oakeson’s team is currently has a goal to sequence 75% of all the positive PCR tests. 

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