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Local experts say omicron variant easier to spot than other strains

University of Missouri
The Coronavirus Sewershed Surveillance Project works to detect variants in wastewater from across the state.

The first confirmed case of the omicron variant in the U.S. was identified Wednesday, little more than a week after its initial discovery in South Africa. While the World Health Organization has already listed omicron as a variant of concern, there is still a lot experts need to learn about the new strain.

But, in contrast with earlier harmful variants, omicron’s early detection could help scientists get up to speed quickly.

Detecting coronavirus variants has been a challenge for American health officials over the course of the pandemic. The U.S. lags behind other industrialized countries when it comes to genomic sequencing — that’s the process by which scientists are able to analyze differences in the virus’s genetic code.

The Missouri Department of Health and Senior Services takes a certain number of positive tests from around the state to sequence in search of variants. That offers a limited picture of what variants might be circulating. But according to Dr. Laura Morris, MU Health’s vaccine co-chair, omicron might actually be simpler to detect than previous variants.

“There’s an interesting feature with this variant, though, that makes it detectable using PCR techniques instead of genomic sequencing," Morris explained. "So it’s possible that we’ll be able to monitor for this a little bit easier”

PCR, which stands for polymerase chain reaction, detects genetic material from the virus that causes COVID-19. Specifically, PCR tests, which are some of the most common coronavirus tests, have three genetic probes to look for the virus.

Scientists in South Africa, where the omicron variant was first identified, discovered the new strain only shows up in two of the three probes.

Marc Johnson is a professor of molecular microbiology and immunology at the MU School of Medicine, who will be on the look out for omicron as leader of the Coronavirus Sewershed Surveillance Project. According to Johnson, the PCR technique isn't perfect, because the alpha variant has the same characteristic. But, "The [alpha] variant is all but extinct at this point,” he said.

Johnson's project is a collaboration between the state health department, the Missouri Department of Natural resources and M-U. His team analyzes waste-water from across the state to look for signals of potential outbreaks, and coronavirus variants. Per Johnson, the changes in omicron that make it concerning, also make it easier to spot in the genetic material he samples.

“It will be very easy to tell from sequencing this one little chunk if it’s omicron or not," Johnson said. "It’s got lots of mutations in that region.”

The sewershed surveillance project was one of the first to identify the presence of the delta variant, which caused a big spike in cases last summer. Delta has since become the dominant coronavirus variant in the state, and Johnson says the biggest lesson he took from the summer was how quickly it spread.

"We’re not a big metropolis, we’re mostly a bunch of little towns that are very well separated," Johnson said. "But it was really eye-opening to me just that there’s enough interaction amongst this state that something can go very quickly from Branson to Linn County ... just like that."

While omicron has spread quickly in some of the countries where it has been detected, Dr. Morris said it’s too early to tell how it might spread in the U.S.

"It depends on geography, it depends on how quickly this variant enters into the united states and into our region but it also maybe depends on some things we don’t know,” she explained.

Regardless, Morris said, from the little we know so far, there’s nothing to suggest the current best practices — masking and vaccination — will change.

Sebastián Martínez Valdivia was a health reporter at KBIA and is documentary filmmaker who focuses on access to care in rural and immigrant communities. A native Spanish speaker and lifelong Missouri resident, Sebastián is interested in the often overlooked and under-covered world of immigrant life in the rural midwest. He has a bachelor's degree in broadcast journalism from the University of Missouri and a master's degree in documentary journalism at the same institution. Aside from public health, his other interests include conservation, climate change and ecology.