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Omicron’s mutations are concerning, but also make the variant easier to detect

By Sebastián Martínez Valdivia, Side Effects Public Media | Published on in Education, Health, Science
The Coronavirus Sewershed Surveillance Project in Missouri works to detect variants in wastewater from across the state. (Provided by the University of Missouri)

The first confirmed case of the omicron variant in the U.S. was identified Wednesday, a 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, experts are still trying to learn about the new strain.

But, in contrast with other harmful variants of COVID-19, omicron’s early detection could help scientists get up to speed quickly.

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

In Missouri, the state’s department of health and senior services samples positive tests from around the state to sequence in search of variants. It’s what many state health labs do – often in partnership with area hospitals – and it offers a limited picture of which variants may be circulating.

But according to Dr. Laura Morris, University of Missouri Health Care’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 said. “So it’s possible that we’ll be able to monitor for this [variant] 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 is only detectable in two of the three probes. It’s a molecular signature that certain PCR tests can pick up – and fast. Those samples can then be prioritized for genetic sequencing.

In other words, the changes in omicron that make the strain concerning also make it easier to spot, said Marc Johnson, professor of molecular microbiology and immunology at the MU School of Medicine.

“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 PCR approach to tracking the omicron variant isn’t perfect, because the alpha variant has the same characteristic, Johnson said, but, “the [alpha] variant is all but extinct at this point.” And the delta variant lacks that molecular signature.

Johnson will be on the lookout for omicron as leader of the Coronavirus Sewershed Surveillance Project, which is a collaboration between the state health department, the Missouri Department of Natural resources and the University of Missouri. The team analyzes wastewater from across the state to look for signals of potential outbreaks and tracks coronavirus variants.

The sewershed surveillance project was one of the first to identify the presence of the delta variant in Missouri, which caused a big spike in cases last summer. Delta has since become the dominant coronavirus variant across the U.S., and Johnson said the biggest lesson he learned this summer was how quickly it spread.

In Missouri, “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 [one town to another] just like that.”

While omicron has spread quickly in some of the countries where it has been detected, 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 … our region. But it also maybe depends on some things we don’t know,” she said.

For example, will it be more transmissible? Will it make patients sicker?

“So far, that does not appear to be the case, but there are so few cases and not enough time has passed to … say that for sure,” Morris said.

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

This story comes from a reporting collaboration that includes KBIA and Side Effects Public Media — a public health news initiative based at WFYI. Follow Sebastian on Twitter: @sebastiansings.