Oregon State University
A team at Oregon State University is testing wastewater samples around the state for Covid-19. It will start testing for Omicron this week. (Photo by Oregon State University)

The new strain has quickly become dominant in South Africa and is infecting people who’ve already had Covid-19

The latest Covid-19 variant of concern has never appeared in Oregon – ever. 

Dr. Melissa Sutton, the Oregon Health Authority’s medical director of respiratory viral pathogens, reviewed all of the state’s genome sequencing data on Covid-19 samples last week. She told the Capital Chronicle that none of the samples resembled Omicron. 

But that’s likely to change soon, perhaps in the next few days.

Though scientists still have a lot to learn about this variant, they already know enough to be concerned. In South Africa, it appears to have quickly overtaken the Delta variant, becoming the dominant strain. 

Sutton, whose work involves catching emerging viruses in Oregon, is worried.

“That’s absolutely concerning,” Sutton said. “More transmissible variants mean more cases. And of course, more cases translate to more severe cases, hospitalizations and deaths.”

Scientists don’t know whether Omicron causes a higher percentage of more severe illnesses than other variants. But in South Africa, people who’ve already had Covid-19 are becoming reinfected. Omicron appears to have genetic advantages that enable it to more easily invade human cells.

“The Omicron variant has about 50 unique mutations, and about half of those mutations occur in the region of the spike protein,” Sutton said. “The spike protein governs infection and immunity. So one of the reasons that we are concerned is that Omicron may impact vaccine effectiveness.”

Another potential concern is treatment. Scientists don’t know whether monoclonal antibody infusions will work against Omicron. Such infusions contain lab-manufactured antibodies to fight the virus and are most useful early in an infection before the virus takes a strong hold. Scientists are studying that, too.

Leaders at Pfizer and Moderna said they’re working on tailoring their vaccines to fight Omicron. One of the advantages of the technology used to produce the Prizer and Moderna vaccines is that it can be readapted fairly quickly, but still the tweaked vaccines would have to be tested in people. Pfizer said the earliest it could have a vaccine out would be 100 days. 

In the meantime, public health officials say that everyone should get fully vaccinated or get booster shots. Though the current vaccines aren’t targeted at Omicron, they were designed to be effective against a range of variants, Sutton said.

The state, meanwhile, is adding lab equipment to bump up its genomic sequencing of Covid-19 samples. Right now it can sequence 200 samples from Covid-19 tests a week. Oregon Health & Science University is sequencing about 700 samples a week but has the capability to analyze thousands of specimens. The University of Oregon, which is also analyzing Covid-19 samples, can sequence 3,000 samples a week.  There’s also a genomic sequencing lab at Oregon State University.

“Compared to other states, Oregon does a lot of sequencing,” Sutton said. “We rank 11th nationally in terms of sequencing volume. To date, we’ve sequenced about 7.1% of all positive molecular specimens.”

Though that doesn’t sound like much, she said only a fraction needs to be analyzed to get a good picture of the evolution and spread of Covid-19 in Oregon. Besides the surveillance of individual samples, Oregon State University is conducting wastewater sampling for Covid in 40 communities across the state.

“That’s something that’s really pretty unique to Oregon,” Sutton said.

OSU will check wastewater for Omicron

The team that oversees the wastewater project plans to start looking for Omicron this week.

“We have now added the Omicron sequence signature to our algorithm and will start looking for its presence in wastewater from samples taken” last week, according to an email from Tyler Radniecki, who oversees the program. “We plan to continue sequencing efforts on a weekly basis.”

The program can sequence up to about 180 wastewater samples a week. Radniecki said that could be doubled if needed.

The Omicron variant’s mutations make it relatively easy to detect, according to Brian O’Roak, an associate professor of molecular and medical genetics at OHSU.

“One of Omicron’s mutations is easily flagged as it disrupts a probe used to detect Covid-19 in some standard PCR tests, including one of the tests used at OHSU,” O’Roak said in an email. “Once we see this flag in our clinical test results, we can prioritize screening those samples.”

He said the university has streamlined its analysis so that the variant could be analyzed in an afternoon. Normally, it would take a lab about 48 hours to extract and analyze the genetic data from the sample. 

One unknown about Omicron is its ancestry.

Since early in the pandemic, scientists around the world have uploaded their sequencing information to GISAID, a public database that’s run by a German nonprofit with the cooperation of the governments of Germany, Singapore and the United States. It’s more than a decade old and has been used to track worldwide infections, for example, of influenza. It’s been a crucial tool for tracking Covid-19 variants.

The data enable scientists to see the gradual evolution of variants and how they change their genetic structure. 

Such information hasn’t been established for Omicron. 

It’s as if a branch suddenly sprouted from the family tree containing dozens of new mutations, O’Roak said. 

“This is something we’ve seen with other variants of concern,” he wrote.

He said that the variant could have evolved in a patient with a long infection, giving the virus opportunity to mutate as it replicates in the body. Another theory is that it evolved in a population where there is little genomic sequencing.

That is not South Africa, which has a robust surveillance system. Though it was first identified in neighboring Botswana, it’s not clear where it came from. Scientists in Europe have already determined that it was there before it was identified in South Africa.

“Although the number of new mutations in the Omicron variant are concerning, I believe the U.S. should still be more concerned with Delta, which is widespread here and continues to cause a lot of suffering and death,” O’Roak wrote.

Cases start rising

The Delta variant surged this summer but since late October, cases have gradually dropped, reaching a low in Oregon on Nov. 26, when about 450 cases were reported. Since then, they’ve been climbing, hitting about 1,350 last Thursday, according to Oregon Health Authority data. The wastewater program is finding Covid-19 samples about everywhere it looks, especially in central, eastern and southern Oregon, Radniecki said. 

Hospitals remain full, and vaccination rates have stagnated.

Though U.S. officials say the country has enough vaccine, some people in Oregon have had trouble getting their shots. 

The state has a vaccine website at GetVaccinated and the state’s hospital systems and pharmacies also have information about the shots.

Public health officials advise people to keep trying. The more who are vaccinated, the less likely it will be that new variants will emerge, Sutton said.

“People who are vaccinated and develop infection can potentially transmit to others,” Sutton said. But vaccination helps stem overall transmission.

“Vaccination really is the key,” Sutton said. “It’s the path forward.”

The state has no plans yet to change any of the Covid-19 restrictions. But masks are still required indoors in public places. Sutton said this new variant does not mean the pandemic is beginning anew.

“We’re not starting over in many ways because we know so much about how to protect ourselves and how to protect other individuals,” Sutton said. “And we do have protections in place for the broader community, like universal masking in school and an indoor mask mandate.”

Oregon Capital Chronicle is part of States Newsroom, a network of news bureaus supported by grants and a coalition of donors as a 501c(3) public charity. Oregon Capital Chronicle maintains editorial independence. Contact Editor Les Zaitz for questions: info@oregoncapitalchronicle.com. Follow Oregon Capital Chronicle on Facebook and Twitter.