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December 1, 2021

Montana ramps up sequencing efforts to monitor for new omicron variant

The state health department and its partners have increased their capacity to conduct sequencing of COVID-19 samples in an effort to monitor for the new omicron variant as it continues to pop in various countries around the world, including Wednesday’s report that it’s in America.

“As a new variant emerges, we want to double or even triple sequencing to understand what the prevalence of this new variant might be,” said Vik Ghai, a senior research scientist at FYR Diagnostics in Missoula. Outside of the state laboratory, Montana partners with three other labs — University of Montana, Montana State University and FYR Diagnostics — that conduct COVID-19 sequencing.

The Centers for Disease Control and Prevention confirmed the first known case of omicron in the U.S. was found in California on Wednesday. In a statement, the CDC said the case was confirmed in a traveler who returned from South Africa, where the variant was first identified last week, on Nov. 22.

“The individual, who was fully vaccinated and had mild symptoms that are improving, is self-quarantining and has been since testing positive,” the statement read.

So far, no samples have shown to be the omicron variant, and delta continues to be the prominent variant in the state, which has been status quo since July, said Jon Ebelt, spokesman for the Department of Public Health and Human Services.

“Delta is the only variant of concern at this time, and it is the dominant circulating strain in Montana. Of specimens collected and sequenced in October and November, 1,867/1,873 are delta,” read a DPHHS report from November 19. “Aside from delta, all other former variants of concern and interest have been re-classified as variants being monitored.”

For the delta variant, it was only a matter of a few weeks before it took hold of the state, Ghai said.

Over a couple of weeks, delta went to 15 to 25 percent, and within three weeks, it was 100 percent of samples,” he said.

Ghai said he would not be surprised if the new variant was already in the U.S. but going undetected.

“It’s already in North America, and I wouldn’t be surprised if it’s here. South Africa has an amazing sequencing surveillance program, and that’s why they were able to detect it,” he said.

To that point, Ghai said it is critical that Montanans continue to get PCR tests so labs can continue sequencing samples for the variant.

According to state data, 585 new positive cases of the virus were reported on Wednesday, with 220 active hospitalizations. In the past week, 1,825 new cases were reported, along with 66 deaths and a positive test rate of 6.72 percent, according to data from Johns Hopkins University. And the positive case rate is trending down. The seven-day average for new daily cases in the state was 671 on November 1, compared to 235 on Tuesday, according to Johns Hopkins.

The first known confirmed omicron infection was from a specimen collected on Nov. 9 in the Tshwane region of Gauteng Province, South Africa, on Nov. 9. It has since been detected in more than 20 countries, including six cases in Canada and one case in the U.S.

And in South Africa, where the delta variant has dominated in recent months, omicron accounted for 76 percent of positive cases in November.

“The data is still young; we just have to wait and see what will happen. It is certainly overtaking delta in some capacity in South Africa, but it is unclear if that will happen in other places,” Ghai said.  Adding, “no one really knows what makes a variant prime to take over, but based on the number of mutations and the types of mutations, people are more concerned about this variant.” 

While the variant shares many key mutations with past variants like alpha and delta, it also has 32 mutations on its spike protein compared to the delta variant which has nine.

“It’s hypothesized the mutation profile of omicron may cause it to escape the immune response that your body may have or that the vaccine may give you,” Ghai said.

Public health officials have maintained vaccination against COVID-19 is the best protection against the new variant. But have said more time is needed to research how omicron’s mutations affect its transmission rate and ability to cause more severe illness.

The World Health Organization said that it is unknown whether omicron is more transmissible compared to other variants like delta.

“The number of people testing positive has risen in areas of South Africa affected by this variant, but epidemiologic studies are underway to understand if it is because of omicron or other factors,” the organization said in a release.

WHO also said whether the variant causes more severe illness remains unknown at this point. The WHO acknowledged hospitalizations in South Africa have risen since the variant was discovered, it said that may just be the result of the overall numbers of infected people.  Additionally, the WHO said there is no information to suggest that symptoms of omicron differ from other variants.

At the same time, the CEO of Moderna, one of the three major vaccine developers, shared concerns about the vaccine’s capability to fight off omicron.

“There is no world, I think, where [the effectiveness] is the same level … we had with [the] delta [variant],” he told the Financial Times.

On Monday, President Joe Biden said the emergence of omicron is not “a cause for concern, not a cause for panic.” And, according to CBS News, said his approach to the new variant will not be met with “shutdowns or lockdowns, but with more widespread vaccinations, boosters, testing and more.”

In response to the spread of omicron in other countries, the White House has restricted the entry of travelers into the U.S. from eight nations, including South Africa. The Washington Post also reported on Wednesday that the Biden administration is preparing to require all inbound international travelers to be tested for COVID-19 one day before departure, regardless of vaccination status, and are considering a requirement that all travelers get retested within three to five days of arrival.

Biden is also expected to announce a new winter COVID-19 strategy on Thursday. As part of that plan, the Post reported U.S. officials are debating a proposal that would require all travelers, including U.S. citizens, to self-quarantine for seven days, even if their test results are negative.

And recently, the CDC upgraded its guidance and recommended everyone ages 18 and older to get a booster shot.

In Montana, vaccination rates have remained mostly stagnant for months, hovering around 50 percent of eligible residents being fully vaccinated. To jumpstart things, DPHHS has launched a new series of public service announcements promoting the COVID-19 vaccine featuring Montanans who have experienced COVID infection.

“Vaccination will keep you and your loved ones safe. DPHHS encourages all eligible Montanans to do their part by getting fully vaccinated and to get their booster shot. Clinical trials have consistently found that the COVID-19 vaccines are safe and effective at preventing severe COVID-19-related outcomes,” Ebelt said. “Vaccine coverage in our state will drive how many Montanans will be hospitalized and/or die from this disease.”