What we know about omicron variant in CT

As strain emerges, experts have more questions than answers

Gov. Ned Lamont announced this weekend that one Connecticut resident has been infected with the omicron variant of the coronavirus.

It has not been long since the variant was first discovered in South Africa, though more is being learned about omicron as more cases are uncovered and as research progresses.

“We know very little,” Rick Martinello, head of infection prevention at Yale New Haven Health, said when asked what we know about omicron.

“I would say, it’s still fair to state that we remain with more questions than we do have answers,” he said.

Here are five questions about omicron, and what we know so far:

1. How transmissible is it?

Exactly how transmissible omicron is, and how much more transmissible it might be compared to other coronavirus variants, is unknown.

“Right now, our information is really based upon the epidemiology that we’re seeing within different communities as it gets introduced into those communities,” Martinello said. “What they’re finding, it’s just highly concerning with the rapidity in which it is being spread.”

Though with the caveat that it is not yet published and had wide margins for error, Martinello pointed to one study “where they estimated that it may be twice as easily spread as the delta variant.”

Nathan Grubaugh, associate professor the Yale School of Public Health, said during a recent Q&A that some of the mutations that make the variant unique are thought to increase transmissibility.

“With 47 defining mutations, omicron is the most divergent SARS-CoV-2 variant yet identified,” Grubaugh said. “Though it evolved independently of other variants, they share several key mutations, some of which have been previously associated with enhanced transmissibility and/or immune escape.”

That said, omicron’s quick spread to six continents around the world has made some researchers take notice, as noted in a study produced by private medical data analysis firm, nference.

“The emergence of a heavily mutated SARS-CoV-2 variant (B.1.1.529, omicron) and its spread to six continents within a week of initial discovery has set off a global public health alarm,” the study said.

2. Is omicron more virulent?

Initial studies suggest that symptoms produced by omicron are less severe than those caused by previously identified variants.

The World Health Organization noted that in South Africa, where the variant was first identified, there was an increase in hospitalizations, though that may be circumstantial evidence.

“Preliminary data suggests that there are increasing rates of hospitalization in South Africa, but this may be due to increasing overall numbers of people becoming infected, rather than a result of specific infection with omicron,” the WHO wrote. “There is currently no information to suggest that symptoms associated with omicron are different from those from other variants.”

Manisha Juthani, commissioner of the Connecticut Department of Public Health, said Monday that, “we have a lot to still learn about omicron.”

“We don’t know what kind of impact it’s going to have. Luckily, for our first few cases here in Connecticut, it seems that it has been mild disease so far,” she said. “That is welcome news.”

While only one omicron case had been confirmed in Connecticut as of Monday, Juthani was referring to other infections that are suspected to contain the variant.

Martinello, however, said that data was largely anecdotal.

“We’ve seen anecdotes, where individuals have said that the cases that they’re seeing are relatively mild,” he said. “I think we need to really take that with a big grain of salt.”

3. Can it evade immune responses?

Grubaugh said that’s something we might learn in the next two to four weeks.

“We currently do not have any data to know for sure the impact that omicron will have on immune evasion, both from vaccines and previous infection,” Grubaugh wrote. “Omicron has 30 mutations in the spike protein, many previously associated with antibody escape, so we expect that it will have some effect. But exactly how much is very difficult to predict at this point.”

There are some initial indications that patients can be reinfected with omicron. Juliet R.C. Pulliam, of the South African Centre of Excellence in Epidemiological Modelling and Analysis, was among several researchers who published a study suggesting that omicron could evade immune responses, at least in patients with some degree of natural immunity.

“Population-level evidence suggests that the omicron variant is associated with substantial ability to evade immunity from prior infection,” the study says. “In contrast, there is no population-wide epidemiological evidence of immune escape associated with the beta or delta variants.”

That study has not yet been peer-reviewed.

Local, national and international officials continue to encourage vaccinations, both the initial course and boosters.

“The recent emergence of the omicron variant further emphasizes the importance of vaccination, boosters, and general prevention strategies needed to protect against COVID-19,” the Centers for Disease Control and Prevention wrote.

At an event in New Haven Monday, U.S. Sen. Richard Blumenthal said, “omicron is one of a series, it’s a preview of coming attractions.”

“If we fail to get vaccinated and use the booster as long as this virus is spreading, it will be mutating and if it’s eventually going to find a way to defeat the vaccine and booster unless we act promptly and effectively to get everybody vaccinated around the world, not just here in the United States,” he said.

4. How widespread is it in Connecticut?

There has only been a single case of omicron detected and announced so far in Connecticut, though it may be more widespread.

Grubaugh, who runs the laboratory that conducts most of the genetic testing of coronavirus variants in Connecticut, said last week that there are as many as 650 samples tested weekly in the state.

Before omicron was identified in Connecticut, Grubaugh postulated that it was already here, but not “yet at a high prevalence.”

Omicron has so far been detected in 17 states, according to national news reports.

The variant that is causing the most infections in Connecticut is still delta, which Grubaugh said has been found in 100 percent of samples tested in recent weeks.

“The delta variant is still very much here,” Juthani said. “It is what is causing most of our problems right now and resulting in severe disease, particularly in the unvaccinated.”

5. Can coronavirus tests identify omicron?

Early indications suggest that tests in use around Connecticut and elsewhere can accurately identify a coronavirus infection if it is caused by omicron.

Abbott Labs, which manufactures both PCR and antigen tests for the coronavirus, said recently that its tests can detect omicron.

“We have already conducted an assessment of the omicron variant and we’re confident our rapid and PCR tests can detect the virus,” Abbott said in a release. “While the omicron variant contains mutations to the spike protein, Abbott’s rapid and molecular tests — antigen and PCR — do not rely on the spike gene to detect the virus.”

Mutations to that spike gene, specifically a “9 nucleotide deletion,” actually make it easier for Grubaugh and his colleagues to identify omicron. When that absence is noted, it’s probably omicron.

“With omicron, we actually have a method for rapid detection,” Grubaugh explained. “Omicron has a 9-nucleotide deletion in its spike gene, the same that alpha had. There is a particular PCR assay that targets this spike gene region as well as two other genes. When viruses that have this deletion are tested, the other genes are positive but the spike is negative.”