What We Know So Far as Omicron Variant Identified in US

The first Midwest case of the omicron COVID variant was confirmed in Minnesota via a specimen from a resident "with recent travel history to New York City."

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The new omicron COVID variant has been identified in the United States, officials announced Wednesday, but what do we know about the first U.S. case, the variant itself and why experts are concerned?

Here's a breakdown of what we know so far.

What do we know about the first US omicron case?

A person in San Francisco, California who had been vaccinated against COVID-19 became the first in the U.S. to have an identified case of the omicron variant, the White House announced Wednesday as scientists continue to study the risks posed by the new virus strain.

Dr. Anthony Fauci told reporters that the person was a traveler who returned from South Africa on Nov. 22 and tested positive on Nov. 29. Fauci said the person was vaccinated but had not received a booster shot and was experiencing “mild symptoms.”

Officials said they had contacted everyone who had close contact with the person and they had all tested negative.

Genomic sequencing was conducted at the University of California, San Francisco and the sequence was confirmed by the Centers for Disease Control and Prevention.

Have any cases been reported in Chicago or Illinois?

Though the new omicron COVID-19 variant has not yet been identified in Illinois, the state and city of Chicago are preparing for cases to be reported here.

Illinois' top doctor said Wednesday, following news of the first U.S. case, "we anticipate there will be cases in Illinois."

"We knew it was only a matter of time before the Omicron variant was identified in the U.S. and we anticipate there will be cases in Illinois," Illinois Department of Public Health Director Dr. Ngozi Ezike. "IDPH continues to perform sequencing to identify the variant. IDPH has renewed its request for hospitals and laboratories to provide positive specimens for sequencing. As soon as the Omicron variant is identified in Illinois, IDPH will share this information.

Similarly, Chicago officials said the variant will likely arrive in the city in the near future.

"We don't have any reason to believe at this moment that omicron is here, but given the way in which this virus' variants spread, I think we have to assume that it will get here at some point," Chicago Mayor Lori Lightfoot said this week.

Where else have cases been reported so far?

The extent of the actual spread of the omicron variant around the world still remains unclear as countries discover new cases each day.

The WHO reported Wednesday that 23 countries have identified omicron cases so far, up from 18 just two days ago, and that number is expected to rise in the coming days and weeks.

The Dutch public health authority confirmed that 13 people who arrived from South Africa on Friday have so far tested positive for omicron. They were among 61 people who tested positive for the virus after arriving on the last two flights to Amsterdam’s Schiphol airport before a flight ban was implemented. They were immediately put into isolation, most at a nearby hotel.

Canada’s health minister says the country's first two cases of omicron were found in Ontario after two individuals who had recently traveled from Nigeria tested positive.

Authorities in Australia said two travelers who arrived in Sydney from Africa became the first in the country to test positive for the new variant. Arrivals from nine African countries are now required to quarantine in a hotel upon arrival. Two German states reported a total of three cases in returning travelers over the weekend.

A new surge was long anticipated and even a new variant, but the speed with which omicron hit came as a “shock” to South Africa’s health experts.

While numbers of confirmed cases are still relatively low, they have been increasing at a high rate. The new spike started after some student parties in Pretoria. Numbers quickly jumped from a few hundred cases a day to thousands. South Africa announced 3,220 new cases Saturday, of which 82% are in Gauteng province — home to Pretoria and South Africa's largest city of Johannesburg, according to the National Institute for Communicable Diseases. That's still well below the peak of the last wave, when more than 25,000 were confirmed in a day.

As many as 90% of the new cases in Gauteng province are caused by omicron, Tulio de Oliveira, director of the KwaZulu-Natal Research Innovation and Sequencing Platform, said in a tweet, citing the results of diagnostic tests.

What are the symptoms of omicron?

COVID symptoms linked to the omicron variant have been described as "extremely mild" by the South African doctor who first raised the alarm over the new strain.

Dr. Angelique Coetzee, chair of the South African Medical Association, told the BBC on Sunday that she started to see patients around Nov.18 presenting with "unusual symptoms" that differed slightly to those associated with the delta variant, which is the most virulent strain of the virus to date and globally dominant.

"It actually started with a male patient who's around the age of 33 ... and he said to me that he's just [been] extremely tired for the past few days and he's got these body aches and pains with a bit of a headache," she told the BBC.

The patient didn't have a sore throat, she said, but more of a "scratchy throat" but no cough or loss of taste or smell — symptoms that have been associated with previous strains of the coronavirus.

Coetzee said she tested the male patient for COVID, and he was positive, as was his family, and then said she saw more patients that day presenting with the same kinds of symptoms that differed from the delta variant.

Other patients she had seen so far with the omicron variant had also experienced what she described as "extremely mild" symptoms, and she added that her colleagues had noted similar cases.

"What we are seeing clinically in South Africa — and remember I'm at the epicenter of this where I'm practicing — is extremely mild, for us [these are] mild cases. We haven't admitted anyone, I've spoken to other colleagues of mine and they give the same picture."

Here's a complete breakdown of symptoms by variant.

Similarly, in the U.S. case, Fauci said the person was vaccinated but had not received a booster shot and was experiencing “mild symptoms.”

But Moderna CEO Stephane Bancel told CNBC on Monday that omicron symptoms reported in South Africa may not be a good predictor of the variant's virulence in other parts of the world, because the country has a much younger and healthier population than European nations and the United States.

"The trick is you're not going to be able to tell the difference between omicron, delta lambda, plain COVID from the beginning," Landon said. "Influenza or even common rhinovirus causes most of our common colds in the winter. You're not going to know the difference between those if you just look at your symptoms. For many people, those symptoms are overlapping. And while there are some parts of the Venn diagram like taste, loss of taste and smell, or common COVID than these other things, there's a lot of overlap. You're just not going to know especially at the beginning of an illness, what kind of illness you have. You have to get tested."

But getting tested won't necessarily tell you if you have the omicron variant, Landon said.

"When you get a COVID test they're just looking for whether or not you have COVID," she said. "They're not on which kind of in order to figure out the exact strain of COVID. You have to do this thing called sequencing, which takes a lot longer. It's much more intensive. You certainly can't get that back in 24 hours, and it's only done by specialized labs."

What makes omicron a variant of concern?

Despite the global alarm there is still little understanding about the variant and how virulent it may be.

The World Health Organization announced last week that omircon has been classified as a "variant of concern."

Hospitalizations are rising across South Africa, but it's still too early to know whether the omicron variant is driving an increase in severe Covid-19 cases, according to the World Health Organization.

Maria Van Kerkhove, Covid technical lead for the WHO, said Wednesday that some patients infected with omicron are showing mild symptoms, but there are also reports of cases in which the disease becomes more severe. Hospitalizations could be rising due to a general increase in Covid cases and not necessarily because omicron is more lethal, Van Kerkhove said.

"With regards to severity, there are studies that are underway looking at hospitalizations, looking at those individuals who are hospitalized, whether or not they have this variant or not," Van Kerkhove told reporters during an update in Geneva. "We're also getting a picture of some of the cases that are detected in other countries."

Van Kerkhove said early evidence on omicron, known by the technical term B.1.1.529, shows that the variant has a large number of mutations, some of which have concerning characteristics.

Omicron has also shown to have an increased risk of reinfection compared to other highly transmissible variants, indicating that people who contracted COVID and recovered could be more subject to catching it again with this variant.

"[The omicron variant is] outcompeting the delta variant, outcompeting the beta variant and very quickly," Chicago Department of Public Health Commissioner Dr. Allison Arwady said Tuesday. "So, it is probably more infectious, more contagious than delta."

Arwady noted that within just 12 days, 90% of COVID-19 cases in South Africa have been detected as the omicron variant. Whereas both the delta and beta variants took about 100 days to saturate 80-90% of the the country.

The leading infectious disease expert for the U.S., Dr. Anthony Fauci, added that public health experts are trying to find answers to questions such as whether the omicron variant causes more severe illness and whether it can evade protection from vaccines or treatments.

"It also has a bunch of mutations that would suggest it could evade the protection, for example, of monoclonal antibodies and perhaps even convalescent plasma for people who have been infected and recovered, and possibly vaccine. These are all maybes, but the suggestion is enough," Fauci said.

The quick spread of the variant is also concerning, Fauci said.

"It seems to have really spread rather rapidly in South Africa, even though the numbers are relatively small, its ability to infect people who have recovered from infection and even people who have been vaccinated make us say, 'This is something you've got to pay really close attention to, and be prepared for something that's serious,'" Fauci explained. "It may not turn out that way, but you really want to be ahead of it, and that's the reason why we're doing what we're doing."

Dr. Scott Gottlieb, a Pfizer board member and a former commissioner of the U.S. Food and Drug Administration, told CNBC on Wednesday that there was a mini-delta surge in South Africa as well as an uptick in a separate variant, C.1.2, which complicates efforts to gain clarity on omicron's transmission and virulence.

"All we know is really the basic science," said Dr. Emily Landon, infectious disease specialist and chief hospital epidemiologist at University of Chicago Medicine. "That means that we know the sequence of the virus and that means we can tell what the spike protein looks like compared to what the usual spike protein looks like. The mutations that are present in the spike protein are concerning. Some of them are the same ones that have made delta variant very, very transmissible. There are also additional changes in the spike protein that we're seeing in the beta variant and the lambda variant. Those are the two that we were concerned might be able to bypass immunity from the vaccine."

Still, doctors say more time is needed to truly determine the severity of the new variant.

"It's important to know that just because we see these changes and they're changes that we've registered before as being consistent with or going along with less vaccine immunity, sort of the vaccine being not quite as good or being more likely to transmit more quickly and more easily from person to person, does not necessarily mean that this particular virus is going to take over and be the most common variant when that's the case ," Landon said. "We just don't know yet."

Dr. Emily Landon, infectious disease specialist and chief hospital epidemiologist at University of Chicago Medicine answers questions on the new omicron COVID variant.

What about vaccines and prevention of the new variant?

Earlier this month, the Centers for Disease Control and Prevention cleared the way for all adults to get a COVID-19 booster shot, if they want one. But now, with the emergence of the new omicron variant, the CDC is intensifying that message — saying those over 18 years old should get one.

"Everyone ages 18 and older should get a booster shot ... when they are six months after their initial Pfizer or Moderna series," CDC Director Dr. Rochelle Walensky said in a statement Monday.

"The recent emergence of the omicron variant (B.1.1.529) further emphasizes the importance of vaccination, boosters, and prevention efforts needed to protect against COVID-19," she added.

Similarly, Chicago health officials urged residents to get their booster shots or get vaccinated if not already.

"I want people to get a booster now," Arwady said. "Why do I want people to get a booster now? Because right now -- forget omicron -- delta [variant] is doing a job on Chicago and on the upper Midwest."

Moderna's Chief Medical Officer Paul Burton said Sunday the vaccine maker could roll out a reformulated vaccine against the omicron coronavirus variant early next year.

The vaccine maker "mobilized hundreds" of workers starting early Thursday morning, on Thanksgiving, to start studying the new variant, the company said in a statement.

Current vaccines could provide some protection, depending on how long ago a person was injected, Burton said. Still, he said unvaccinated people should get vaccinated or receive their booster shots, if eligible.

It's not clear whether new formulations will be needed, or if current COVID vaccinations will provide protection against the new variant that has begun to spread around the globe.

"We should know about the ability of the current vaccine to provide protection in the next couple of weeks, but the remarkable thing about the mRNA vaccines, Moderna platform is that we can move very fast," Burton said on BBC's "Andrew Marr Show."

"If we have to make a brand new vaccine I think that's going to be early 2022 before that's really going to be available in large quantities," the Moderna chief added.

According to Van Kerkhove, the WHO Technical Advisory Committee for Virus Evolution will be meeting "regularly" concerning the new variant.

She noted, however, that tests can take days and weeks to receive results that could provide a better understanding of the impacts with omicron.

Until more information is found, Van Kerkhove encouraged people to prevent their exposure to COVID infection by distancing, wearing a mask, avoiding crowded spaces, consistently washing hands and getting vaccinated.

Where is travel being restricted?

As cases of the variant are confirmed around the world, an increasing number of nations are tightening their borders despite pleas for caution and outbursts of dismay from some. 

Effective Monday, the U.S. has restricted travel from South Africa and seven neighboring countries: Botswana, Zimbabwe, Namibia, Lesotho, Eswatini, Mozambique and Malawi.

Israel moved to ban entry by foreigners and mandate quarantine for all Israelis arriving from abroad.

And Japanese Prime Minister Fumio Kishida said Monday that Japan is considering stepping up border controls. Kishida told reporters that he planned to announce new measures in addition to the current 10-day quarantine requirement for travelers from South Africa and eight other nearby countries. Japan still has its border closed to foreign tourists from any country.

Morocco's Foreign Ministry tweeted Sunday that all incoming air travel to the North African country would be suspended to “preserve the achievements realized by Morocco in the fight against the pandemic, and to protect the health of citizens.” Morocco has been at the forefront of vaccinations in Africa, and kept its borders closed for months in 2020 because of the pandemic.

Many countries are introducing such bans, though they go against the advice of the WHO, which has warned against any overreaction before the variant is thoroughly studied.

In a statement to NBC 5, Chicago-based United Airlines said that it is monitoring how the new travel restrictions will impact demand for flights, but says that it has not made any adjustments to its schedule.

Which variants are in Illinois as of now?

These were the COVID variants in Illinois, as of Friday:

Alpha (B.1.1.7): 7,063
Beta (B.1.351): 112
Delta (B.1.617.2): 16,486
Delta (AY.1): 34
Delta (AY.2): 29
Delta (AY.3) 3,104
Gamma (P.1): 2,687

What is the Chicago-area doing about the new variant?

Illinois encouraged residents to get vaccinated as soon as possible as concerns around the new variant rise.

"At this time, IDPH urges everyone 5 years and older to get vaccinated and all eligible adults to get a booster," Ezike said. "People should continue to take the public health precautions we’ve recommended – vaccinate, booster, wear a mask, avoid crowds, test, and physically distance. As public health officials and scientists worldwide learn more about omicron – transmissibility, severity, and vaccine effectiveness – IDPH will share that information with the public."

Chicago officials are also preparing for the new omicron COVID variant, though they said there are still many questions to be answered about the emerging variant of concern.

In a statement Monday, Lightfoot and Arwady said the city is "very engaged in the heightened discussions regarding the omicron variant of the COVID-19 virus, particularly with our federal partners."

"At this point, there are many questions which scientists across the world, and at the Chicago Department of Public Health, are actively working to address all while closely monitoring this strain," the statement read. "While that work continues, we must as a city, and importantly as individuals, continue to follow the public health guidance: get vaccinated, and if vaccinated, get your booster; wear a mask indoors and when you're around other people; and if you are feeling sick, stay home to save lives. The unvaccinated remain the most at risk to themselves and others so please get vaccinated as soon as possible."

Scientists across Chicago are working day and night to determine if the latest COVID-19 variant has hit our area. NBC 5's Chris Hush goes inside a laboratory where hundreds of samples are being examined for the omicron variant.

Similarly, Cook County's health department said on Friday it was watching the variant "very carefully."

"We don't know if the variant has reached the United States, but given the global concern about the virus, it is more important than ever to continue to follow public health recommendations: Mask Up, Wash Your Hands, Stay Physically Distant, and most importantly, get vaccinated and get your booster as soon as you are eligible," said Dr. Rachel Rubin, co-lead and senior medical officer for the Cook County Department of Public Health. "The longer people do not get vaccinated, the risk of deadlier variants increases."

What are other states and countries doing about omicron?

In addition to travel bans, on Friday, New York Gov. Kathy Hochul declared a state of emergency amid a recent surge in coronavirus metrics and concern for potential spikes due to both the Delta and Omicron variants.

Going into effect on Dec. 3,the order will allow New York to acquire pandemic-fighting supplies, increase hospital capacity and fight potential staffing shortages. It would also allow the state Health Department to limit non-essential and non-urgent procedures at hospitals.

In advice to its member states, the U.N. agency urged them to accelerate COVID-19 vaccination coverage "as rapidly as possible," particularly among high-priority groups, and to enhance surveillance and sequencing efforts.  

Spain announced it won't admit unvaccinated British visitors starting Dec. 1. Italy was going through lists of airline passengers who arrived in the past two weeks. France is continuing to push vaccinations and booster shots.

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