The first U.S. Omicron case was reported in California, the C.D.C. said today, signaling the arrival of a potentially dangerous new phase of the pandemic in the country.

The patient, who returned to the state from South Africa on Nov. 22, is in isolation, and aggressive contact tracing is underway. The individual was fully vaccinated, was not hospitalized and had mild symptoms that were improving. People in close contact with the individual have tested negative.

Gov. Gavin Newsom said the patient had received two doses of the Moderna vaccine but was within the six-month window and had thus not received a booster.

California health officials said the state was increasing coronavirus testing at airports, focusing on arrivals from countries identified by the C.D.C. as potential sources of the virus. Newsom said that the state would not be intensifying public health restrictions, at least in the short term.

The discovery prompted Biden administration officials to renew their urgent calls for Americans to get fully vaccinated and, if eligible, a booster shot.

“We’re learning more every single day,” Biden said at the White House today. He vowed that the administration would “fight this variant with science and speed, not chaos and confusion.”

Dr. Anthony Fauci stressed the additional protection that booster shots provide across variants of the virus and said Americans should not wait for pharmaceutical companies to develop a booster shoot against Omicron.

“Get boosted now,” Fauci said. “We may not need a variant-specific boost.”

More Omicron cases in South Africa

South Africa’s National Institute for Communicable Diseases said today that Omicron had been found in nearly three quarters — 74 percent — of all virus genomes sequenced in the country in November. Omicron has now overtaken Delta as the most prevalent variant in South African samples.

My colleague Lynsey Chutel, who covers southern Africa for The Times, told me that scientists now know the variant was present in the country as early as Nov. 8.

Virus cases are also surging in South Africa. In the last 24 hours, the country’s test positivity rate jumped to 16.5 percent, from 10.2 percent. In mid-November, before the detection of the Omicron variant, the positivity rate hovered around 1 percent.

Many questions remain about whether the new variant causes more severe illness than others. Officials in South Africa reported Omicron cases with symptoms that ranged from “mild disease all the way to severe disease,” but no deaths to date.

Tulio de Oliveira, director of the KwaZulu-Natal Research and Innovation Sequencing Platform, said that Omicron “seems to cause much more breakthrough infections than the previous ones.” But there is still much we don’t know.

For the latest on Omicron in South Africa, I spoke with Lynsey.

What do we know about the people infected with Omicron in South Africa and how they’re doing?

At this point, we just don’t know much. Hopefully, once we have data on the link between hospitalizations and the Omicron variant, we’ll also have a clearer idea about the severity of illness caused so far.

It’s worth noting, though, that the spike in infections has largely been among young people under the age of 35. This also happens to be the cohort that is least vaccinated, and the most socially active group, according to epidemiologists. In Pretoria, where we first saw infections spike, scientists have also seen an increase in hospitalizations among people ages 20 to 44.

Worryingly, there is also an increase in hospitalizations in children younger than 2. These are just some of the concerning patterns that we’re hoping to have more insight into soon.

How did we get here?

Before the detection of the new variant, South Africa recorded its lowest daily new cases since the start of the pandemic. To some scientists, it seemed a form of herd immunity had been reached through an overlap of vaccinations and previous infections.

The uptick in cases was the first sign that South Africa was most likely entering a fourth wave. By the end of November, the number of new infections shot up to 4,373. Most of these are in Gauteng province, South Africa’s densely populated economic hub, which is also home to the administrative capital, Pretoria, and the largest city, and my home: Johannesburg.

How is the government responding?

News of the new variant could not have come at a worse time for South Africans. December is the holiday season here, and it is also the height of summer. Millions of people travel from cities to rural areas, coming together at social gatherings. In the first few days after the announcement of the detection of the Omicron variant, South Africans were holding their breath for another lockdown. In the past, we’ve seen inter-provincial travel banned, beaches closed and a strict curfew. All of this was not only bad for morale, our already battered economy took a knock.

However, we’re not going into lockdown yet, and the state’s public health response has emphasized vaccines. In fact, President Cyril Ramaphosa announced on Sunday that his cabinet was considering introducing vaccine mandates.

South Africa now has enough vaccines to cover the adult population and has also started vaccinating children ages 12 to 17. However, uptake has plateaued, with vaccine hesitancy becoming a worrying issue. So far, 36 percent of adults are fully vaccinated, but that is only half of the vaccination target the government set for the end of December.

How are people feeling?

The travel bans seem to be the most important topic in the public conversation. For one, it hurts our economy after two tough years that saw tourist numbers drop.

But more than that, South Africa is smarting from feeling punished for sharing scientific data and being transparent. Botswana’s health minister lamented the early use of the term “Botswana variant” and asked why scientists from this small African nation weren’t celebrated instead. Now, in South Africa at least, news that the variant was likely in Europe long before the announcement is being met with a bit of schadenfreude.

More in Africa: Lynsey and Max Fisher explored how vaccine skepticism is slowing the rollout across the continent. And Nigeria and Ghana are the latest African countries to detect the Omicron variant.

OMICRON AND OTHER CORONAVIRUS VARIANTS: WHAT YOU NEED TO KNOW
By Louis Jacobson, PolitiFact, Kaiser Health News PUBLISHED ON DEC 2, 2021

Americans, already weary of a pandemic nearly two years long, were dealt a new blow during the long Thanksgiving weekend: the announcement that a new coronavirus variant had emerged.

The omicron variant, officially known as B.1.1.529, surfaced in November in several southern African nations. It set off alarm bells worldwide when public health officials in South Africa saw it beginning to outcompete the previous reigning variant, delta. This suggested that omicron could eventually spread widely. Indeed, omicron has since been reported on multiple continents, likely due to international travel by people unknowingly infected.

After the emergence of omicron was announced, several nations imposed travel bans hoping to contain the virus. Whether those bans will effectively slow the spread remains unknown. “Travel bans don’t help once the horse is already out of the barn, as we’ve seen before and are seeing now,” said Tara Smith, a Kent State University epidemiologist.

Scientists caution that it’s still too early to say whether omicron will prove as dangerous as delta. Other variants that initially seemed worrisome have flamed out.

For now, here’s what we know, and don’t know, about the omicron variant.

What Is a Variant?

A variant of a virus is one that has mutated in a way that bolsters its spread or severity compared with the original strain that emerged in Wuhan, China. “RNA viruses like the coronavirus can mutate when they replicate, especially when circulating at high rates,” said Dr. Monica Gandhi, professor of medicine at the University of California-San Francisco.

Coronaviruses do not mutate as readily as influenza viruses do, but they do mutate over time. The variants generally produce the same range of symptoms as the original strain of the coronavirus. But the mutations may help the virus spread more effectively from person to person, or have an advantage in sneaking past either natural or vaccine immunity.

What Variants Were Already Circulating in the United States?

To date, public health officials have noted five “variants of concern,” plus two “variants of interest” not yet considered as worrisome. So far, no variants have emerged that fit the most worrisome of the three official categories — “variants of high consequence.”

The World Health Organization decided early this year to name the variants after Greek letters, both to simplify the discussion and to limit the stigma of having a variant named for a country.

The first four “variants of concern” — alpha, beta, gamma and delta — have been circulating in the United States for most of this year. But the most dominant variant has been delta, due to its ability to spread from person to person more quickly than other variants. For months, delta has accounted for more than 99% of coronavirus infections in the U.S.

There were no confirmed cases of omicron in the United States as of midday Nov. 29, but experts warn it’s just a matter of time. It could be in the U.S. already, merely undetected.

How Did Omicron Emerge?

Though scientists aren’t sure precisely where omicron first surfaced, it was most likely in a southern African nation.

Experts say low vaccination rates in that part of the world probably played a role in creating a favorable environment for the mutations that produced omicron. (It can be pronounced either AH-mi-crahn or OH-mi-crahn.)

“Many countries in Africa have populations with very low immunity — about 30% in South Africa are vaccinated,” Smith said. “In a largely non-immune population, the virus can sweep through, and each new person infected is a chance for the virus to mutate.”

Why Did Public Health Officials React So Urgently to Omicron?

The concern stems from the scope and nature of the new variant’s mutations. South African health officials noted 50 notable mutations, 30 of which are on the spike protein, a key structure in the virus, New York magazine reported. That’s more than previous variants have had.

“If we were looking out for mutations that do affect transmissibility, it’s got all of them,” University of Oxford evolutionary biologist Aris Katzourakis told Science magazine.

Still, what’s uncertain at this point is how effectively those mutations will work together in creating a variant that can consistently outcompete delta.

What Do We Know About Omicron’s Degree of Infectiousness?

The omicron variant is so new that scientists are just beginning to learn about its characteristics. Because of this, experts urge caution in drawing conclusions, especially from anecdotal evidence.

That said, scientists say they would not be shocked if omicron becomes as easily transmissible as delta.

“The answer is uncertain, of course, but it looks as though it will be at least as infectious as delta,” said Dr. William Schaffner, a professor of preventive medicine at Vanderbilt University School of Medicine.

One complicating factor, Schaffner said, is that the initial areas of fastest spread have been in areas of Johannesburg populated by young adults and college students, who tend to have lower vaccination rates. The vulnerability of these groups to infection may be exaggerating how rapidly omicron seems to be spreading.

What Do We Know About Whether Omicron Makes Patients Sicker?

The early evidence is somewhat conflicting, but there are signs that symptoms from omicron may not be more severe than previous variants. Dr. Angelique Coetzee, who chairs the South African Medical Association, has said that the early cases being seen among the unvaccinated are mild.

It remains to be seen, however, whether older and unhealthier patients will also see milder symptoms. Another caveat is that it may be too early in omicron’s spread to see cases that have seriously progressed.

Will Existing Vaccines Be Effective Against the Omicron Variant?

Scientists are cautiously optimistic that existing vaccines will also be effective against omicron, just as they have been against delta, at least in being able to prevent illness severe enough to require hospitalization.

“Scientists in South Africa and Israel, where the variant has also been detected, have indicated that they are not seeing severe disease among the vaccinated,” Gandhi said.

Gandhi added that the immunity-providing B cells produced by the vaccines have been shown to produce antibodies against variants, and that T-cell immunity, which protects against severe disease, is robust and should not be at risk from the mutations being seen in omicron. The vaccines also produce polyclonal antibodies that work against multiple parts of the spike protein, she said. Finally, booster shots have been shown to be effective in strengthening immunity quickly.

“Most scientists believe we should still have protection against severe disease with vaccinations, and vaccination remains the mainstay of control,” Gandhi said.

Bottom line: If you haven’t been vaccinated, and especially if you haven’t had the disease yet, get vaccinated. And if you’ve already been vaccinated, get a booster.

How Long Will It Be Before We Have a Better Handle on the Threat From Omicron?

Moderna, Pfizer-BioNTech and Johnson & Johnson are all testing the effectiveness of their existing vaccines against omicron in the lab, based on variant-analysis protocols developed early this year. Those results should be available in a week or two.

Other questions — including whether omicron makes you sicker, and whether it’s more transmissible — will take longer to answer because they require careful contact tracing and accurate diagnoses of those infected.

To better answer those questions, Smith said, “I think, at a minimum, it will take a month to get some preliminary data, and quite possibly longer to really know the fuller picture. We also won’t know about real-world experience in vaccine breakthroughs until that time.”

Can We Expect a Specific New Booster to be Developed for Omicron?

It’s unknown whether the omicron variant will require a reformulated booster. A newly formulated booster wasn’t necessary for delta, because researchers determined that the existing formulation was still effective.

That said, vaccine makers can jump in with a new booster quickly if they have to.

In the event that such a variant emerges, Pfizer and BioNTech “expect to be able to develop and produce a tailor-made vaccine against that variant” within 100 days, pending regulatory approval, a Pfizer spokesperson told The Washington Post.

Dr. Matthew Laurens, a specialist in pediatric infectious diseases at the University of Maryland School of Medicine, said he’s confident boosters could be developed and tested quickly if needed, “likely within a few months.”

What Happened to the Other Variants?

Between May 2021, when delta was named a variant of concern, and November 2021, when omicron was given the same label, two other variants were elevated to the lower “variant of interest” status: lambda from Peru and mu from Colombia. Other variants, such as one discovered in Nepal called “delta-plus,” attracted notice during that period as well. But none of these managed to outcompete delta in a consistent way, so they were never elevated to “variant of concern.”

This is the most hopeful outcome for omicron. The other variants “all had similar concerns around them, but they didn’t expand to any significant degree after the initial reporting,” Gandhi said.

Is It Reasonable to Think the U.S. Is in a Better Position to Handle Omicron Than It Was for Delta?

Experts generally agreed that the United States should be better prepared to battle omicron than it was when delta emerged earlier this year.

“We are in a much better position since we have higher rates of vaccination, the availability of boosters for everyone over 18 and vaccine eligibility down to 5 years old,” Gandhi said. “We also have higher rates of natural immunity in this country due to the delta variant’s spread since July 2021. And we have oral antiviral therapeutics on the horizon. So we have the tools to fight this new variant.”

The challenge, Schaffner said, will be to make sure Americans continue to get vaccinated and boosted, and to make use of testing and maintain safe behavior in public.

“All these tools are available,” he said. “The big question is how inclined the general public is to use these tools.”

Is the Coronavirus Going to Be Around Permanently, Like the Flu?

Experts now believe it’s unlikely that the coronavirus will either be eradicated from the globe, like smallpox has been, or even eliminated in the United States, as polio was following near-universal vaccination. The combination of rapid mutations and too-low vaccination rates make it likely that covid-19 won’t follow smallpox and polio into submission.

“This will more likely be the influenza model, where we have to track mutations annually and alter the boosters accordingly,” Schaffner said. In fact, he said, efforts to create combined coronavirus-flu shots are already underway.

This story was produced by KHN (Kaiser Health News), a national newsroom that produces in-depth journalism about health issues. Together with Policy Analysis and Polling, KHN is one of the three major operating programs at KFF (Kaiser Family Foundation). KFF is an endowed nonprofit organization providing information on health issues to the nation.