The first inkling of a new, potentially fearsome threat arrived a few days ago. The latest variant of the coronavirus was on the move, the Biden administration was told. And, before long, evidence emerged that the variant — which would be dubbed omicron — carried worrisome mutations.
On Saturday, covid-19 cases caused by the omicron variant were confirmed or suspected in a widening circle of nations, including Britain and Germany. The pharmaceutical companies whose vaccines had appeared to chart a path out of the pandemic expedited development of new formulations targeting the omicron variant.
“This is the highest level of alert we’ve ever been on, by far,” since devising the initial batch of vaccines last year, said Stephen Hoge, Moderna’s president. “What’s most scary about this virus is it’s managed to put all of its greatest hits into one [omicron] variant, and then has added maybe 10 mutations that we don’t even know what to think of yet.”
The frenzy of activity comes as the world waits to learn how far the new variant has spread and whether it can evade current vaccines — answers that are probably weeks away.
“We’re doing all these things, which may seem somewhat draconian,” Anthony S. Fauci, President Biden’s top coronavirus adviser, said in an interview. “It’s only because you want to be better safe than sorry. . . . You’ve got to prepare for the worst, and hope it’s not going to be the worst at all.”
Just as a person’s immune system is primed to react to known pathogens, senior government officials and scientists said they were poised to respond quickly to this latest threat after two years of lessons learned from the pandemic. The United States, the European Union and other nations, including Israel, have already moved to cut travel to South Africa and nearby countries, despite sharp rebukes from African officials and public health experts, who called the moves counterproductive.
“This latest round of travel bans is akin to punishing South Africa for its advanced genomic sequencing and the ability to detect new variants quicker. Excellent science should be applauded and not punished,” the South African government said in a statement Saturday.
White House officials said that the world’s failure to contain the rapid spread of a coronavirus variant known as delta this spring demonstrated the need to be overly vigilant in staving off omicron, which public health experts fear could sicken vaccinated people and spread more rapidly than delta.
“The delta wave changed everything” by reversing the sharp decline of coronavirus cases and deaths in the United States, said an administration official who spoke on the condition of anonymity to describe internal deliberations. “We have to do everything we can to avoid that [scenario] again.”
Biden and White House officials this weekend also urged unvaccinated Americans to get inoculated and called on eligible adults to get booster shots, saying that the vaccines remain the best protection against the virus.
Experts cautioned that the flurry of activity to fight omicron may turn out to be largely unnecessary, as researchers learn in the coming days whether current vaccines can ward off the variant or successfully limit symptoms.
“Bottom line — too soon to know if this will become a dominant strain and if it does, will it be more problematic in terms of vaccine protection,” Susan Weiss, a virologist who helps lead the University of Pennsylvania’s coronavirus research center, wrote in an email, adding that there is “NO evidence that it will cause worse disease.”
But early data from South Africa, where officials say omicron fueled a recent outbreak at breathtaking speed, suggests the new variant is already spreading more quickly than delta. In the populous Gauteng province around Johannesburg, the share of swabs that tested positive for the coronavirus spiked from 3.6 percent Wednesday to 9.1 percent Friday. The country is bracing for the possibility of its public health systems becoming overwhelmed.
Those findings come as many countries continue to struggle with delta. Europe is facing a severe late autumn wave of cases, with deaths rising, sending some countries back into lockdown. A handful of European Union nations have increasingly been targeting the unvaccinated, barring them from restaurants and workplaces.
“Please get vaccinated as soon as possible, if not done yet,” European Commission President Ursula von der Leyen said Friday, adding that Europe was taking the new variant “very seriously.”
In the United States, officials are grappling with an uptick of delta-driven cases and a death toll that has persistently surpassed more than 1,000 average deaths per day since the summer, according to The Washington Post’s daily tracker. Virus-linked hospitalizations have increased more than 10 percent since the start of the month, driven by a surge of cases in Michigan, even as more interactions shift indoors because of the cold weather and holiday gatherings.
Against that backdrop, administration officials said they quickly jumped into action after learning earlier this week that the new variant contained long-feared mutations, such as the potential ability to evade vaccinations, and appeared to descend from a different genetic lineage than delta. Senior officials such as Fauci, Centers for Disease Control and Prevention Director Rochelle Walensky and others began discussions with government scientists, South African officials and vaccine manufacturers that intensified on Thanksgiving Day.
“By the end of Thursday, we had no definitive conclusions on the variant,” said Natalie Quillian, deputy coordinator of the White House’s covid response team. “But our mandate has always been to prepare for every scenario and not be caught flat-footed whenever possible.” So senior officials on Friday morning began preparing potential restrictions that limited travel from South Africa and seven other African countries.
Fauci and other senior officials briefed Biden on Friday, recommending the travel restrictions that the president formally announced later in the day.
While Vice President Harris and other administration officials last year criticized the Trump administration’s decision to restrict travel in the early days of the pandemic — a strategy that was also panned by some public health experts — senior leaders said they had come to believe the tactic could be useful in at least slowing the spread of new variants.
“No matter what you do, this is ultimately going to spread around the world because it appears to be quite transmissible,” Fauci said. But officials can “try to slow it down by blocking the travel from a country that clearly, at this point, is the epicenter,” he added.
Some outside experts criticized the administration’s decision. Scott Gottlieb, the former Food and Drug Administration commissioner, said he supported robust safety checks but not outright bans on travelers from South Africa and other countries until more information about omicron was known.
“Ready, fire, aim is not prudent public health policy,” Gottlieb wrote on Twitter.
The travel measures also likely come too late to stop omicron’s spread, said Jeffrey V. Lazarus, a health systems and policy professor at the Barcelona Institute of Global Health. The World Health Organization said the first confirmed omicron infection came from a specimen collected Nov. 9.
“Travel restrictions give a false sense of security,” Lazarus said, adding that it would be wiser to include strong safeguards for those who fly.
Global policy experts said that the emergence of omicron in southern Africa, where vaccination rates lag behind Western nations, underscores the need to inoculate people in all regions and curb the risk of new outbreaks and variants.
“This may be the moment that shocks the world,” said J. Stephen Morrison, director for global health policy at the Center for Strategic and International Studies. Morrison added that “serious and sustained” cooperation is needed for countries to take actions required to distribute vaccines more widely. “Hopefully this shakes loose more focus on what needs to happen,” he said.
But Fauci and others said that millions of doses of vaccines shipped to nations in lower-income countries have gone unused, demonstrating the complexity of the global challenge. South African officials recently asked vaccine manufacturers to slow their shipments so the country could maximize its existing stock.
Meanwhile, officials at Moderna and Pfizer said that they have been working around-the-clock to prepare new versions of their vaccines, if they’re deemed necessary.
The first data on omicron “scared the heck out of us, because it was like a Frankenstein mixture of the greatest hits,” said Hoge, Moderna’s president. The company on Friday announced a three-part strategy to combat the new variant, including work on targeted booster shots. “The world is primed to fight this thing again,” Hoge said.
While pharmaceutical companies have the capability to make versions of their vaccines targeted to specific variants, they have not previously produced them because existing formulations have been able to provide significant protection — and because shifting the manufacturing process has far-reaching implications, such as slowing down global vaccine production.
“Those sorts of large-scale changes to manufacturing production lines — you don’t want to do those willy-nilly,” Hoge said.
Scientists said they are bracing for the possibility that omicron is the virus variant they’ve long feared: one that forces the world to rapidly adjust its coronavirus-fighting strategy.
“The [genomic] sequences are terrifying when you look at them, because of the number of mutations. It’s another leap in terms of magnitude,” said Jeremy Luban, a virologist at the University of Massachusetts Medical School who directs the variant research program for a consortium of academic and medical institutions in that state.
The sudden appearance of a variant with 30 mutations raises the possibility that it evolved in stealth fashion in a region with little testing, Luban said. South Africa, he said, does have excellent genomic surveillance, which may be why it was the first country to sound the alarm about a new variant.
“Most of the world doesn’t have any monitoring, any sequencing, and we don’t have any idea what’s going on,” Luban said. The lack of genomic surveillance, he said, “is one of the biggest shortcomings of the whole world’s effort to stop this pandemic. We need to vaccinate people and we need to know what’s going on around the planet in places where we don’t have information.”
Epidemiologists have speculated that omicron could have evolved in, and been transmitted by, an immunocompromised patient unable to clear the virus for an extended period. A similar theory arose last year when an earlier variant known as alpha appeared suddenly with a large suite of mutations. Highly mutated viruses have been detected in immunocompromised patients, but there are no documented cases of those viruses causing an outbreak among other people, Luban said.
A major unknown at the moment is whether omicron leads to more severe illness. The opposite could also be true. Epidemiologists say the documented spread of the variant remains limited, and there just isn’t enough data to reach any conclusion.
“It is possible that this thing is much more transmissible than even Delta, but it’s less pathogenic,” Luban said, adding, “That would be very lucky.”
Nor is it known whether the variant actually erodes the immune system’s protections against infection or severe disease.
Immunity can be conferred by either recovery from infection or by vaccination, with the vaccination-induced protection being more consistent, according to recent research from the CDC.
But immunity is not an either-or situation; some protection may remain even if diminished to some degree. Immunity is rarely absolute, and a vaccinated or infection-recovered person potentially can get an infection from the dominant delta variant. Those infections are less likely to result in severe illness compared with infections among people who are unvaccinated or without prior exposure to the virus.
Inside the White House, the president’s top coronavirus adviser said he’s waiting for more data before rendering a verdict on omicron’s risks.
“The big unknown in this whole story, which we will find out, I think within the next couple of weeks: Is the severity of this infection different than the severity of delta in a vaccinated or unvaccinated person,” Fauci said.
Diamond and Achenbach reported from Washington. Harlan reported from Rome. Wroughton reported from Cape Town, South Africa. Annie Linskey, in Nantucket, Mass., contributed to this report.