New Covid Variant Omicron, Most Alarming Yet


By Meryl Kornfield, Adela Suliman, Christine Armario & María Luisa Paúl 

A new variant of the coronavirus that causes covid-19 is raising concern around the globe.

South Africa on Thursday confirmed that scientists there had detected a variant with a high number of mutations that could make it more easily transmissible. On Friday, the World Health Organization labeled it a “variant of concern,” a classification it has given to four other variants. The global health agency also gave it a Greek letter designation: omicron.

Several countries, including the United States, moved to curb flights Friday and Saturday from southern Africa, while epidemiologists began working to identify how far the variant may have spread. Cases have been identified in at least eight nations, most but not all tied to recent travel to Africa.

There is too little research to draw conclusions, with experts urging caution but not panic. Studies are underway to examine how vaccines hold up against the new variant, with some experts expressing initial optimism that they will offer protection. Officials in South Africa said most of those hospitalized with omicron had not gotten immunized.

“This is the most concerning variant we’ve seen since delta,” Eric Topol, director of the Scripps Research Translational Institute, said in an interview Friday. “It’s going to take a really high bar for something to take over for delta, and we don’t know whether this is going to do it.”

Where has omicron been confirmed?

Although it is unknown where the variant came from, it was first detected in southern Africa. On Tuesday, scientists in South Africa made data of the variant public. Noticing the distinct sequence, a virologist at Imperial College London, Tom Peacock, raised alarms about the “really awful Spike mutation profile.”

In South Africa, where nearly 25 percent of the adult population is fully vaccinated, the variant has spread rapidly. There were 50 new daily cases of coronavirus per 100,000 people in South Africa from Nov. 20 to Saturday, a 592 percent increase from the previous week.

At a news conference Friday, Ian Sanne, an infectious-disease specialist and member of South Africa’s Ministerial Advisory Council on COVID-19, said that the new variant was becoming the dominant type and that “overall, we do think it’s more transmissible.”

Cases have also been identified in Britain, Belgium, Botswana, Germany, Hong Kong and Israel. Reuters reported that Italy — once the epicenter of the pandemic — had confirmed omicron infection there. Most of the cases outside Africa appear to involve people who had traveled to the continent. Dutch health authorities said Saturday that testing of about 600 passengers who arrived from South Africa found 61 were infected with the virus — though with which variant was still unknown.

The Centers for Disease Control and Prevention said Friday that omicron had not been detected in the United States, but that doesn’t have officials resting easy. New York Gov. Kathy Hochul (D) declared a state of emergency Friday in response to a cold-weather surge of infections and the threat of the new variant, saying, “It’s coming.”

What do we know about the new variant?

Omicron’s genetic profile is unique from other circulating variants, meaning it represents a new lineage of the virus.

It is distinct from other variants in another critical way: There’s a greater number of mutations. Tulio de Oliveira, director of the Center for Epidemic Response and Innovation in South Africa, said there are more than 30 mutations in the spike protein, the part of the virus that binds to human cells, allowing it to gain entry.

Scientists say omicron could be more transmissible and better at evading the body’s immune defenses, making vaccines less effective. The World Health Organization said Friday that preliminary evidence suggests an “increased risk of reinfection” compared to other variants.

“The one good news, if there’s any good news, is that this variant, the B. 1.1.529, can be detected by one particular PCR assay,” de Oliveira said at a news conference, meaning diagnostic labs can quickly identify the new variant.

Jesse Bloom, a virologist at the Fred Hutchinson Cancer Research Center who has conducted mutational scanning experiments for the B. 1.1.529 variant, noted that three mutations of the variant could make the virus a more elusive target for antibodies produced through vaccines or prior infection, but cautioned that there is still much to learn.

“What that’s going to mean for how likely people are to get infected, even if they’ve been vaccinated, it’s too early to say,” Bloom said, noting that more traditional experiments should provide more data. “But having a drop in the antibody neutralization is never a good thing.”

Linda Bauld, a professor of public health at the University of Edinburgh, said there were “genuine” causes for concern given that “it does look like a more transmissible variant.” But she added: “I think it’s premature to panic. … There’s just a lot we don’t know at the moment.”

What’s being done to halt the spread of omicron?

Within days of the discovery of the variant, several countries began imposing restrictions on flights to and from South Africa and its neighbors.

Israel closed its borders to “foreigners from all countries.” Australia, Britain, Japan, Thailand and others introduced travel bans or quarantine rules for air passengers arriving from the southern African region. The European Union and the United States have also announced restrictions.

The U.S. restrictions will apply to travelers from South Africa, Botswana, Zimbabwe, Namibia, Lesotho, Eswatini, Mozambique and Malawi. They do not apply to American citizens and lawful permanent residents. President Biden, in a statement, said the move is “a precautionary measure,” and urged Americans to get vaccinated and get booster shots.

“If you have not gotten vaccinated, or have not taken your children to get vaccinated, now is the time,” he said.

Officials in South Africa expressed concern about the travel bans, while some experts cast doubt on the efficacy of the restrictions and whether they could “give a false sense of security.” The nation’s health minister, Joe Phaahla, characterized them as a “draconian reaction.”

“It really doesn’t look scientific in any way,” he said. “That kind of reaction is quite a knee-jerk and panicked and almost wants to put a blame on other countries rather than work together.”

Before the novel coronavirus spread through the world, a study published in February 2020 in the Journal of Emergency Management found that a travel ban could delay the arrival of an infectious disease in a country by days or weeks. However, little evidence suggested it eliminated the risk of it jumping borders in the long term.

Amesh Adalja, an infectious-disease physician and professor at Johns Hopkins University, said the measure would do little or nothing for curbing the spread of a variant that may have been “spreading for probably several days or weeks before it was noticed.”

When “full containment is not ever going to be possible,” he said, the focus should shift toward improving nations’ testing capabilities and boosting vaccinations — particularly in places where the virus continues surging, such as the United States and Europe.

Like other experts, Adalja praised South Africa’s robust surveillance system, saying it doesn’t deserve punishment, especially because its infections per capita are below that of the United States.

“What should be happening is South Africa should be getting praised, not punished, not penalized, not stigmatized,” he said. “Not because of anything they did wrong, but because of something they did right. Because they’re better at sequencing than the U.S.“

Do we know whether vaccines are effective against omicron?

Even if the variant limits the effectiveness of vaccines, it probably will not completely subvert the protections that vaccines provide, experts say.

“My expectation would be that the mutations in this variant are not going to ablate or completely escape that type of antibody neutralization” from vaccines or prior infection, Bloom said.

“Regardless of whether or not this new variant ends up spreading, I would suggest that people do what they can to minimize their chances of getting infected with SARS-CoV-2,” Bloom added, referring to the virus by its technical name. “There are certain obvious things you can do: Get vaccinated, get a booster vaccination, wear a mask.”

Though the sample size is small, Sanne said physicians have seen a higher rate of breakthrough infections among those previously vaccinated in South Africa. But he added that initial data indicates the vaccines are still proving effective, with the majority of hospitalizations being among those who hadn’t gotten immunized.

“We have every indication that the vaccines are still effective in preventing severe disease and/or complications,” he said. “The data, however, is small and early.”

Meanwhile, vaccine makers, which have done preliminary research using vaccines with formulas tailored for other variants, are working to understand how well their vaccines can counter omicron.

“In the event that vaccine-escape variant emerges, Pfizer and BioNTech expect to be able to develop and produce a tailor-made vaccine against that variant in approximately 100 days, subject to regulatory approval,” a Pfizer spokesperson said in a statement.

Given the spread of B. 1.1.529 in South Africa, several experts have pointed to the critical need to vaccinate underserved countries to bolster the world’s protection from future, more-evasive variants.

“I think vaccine equity is a really important issue,” said Bauld, noting the low vaccination rates in many African countries and the fact that high prevalence of the virus means it can undergo many genetic changes each time it jumps between individuals.

However, Bauld added, transmission of the coronavirus probably will not be eliminated even with a vaccine, as seen with the delta variant, with mutations ultimately able to “occur in any country.”

Viral immunologist Kizzmekia Corbett, from the Harvard T.H. Chan School of Public Health, tweeted that “by the time you detect one variant another is already circulating under the radar somewhere,” and that a combination of surveillance lags, low vaccine uptake and inequitable vaccine access meant “we will be chasing variants endlessly.”

Could omicron evade treatments?

We don’t yet know how omicron might stand up to therapeutics developed to treat covid-19, including antivirals and monoclonal antibodies.

Bloom, whose scanning experiments could inform further research about omicron, said it is too soon to base clinical recommendations on available information. Because multiple mutations could combine in a way that dulls the impact of monoclonal antibody treatments, he said it’s difficult to assess which would be effective.

“I have low confidence in assessments at this point of which antibodies will still work,” Bloom said Saturday.

Companies that have developed cocktails, including Roche and AstraZeneca, say they are monitoring the variant.

Bloom said his experiments show initial indications that the Regeneron-Roche cocktail could “take a hit.”

“I think this shows the importance of work going on in academia and in industry to continue to find more antibodies against SARS-CoV-2 because it’s clear the reason people were doing this is we know that new variants were arising,” Bloom said. “It’s clear that’s going to continue to happen.”

How far might omicron have already spread?

Public health experts say there is a high probability that the new variant is already spreading in a number of countries beyond those where cases have been detected, noting that the first infection in Hong Kong involves a passenger who landed on Nov. 11.

“That is two weeks ago, which is a forever in the pace of a pandemic,” said Eric Feigl-Ding, a senior fellow with the Federation of American Scientists.

There are several other troubling signs. One of the first cases identified in Belgium, for example, involves a young woman who did not travel to sub-Saharan Africa. Health officials there said she developed symptoms 11 days after traveling to Egypt via Turkey. She had not been vaccinated and had not developed signs of severe disease.

Feigl-Ding also expressed concern at the large number of people who tested positive for the virus on two flights from South Africa that arrived in the Netherlands — about 10 percent of all passengers: “That’s quite a statistic, even if it’s not all omicron.”

Anthony S. Fauci, the nation’s leading infectious-disease expert, said Saturday that he “would not be surprised” if the variant was already circulating in the United States.

“When you have a virus like this it almost invariably is ultimately going to go essentially all over,” he said.

Scientists can get a good indication that a person probably has the new variant through a traditional PCR test that can detect whether a specific part of the virus is missing, signaling a mutation in line with omicron, though more complete genome sequencing is needed to confirm this, Feigl-Ding said.

Countries such as Belgium are now on the hunt to see whether there are signs of transmission within their country by retroactively examining those tests.

Faheem Younus, an infectious-disease specialist at the University of Maryland, said that by the time travel bans are imposed, “the new variant has already traveled out of the country.” He noted that the O.R. Tambo International Airport near Johannesburg serves more than 1 million travelers a month.

“These bans also come at a cost and will disincentive other countries in the future,” he said. “‘Why alert the world promptly if that means your people will be punished and your economy crushed?’ they might wonder.”

Will omicron upend plans to return to ‘normal’?

After nearly two years of a pandemic, many are nervous about what challenges the new variant might bring and whether hard-fought gains will be lost. Public health experts are urging people not to jump to conclusions.

“I have never before experienced such an absolutely anguished outpouring as I have around this,” said Bill Hanage, an associate professor of epidemiology at T.H. Chan. The response, he said, has “as much to do with humans as it does with the virus.”

Hanage said he is in a state of “weary alertness” waiting for more information. He suspects omicron’s consequences will be more serious in some places than others, particularly those with low vaccination rates.

“This is certainly a curveball,” he said. “But exactly how serious it is remains to be seen.”

Stuart Ray, an infectious-disease specialist at the Johns Hopkins University School of Medicine, said people should follow the “new wisdom” on the virus: keeping track of local infection rates to determine how vulnerable they are while using common-sense protection including vaccination, boosters and high-quality masks such as KN95 and N95s.

“It’s still early days,” he said. “But this is probably not the last variant that we’ll see, so I think we should see this as part of the learning about this virus.”


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