ImageA view of San Francisco in late October.
Credit…Carlos Barria/Reuters

The first United States case of the Omicron variant of the coronavirus was reported in California on Wednesday, prompting Biden administration officials to renew their urgent calls for Americans to get fully vaccinated and, if eligible, a booster shot.

The patient, a traveler who returned to California from South Africa on Nov. 22, is in isolation, and aggressive contact tracing is underway, the Centers for Disease Control and Prevention said in a statement, adding that the individual was fully vaccinated and had mild symptoms that are improving. Close contacts of the individuals have tested negative, the agency said.

The World Health Organization has warned that the risk posed by the variant, a new iteration of the coronavirus first detected in southern Africa, is “very high.” More than 20 countries have found the variant so far.

Public health officials around the world have said for days that they expected the new, mutated form of the virus would quickly find its way to the United States despite its imposition of a travel ban on international travelers from eight southern African nations, a move several other countries also took.

But confirmation of the variant’s presence nonetheless was a jolt to President Biden’s efforts to make good on his campaign promise to bring the pandemic to a swift and conclusive end. At the White House on Wednesday, Mr. Biden said that “we’re learning more every single day,” and he vowed that the administration would “fight this variant with science and speed, not chaos and confusion.”

Shortly afterward, Dr. Anthony S. Fauci, the president’s top medical adviser, told reporters that confirmation of the new variant in the United States should persuade unvaccinated Americans to get shots immediately.

“We have 60 million people in this country who are not vaccinated who are eligible to be vaccinated,” Dr. Fauci said. “Let’s get them vaccinated. Let’s get the people vaccinated, boosted. Let’s get the children vaccinated.”

Dr. Fauci expressed optimism that the country would eventually emerge from the grip of the pandemic, saying that “there’s no doubt that this will end.” But he also urged caution, saying there was much that health officials still did not know about the new variant.

Omicron carries more than 50 genetic mutations that in theory may make it both more contagious and less vulnerable to the body’s immune defenses than previous variants. More than 30 of the mutations are in the virus’s spike, a protein on its surface. Vaccines train the body’s immune defenses to target and attack these spikes.

Available vaccines may still offer substantial protection against severe illness and death following infection with the variant, and federal officials are calling on vaccinated people to get booster shots. The makers of the two most effective vaccines, Pfizer-BioNTech and Moderna, are preparing to reformulate their shots if necessary, but that will take time.

In California, Gov. Gavin Newsom said the infected person had not been hospitalized. The governor said the individual started feeling mild symptoms on Nov. 25. The person was tested on Sunday, and got a positive result on Monday. Within a day, scientists at the University of California, San Francisco had determined that it was Omicron.

The person had received two doses of the Moderna vaccine but was within the six-month window and had thus not received a booster, Mr. Newsom said.

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. Mr. Newsom said the state would not be intensifying public health restrictions, at least in the short term, but that “we should assume that it’s in other states as well.”

“There is no reason to panic, but we should remain vigilant,” he said in a statement.

The health director of the city of San Francisco, Dr. Grant Colfax, added that “we are still learning about the Omicron variant, but we are not back to square one with this disease.”

In California, some 79 percent of residents have gotten at least one dose of the vaccine, after months of campaigning by state officials. Cases and hospitalizations have largely been trending downward since a Delta variant-driven summer rise. 

Following news of the variant’s spread in South Africa, countries around the world curtailed air travel to and from southern Africa, measures that officials there described as unduly punitive, especially in light of the fact that Western countries have failed to deliver sufficient vaccines and logistical support to the continent.

Dutch officials said on Tuesday that they identified cases of the variant a week before Friday, when 13 passengers who arrived on flights from South Africa tested positive for it, signaling that the variant was already present.

The W.H.O. says the emergence of Omicron resulted from vaccine inequity in poor countries. Even so, some nations, including Britain and the United States, have renewed efforts to persuade citizens to get vaccine booster shots as quickly as possible.

Credit…Mike Kai Chen for The New York Times

As officials scrambled to contain alarm over the detection of a case of the Omicron variant in California, state leaders portrayed the finding as an encouraging — and inevitable — result of the state’s efforts to be prepared.

“This was predictable,” said Gov. Gavin Newsom, speaking at a news conference on Wednesday in the Central Valley, where he encouraged residents to get vaccinated and get booster shots. “And it was not surprising that the state of California detected it.”

State health officials said the discovery of the Omicron variant would prompt increased Covid-19 testing at California airports, focusing on arrivals from countries identified by the C.D.C. as potential sources of the variant.

However, Mr. Newsom — who beat back a recall effort in September that was fueled in part by resistance to the state’s pandemic health restrictions — suggested that for now at least, the state would not tighten public health rules or close schools.

Mr. Newsom said there were “no indications” that such restrictions would be needed “as long as we continue our nation-leading efforts.”

State officials had said it would be only a matter of time until the Omicron variant appeared on the West Coast. California is a first U.S. stop or a destination for millions of global travelers, and as recently as Sunday, the state’s Department of Public Health had said that officials were monitoring for signs that the variant had arrived.

Mr. Newsom said the infected patient — a fully vaccinated resident of San Francisco between the ages of 18 and 49 — had been tested after traveling to South Africa, the region where the variant was first detected.

The patient, he said, had landed in California on Nov. 22, developed Covid-19 symptoms three days later and was tested on Nov. 28. The variant was confirmed by scientists at the University of California, San Francisco, the next day.

San Francisco public health officials said the individual was self-isolating, experiencing mild symptoms and assisting with contact tracing.

The governor said the state has partnered with top scientists at the University of California, San Francisco, to sequence Covid-19 cases, built up testing and succeeded in vaccinating many of its residents.

Dr. Mark Ghaly, the state’s secretary of health and human services, went so far as to say that Californians were “proud” to have identified the Omicron case.

Almost 80 percent of California residents have gotten at least one dose of the vaccine, after months of campaigning by state officials. Cases and hospitalizations have been inching mostly downward since a summer rise driven by the Delta variant — though hospitals in areas like the Central Valley, where fewer residents are vaccinated, have filled.

In San Francisco, officials sought to reassure residents.

“San Francisco has one of the highest vaccination rates and lowest death rates in the country because of the actions our residents have taken from the beginning of this pandemic to keep each other safe,” San Francisco Mayor London N. Breed said in a statement. “We knew that it was only a matter of time until the Omicron variant was detected in our city, and the work that we have done to this point has prepared us to handle this variant.”

In the Bay Area, longstanding mask mandates — some of the state’s most enduring restrictions — have recently been relaxed as the spread of the virus has slowed. Local governments in the Bay Area and in other parts of the state have begun to require businesses to verify vaccination status for entry, and more workers have been required to get their shots — a trend that officials have credited with helping to curtail the transmission of Covid.




First U.S. Omicron Case Is Detected in California

Dr. Anthony S. Fauci said the first case of the coronavirus variant was reported in the United States, after a vaccinated traveler returned to California from South Africa.

The California and San Francisco Departments of Public Health, and the C.D.C. have confirmed that a recent case of Covid-19 among an individual in California was caused by the Omicron variant. The individual was a traveler who returned from South Africa on November the 22nd and tested positive on November the 29th. The individual is self-quarantining and all close contacts have been contacted, and all close contacts thus far have tested negative. The individual was fully vaccinated and experienced mild symptoms, which are improving at this point. This is the first confirmed case of Covid-19 caused by the Omicron variant detected in the United States. And as all of you know, of course, we’ve been discussing this, we knew that it was just a matter of time before the first case of Omicron would be detected in the United States. And as you know, we know, I’ve been saying it and my colleagues on the medical team, and others have been saying, that we know what we need to do to protect people: get vaccinated. If you’re not already vaccinated, get boosted. If you’ve been vaccinated for more than six months with an mRNA, or two months with J.&J. and all the other things we’ve been talking about — getting your children vaccinated, masking in indoor congregate settings.

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Dr. Anthony S. Fauci said the first case of the coronavirus variant was reported in the United States, after a vaccinated traveler returned to California from South Africa.CreditCredit…Doug Mills/The New York Times

As the first case of the Omicron coronavirus variant was reported in the United States, Dr. Anthony S. Fauci, the nation’s top infectious disease expert, cast the detection as a reason for Americans to get vaccinated or boosters and said that public health recommendations had not changed in the presence of the fast-spreading variant.

“We knew that it was just a matter of time before the first case of Omicron would be detected in the United States,” Dr. Fauci said.

The patient, a traveler who returned to California from South Africa on Nov. 22, is in isolation, and aggressive contact tracing is underway, according to the Centers for Disease Control and Prevention. The individual was fully vaccinated and had mild symptoms that are improving. Gov. Gavin Newsom of California said the person had received two doses of the Moderna vaccine but was within the six-month window and had thus not received a booster.

Dr. Fauci said he did not necessarily favor vaccine requirements for domestic air travelers, preferring instead to push to inoculate the remaining unvaccinated people in the country.

He said he was “not so sure” that new testing requirements administration officials are currently weighing for international travelers would have helped catch the case sooner — because the patient took a test immediately after beginning to experience what he described as mild symptoms. And he said it was possible that in the future, the federal government could change its definition of “fully vaccinated” to require international travelers to have received booster shots before entering the United States.

Dr. 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 designed for Omicron.

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

Asked if Americans should feel free to attend holiday parties and drink holiday beverages unmasked, he said it depended on the size of the gathering.

“In a situation with the holiday season, indoor-type settings with family that you know is vaccinated, people that you know, you could feel safe with not wearing a mask and having a dinner, having a reception,” he said. But in larger public settings where it is unclear if everyone is vaccinated, he said, people should wear masks except to eat or drink.

Jill Cowan contributed reporting.

Credit…Spencer Platt/Getty Images

Federal health officials have directed airlines to provide the Centers for Disease Control and Prevention with the names and contact information of all passengers who boarded flights bound for the United States since Nov. 29 and who had been in southern Africa during the prior two weeks.

The directive, issued Wednesday, applies to passengers who spent time in Botswana, the Kingdoms of Eswatini and Lesotho, Malawi, Mozambique, Namibia and South Africa in the two weeks before flying to the United States. The airlines were directed to provide their names, addresses while in the United States, phone numbers, email addresses, dates of birth and flight information, including seat numbers.

“C.D.C. is issuing this directive to prevent the importation and spread of a communicable disease of public health importance,” a statement from the agency said, an apparent reference to the new Omicron variant of the virus that causes Covid.

Last week, the White House announced a ban on travel from eight countries in southern Africa. And late Tuesday night, the C.D.C. said it planned to toughen virus testing and screening of people flying to the United States by requiring all international passengers to provide a negative result from a test taken within 24 hours of departure.

The new directive was issued under an Oct. 25 order that instructed airlines and aircraft operators to collect specific information from all passengers before boarding, retain the information for 30 days, and transmit it to C.D.C. within 24 hours if requested to do so.

The C.D.C. can share the information with state and local health departments at passengers’ destinations, enabling local health authorities to monitor travelers for Covid, identify symptomatic individuals, notify their contacts, and direct those who are infected to isolate and their contacts to quarantine to avoid further disease spread. They can also use the information to ensure infected individuals get appropriate care.

The order applies to flights that have departed for the United States since Monday morning. Two flights left Johannesburg for the United States that day: a Delta Air Lines flight with more than 300 seats that was headed for Atlanta, and a United Airlines flight with more than 250 seats that was headed for Newark, N.J.

Both flights landed in the United States on Tuesday morning, according to schedules from Cirium, an aviation data provider. Two more United flights are scheduled to leave South Africa for Newark on Wednesday, one from Cape Town and one from Johannesburg.

Delta and United are currently the only two carriers that offer direct or single-layover flights between the countries covered by the C.D.C. order and the United States, according to Cirium schedule data. Delta operates three weekly flights between Johannesburg and Atlanta. United operates five flights a week between Johannesburg and Newark. It also plans to restart seasonal flights between Cape Town and Newark on Wednesday.

Both airlines have said that they are not planning to adjust their flight schedules in response to the administration’s ban on travelers from the region, which took effect on Monday and does not apply to American citizens or lawful permanent residents. The airlines also said that they plan to comply with the C.D.C. order.

Sixty-one people who arrived in the Netherlands on Friday aboard two flights that departed from South Africa tested positive for the virus that causes Covid, including over a dozen who were carrying the new Omicron variant. The number of overall positive cases represented more than 10 percent of the 600 passengers tested.

Credit…Sheba Medical Center

Elad Maor initially feared that he might have exposed hundreds of people to the virus when he became the first Israeli to test positive for the new Omicron variant on Saturday morning.

In the three days before his positive results, Dr. Maor, a cardiologist, had attended a large staff meeting at his hospital east of Tel Aviv. He had inserted stents into the arteries of 10 patients. And he had driven to a cardiology conference north of Tel Aviv, sharing the 90-minute car journey with a 70-year-old colleague, and lunched there with five others in a crowded canteen.

Dr. Maor, 45, had attended a piano recital with dozens in the audience, where his 13-year-old played a short piece by Stephen Heller, a Hungarian composer. And finally, last Friday night, Dr. Maor had eaten sea bass at the home of his in-laws, together with his wife and nine other family members.

But of these many people, most of whom had received three shots of the Pfizer-BioNTech vaccine, only his 70-year-old colleague has so far tested positive for the Omicron variant in the five days since.

That number may yet rise, as the virus can take several days to show up in tests, and not every contact has been tested. But at least 50 people have already been screened with a P.C.R. test by Dr. Maor’s hospital, the Sheba Medical Center, and at least 10 of those have been tested at least three times.

These initial results have led the infectious disease experts at Sheba, which houses one of Israel’s leading coronavirus laboratories, to cautiously hope that people who have been vaccinated three times may not be as vulnerable to Omicron as was first feared.

Though Dr. Maor met with many people last week, almost all of them were health care workers or close family members. And the people he had spent the most time with were fully vaccinated and had even recently had a third “booster” shot.

It is important not to extrapolate too much from isolated cases, said Prof. Gili Regev-Yochay, director of the infectious disease epidemiology unit at Sheba, who has helped lead research into the virus. “But this does tell us that, in some cases, Omicron is not as infectious if you’re vaccinated,” Prof. Regev-Yochay said. “And I think that’s a major thing.”

To Dr. Maor, who was still in isolation at home on Wednesday night, it was still concerning that he had been hit so hard by the virus, despite being fully vaccinated himself, and despite being a fit non-smoker without any chronic medical conditions. The cardiologist spent Saturday and Sunday in bed with a fever, sore throat and aching muscles — and only began to feel considerably better on Wednesday afternoon.

“Despite everything, despite the vaccines and the booster, I was in bed for 48 hours,” Dr. Maor said in a phone interview. “If I didn’t have the vaccine, I probably would have ended up in the hospital.”

To Prof. Regev-Yochay, the coronavirus expert, her colleague’s experience highlighted the need for travelers to keep testing themselves and avoid busy places for a few extra days after arriving from a country with high infection rates.

Dr. Maor arrived back last Wednesday from London, where he had attended another crowded cardiology conference. Because he had tested negative twice in London, and a third time on arrival back in Israel, he had thought he was safe to operate as normal. But his experience highlighted how the virus may not show up in tests for several days.

That shows that ideally, each new arrival to the country would be tested every morning for at least five days after they land, said Prof. Regev-Yochay.

“People should be cautious,” she said. “Every day on a daily basis.”

Credit…Bryan Anselm for The New York Times

Travelers reacted with dismay and confusion on Wednesday after the Centers for Disease Control and Prevention said that it plans to toughen coronavirus testing requirements and screening of international fliers bound for the United States because of concern about the Omicron variant.

The agency is considering requiring travelers to provide a negative result from a test taken within 24 hours before departure, among other steps, a spokesman said Tuesday night.

Though the C.D.C. has yet to officially announce any changes, the prospect of them sent travelers searching for updates, booking pre-emptive tests where they could, and scouring airline websites for reservation changes, as the pandemic threatened to upend another December travel season.

“It’s a shame, because travel just opened up again,” said Giritharan Sripathy, who was scheduled to fly to New York from London on Thursday. Mr. Sripathy, who had already taken a P.C.R. test three days before his flight, as required, said he had scheduled a new rapid test for Wednesday as a precaution, “in case they change the rules tomorrow.”

Mr. Sripathy, a Singaporean film producer, said he was concerned that the United States might close off entry to people who are not American citizens or permanent residents. Last year, restrictions like that kept him from returning to the United States, where he works, from a holiday in Singapore for eight months.

“I don’t want a repeat of that,” he said.

The plans to tighten testing requirements reflect growing concern about Omicron, a highly mutated form of the virus that was first documented by researchers in southern Africa and has since been detected in more than a dozen countries around the world, including Britain. Experts say it may be weeks before they will know enough about it to assess how readily it spreads or whether it can evade existing vaccines. In the meantime, countries around the world have imposed travel restrictions, and stock markets have tumbled.

The C.D.C. spokesman, Jason McDonald, said that requiring a negative test within a day of departure, instead of three days, would strengthen the United States’ “already robust protocols” for international travelers, including a requirement that they be fully vaccinated. It was unclear whether the new 24-hour rule would require a particular type of rapid test.

President Biden has said he would announce plans on Thursday for stepping up the fight against the pandemic. It was not clear whether his announcement would include the tighter testing requirements for international travelers, which were first reported by The Washington Post. Mr. McDonald offered no timeline for the C.D.C.’s action.

Mr. McDonald said the C.D.C. continues to recommend that all travelers get a coronavirus test three to five days after arrival in the United States. Unvaccinated travelers should self-isolate and quarantine for seven days after arrival, even if they test negative, the agency says.

Natalie Quillian, the deputy coordinator for the Covid response at the White House, said in an interview on Monday that the administration was “assessing all of our tests to make sure they’re effective in picking up” the Omicron variant, and would remove from the accepted list any tests that were not.

Some travelers said a 24-hour testing rule could make visiting the United States difficult. Paula Tolton, 23, a student in Taipei, Taiwan, who plans to visit relatives in Florida in January, said that she found even the current 72-hour rule nerve-racking because of delays in test processing.

“I’ve had that stress before, when a P.C.R. test didn’t come back when I was supposed to fly here in April,” she said. “I was freaking out.”

Carlos Valencia, a dual Spanish and American citizen whose Seville-based company runs a study-abroad program for American students, said he would put a planned January trip to return to the United States on hold until “there is at least some clarity about whether the new rules make a trip feasible.”

He said shifting rules had driven students in his program “completely crazy” and hampered his business, especially “when you know that variants are going to keep coming.”

Credit…Tafadzwa Ufumeli/Getty Images

The Omicron variant has become by far the most prevalent version of the coronavirus spreading in South Africa, replacing the fading Delta variant, health officials said on Wednesday.

Nearly three-quarters of the 249 positive test samples that were checked genetically in South Africa in November were found to involve the Omicron variant, the National Institute for Communicable Diseases announced.

New cases are rising sharply in South Africa, after having dropped to low levels in recent months. The institute said that there were 8,651 new cases reported on Wednesday, almost twice as many as the day before; as recently as early November, the country was averaging fewer than 300 new cases a day. The share of tests that are coming back positive rose to 16.5 percent, from 10.2 percent on Tuesday, the institute said.

The first Omicron case detected in the United States was announced on Wednesday. The World Health Organization said that at least 23 other countries around the world have reported cases of Omicron, and that it expects that number to grow as scientists around the world sequence more test samples.

In a virtual news conference, W.H.O. experts said that “it is early days” in determining whether the mutations seen in the new variant made it more transmissible or better able to evade vaccine protection, as some experts fear. Dr. Maria Van Kerkhove, the technical lead of the W.H.O.’s coronavirus response, said she expected more information on those issues “within days,” but she emphasized that so far, “there is no evidence to suggest that the vaccines don’t work” against Omicron.

“Vaccines are saving lives,” she said.

Many questions remain about whether this variant causes more severe illness than others, she said, adding that officials in South Africa had seen reports of Omicron cases with symptoms that ranged from “mild disease all the way to severe disease.” To date they had seen no deaths associated with the variant.

Tulio de Oliveira, director of the KwaZulu-Natal Research and Innovation Sequencing Platform, said that the Omicron variant “seems to cause much more breakthrough infections than the previous ones.” He said that he was concerned about the threat of such infections among health workers, which would sap the country’s ability to cope with a surge in cases.

But Mr. de Oliveira cautioned against reading too much into head-to-head comparisons between Omicron and Delta. Omicron might swiftly supplant Delta in countries like South Africa where the older variant was fading, but perhaps not as readily where Delta is still spreading actively, he noted.

The W.H.O. panel emphasized the need for countries to speed up vaccination efforts as much as possible, particularly for vulnerable populations.

The panel also called on health authorities to strengthen sequencing, surveillance and field investigations, including community testing.

The agency strongly advised against imposing “blanket travel bans,” calling instead for “a tailored approach” to travel restrictions that could include quarantine and testing requirements for arrivals.

“Our concern here is that we apply public health principles, not political principles, to select the measures that are used,” said Dr. Michael Ryan, the head of the emergencies program at the W.H.O.

Credit…Pool photo by Fabrice Coffrini

The World Health Organization’s member states on Wednesday took the first step toward what many governments hope will be a legally binding treaty aimed at strengthening global defenses against pandemics.

A rare special session of the W.H.O.’s governing body agreed to set up an intergovernmental negotiating body that is to meet no later than March to begin negotiating an international agreement intended to ensure a more coherent and equitable response to future pandemics. But the United States and other countries have pushed for a weaker mechanism that would not carry legal obligations for member states.

The W.H.O. director-general, Dr. Tedros Adhanom Ghebreyesus, a strong advocate of a legally binding treaty, hailed the decision as historic, calling it “a once-in-a-generation opportunity to strengthen the global health architecture to protect and promote the well-being of all people.”

The decision marked only the beginning of what promises to be arduous negotiations to try to achieve consensus among the W.H.O.’s 194 member countries. The agreement calls for negotiators to deliver the result of their deliberations in May 2024.

The European Union and Britain have pushed for months for an ambitious treaty or convention that carries legal force. The discovery of the Omicron variant, which has prompted a new wave of travel rules and border closures, primarily targeted at southern African nations where the variant was first identified, has renewed criticism that countries worldwide are acting in a patchwork and discriminatory fashion.

“No better response to the emergence of the Omicron variant than this coming together of the international community behind the effort to strengthen the legal framework underpinning our collective response to pandemics,” Simon Manley, Britain’s ambassador in Geneva, said on Twitter.

The United States described the initiative in a statement as “a momentous step” but, with support from Brazil and other countries, it refused to commit to anything that is legally binding, and kept open the possibility of a weaker instrument.

The international agreement is intended to avoid any repetition of the “fragmented and splintered” steps by nations that Dr. Tedros has said weakened the global response to Covid-19. Proponents of a treaty want commitments to share data, virus samples and technology, and to ensure an equitable distribution of vaccines.

Those issues raise politically sensitive questions of national sovereignty over access to the sites of outbreaks, and potential investigations into origins of diseases — a source of tension between Western governments and China, which has resisted calls for an independent inquiry into the emergence of Covid-19 in the Chinese city of Wuhan in early 2020.

China said this week that it agreed “in principle with the ideas of further strengthening compliance, financing, sharing and information management.” But Beijing appeared wary of a new treaty and cautioned against “politicization, stigmatization and instrumentalization.”

Credit…Jeff J Mitchell/Getty Images

The secretary general of the United Nations, António Guterres, expressed strong criticism of the international response to the Omicron variant, saying that the rush to close borders has especially penalized African nations where the variant was first detected and vaccines were slow to arrive.

“The people of Africa cannot be blamed for the immorally low level of vaccinations available to them,” Mr. Guterres told reporters Wednesday after a meeting with the chairman of the African Union Commission, Moussa Faki Mahamat, at U.N. headquarters in New York. “Nor should they be collectively punished for identifying and sharing crucial science and health information with the world.”

The United States and several European countries were quick to temporarily bar travelers from southern Africa in a defensive move against the spreading of the newly discovered variant. Some countries, including Israel, Japan and Morocco, went further, temporarily barring all foreign travelers.

The borderless nature of the virus, Mr. Guterres said, means that “travel restrictions that isolate any one country or region are not only deeply unfair and punitive — they are ineffective.”

He appealed to “all governments to consider instead repeated testing for travelers, together with other appropriate and truly effective measures.”

“This is the only way to reduce the risk of transmission while allowing for travel and economic engagement,” he said.

Mr. Mahamat, a Chadian statesman who leads the administrative branch of the African Union, joined Mr. Guterres in denouncing the attempts by Western and other non-African countries to effectively isolate Africa because of the Omicron variant, which was first discovered in southern Africa last month.

“As a result of being transparent, much of Africa has been stigmatized,” he said. “This stigmatization cannot be justified.”

Also on Wednesday, the director general of the World Health Organization, Dr. Tedros Adhanom Ghebreyesus, thanked South Africa and Botswana for identifying the new variant and reporting it to global health authorities.

Dr. Tedros said that the two countries should not be discouraged by the “unnecessary” travel bans from other nations in response to the Omicron variant.

Credit…Joao Silva/The New York Times

The detection of the Omicron variant in southern Africa signals the next stage of the battle against Covid-19: getting many more people inoculated in poorer nations where vaccines have been scarcest in order to deter new mutations from developing.

But while world leaders sometimes talk about this as if it is largely a matter of delivering doses overseas, the experience of South Africa, at least, hints at a far more complex set of challenges.

Like many poor countries, South Africa was made to wait months for vaccines as wealthier countries monopolized them. Many countries still do not have anywhere near enough vaccines to inoculate their populations.

The problems have not ended as shots began arriving in greater numbers.

Neglected and underfunded public health infrastructure has slowed their delivery, especially to rural areas, where storage and staffing problems are common.

And now, there are growing signs in parts of Africa, as well as South Asia, that skepticism or outright hostility toward the Covid vaccines may run deeper than expected.

Deep distrust of governments and medical authorities, especially among rural and marginalized communities, may already be stalling out vaccination drives. The legacy of Western exploitation and medical abuses during and after colonialism is weighing heavily, too.

Misinformation circulating on social media often fills the vacuum, some of it floating in from the United States and Europe, where vaccine refusal has also been an issue.

“There’s no doubt that vaccine hesitancy is a factor in the rollout of vaccines,” said Dr. Matshidiso Moeti, the Africa director of the World Health Organization. News or rumors of potential side effects, she said, “gets picked out and talked about, and some people become afraid.”

Just days before the Omicron variant was first detected, health officials in South Africa turned away shipments of doses from Pfizer-BioNTech and Johnson & Johnson, worried that their stockpile of 16 million shots might spoil amid insufficient demand.

Though only 36 percent of South African adults are fully vaccinated, daily vaccinations have already been flatlining, according to government statistics.

Namibia, Zimbabwe, Mozambique and Malawi have also asked vaccine manufacturers and donors to hold off on sending more shots because they can’t use the supplies they have, according to several health officials involved in the effort to distribute vaccines to developing nations.

Credit…Ruth Fremson/The New York Times

President Donald J. Trump tested positive for coronavirus three days before his first debate with Joseph R. Biden Jr. in 2020, two former administration officials said Wednesday.

The White House did not announce the positive test at the time, and the president received a negative result shortly afterward and carried on with a campaign rally and the debate, the officials said. The account was first reported by The Guardian, which cited a forthcoming book by Mr. Trump’s chief of staff, Mark Meadows.

The two former officials, who spoke on condition of anonymity because they were not authorized to discuss the matter publicly, confirmed the timeline on Mr. Trump’s test results contained in “The Chief’s Chief,” by Mr. Meadows, Mr. Trump’s fourth and final White House chief of staff.

The revelation came nearly a year after widespread speculation that Mr. Trump was sick when he first shared a stage with Mr. Biden for their first presidential debate on Sept. 29, months into the pandemic.

The White House declined repeatedly at the time to give a precise chronology of when precisely Mr. Trump first received a positive coronavirus test result. The administration first told the public in the early hours of Oct. 2 that Mr. Trump had tested positive. Mr. Trump was hospitalized later that same day.


Credit…Peter Byrne/Press Association, via Associated Press

England’s return to some Covid restrictions on Tuesday provoked a range of emotions: anger, dismay, weariness, and, for some, indifference. From London, festooned with Christmas lights, to Bradford, in northern England, the feeling on the streets was, above all, one of weary resignation.

“I expected it, because the British took so long,” said Ali Hasan, 31, a medical consultant at a hospital in Bradford, referring to the nation’s first lockdown, in March 2020, which he said should have been imposed sooner, were it not for what he described as the “laziness” of the country’s political parties.

The British government ended virtually all restrictions in England over the summer, and has seen a high but relatively stable coronavirus caseload in recent weeks. Even now, it is stopping short of the health pass systems, vaccine mandates and lockdown measures that have been implemented to stem surges elsewhere in Europe.

But it has responded to news of the Omicron variant by severely restricting travel from 10 African countries, reinstating testing and self-isolation requirements for other arrivals, and making face masks compulsory on public transportation and in shops.

Many in England had been anticipating restrictions for a while, and some had started to take matters into their own hands. Though masks are not mandatory in restaurants or cafes, Audrey Mekki, 35, a waitress at Pera, a Mediterranean restaurant in North London, makes a point of wearing one throughout her shift.

“I’m wearing it for my safety, and also for the customers,” she said. “Most don’t mind, but some may not feel comfortable if the waitresses serving their food are not masked.”

Helen Daly, 62, who was in London on a holiday from Cork, Ireland, said she had been surprised by the lax British attitude.

“There’s very little mask-wearing here,” she said. “We were at the theater last night. There were four of us, and we were the only four wearing masks.”

For Matthew Leonard, 22, however, the change on the subway was sudden and visible. He said he arrived in London the night before the new regulations took effect. “It was pretty much how it was before, sort of 50-50,” Mr. Leonard said, “but then this morning I noticed almost all people wearing masks.”

At schools, students age 11 and older are now advised to wear masks in communal spaces. Lucy Long, 41, who has a 10-year-old-daughter, explained that the school drop-off had also changed; parents no longer gather for a conversation at the gates. She supports requiring children to wear masks.

“We don’t know what’s going to happen to these children in 20 years’ time after any infection,” she said.

In Bradford, where Ursula Sutcliffe runs a small plant shop and cafe, she said the successive lockdowns had taken a toll — to say nothing of Brexit, which drove up the cost of her plants, which are imported from the Netherlands.

“We’ve just been in an uphill battle,” Ms. Sutcliffe said. Referring to Britain’s prime minister, she added: “Boris Johnson should never have stopped wearing face masks in the first place. If we’d just kept face masks on, we probably could have just gone about our lives. But he is so eager to say, ‘Yay, we’re back to normal.’ We’re not!”

In other news from around the world:

  • Japan asked airlines to stop accepting new bookings for inbound all flights for the rest of the year. However, existing bookings would not be affected. Japan also confirmed its second Omicron case on Wednesday.

  • The incoming chancellor of Germany, Olaf Scholz, said he wanted vaccinations in the country to be mandatory, possibly as soon as February. He told a German newspaper that the high rates made the move necessary.

  • Ghana and Nigeria are the latest African nations to confirm cases of the variant. In Nigeria, three travelers from South Africa tested positive for the variant, and Ghana detected the variant on Nov. 21.

Credit…The New York Times

Among the many unknowns surrounding the new coronavirus variant called Omicron, named after the 15th letter of the Greek alphabet, one has stood out to many English speakers: How is it pronounced?

There is no single, agreed-on English pronunciation, experts say.

One pronunciation, according to Merriam Webster, is “OH-muh-kraan,” with a stress on the first syllable.

A World Health Organization official, Dr. Maria Van Kerkhove, recently said it that way when announcing that the variant was of concern.

Pronouncing ‘Omicron’

There are several widely accepted ways in English to pronounce “Omicron,” a variant of the coronavirus named after the 15th letter of the Greek alphabet.

In the United States, it is often pronounced “AH-muh-kraan,” Merriam Webster says. Less common are “OH-mee-kraan,” as Prime Minister Boris Johnson of Britain pronounced it this week, or “OH-my-kraan.”

On the New York Times podcast “The Daily,” Apoorva Mandavilli, who reports on the coronavirus and its variants, said she was going with “AH-muh-kraan.”

“I don’t think it really matters that much, honestly,” she said.

The New Oxford English Dictionary gives a pronunciation that differs from those in Merriam-Webster, according to Dr. Andreas Willi, a comparative linguistics professor at Oxford University. “Namely rather like an English phrase ‘o-MIKE-Ron,’” he said.

The word is a compound from the Greek “o mikron,” meaning “small o.” In classical Greek, the word was pronounced with the second syllable sounding like an English “me,” Dr. Willi said.

Peter Sokolowski, editor at large at Merriam Webster, said that because the Greek word is transliterated for pronunciation into English, sounding much as the word “omnipotent” is different from its Latin “omni-potent” origin, then the “AH-muh-kraan” pronunciation “makes perfect sense.”

But, he added, “There isn’t a wrong answer.”

“The question of British versus American pronunciation of the first syllable isn’t really specific to this particular word,” Dr. Willi said. “Compare the British versus American pronunciation of ‘god.’”

The divergences are to do with the name having been adopted as a loanword and used by English speakers in different places at different times, Dr. Willi said.

“When we speak of ‘Paris’ in English, that is also very different from the ‘proper’ French way of pronouncing the same name,” he said. “But it is hardly wrong in a strict sense.”

Stocks on Wall Street slid on Wednesday for a second consecutive session, continuing their tumultuous ride since the discovery of the Omicron variant of the coronavirus last week.

The S&P 500 fell 1.2 percent, as an early gain quickly faded after news that the variant had been detected in the United States. The Nasdaq composite lost 1.8 percent.

Early gains by oil futures also faded. West Texas Intermediate, the U.S. benchmark, fell about 1 percent to $65.57, erasing earlier gains of as much as 5 percent.

Shares of companies likely to be most affected by an increase in pandemic precautions were among the hardest hit. American Airlines fell 8 percent and was one of the worst performers in the S&P 500. United Airlines was down nearly as much, as were the cruise lines like Norwegian and Carnival.

Even as they have cautioned against overreacting to the news of a new variant before much is known about it, several world governments have put in place restrictions on travel — including limits on entry for visitors from southern Africa, where the variant was first detected, and blanket bans on all foreigners.

In the United States, the Centers for Disease Control and Prevention has said it plans to toughen coronavirus testing and screening requirements for international fliers bound for the country. The agency is considering requiring travelers to provide a negative result from a test taken within 24 hours before departure, among other steps, a spokesman said Tuesday night.

Investors also snapped up shares of companies that could benefit from a renewed vigilance to a spreading virus. Clorox rose nearly 2 percent. Quest Diagnostics, a lab company with a fast-growing Covid testing business, rose 1.7 percent. Becton Dickinson and Company, which makes an at-home Covid test, rose 1.9 percent.

As they consider the risk of the Omicron variant, and the potential impact on the global economy as governments again restrict travel and tighten testing requirements, investors are also grappling with a shifting outlook for interest rates.

On Tuesday, the S&P 500 declined 1.9 percent when the head of the Federal Reserve said the central bank might speed up its plan to reduce support for the economy because of high inflation. The back-to-back declines added up to a 3.1 percent drop for the U.S. benchmark index, its worst two-day dive since October 2020.

A measure of volatility in the U.S. stock market surged to its highest since early March on Friday after the Omicron variant was reported by researchers in South Africa. The VIX index has declined a little since then, but it remains above levels seen in the past two months.

Traders had pushed back their expectations about when the Fed might eventually raise interest rates, in light of the news about the variant and some predictions that current vaccines will be less effective against it. But Jerome H. Powell, the Fed chair, said on Tuesday that the risk of higher inflation had increased. If the central bank finishes tapering its bond-buying program sooner than expected, it could also raise interest rates sooner.

Yields on long-term Treasury bonds dropped, suggesting that investors were moving money out of shares and into the safety of government securities as they await more information about the Omicron variant. (Yields on Treasury bonds fall as prices rise.)

The yield on the 10-year Treasury note, often viewed as a barometer of the market’s expectations for economic growth and inflation, dropped to about 1.43 percent, the lowest level in over two months.

The Omicron variant could prolong the bottlenecks and shortages that have caused inflation to run hotter than expected, a risk Fed officials will assess as they “grapple” with how quickly to remove economic support, another Fed official said.

“Clearly, it adds a lot of uncertainty to the outlook,” John C. Williams, president of the Federal Reserve Bank of New York, told The New York Times in an interview that was published on Wednesday.

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