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Health officials in Brazil recently began giving the first Covid-19 vaccinations after the country’s health regulator approved two vaccines for emergency use.CreditCredit…Victor Moriyama for The New York Times

Brazil on Monday kicked off its nationwide coronavirus vaccination campaign, providing a glimmer of hope in a nation where political infighting, a strained health care system and lax precautions have given the virus free rein.

But the rollout is expected to be painfully slow, even as Brazil battles two worrisome new variants of the virus, at least one of which is more contagious and could be contributing to the country’s recent surge of cases.

The government is scrambling to buy more vaccine after months of taking a lackadaisical approach, as President Jair Bolsonaro argued that scientists and the media were hyping the seriousness of a virus that has killed more than 210,000 Brazilians. The country now has just six million doses of vaccine on hand for a nation of 213 million.

The potential menace of the new variants became clear last week as patients in the northern state of Amazonas asphyxiated to death because hospitals ran out of oxygen amid a sharp rise in critically ill patients. Prosecutors investigating the calamity said at least 16 patients had died.

The oxygen shortage “is the saddest and most outrageous expression of the government’s abject failure at all levels,” Alex Machado Campos, a director of the country’s health regulatory agency, said in televised remarks Sunday. “Is this a civilized nation or one living through a barbaric dystopia?”

The lack of vaccine doses is just one of myriad missteps that have hampered the country’s ability to protect its people against the pandemic. Mr. Bolsonaro has been criticized for repeatedly downplaying the threat of the virus, promoting a useless treatment, refusing to wear a mask, sabotaging other officials’ lockdown measures and, most recently, fueling unfounded fears about the safety of vaccines.

Last month, the president, who had Covid-19 and recovered, said he had no intention of getting a vaccine and criticized vaccine providers for asking buyers to sign hold-harmless agreements.

After peaking in July, when Brazil regularly had 1,200 coronavirus deaths per day, cases and fatalities dropped gradually for a few months but began to inch up in November. In recent weeks, the country has often reported more than 1,000 deaths a day, and Brazil’s death toll is second only to that in the United States.

Brazilian scientists say the new variants discovered in Brazil could be contributing to the resurgence of the virus there. The one in Amazonas contains a mutation that has been linked with higher contagiousness, and both variants have another mutation that may weaken the efficacy of vaccines.

The two mutated viruses have slipped the country’s borders and turned up in other parts of the world, with the latest discovery occurring in South Korea.

While virus mutations are common, experts say hard-hit countries like Brazil provide fertile ground for new variants that could hamper the global response. Despite a rise in cases, bars and restaurants are doing brisk business and mask wearing is spotty.

“The appearance of these variants is directly proportional to people’s lack of care,” said Luiz Vicente Rizzo, the head of research at Israeli Albert Einstein Hospital in São Paulo.

Cemetery workers prepared graves in Chitungwiza, Zimbabwe, on Monday.
Credit…Aaron Ufumeli/EPA, via Shutterstock

Governments and public health organizations around the world responded slowly and ineffectually to the coronavirus outbreak, according to an interim report by a World Health Organization panel that laid bare a yearlong cascade of failures.

The report, an early blueprint for accountability, questions the faulty assumptions, ineffective planning and sluggish responses that helped fuel a pandemic that has killed more than two million people and infected more than 95 million.

“We have failed in our collective capacity to come together in solidarity to create a protective web of human security,” the Independent Panel for Pandemic Preparedness and Response wrote.

Many of the failings, such as the inability of governments to obtain protective equipment, have long been painfully clear. But the report is stark in its assessment that, time and again, those who were responsible for protecting and leading too often failed to do either.

The panel, led by Helen Clark, the former prime minister of New Zealand, and Ellen Johnson Sirleaf, the former president of Liberia, is still conducting its investigation. But an interim report, laying out the scope of its inquiry, made clear that the world needs to rethink its approach to outbreaks. The panel called the pandemic alert system “slow, cumbersome and indecisive.”

Investigators said they did not understand why a World Health Organization’s committee waited until Jan. 30 to declare an international health emergency. But even when the world health body did send up clear warning signals, the report noted, “In far too many countries, this signal was ignored.”

The report also faulted public health leaders for responding so slowly to early evidence that people without symptoms could spread the new coronavirus. Instead, leading health agencies, including the World Health Organization, provided contradictory and sometimes misleading advice, a New York Times investigation previously found.

The report was scheduled to be released Tuesday. Agence France-Presse reported details of the report on Monday evening. A copy was obtained by The Times.

The Trump administration ended a ban on travelers from Europe and Brazil on Monday. 
Credit…Ariana Drehsler for The New York Times

President Trump on Monday ordered an end to the ban on travelers from Europe and Brazil that had been aimed at stopping the spread of the coronavirus to the United States, a move that was quickly rejected by aides to President-elect Joseph R. Biden Jr., who said Mr. Biden will rescind the move when he takes office on Wednesday.

In a proclamation issued late Monday, Mr. Trump said that the travel restrictions, which applied to non-citizens trying to come to the United States after spending time in those areas, would no longer be needed on Jan. 26, the date on which those passengers will be required to present proof of a negative coronvirus test before boarding a flight.

Mr. Trump wrote that Alex Azar, the secretary of health and human services, had recommended ending the restrictions on travel from most parts of Europe and Brazil, while maintaining restrictions on Iran and China, which Mr. Trump said had not been cooperative.

“I agree with the secretary that this action is the best way to continue protecting Americans from Covid-19 while enabling travel to resume safely,” the president said in the proclamation.

But Jen Psaki, the incoming White House press secretary for Mr. Biden, said the new administration would not allow Mr. Trump’s directives to take effect.

“With the pandemic worsening, and more contagious variants emerging around the world, this is not the time to be lifting restrictions on international travel,” Ms. Psaki tweeted shortly after the White House issued Mr. Trump’s proclamation.

“On the advice of our medical team, the administration does not intend to lift these restrictions on 1/26,” she said. “In fact, we plan to strengthen public health measures around international travel in order to further mitigate the spread of Covid-19.”

Mr. Trump’s attempt to alter policy related to the pandemic just two days before he leaves office is in keeping with the unorthodox way he has conducted the transition to a new administration. Normally, departing presidents refrain from issuing new executive orders without consulting with the incoming president.

But Mr. Trump has refused to abide by those norms. On Monday, he also issued several other executive orders that will most likely be rescinded or reversed by Mr. Biden, including one that would allow federal agencies to issue new regulations only at the instigation of political appointees.

He also issued an executive order directing the federal government not to purchase drones “that present unacceptable risks and are manufactured by, or contain software or critical electronic components from, foreign adversaries.”

The proclamation on the travel restrictions appeared to be an effort to help the airlines and the hospitality industries, which have been hard hit by the ban. In the proclamation, Mr. Trump said that the ban was no longer needed because unrestricted travel into the United States “is no longer detrimental to the interests of the United States” and added that it was “in the interest of the United States to terminate the suspension of entry into the United States of persons who have been physically present in those jurisdictions.”

A CVS pharmacist preparing a Covid-19 vaccination for residents of a nursing home in Harlem on Friday. Nearly a third of nursing home workers in New York State have declined to be vaccinated.
Credit…Yuki Iwamura/Associated Press

The number of nursing home workers in New York State who have declined the coronavirus vaccine rivals the number of workers who have been inoculated, raising concerns about vaccine hesitancy among those who are in contact with some of the individuals at highest risk of a severe coronavirus infection.

As of Monday, about 37 percent of the more than 130,000 people working in “skilled nursing” facilities in the state have been vaccinated, according to the governor’s office.

But 32 percent of the workers have declined to be vaccinated.

In some parts of the state, the number of staff members who have declined a shot outnumber those who have been vaccinated. On Long Island, 46 percent of workers declined while 34 percent have been vaccinated.

Officials cautioned that the vaccination process for long-term-care facilities was still in its early stages — the first of three inoculation phases concluded on Sunday, and there are still many workers who have not had the chance to get vaccinated. They said they hoped the proportion of staff members declining to be inoculated would decrease as they saw their colleagues getting vaccinated safely.

Gov. Andrew M. Cuomo said at a news conference on Monday that the state had earmarked 225,000 doses for residents and workers in long-term-care facilities and that 105,000 had been used. The 120,000 unused doses will be reallocated to the main vaccination program, he said.

The vaccination rate among residents was higher: 67 percent of residents have been inoculated, while 16 percent have declined. Workers and residents who are medically able to get the vaccine but had previously declined will still be able to get a shot if they decide to.

The state health department has done online events and other educational outreach with nursing homes, largely to address vaccine hesitancy.

Many of the workers are lower-income and people of color, communities that tend to have higher rates of vaccine hesitancy. In a speech on Monday marking Martin Luther King’s Birthday, Mr. Cuomo said he understood their distrust, citing the decades-long Tuskegee experiment in which government researchers withheld treatment from Black men infected with syphilis.

“No one can ameliorate or justify the victimization and discrimination the Black community has endured,” Mr. Cuomo said.

But, he said, “we have had New York’s doctors, the best on the planet, review the vaccine, and they vouch for it. I will take it as soon as I am eligible.”

State officials have also cited the results of an antibody survey as a possible factor in low vaccination rates. The survey found that high numbers of workers in long-term-care facilities had most likely been infected previously; some workers, then, may have declined the vaccine because they already had antibodies.

New York is not the only state where significant rates of workers in long-term-care facilities are declining the vaccine. Gov. Mike DeWine of Ohio said last month that roughly 60 percent of nursing home workers offered a vaccine had declined.

A pharmacist prepared a dose of Moderna’s coronavirus vaccine in Santa Rosa, Calif., last week.
Credit…Jim Wilson/The New York Times

The California state epidemiologist has recommended that the state pause the distribution of more than 330,000 doses of the Moderna vaccine after a “higher than usual” number of people showed signs of a possible severe allergic reaction.

The recommendation comes at a dire moment in California, which is experiencing one of the most acute outbreaks in the nation. About 40,000 people are testing positive each day — the equivalent of the daily caseload for the entire United States as recently as September — and California’s hospital beds are filling up.

The state epidemiologist, Dr. Erica S. Pan, made the recommendation “out of an extreme abundance of caution” after several people who received the vaccine at one community clinic needed medical attention in the span of 24 hours. Each appeared to experience a possible “severe” allergic reaction, and officials recommended not using other vaccines from that batch until an investigation was completed, the health department said in a statement on Sunday.

According to the Centers for Disease Control and Prevention, an example of a severe allergic reaction is if a patient needs to go to a hospital or be treated with epinephrine.

The recent reactions were related to a vaccine distribution at Petco Park in San Diego, a spokesman for the California Department of Public Health said. It was not immediately clear how the delay would affect the state’s overall rollout of vaccines, which has been choppy and plagued with confusion.

The possible allergic reactions had stemmed from the same batch of Moderna vaccines, which included more than 330,000 doses, among 3.5 million vaccines allocated to the state. California has distributed less than a third of its allocated vaccines, below the national average, with 2.2 percent of the state’s population having received a first dose, according to a New York Times vaccine tracker.

Allergic reactions are a rare response to some vaccines. Some estimates suggest that for a similar type of coronavirus vaccine, made by Pfizer-BioNTech, the risk of severe allergic reaction is about 1 in 100,000.

A doctor administered a coronavirus test last April at Pinn Memorial Baptist Church in Philadelphia.
Credit…Matt Rourke/Associated Press

As the United States paused to remember Dr. Martin Luther King Jr. on Monday, Black Americans remained in greater danger of dying from Covid-19 than white Americans.

To help turn the tide, a group of clergy and community leaders is working to provide testing, inoculations and counseling in five cities, with plans to expand their community-based approach.

The initiative, called Choose Healthy Life, is centered on Black churches in New York, Newark, Detroit, Atlanta and Washington, in partnership with United Way, Quest Diagnostics, local health departments and community-based organizations. It aims to give churches resources, training and support to connect people to services.

Dozens of its leaders were joined in a video call on Monday by Anthony S. Fauci, the nation’s top infectious disease expert, and other top figures in the effort to stop the pandemic.

Speakers included the Rev. Al Sharpton of the National Action Network and the Rev. Calvin O. Butts III of the Abyssinian Baptist Church in Harlem, who serve as chairs for the project; the Rev. Raphael Warnock, who will be Georgia’s first Black senator; and Dr. Marcella Nunez-Smith, the incoming chair of President-elect Joseph R. Biden Jr.’s Covid-19 Racial and Ethnic Disparities Task Force.

“The same disparities that are ingrained in our economy, our housing system, our food system, our justice system and so many other areas of our society, we know are conspiring in this moment to create this grief gap,” Dr. Nunez-Smith said on the call. “We cannot become numb in the face of such tragedy.”

Sheena Wright, the president and chief executive of United Way of New York City, said in an interview that the project would seek to harness the power of Black churches, which are “credible, trusted messengers as well as caregivers in the community.”

“We’re focused on spreading awareness, education and access to testing, vaccines and other care,” she said.

That care could include helping someone make an appointment; figuring out food delivery or child care arrangements for someone who is sick or needs to quarantine; or addressing concerns and hesitation around vaccines. Unethical medical research, such as the U.S. government’s 40-year-long Tuskegee study, have contributed to lingering mistrust in the medical establishment among many communities of color — particularly among Black men, who were the unwilling subjects of the Tuskegee experiment.

“There’s critical information that we as a community need to hear and digest and execute as it relates to our own health and safety, coming from trusted leaders who can say it in a culturally responsive way,” Ms. Wright said.

Rebekah Jones, a former manager of the Florida Department of Health’s coronavirus dashboard, in Tallahassee last month.
Credit…Aileen Perilla for The New York Times

Rebekah D. Jones, a data scientist who helped manage the Florida Department of Health’s coronavirus dashboard before she became a cause célèbre when she was fired in May, was arrested on Sunday after the authorities charged her with accessing a state computer system and downloading a file without authorization.

Court records show that Ms. Jones surrendered to the police in Tallahassee, Fla., on Sunday. She spent the night in jail and was released after posting bond on Monday.

Agents from the Florida Department of Law Enforcement found that Ms. Jones’s computer, which they seized last month, was used to log into the health department’s internal emergency alert system on Nov. 10, the day that unauthorized messages were sent to 1,750 department employees, according to an arrest affidavit.

“It’s time to speak up before another 17,000 people are dead,” the messages read. “You know this is wrong. You don’t have to be part of this. Be a hero. Speak out before it’s too late.” (The Florida death toll is now more than 24,000.)

Investigators also found that Ms. Jones had downloaded and saved to her devices a file containing the personal information for 19,182 people who had given their data to the health department to be contacted in an emergency, the affidavit said.

Ms. Jones denied having anything to do with the messages when agents served a search warrant on her Tallahassee townhome on Dec. 7. Lawyers for Ms. Jones did not respond to requests for comment on Monday.

Ms. Jones told reporters in Tallahassee that she had tested positive for the coronavirus while in custody.

They noted last month that the login information for the emergency alert system was easily available to many health department employees and, for months, was even posted online.

“Censored by the state of Florida until further notice,” Ms. Jones wrote on Twitter on Sunday before turning herself in. She had written on Saturday that one of the likely conditions of her release would be having no access to computers, the internet or electronic devices.

Ms. Jones had also insisted that agents had found no evidence that she had sent the unauthorized emergency alert messages, though the affidavit made public on Monday said they did.

After she was fired for insubordination, Ms. Jones created her own dashboard to rival the state’s and filed a formal whistle-blower complaint. She also raised hundreds of thousands of dollars online to support her work.

Members of the Park Police patrolling the Lincoln Memorial last week.
Credit…Oliver Contreras for The New York Times

President-elect Joseph R. Biden Jr., who ran on a platform of addressing the pandemic with competence and compassion, will preside over a national memorial honoring the nearly 400,000 people who have died of the coronavirus shortly after arriving in Washington on Tuesday, his inaugural committee said Monday.

Mr. Biden, Vice President-elect Kamala Harris and their families plan to participate in the lighting of 400 lights to illuminate the perimeter of the reflecting pool in front of the Lincoln Memorial in their first stop in the city ahead of Wednesday’s inauguration, the committee said.

Each light is meant to represent approximately 1,000 Americans who will have perished related to the virus at the time of his swearing-in.

Tuesday’s ceremony will kick off “a national moment of unity” at 5:30 p.m. Eastern that will include similar memorials at the Empire State Building, the Space Needle in Seattle and other landmarks across the country, with events also planned for Mr. Biden’s hometowns of Scranton, Pa., and Wilmington, Del.

The inauguration “represents the beginning of a new national journey — one that renews its commitment to honor its fallen and rise toward greater heights in their honor,” the committee’s chief executive, Tony Allen, president of Delaware State University, said in a statement.

Cardinal Wilton Gregory, the archbishop of Washington, will deliver the invocation at the Lincoln Memorial event. The gospel singers Yolanda Adams and Lori Marie Key will perform at the commemoration.

In recent days, the committee’s staff has reached out to church and civic leaders around the country to participate in the memorial, with a particular focus on involving Black and Latino communities, which have been disproportionately hit by the pandemic.

On Sunday, Ron Klain, the incoming White House chief of staff, had a dire forecast for the course of the coronavirus outbreak in the new administration’s first weeks, predicting that half a million Americans will have died from the coronavirus by the end of February. The current death toll is nearing 400,000 and on Monday, the United States surpassed 24 million cases of the virus.

“The virus is going to get worse before it gets better,” Mr. Klain said in an appearance on CNN’s “State of the Union.” “People who are contracting the virus today will start to get sick next month, will add to the death toll in late February, even March, so it’s going to take awhile to turn this around.”

On Friday, federal health officials warned of a fast spreading, far more contagious variant of the virus that is projected to become the dominant source of infection in the country by March, potentially fueling another wrenching surge of cases and deaths.

Community Hospital of Huntington Park in Los Angeles earlier this month.
Credit…Philip Cheung for The New York Times

For nearly the entire pandemic, political polarization and a rejection of science have stymied the United States’ ability to control the coronavirus.

That has been clearest and most damaging at the federal level, where President Trump claimed that the virus would “disappear,” clashed with his top scientists and abdicated responsibility for a pandemic that required a national effort to defeat it, handing key decisions to states under the assumption that they would take on the fight and get the country back to business.

But governors and local officials who were left in charge of the crisis squandered the little momentum the country had as they sidelined health experts, ignored warnings from their own advisers and, in some cases, stocked their advisory committees with more business representatives than doctors.

Nearly one year since the first known coronavirus case in the United States was announced north of Seattle on Jan. 21, 2020, the country is hurtling toward 400,000 total deaths, and cases, hospitalizations and deaths have reached record highs.

The situation has turned dire just as the Trump administration, in its final days, begins to see the fruits of perhaps its biggest coronavirus success, the Operation Warp Speed vaccine program. But already, a lack of federal coordination in distributing doses has emerged as a troubling roadblock.

The incoming president, Joseph R. Biden Jr., has said he will reassert a federal strategy to bring the virus under control, including a call for everyone to wear masks over the next 100 days and a coordinated plan to widen the delivery of vaccines.

“We will manage the hell out of this operation,” Mr. Biden said on Friday. “Our administration will lead with science and scientists.”

The strategy signals a shift from the past year, during which the Trump administration largely delegated responsibility for controlling the virus and reopening the economy to 50 governors, fracturing the nation’s response. Interviews by The Times with more than 100 health, political and community leaders around the country and a review of emails and other state government records offer a fuller picture of all that went wrong.

People waiting in line at a coronavirus testing site in Los Angeles this month.
Credit…Alex Welsh for The New York Times

As the total number of U.S. coronavirus cases surpassed 24 million on Monday, Los Angeles County, one of the hardest-hit areas, may face even more dire weeks ahead. Deaths in the county have continued to climb as the national death toll nears 400,000.

Hospitals have run out of room in intensive care units, though new cases and hospitalizations appear to be leveling off in recent days. The county records a coronavirus-related death roughly every seven minutes, and last week was its highest recorded ever for Covid-19 fatalities.

On Saturday alone, 253 people died of Covid-19, and with variants of the virus that could be more contagious now circulating in California, those numbers may rise.

It took nearly 10 months for the county, America’s most populous, to hit 400,000 cases, but little more than a month to add another 400,000, from Nov. 30 to Jan. 2, according to a New York Times database. On Saturday, the county became the nation’s first to surpass one million recorded coronavirus infections, a number only four states other than California have exceeded: Illinois, New York, Florida and Texas. (California on Sunday became the first state to have recorded more than three million cases.)

And the true scale of infections may be much higher than reported: One in three Los Angeles residents is believed to have been infected with the virus since the beginning of the pandemic, according to the Los Angeles Department of Health. To help quell the spread, the county’s public schools have asked health authorities for permission to begin providing Covid-19 vaccinations.

The virus is surging across California, where daily deaths are averaging 528, an increase of over 15 percent from a week ago. Much of the state, including the southern region, remains under a stay-at-home order.

The crisis has led to a backlog of bodies so severe that the air quality regulator for much of Southern California issued an emergency order on Friday temporarily suspending limits on cremations in Los Angeles County, at the request of the county’s coroner and health department.

The state is among many dealing with the arrival of a more contagious viral variant, first discovered in Britain; the first confirmed case in Los Angeles was reported on Saturday. It is believed to be potentially 50 percent more transmissible than the initial version of the virus.

Officials said they thought the variant, which has caused infections to soar in London and southeast England, has been spreading through Los Angeles for some time. While more contagious, the variant does not appear to cause more severe illness.

On Sunday night, the California Department of Public Health reported another variant that had grown more common across the state since December. Known as L452R, it was first detected in Denmark in March and appeared in California in May. In December, researchers at the University of California, San Francisco, sequenced genomes of coronavirus gathered around the state and found that the variant was present in just 3.8 percent of their samples. By January, it had jumped to 25.2 percent.

Charles Chiu, who led the sequencing, cautioned that he and his colleagues worked with a small sample size, so they have not yet proven that this variant is more contagious. “But there are worrisome signs that this variant may be highly transmissible,” he said.

Dr. Chiu and his colleagues are now looking more carefully for this variant across the state and are trying to understand how its mutations have altered it. They want to see if the variant can escape from monoclonal antibodies and perhaps even make vaccines less effective. “These are critical studies that need to be done,” Dr. Chiu said.

After weeks under a stay-at-home order, the county’s positivity rate is starting to taper. Dr. George Rutherford, an epidemiologist at the University of California, San Francisco, said the state and Los Angeles seemed to be “in the process of sort of gradually turning a corner here.”

He cautioned against panicking about the more transmissible variant, noting the same cautious behavior will help keep it at bay: stay home, wear a mask, physically distance.

Members of the National Guard last week outside the U.S. Capitol, where up to 25,000 troops are expected for the inauguration on Wednesday.
Credit…Jason Andrew for The New York Times

In recent days, tens of thousands of National Guard troops have flooded into Washington from across the country to protect lawmakers and ensure a smooth transition to the next administration.

The soldiers — several times more troops than are deployed to Iraq, Afghanistan, Somalia and Syria — may also be dealing with another risk: the coronavirus. At least 43 troops deployed to Washington contracted the virus, The Military Times reported, though none while on duty in the city, according to Air Force Capt. Tinashe T. Machona.

A spokesman for the National Guard Bureau, Maj. Matt Murphy, said that while Guard members with symptoms were directed to get tested and seek medical care, not all Guard members would be tested. Members underwent temperature checks and filled out questionnaires about their symptoms and exposure, he said.

“All 50 states, three territories and the District of Columbia are involved in this operation,” Major Murphy said. “To track down all 54 surgeon generals to see if they’re able to release numbers regarding their troops at this time would overwhelm us.”

Linsey Marr, a professor of civil and environmental engineering at Virginia Tech, said that while it was “very important for them to be there,” Guard members “should be doing everything reasonably possible” to prevent the spread, including wearing masks, getting tested and exercising extra caution in higher-risk settings like being in vehicles together, resting in the Capitol (as many have been pictured doing) and eating indoors.

“It’s almost certain that some of them are carrying the virus” with such a large crowd, Dr. Marr said.

Credit…T.J. Kirkpatrick for The New York Times

The troops are frequently photographed in masks, standing at a distance. But many had to sleep huddled in crowded spaces in the Capitol, making room for lawmakers to continue business.

Dr. Ashish Jha, the dean of Brown University’s School of Public Health, said that systematic testing should be a priority for a group of that size, including for asymptomatic cases. “These folks are there to protect our political leaders, but we should not be putting them in harm’s way unnecessarily by not doing what we can to protect them from the virus,” he said.

The troops are mostly processed through the D.C. Armory, where they fill out a medical questionnaire, receive credentials and find out about their assignments and other logistics.

Earlier this summer, when the National Guard deployed troops to Washington for Black Lives Matter protests, a few tested positive, McClatchy reported at the time. The infected Guard members stayed in the city and quarantined while others went back to their home states.

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Ahmed Nafei via FacebookCreditCredit…Ahmed Nafei via Facebook

A nurse’s cry pierced the night from the balcony of an Egyptian hospital. She was screaming that the patients in the Covid-19 intensive care unit were gasping for air.

Ahmed Nafei, who was standing outside, brushed past a security guard, dashed in and saw that his 62-year-old aunt was dead.

Furious, he whipped out his phone and began filming. It appeared that the hospital had run out of oxygen. Monitors were beeping. A nurse was distressed and cowering in a corner as her colleagues tried to resuscitate a man using a manual ventilator.

At least four patients died.

Mr. Nafei’s 47-second video this month of the chaos at El Husseineya Central Hospital, about two and a half hours northeast of Cairo, spread rapidly on social media.

As outrage grew, the government denied that the hospital had run out of oxygen.

An official statement issued the following day concluded that the four who died had suffered from “complications” and denied that the deaths had “any connection” to an oxygen shortage. Security officers interrogated Mr. Nafei, and officials blamed him for violating rules barring visits and filming inside hospitals.

A New York Times investigation, however, found witnesses, including medical staff and relatives of patients, who said in interviews that the oxygen had fallen to precipitously low levels. At least three patients, they said, and possibly a fourth, had died of oxygen deprivation. A close analysis of the video by doctors in Egypt and the United States confirmed that the chaotic scene indicated an interruption in the oxygen supply.

The oxygen shortage was the result of a cascade of problems at the hospital, The Times’s investigation found. By the time patients were suffocating, a relief delivery of oxygen was already hours late and a backup oxygen system had failed.

“We’re not going to bury our heads in the sand and pretend everything is OK,” a doctor at the hospital said, speaking on condition of anonymity because he feared arrest. “The whole world can admit there’s a problem, but not us.”

The government’s rush to deny the episode is only the latest example of the lack of transparency in its response to the pandemic, which has led to cynicism and distrust of its public assurances.

The City of Los Angeles opened a mass vaccination site at Dodger Stadium last week.
Credit…Pool photo by Irfan Khan

Public schools in Los Angeles, which are already administering a huge coronavirus testing and tracing program for students, teachers and families in the nation’s second-largest district, have asked the state and county health authorities for permission to begin providing Covid-19 vaccinations, the superintendent said on Monday.

Austin Beutner, the superintendent, said the Los Angeles Unified School District was “uniquely situated — and uniquely qualified — to help in the vaccination effort,” with a dozen licensed clinics, 42 testing locations, more than 450 registered school nurses and partnerships with insurers that would allow them to begin administering inoculations immediately.

Though school districts in New York, Kansas City and the California cities of Riverside, Ventura and Long Beach have committed to vaccinate or have begun vaccinating school employees, schools have yet to be broadly deployed for general distribution of coronavirus vaccines.

But Los Angeles Unified, which has more than 1,400 K-through-12 schools and serves nearly 700,000 mostly low-income students across 710 square miles of Southern California, has throughout the pandemic operated not only as a school system, but as a large-scale social service and relief organization, distributing nearly 100 million free meals, as well as pandemic supplies and virus tests, to students and employees and to their families. The district is also in a county with soaring rates of coronavirus infection: One-third of Los Angeles County residents are now estimated to have contracted the virus.

“We’re raising our hand and saying, ‘Put me in, coach — we can help,’” Mr. Beutner said.

Last week, counties and cities throughout the state began opening mass inoculation sites by appointment to accommodate patients unable to obtain vaccines from their pharmacists or doctors. The City of Los Angeles opened a site at Dodger Stadium, and Los Angeles County has said it will open five more such sites on Tuesday.

It is unclear whether the public health authorities will take the school district up on its offer. But Mr. Beutner called the notion of school-based community vaccination centers “just common sense.”

Schools have been integral to vaccine distributions in the past, operating as sites in the 1950s for the inoculation of millions of schoolchildren against polio, for instance, and in 2009 for the distribution of millions of doses of vaccines for the H1N1 swine flu virus.

A doctor at the Jeffrey Cheah Biomedical Centre, in Cambridge, Britain analyzing samples of the coronavirus last week to determine how the virus is mutating.
Credit…Mary Turner for The New York Times

At the heart of each coronavirus is its genome, a twisted strand of nearly 30,000 “letters” of RNA. These genetic instructions force infected human cells to assemble up to 29 kinds of proteins that help the coronavirus multiply and spread.

As viruses replicate, small copying errors known as mutations naturally arise in their genomes. A lineage of coronaviruses will typically accumulate one or two random mutations each month.

A coronavirus variant first reported in Britain, named Variant of Concern 202012/01 by Public Health England, is part of the B.1.1.7 lineage of coronaviruses, and is believed to be potentially 50 percent more transmissible than the initial version of the virus.

Some mutations have no effect on the coronavirus proteins made by the infected cell. Other mutations, like those in B.1.1.7, might alter a protein’s shape by changing or deleting one of its amino acids, the building blocks that link together to form the protein.

Through the process of natural selection, neutral or slightly beneficial mutations may be passed down from generation to generation, while harmful mutations are more likely to die out.

The B.1.1.7 lineage has now been detected in over 50 countries, including the United States. Britain has responded to the surge of B.1.1.7 with stringent lockdowns, and other countries have tried to prevent its spread with travel restrictions.

Federal health officials warn that it may become the dominant variant in the United States by March. It is no more deadly than other forms of the coronavirus. But because it can cause so many more infections, it may lead to many more deaths.

B.1.1.7 has been detected in at least 14 states, but the United States has no national surveillance program for determining the full extent of its spread.

A woman received a coronavirus vaccine during a pop-up event at the Grace Cathedral International in Uniondale, Long Island on Monday.
Credit…Laylah Amatullah Barrayn for The New York Times

Shortly after Bishop Robert Harris sent out an email last week telling parishioners that his church in Uniondale, N.Y., would be a pop-up site for Covid-19 vaccinations on Martin Luther King Jr. Day, the phone in the office at Grace Cathedral International Church started ringing nonstop.

Members of several other churches in Uniondale had received the emails, and word spread quickly beyond the immediate community, triggering even more calls to register for shots.

“One woman called me crying, saying, ‘Thank you so much,’ that they’ve just been waiting so long for this,” said Shareese Harris, the bishop’s granddaughter, who was answering the phones at the church office on Friday.

“She said she hasn’t been able to see her newborn grandson because she didn’t want to be around him and risk his health, and she just broke down crying. She said it was a prayer answered.”

The vaccination drive is an element of a health equity outreach project sponsored by Northwell Health, as part of a statewide effort led by Gov. Andrew M. Cuomo that aims to take critical Covid-19 health care services into Black and Hispanic communities that were hard-hit by the epidemic. The clinical sites at churches in diverse neighborhoods allow residents without transportation easy access to care at a trusted institution.

Many Black and Hispanic churches participated in similar initiatives last spring, when they became temporary sites offering tests for Covid-19 and for antibodies.

People of color, including Black, Hispanic, Native American and, to a lesser extent, Asian-Americans, have been disproportionately impacted by the pandemic.

Another Long Island church, the Prayer Tabernacle Church of God In Christ in Amityville, also hosted a one-day pop-up vaccination clinic on Monday. The two sites hoped to dispense 250 vaccine doses each, and Northwell officials said they hoped to continue the program as long as supplies last.

Public opinion surveys have found that Black Americans are more likely than others to be concerned about the safety of the Covid-19 vaccines, with a recent Kaiser Family Foundation survey reporting that while about one-quarter of Americans are hesitant about the new vaccines, 35 percent of Black Americans said they definitely or probably would not get the vaccine because of concerns about its safety and novelty.

But Bishop Harris said the community has lost so many people to Covid-19 that the vaccine will be welcomed.

“We don’t have a history about the long-term impact of the vaccine, but we’ve got 4,000 people dying a day,” said Mr. Harris, 78, who has been vaccinated. “I’d rather take a gamble with the vaccine than not. You become fearful when it comes so close.”

global roundup

Attending to a patient at the Covid-19 emergency room of Santa Maria hospital in Lisbon last week. Portugal has one of Europe’s smallest intensive-care capacities.
Credit…Patricia De Melo Moreira/Agence France-Presse — Getty Images

Portugal’s hospitals are on the brink of becoming overwhelmed with coronavirus cases, with fears the country’s hospital system could buckle in the face of steadily rising infections. The country has registered more than 10,000 new cases of Covid-19 daily for the last five days.

Portugal has one of smallest intensive care unit capacities of any country in Europe, with just 672 beds available, and by Sunday, 647 intensive care patients were being treated for the coronavirus, according to the health ministry.

After visiting a hospital on Sunday, President Marcelo Rebelo de Sousa of Portugal told journalists that there was now pressure on health care structures that were greater than the first peak of the outbreak in March. The rate of infections, he added, could rise significantly in the coming weeks and necessitate “a much longer lockdown.”

Portugal began a month of nationwide restrictions on Friday, with measures similar to those the country enforced last spring, including the closure of nonessential stores and an order for citizens to stay at home.

Marta Temido, Portugal’s health minister, said the country was “very close to the limit” after visiting a hospital in Almada on Sunday and called on citizens to follow the latest lockdown rules in order to help reduce the “very high” pressure on hospitals.

“Everybody needs to make sacrifices,” she said.

Here’s what to know from elsewhere in the world:

  • European leaders are set to debate a proposal this week for coronavirus “passports” that would let vaccinated people travel freely within the bloc. Prime Minister Kyriakos Mitsotakis of Greece, where travel restrictions have hit the tourism industry hard, said in a letter to the president of the bloc’s executive arm that it was “urgent” for member states “adopt a common understanding” on vaccination certificates, according to Reuters. The issue is expected to be discussed during a video conference on E.U. coronavirus coordination on Friday.

  • Australia’s health secretary said the country was unlikely to fully reopen its borders in 2021, despite vaccination efforts and pressures from the tourism industry. Speaking to ABC News on Monday morning, the minister, Brendan Murphy, said that restarting international travel remained “a big question.”

    “I think that we’ll go most of this year with still substantial border restrictions,” he said.

  • Germany’s health ministry has announced plans to systematically sequence coronavirus samples in order to detect and track variants of the virus that have the potential to spread more swiftly. “We want to be able to understand even better where known mutations are spreading and whether new mutations are occurring,” Jens Spahn, the health minister, said on Monday. The goal is to sequence at least 5 percent of new infections. Mr. Spahn said that while the variant that spread rapidly in England had been found in Germany, it was mostly linked to patients who had traveled from Britain.

  • In Japan, the health ministry reported three new cases on Monday of the variant that spread in Britain, the first to be discovered among residents with no travel history. Japan has reported a total of 45 cases of three different coronavirus variants, all but these latest three among people who had recently traveled or were close contacts of travelers from Britain, South Africa or Brazil. The three new cases were all confirmed in Shizuoka Prefecture, south of Tokyo and the home of Mt. Fuji, Japan’s highest peak.

Vaccinations at a government hospital in Ahmedabad, India, on Saturday.
Credit…Ajit Solanki/Associated Press

India’s coronavirus vaccine rollout, one of the largest in the world, has been hobbled by technical glitches in a mobile phone application, leaving the country far short of its vaccination goals in the first few days of the campaign.

State officials complained of problems with a digital platform called the Covid Vaccine Intelligence Network, or CoWIN, which is used by both vaccine providers and recipients to monitor the campaign’s progress. It is mandatory for vaccine recipients to register on the app in order to be inoculated.

Dr. Ajoy Kumar Chakraborty, director of health services in the state of West Bengal, said Monday that the software had become overwhelmed and didn’t work at many vaccination sites, and that vaccinations were curtailed as a result.

In the first phase of the campaign, which began on Saturday, government officials plan to vaccinate 30 million health and frontline workers. On the first day, about 300,000 health care workers were set to be inoculated; the actual number was about 207,000. On Sunday, the number dropped to 17,072.

Dr. Manohar Agnani, a senior official in the federal Ministry of Health and Family Welfare, said on Sunday that feedback was being collected from states to “identify bottlenecks and plan corrective action.”

India has approved two vaccines for emergency use. One is the vaccine developed by AstraZeneca and Oxford University, which is manufactured by the Serum Institute of India and is known in the country as Covishield. The other is Covaxin, which was developed by India’s National Institute of Virology with Bharat Biotech, a local pharmaceutical company.

The government of India, which has a population of 1.3 billion people, has so far purchased 11 million doses of Covishield and 5.5 million doses of Covaxin, both of which require two doses per person. Unlike the Oxford-AstraZeneca vaccine, no Phase 3 clinical trial data has been released showing that Covaxin is safe and effective. Officials have said that vaccine recipients will not get to choose between the two.

Doubts about transparency are only one of the obstacles officials face in trying to end one of the largest outbreaks in the world. India has the second-highest number of cases after the United States, and the third-highest number of deaths after the United States and Brazil, according to a New York Times database.

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The head of the World Health Organization says that the promise of equitable access to the vaccines “is at serious risk.”CreditCredit…Tim Gruber for The New York Times

The head of the World Health Organization has warned that the world is on the brink of a “moral failure” in ensuring coronavirus vaccines are distributed among the world’s poorest populations, and that the promise of equitable access to the vaccines “is at serious risk.”

Dr. Tedros Adhanom Ghebreyesus, the director general of the World Health Organization, speaking at the opening session of a meeting of its executive board, said the world had the opportunity to “write a different story” than those of past pandemics in which rich countries benefited from widespread access to vaccines while the world’s poor were neglected.

“We now face the real danger that even as vaccines bring hope to some, they become another brick in the wall of inequality between the world’s haves and have-nots,” he said.

While the “stunning scientific achievement” of developing a vaccine in under a year has become “a much-needed source of hope,” Dr. Tedros warned that the world must do more to ensure the equitable distribution of the finite supply of approved vaccines to poorer nations.

In recent months, rich nations like the United States and Britain have cut deals with drug manufacturers and secured enough vaccine doses to ensure their citizens could be vaccinated, often multiple times over, and programs have already begun in most.

“Its right that all governments want to prioritize vaccinating health workers and older people first,” he said. But it was “not right” for young, healthy people in rich countries to be vaccinated before the more vulnerable.

Many nations have also committed to taking part in a complex vaccine-sharing scheme called Covax, a collaboration between international health organizations and global partners, designed to ensure that the world’s poorest nations can access vaccines. But Dr. Tedros said that in recent weeks, worrisome reports had made him fear wealthier nations would not follow through on their commitments.

“I need to be blunt: The world is on the brink of a catastrophic moral failure, and the price of this failure will be paid with lives and livelihoods in the world’s poorest countries,” he said.

Dr. Tedros noted that even the countries and companies that “speak the language of equitable access” have continued to prioritize bilateral vaccine deals that circumvent the Covax program, drive up prices and see nations “attempting to jump to the front of the queue.”

“This is wrong,” he said.

Jonathan Sumption in London in 2010, two years before he joined Britain’s Supreme Court. He retired from the court in 2018, and has become a prominent anti-lockdown voice.
Credit…Ben Stansall/Agence France-Presse — Getty Images

A former British Supreme Court justice is drawing condemnation after clashing with a woman with cancer during a televised debate over the country’s lockdown.

Jonathan Sumption, 72, who was a Supreme Court justice for six years before retiring in 2018 and has become one of the country’s most prominent anti-lockdown voices, said during a discussion broadcast on the BBC on Sunday that he did not accept that “all lives were of equal value.”

When he argued that the lives of his children and grandchildren were “worth much more” because of potential years ahead, another panelist pushed back.

“I’m the person who you say their life is not valuable,” said Deborah James, who hosts a podcast on the BBC and has stage four, metastatic bowel cancer.

Lord Sumption responded: “I didn’t say it wasn’t valuable, I said it was less valuable.”

“Who are you to question and put a value to life?” Ms. James then continued. “I believe life is sacred and I don’t think we should make those judgment calls.”

The exchange provoked outrage online, with critics calling the former judge’s position “morally deficient,” “inhumane” and reminiscent of arguments for eugenics.

Lord Sumption said later that his comments had been misinterpreted, telling the British newspaper The Daily Mail: “I object extremely strongly to any suggestion that I was inferring that Miss James’s life was less valuable because she had cancer. I thought she was responding to my earlier comments about older people being protected by a total lockdown which is causing immense harm to the young who are unaffected.

“That harm can be to their mental health or through cooping undergraduates up at university or through the loss of jobs. I was saying this should not be inflicted on the young to protect old people like me.”

“One of the problems is that we were talking across each other,” he said on another television show, “Good Morning Britain,” on Monday, adding that he and Ms. James had had a friendly exchange afterward and he regarded the matter as “closed.”

The point he was trying to make, he said, was that policymakers had to make difficult choices including putting a value on human life. “This is a tool for policymakers,” he said. “It’s not a way of valuing individuals.”

A page from the Paycheck Protection Program loan application in May.
Credit…Lucas Jackson/Reuters

The Paycheck Protection Program’s loose rules allowed virtually any small business or company in America to qualify for a government-backed relief loan. Citizens and activist groups have criticized thousands of recipients that they deemed unworthy, including wealthy lawyers, politicians and political lobbyists, publicly traded companies and businesses under government investigation.

Now, an advocacy group that fights online misinformation is drawing attention to a group of loan recipients it finds troubling: anti-vaccine activists.

Six organizations that have challenged the safety of vaccines and made claims that scientists have called false received loans that collectively added up to more than $1.1 million, according to data from the Small Business Administration, which manages the program. (The data was released last month under a court order, in response to a lawsuit filed by The New York Times and other news organizations.)

The groups that received the loans are Children’s Health Defense, founded by Robert F. Kennedy Jr.; the Informed Consent Action Network; the National Vaccine Information Center; Health Resources and Mercola Consulting Services, both affiliated with the prominent vaccine skeptic Joseph Mercola; and the Tenpenny Integrative Medical Center, a medical practice run by Dr. Sherri Tenpenny, a physician and author who opposes vaccines.

The loans, which were made by banks and backed by the government, ranged in size from $72,500 to Dr. Tenpenny’s medical center to $335,000 to They do not appear to violate Small Business Administration rules: P.P.P. loans were widely available to any small company or nonprofit (generally those with 500 or fewer workers) willing to certify that “current economic uncertainty makes this loan request necessary” to support their continuing operations.

The Center for Countering Digital Hate, a London-based advocacy group, uncovered the loans and alerted The Washington Post, which first reported on them. Imran Ahmed, the group’s chief executive, called it “bananas” that such groups were eligible for taxpayer-funded relief money.

“There’s an anomaly here,” Mr. Ahmed said. “The P.P.P. was needed to deal with the economic shock of Covid, and the anti-vaxxers fundamentally inhibit our ability to defeat Covid and move past this.”

Barbara Loe Fisher, the president of the National Vaccine Information Center in Sterling, Va., said by email that her group applied for the loan “when it became apparent that lockdowns and social distancing restrictions directly threatened the job security of a number of our employees and jeopardized continued rental of our Virginia headquarters office.” The group used the loan to retain all of its 21 workers, she said.

Ms. Fisher disputed the notion that her group is anti-vaccine. The organization “does not make vaccine use recommendations and encourages everyone to become fully informed about the risks and complications of infectious diseases and vaccines,” she said.

The Paycheck Protection Program distributed $523 billion to more than five million small companies from April to August to help them endure the shutdowns and other economic shocks caused by the coronavirus pandemic. So long as recipients use most of the money to pay their workers and comply with other rules, the loans are eligible to be fully forgiven and paid off by the U.S. government.

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Gov. Andrew M. Cuomo of New York said on Monday that he had asked the pharmaceutical giant Pfizer to directly sell doses to the state, so that it does not have to depend solely on the federal government to distribute doses.CreditCredit…James Estrin/The New York Times

Facing a shortage of coronavirus vaccines in New York, Gov. Andrew M. Cuomo on Monday asked the pharmaceutical giant Pfizer to directly sell doses to New York, so that the state would no longer have to rely solely on the federal government to distribute doses. But it was unclear whether the company would be able to do so.

Speaking at a news conference, Mr. Cuomo noted that Pfizer did not seem to have to follow Moderna’s exact commitments to the Trump administration’s Operation Warp Speed vaccine program, so he wondered whether it might be able to sell doses directly to the state.

But a spokeswoman for Pfizer said Monday that the company would need approval from the federal government to sell directly to state governments. Such a move would seem unlikely within the last 48 hours of President Trump’s tenure; representatives for the federal Department of Health and Human Services and the transition team for President-elect Joseph R. Biden Jr., who will be sworn into office on Wednesday, did not immediately respond to requests for comment.

Under agreements with the Trump administration, Pfizer has committed to selling a total of 200 million doses of its vaccine, developed with BioNTech, to the federal government. The first tranche, of 100 million doses, was committed last summer even before the vaccine was found to be effective. Last month, the company agreed to deliver another 70 million doses by the end of June and an additional 30 million by the end of July.

“Pfizer is a New York company — something I am greatly proud of,” Mr. Cuomo wrote in a letter to Pfizer’s chief executive, Dr. Albert Bourla, adding, “the distribution of any doses obtained directly from Pfizer will follow the rigorous guidance the state has established, while enabling us to fill the dosage gap created this week by the outgoing federal administration.”

Mr. Cuomo said over one million vaccine doses have been administered across the state so far, but said New York urgently needed a solution to its supply issue.