Britain’s Contact Tracing for Coronavirus Falls Short of Promises

Oversold and underperforming: How Britain’s new contact-tracing system went wrong.

When Britain unveiled an ambitious new contact-tracing system to help pinpoint clusters of infections as they emerge, Prime Minister Boris Johnson described it as a “world beating” operation.

As with much of the government’s response to the pandemic, however, the results have fallen short of the promises, jeopardizing the reopening of Britain’s hobbled economy and risking a new wave of death in one of the countries most debilitated by the virus.

The system, staffed by thousands of poorly trained, low-paid workers, was rushed out of the gate on May 28 before it was ready, according to interviews with more than a dozen contact tracers, public health officials and local government leaders.

In the almost three weeks since it began, some contact tracers have failed to reach a single person, filling their days instead with internet exercise classes and bookshelf organizing. And some call handlers, scattered in offices and homes far from the people they speak with, have mistakenly tried to send patients in England to testing sites across the sea in Northern Ireland.

One government minister threatened on a conference call to stop coordinating with local leaders on the virus-tracking system if they spoke publicly about its failings, according to three officials briefed on the call.

The United Kingdom has nearly 300,000 confirmed infections, and more than 40,000 people have died. Contact tracing was supposed to be the bridge between lockdown and a vaccine. Without it, a World Health Organization official said recently, England would be remiss in reopening its economy.

Now, the troubled debut has left public health officials across England trying to battle a virus they still cannot locate.

Reversing course, Arizona and Texas allow some local governments to require masks.

Arizona did not record its first 20,000 cases until June 1, but it took less than three weeks for the state to record 20,000 more. So on Wednesday, its governor, Doug Ducey, said he would switch gears and allow mayors to require mask wearing if they see the need.

“The trend is headed in the wrong direction,” Mr. Ducey said at a news conference.

The state has merely recommended masks, and localities were precluded from drafting more restrictive rules.

But with cases rising swiftly and the mayors of Phoenix and Tucson urging him to let them mandate masks, Mr. Ducey said he would allow local governments to set their own mask policies.

The governor noted that the rise in cases was not due solely to increased testing.

Mayor Kate Gallego of Phoenix and Mayor Regina Romero of Tucson both said they would move to mandate masks in their cities.

In Texas, which also saw record case increases this week, similar tensions have arisen between local officials and the governor, whose statewide reopening orders take precedence. The mayors of nine cities sent a letter to Gov. Greg Abbott urging him to give them the authority to require masks.

“A one-size-fits-all approach is not the best option,” said the letter, whose signers included the mayors of Houston, Dallas, Austin and San Antonio. “We should trust local officials to make informed choices about health policy.”

Although Mr. Abbott has strongly urged wearing face masks, the state’s policies do not require their use, and the governor has resisted calls to do so, saying that he believed in “individual responsibility” and not “government mandates.”

But at least one Texas county got permission to go ahead with a limited mask requirement.

Bexar County, which includes San Antonio, is ordering businesses to require employees and customers to wear face masks when they are unable to observe social distancing. County Judge Nelson Wolff issued the order Wednesday, a day after the county confirmed 436 new cases, its biggest single-day increase.

In a television interview on Wednesday, the governor said he has no quarrel with the Bexar County order since it applies to businesses and not individuals.

“I was surprised that he was OK with it,” Judge Wolff said in a telephone interview. “I’m very pleased. I think it’s going to make a difference.”

U.S. ROUNDUP

Pence dismisses fears of a second wave. Fauci says the U.S. is still in its first.

Vice President Mike Pence argued in a Wall Street Journal opinion piece that concern over a “second wave” of the coronavirus was “overblown” and that “we are winning the fight against the invisible enemy.” Dr. Anthony S. Fauci, the government’s top epidemiologist, also said that the country was not in a “second wave,” but for a very different reason: He warned that the nation was still in the first wave.

“People keep talking about a second wave,” Mr. Fauci said in an interview with The Wall Street Journal on Tuesday. That is not accurate, he said, because “we’re still in a first wave.”

Mr. Pence’s argument appears to have oversimplified a complicated picture, emphasizing regions where the pandemic is waning while explaining away surging infection rates in other states. His rosy picture conformed with President Trump’s desire to reopen the economy and get Americans back to work, but it ignored bad news, especially in the Sun Belt.

In at least 20 states, new cases are increasing, some at alarming rates. Some states, including Texas, South Carolina and Arizona, are seeing their largest surges yet, according to data compiled by The New York Times.

In his op-ed, Mr. Pence said that expanded testing revealed that fewer than 6 percent of Americans tested every week have the virus. On a call with governors Monday, Mr. Pence encouraged them to adopt the administration’s explanation that a rise in testing was behind new outbreaks, a claim that Dr. Fauci rebutted on Tuesday, when he said that the higher percentages of positive tests “cannot be explained by increased testing.”

In other U.S. news:

• With the entire college football season looking tenuous just over two months before its scheduled start, four games involving historically black colleges and universities became the first Division I matches to be canceled because of the pandemic. Southern University and Jackson State each canceled its first two games, including a pair of neutral-site contests: Southern vs. Tennessee State in Detroit on Sept. 5 and Jackson State vs. Tennessee State a week later in Memphis.

• Gov. Gretchen Whitmer of Michigan announced on Wednesday that she would extend her state-of-emergency order, joining at least five other governors — in Vermont, Maine, Minnesota, Missouri and South Carolina — who took the same step during the last week. Along with control over travel restrictions and business closures, the emergency declarations provide a direct line to federal funding for disaster relief. In Michigan, confirmed cases of the virus have steadily declined this month. Restaurants have reopened at limited capacity. Major industries, including construction and manufacturing, have also restarted operations.

• Thousands of citizens-in-waiting may be unable to complete their naturalizations in time to vote in the 2020 election, after the ceremonies were put on hold amid the pandemic.

• U.S. stocks fell on Wednesday, giving up an early gain, as investors regrouped after days of turbulent trading fueled by a cascade of news about the coronavirus and its impact on the global economy.

• Some cities that initially avoided the worst of the virus are seeing a surge in cases since reopening. Charleston, S.C., Joplin, Mo., and Portland, Ore., are seeing major increases, raising concerns among state officials about easing restrictions too soon. Cases are also rising around Tulsa, Okla., Honolulu and Wichita, Kan., none of which were previously hit especially hard.

• Two major labor unions — the United Mine Workers of America and United Steelworkers — filed suit against the Trump administration in a bid to force regulators to protect mine workers. The suit aims to force the Mine Safety and Health Administration to adopt rules to prevent virus transmission, which the unions argue could pose a serious risk to miners who work in close quarters and often already suffer from respiratory illnesses.

• New Jersey will allow colleges and universities to resume in-person clinical, laboratory and hands-on programming as soon as July 1, the governor said. The schools must require masks and need to submit a plan to the state detailing safety procedures. There were an additional 47 deaths.

• Washington is scheduled to enter it second phase of reopening next week. It will now allow gatherings of up to 50 people and indoor dining at restaurants, as long as they operate at no more than 50 percent capacity. Over the past week, the district saw an average of 44 new cases a day. Cases have been dropping since late April.

• Students will not be required to return to campus of the University of California, Berkeley, next fall. Those who choose to live in dorms will have to self-isolate at first, and large lectures will be offered remotely through an online “Semester in the Cloud” program.

GLOBAL ROUNDUP

China’s best-known doctor gives a prescription for fixing disease surveillance.

Zhong Nanshan, an 83-year-old doctor who specializes in respiratory ailments, occupies a status in China roughly similar to Anthony Fauci’s in the United States: that of a widely respected medical expert whose plain-spoken views carry particular weight.

Dr. Zhong in 2003 helped to uncover the coronavirus behind the SARS epidemic in China. This year, he pushed back against local officials reluctant to acknowledge the threat from the new coronavirus, and he warned the government and the public that the virus was spreading from human to human.

On Thursday, Dr. Zhong told an online seminar organized by the University of Sydney that China needed to give its centers for disease control more power, independence, expertise and money to ensure that they serve as independent sentinels against dangerous outbreaks. The changes should not be “prolonged” or “delayed,” he added.

China’s network of centers for disease control is supposed to identify and report on potentially dangerous infectious diseases. But in Wuhan, the central Chinese city where the new coronavirus began to spread late last year, officials slowed the collection and release of information that might have enabled the authorities to act sooner against spreading infections, evidence from doctors and official documents has shown.

“Their position should be elevated so it’s not only for research or just giving some information to the local authorities. They should, in some part, be independent,” Dr. Zhong told the seminar, speaking in English. “The C.D.C. should have the right — should be more independent — to announce what’s their view, what’s their point, in particular in the emerging infectious diseases.”

Chinese leaders, including Xi Jinping, head of the ruling Communist Party, have said that the country’s public health system needs to improve in the wake of the pandemic, but they have not given details. And medical experts like Dr. Zhong appear to be pressing the government to act with greater urgency on their proposals.

The Beijing city government on Thursday reported 21 more cases of patients who tested positive for the virus and showed symptoms, bringing the total number of new symptomatic cases from a recent local outbreak to 158.

Dr. Zhong said that it would be two or three days before it became clear whether the renewed surveillance and controls in the capital had succeeded.

“That’s a big challenge to Beijing,” he said. “We don’t know whether this action will be effective or not.”

In other world news:

• In Germany, schools and day care centers in the northwestern district of Gütersloh remained closed on Thursday after more than 650 workers in a meatpacking plant tested positive for the coronavirus. The infected workers, many of whom travel to Germany from Eastern Europe to work in the slaughterhouse, have been placed under quarantine along with hundreds of other employees at the plant, officials in the district said.

• Prime Minister Scott Morrison of Australia said on Thursday that the economic blow from lockdowns had been “devastating,” as data showed that the country’s unemployment rate had surged to a 19-year high.

• New Zealand on Thursday recorded its third new case of the week, days after declaring itself among the first countries to be free of the virus.

• India had at least 354,000 confirmed cases of the coronavirus as of Wednesday, as efforts in New Delhi and Mumbai to account for previously unrecorded virus-related deaths led to a surge.

• The Israeli military announced that several generals had been quarantined after being exposed to people who tested positive for the coronavirus. All will continue to work remotely, and none has yet developed symptoms, the military said on Wednesday.

• Daily fossil fuel emissions worldwide were roughly 17 percent lower in early April than they were in 2019, a new study found. But they have rebounded sharply as countries relax their lockdowns and traffic surges back onto roads.

• Juan Orlando Hernández, the president of Honduras, announced on Tuesday that he, the first lady and two aides had tested positive for the virus. A government official said that he had been hospitalized on Wednesday and was being treated for pneumonia.

The Premier League is back after a 100-day shutdown.

“Most of all, though,” Rory writes, “as the death tolls mounted and the lockdown gripped, it asked again and again if soccer could return in the world of the coronavirus, or, more pertinent, whether it should. And then it asked, again and again, why everyone was talking about soccer so much.”

Cuomo says New York City is on track to ease more restrictions as soon as Monday.

New York City, once the center of the U.S. outbreak, is “on track” to enter its next phase of reopening as soon as Monday if there isn’t a resurge there, Gov. Andrew M. Cuomo said Wednesday.

It would move the city one step further along its path to recovery after the virus killed more than 21,000 residents.

Under the state’s plan, outdoor dining, some in-store shopping, hair salons, barbershops, and some offices in the city would be allowed to reopen in the second phase, with social distancing and restrictions on capacity. Playgrounds will also reopen then, city officials have said.

On Wednesday, the state reported another 567 cases, or about 0.96 percent of all tests processed the day before, the lowest rate since the beginning of the outbreak, according to the governor, and just 17 new deaths.

Mr. Cuomo has repeatedly emphasized the need for caution as the state eased restrictions, pointing to other states seeing new spikes, and urging New Yorkers to continue wearing masks and social distancing.

“You don’t stay smart, it will come back,” he said on Wednesday.

Earlier this week, Mr. Cuomo threatened to reinstate closures in the city after photos and videos spread online of people flouting social distancing and congregating outside Manhattan bars. Both he and Mayor Bill de Blasio also left open the possibility that the city would delay reopening if test results in the coming days showed a new spike in cases.

Mr. de Blasio has generally sounded a more cautious note about whether the city would be ready to ease more restrictions by next week, declining several times this week to specify a date.

On Wednesday, he reiterated concerns about the virus spreading during the recent huge protests over systemic racism and police brutality.

But Mr. Cuomo later said that state officials currently expected to follow the same precedent set in other regions: allowing Phase 2 to proceed 14 days after the start of Phase 1.

“It’s one set of rules for everyone,” Mr. Cuomo said. “And they have worked everywhere in the state.”

Australian universities plan to fly in some international students.

Australia’s locked-down international borders could see their first major opening next month, as two universities make plans to fly in a select group of international students who have nearly completed their degrees.

The proposal from the Australian National University and the University of Canberra is one of several plans being presented to Australia’s federal government by universities and states seeking travel exemptions that aim to be a model for others.

Under the latest plan, the universities would ask around 350 students to fly to a hub destination, such as Singapore, where they would connect to a charter flight hired by the universities. Both are based in Canberra, Australia’s capital city.

Upon arrival, the students would be quarantined in a hotel for 14 days and tested for Covid-19 at the beginning and end of their stay. The government of the capital territory, which has approved the plan, would take responsibility for managing the quarantine period and clearing the students for a return to campus.

Students with clear practical requirements or research projects that need to be finished would be given priority at first, but university officials said the goal was to create a process that could be broadened over time.

“We need a trial for Australia to build that confidence,” Paddy Nixon, the vice chancellor at the University of Canberra, told Australia’s main public broadcaster.

Another state — South Australia — plans to bring up to 800 international students to Adelaide’s universities.

But there is still a major hurdle: federal government approval.

Prime Minister Scott Morrison has emphasized that state borders would have to fully reopen before international students could return, and that has yet to happen.

The universities in Canberra are hoping to bring students back for the term that begins in August.

The Chinese government has been publicly warning its students to reconsider studying in Australia, citing “racist incidents targeting Asians,” but university officials maintain that their students will not be deterred.

“Our students in China want to get back to campus as much as any of our students do,” said the Australian National University vice chancellor Brian Schmidt. “This is an incredibly safe place, as I think we all know here.”

As states confront new coronavirus infections, Trump sends mixed messages.

The federal government’s leadership in the coronavirus crisis has so faded that state and local health officials have been left to figure out on their own how to handle rising infections and to navigate conflicting signals from the White House.

About 800 Americans a day are still dying of Covid-19, a pace that, if sustained over the next few months, would yield more than 200,000 dead by the end of September. Arizona, Florida, Nevada, Oregon and Texas all reported their largest one-day increases in new cases on Tuesday.

On Wednesday, Oklahoma recorded 259 new cases, a single-day record for the second day in a row, and just three days before President Trump is scheduled to hold an indoor campaign rally in Tulsa in defiance of his own administration’s guidelines for “phased reopening.”

That rally is not the only confusing signal from Washington. The Trump campaign is requiring rally-goers to sign a statement waiving their right to sue the campaign if they get sick.

While the president refuses to wear a mask, Surgeon General Jerome M. Adams has spent this week doing a round of television interviews to implore Americans to do so. Meantime, Vice President Mike Pence insisted in an opinion piece in The Wall Street Journal this week that panic over a second wave was “overblown.”

To public health experts, it is little mystery why Americans are confused. As the White House sends mixed messages, Washington’s public health bully pulpit has largely fallen silent.

Tulsa’s top health official expresses concern over Trump rally, but its mayor is ‘honored.’

The huge indoor gathering is expected to bring tens of thousands of people to the area on Saturday, just days after the city announced 96 new cases, its largest single-day increase. State officials also reported a new one-day high of cases on Wednesday, 259.

Bruce Dart, the executive director of the city’s health department, said he was “absolutely” concerned that the rally could become a “superspreader” event leading to more deaths. Mr. He noted that he had recommended the event be postponed until it was safer to bring large groups together indoors.

Mr. Dart urged people over 60 who are considering attending to “please stay home” and said they should “seek other ways to participate virtually.”

“We’re in the middle of a pandemic,” he said at a news conference. “If you want to use your voice, do it safely, wear a mask, social distance. Coming together is a definite possibility of seeing increased infections and increased deaths from those infections.”

But Tulsa’s mayor, G.T. Bynum, a Republican who is friendly with the Trump campaign, said he was “honored” that his city was chosen to host the president as he returns to the campaign trail. He noted that the event would be the first presidential rally in Tulsa since President George H.W. Bush visited decades ago.

“The fact that this president, coming out of this event, would single out our city and say, ‘That’s a city that did it the right way, that’s a city that’s reopening the right way,’ and want to come here? I do take it as an honor,” Mr. Bynum said.

He said that “any rational person looking at any large group of people” would have concerns about the event, but that it would be up to attendees to wear masks and use hand sanitizer.

Asked why he had disregarded his top health official’s advice to postpone the rally, Mr. Bynum said that it was not his decision and that he did not control bookings at the BOK Center, the sports arena that signed a contract with the Trump campaign.

The Trump campaign manager has said the campaign will distribute masks at the venue, but campaign officials said they would not require people to wear them inside. Attendees have had to waive their right to sue if they contract the virus at the rally.

The Tulsa police chief, Wendell Franklin, said he expected Mr. Trump’s rally to bring an “amount of people that probably Tulsa has never seen before” and noted that the temperature for Saturday was expected to reach 90 degrees. “Prepare for hours and hours inside of a concrete jungle, if you will,” he said.

Mr. Franklin also raised the possibility of mass protests.

In Tulsa, which in 1921 was the site of one of the country’s bloodiest outbreaks of racist violence, Juneteenth protests are expected to be more intense because of Mr. Trump’s initial decision to schedule a rally there on the holiday, which honors the end of slavery in the United States and is celebrated as African-Americans’ Independence Day. After a backlash, Mr. Trump said he would delay his rally by a day. But his visit will still coincide with planned protests and celebrations across the city all weekend.

India records its highest single-day toll as officials move to account for unreported virus deaths.

Efforts in New Delhi and Mumbai to account for previously unrecorded virus-related deaths led to a surge in India’s death toll on Tuesday, bringing the total to nearly 12,000.

Mumbai recorded 1,409 deaths on Tuesday, and the capital, New Delhi, added 437 fatalities, according to data from the federal health ministry. The country now has the eighth-highest death toll worldwide.

Officials in the two cities had been accused of underreporting the death toll. The Delhi health minister, Satyendar Jain, blamed insufficient information from hospitals.

“Every death count must have corresponding documents to back the death, otherwise they are just figures,” Mr. Jain said in a TV interview. On Tuesday, he was hospitalized for a high fever and respiratory symptoms, and later said he had tested positive for the virus.

Haitian migrants face risks after outbreaks at the border.

As the coronavirus spreads across Latin America and the Caribbean, public health officials are flagging outbreaks cropping up in several border regions, particularly the one between Haiti and the Dominican Republic.

The Pan American Health Organization said this week that it was focusing its efforts in these rural frontier areas, where populations are on the move and medical facilities are lacking. Indigenous people and migrants, vulnerable under normal circumstances, face even greater risks now.

Many Haitians live and work in the Dominican Republic, but after the outbreak there, thousands lost their jobs and moved back to Haiti. Some may have brought the virus with them.

According to the International Organization of Migration, there were more than 278,000 border crossings from March 17 to June 7, with a total of 51,000 going to Haiti, an unusually high number, according to Giuseppe Loprete, the organization’s chief of mission in Haiti. He added that the weekly average of 4,000 crossings was about double the normal figure.

For many migrants, the stigma associated with the disease has made some of those safeguards, like contact tracing, even more difficult. Mr. Loprete said that many people returning to Haiti leave inaccurate contact numbers because they do not want community members to treat them as sick.

In addition to Haiti and the Dominican Republic, Dr. Carissa F. Etienne, the director of the P.A.H.O., cited spikes in other border areas, including the one between Costa Rica and Nicaragua and the Amazon region that Brazil shares with its neighbors.

The W.H.O. stops its trial of hydroxychloroquine.

The World Health Organization announced on Wednesday that it was halting its major trial of hydroxychloroquine, the malaria drug hailed by Mr. Trump as a possible treatment for Covid-19. It said there was no evidence that the drug was effective.

Dr. Henao Restrepo, a W.H.O. official, said the decision was based on evidence from the trial and from others conducted elsewhere that showed the drug “does not result in the reduction of the mortality of those patients.”

The decision came two days after the United States Food and Drug Administration revoked emergency-use authorization for hydroxychloroquine and chloroquine, a related drug, after a review determined that the drugs were not effective as a treatment. It also found more than 100 cases of serious heart disorders in Covid-19 patients who took the drugs, including 25 that were fatal, and it found other problems, too.

The F.D.A.’s abrupt decision to revoke the waiver for the drugs has left 66 million doses stranded in the federal stockpile — and officials do not yet know what they will do with them.

U.C. Berkeley says in-person attendance will be optional, and students who live in dorms must self-isolate at first.

Students will not be required to return to campus of the University of California, Berkeley, next fall. Those who choose to live in dorms will have to self-isolate at first. Large lectures will be offered remotely through an online “Semester in the Cloud” program.

As colleges across the country grapple with how and whether to bring students back to campus, leaders at the Berkeley laid out a menu of options on Wednesday.

“You and your family will need to decide which course of action is right for you based on your circumstances, your preferences, your goals, and your judgment of the risk,” campus leaders including Chancellor Carol Christ said in a statement.

Smaller discussion groups or other coursework involving smaller gatherings would be available in-person, as long as students and educators adhere to social distancing and other public health guidelines, including wearing masks.

Tuition and fees will be the same no matter how a student chooses to take classes, the statement said. Officials said as many as 6,500 students will be able to live in dorms and other on-campus housing, but move-in dates will be staggered, and space will be reserved for quarantine.

Students will be prioritized based on their need for housing, according to the statement.

Students moving in will have to be tested for the virus immediately and will have to isolate for a week to 10 days after they arrive. And to avoid the risk of exposure from students traveling home for Thanksgiving, all instruction, and final exams, will be online after the holiday.

U.C. Berkeley’s announcement comes more than a month after the California State University, the largest four-year public university system in the country, said classes at its 23 campuses would be canceled, and instruction would take place almost exclusively online.

A Veterans Affairs medical worker is accused of stealing coronavirus medical supplies.

Federal prosecutors have accused a Washington State man who worked as a respiratory therapist at the Veterans Affairs Medical Center of stealing and selling coronavirus-related medical supplies, including ventilators, starting in January, officials said.

Gene Wamsley, 41, of Bonney Lake, was charged with one count of theft of government property, the United States Attorney’s Office for the Western District of Washington announced on Wednesday.

Citing a criminal complaint, prosecutors said that an investigation had linked Mr. Wamsley to the sale of three bronchoscopes on eBay and that “a further review” of records had revealed that he sold five ventilators in March and April 2020 — the same time that the center learned that it was missing three ventilators.

Records showed “a variety of other respiratory support equipment sold by the account linked to Wamsley,” prosecutors said, noting that Veterans Affairs Medical Center administrators confirmed that the items were used in the respiratory department.

“Right now respiratory support equipment is critical in medical care for those suffering with Covid-19 infections,” said Brian T. Moran, the U.S. attorney for the Western District of Washington. “To steal and sell equipment needed to care for our veterans is a shocking betrayal.”

Mr. Wamsley worked at the center until he was placed on leave on June 9, the U.S. attorney’s office said, the same day that law enforcement seized medical supplies and eBay sales records from his home.

Attempts to reach Mr. Wamsley and his lawyer on Wednesday night were unsuccessful. If convicted, Mr. Wamsley could face up to 10 years in prison.

Emissions are surging as countries and states reopen.

In early April, daily fossil fuel emissions worldwide were roughly 17 percent lower than they were in 2019, as employees stopped driving to work, factories idled and airlines grounded their flights, according to a study published in May in Nature Climate Change.

But by mid-June, as countries eased their lockdowns, emissions had ticked up to just 5 percent below the 2019 average, the authors estimated in a recent update. Emissions in China, which accounts for one-quarter of the world’s carbon pollution, appear to have returned to pre-pandemic levels.

“We still have the same cars, the same power plants, the same industries that we had before the pandemic,” said Corinne Le Quéré, a climate scientist at the University of East Anglia in England and lead author of the analysis. “Without big structural changes, emissions are going to come back as the restrictions end.”

The researchers estimated that global fossil fuel emissions for all of 2020 are likely to be 4 percent to 7 percent lower than in 2019. That would be by far the largest one-year decline since World War II and several times larger than the drop seen in 2009 after the global financial crisis.

U.S. officials don’t know what to do with 66 million doses of two malaria drugs in the federal stockpile.

The Food and Drug Administration’s abrupt decision this week to revoke an emergency waiver for two malaria drugs promoted by Mr. Trump as potential “game changers” against the virus has left 66 million doses stranded in the federal stockpile — and officials do not yet know what they will do with them.

The F.D.A.’s withdrawal on Monday of its “emergency use authorization” for chloroquine and hydroxychloroquine did not go over well at the White House, where top aides to Mr. Trump had rushed in March to fill the federal stockpile. That included accepting a donation from the pharmaceutical giant Bayer of three million tablets from a factory in Pakistan that had not been certified by the F.D.A. as safe.

Medical experts across the country — including those who are researching hydroxychloroquine — on Tuesday applauded the F.D.A.’s withdrawal of the waiver after it concluded the drugs’ potential benefits did not outweigh their risks.

An F.D.A. spokesman said the White House and Health and Human Services Secretary Alex M. Azar II were made aware of the decision before it was announced. But Peter Navarro, Mr. Trump’s trade adviser, said Monday night, “This is a Deep State blindside by bureaucrats who hate the administration they work for more than they’re concerned about saving American lives.”

His anger seemed to capture the futility of the administration’s headlong efforts to yield to the president’s wishes and rush the two drugs into use, yet another example of how politics and science have collided in Mr. Trump’s Washington.

In the end, none of the chloroquine was ever distributed from the stockpile; doctors preferred hydroxychloroquine, which is newer and has fewer side effects, they say. But its prospects as a treatment for Covid-19 also look dim.

As of Monday, the government had distributed 31 million tablets of hydroxychloroquine to state and local health departments, hospitals and research institutions; 63 million tablets remain, according to Carol Danko, a spokeswoman for the Department of Health and Human Services. Officials are working with the companies that donated the drugs to “determine the available options” for the products.

U.S. cities that initially avoided the worst of the virus see surge in cases since reopening.

For months, Charleston, S.C., Joplin, Mo., and Portland, Ore., avoided the worst of the virus. Now, they are seeing major surges, raising concerns among state officials about easing restrictions too soon.

In Charleston County, S.C., more than half the total cases have been reported in the last three weeks. The Oregon governor has paused the state’s reopening plans as new virus cases are emerging at their highest levels yet across the state. And in Joplin, Mo., where case numbers have doubled over the last two weeks, the City Council decided to keep in place occupancy limits at businesses.

Cases are also rising around Tulsa, Okla., Honolulu and Wichita, Kan., none of which were hit especially hard in the pandemic’s early months.

Gov. Laura Kelly of Kansas said this week that cases around Wichita spiked shortly after county leaders relaxed social distancing rules.

“This is not a coincidence,” Ms. Kelly said. She added: “If we do not treat this threat seriously, more lives will be lost.”

Reporting was contributed by Jane Bradley, Keith Bradsher, Chris Buckley, Damien Cave, Michael Cooper, Jill Cowan, Jacey Fortin, Luis Ferré-Sadurní, Michael Gold, Joseph Goldstein, James Gorman, David M. Halbfinger, Andrew Higgins, Carl Hulse, Mike Ives, Miriam Jordan, Annie Karni, Sarah Kliff, Jeff Mays, Patricia Mazzei, Sarah Mervosh, Raphael Minder, David Montgomery, Benjamin Mueller, Aimee Ortiz, Tariq Panja, Brad Plumer, Nadja Popovich, Frances Robles, Dagny Salas, David E. Sanger, Christopher Schuetze, Robert Simonson, Karan Deep Singh, Kirk Semple, Jeanna Smialek, Rory Smith, Mitch Smith, Kaly Soto, Sheryl Gay Stolberg, Eileen Sullivan, Daniel Victor, David Waldstein, Billy Witz, Noah Weiland, Will Wright and Karen Zraick.