Here’s what you need to know:Dr. Deborah L. Birx with President Trump during a White House news conference in July.Credit…Doug Mills/The New York Times

Dr. Deborah L. Birx, who has carefully straddled the line between science and politics as she helps lead the Trump administration’s coronavirus response, delivered a stark private warning on Monday, telling White House officials that the pandemic is entering a new and “deadly phase” that demands a more aggressive approach.

The warning — sent in a private memo to White House officials as the nation — amounted to a direct contradiction of President Trump’s repeated false assertions that the pandemic is “rounding the corner.” In it, Dr. Birx suggested Mr. Trump and his advisers were spending too much time focusing on lockdowns, and not enough on controlling the virus.

“We are entering the most concerning and most deadly phase of this pandemic,” Dr. Birx wrote, adding, “This is not about lockdowns — It hasn’t been about lockdowns since March or April. It’s about an aggressive balanced approach that is not being implemented.”

The report warned against the type of rallies that Mr. Trump has been holding. It also predicted that the United States would continue to see days when the number of new cases exceeded 100,000. Its existence was first reported by The Washington Post; a top White House official who has seen it confirmed its contents.

The blunt message was a striking one for Dr. Birx, who at least in public has resisted disagreeing with Mr. Trump. But with cases soaring around the country, and hospital intensive care units starting to fill up, government scientists and public health experts are growing increasingly concerned that the worst of the pandemic is yet to come.

Dr. Anthony S. Fauci, the government’s top infectious disease expert, has also been offering unusually blunt assessments, and is once again in Mr. Trump’s cross hairs as a result. At a campaign rally in Miami early Monday morning, Mr. Trump attacked the news media for its emphasis on the virus, which prompted the crowd to chant, “Fire Fauci! Fire Fauci!”

To that, the president responded: “Don’t tell anybody, but let me wait until a little bit after the election. I appreciate the advice.” What the president neglected to mention is that Dr. Fauci has Civil Service protections, and it would be extremely difficult for Mr. Trump to remove him.

Unlike Dr. Fauci, who has clashed repeatedly with the White House, Dr. Birx has taken a more measured approach, taking care never to openly criticize the president or his administration.

Dr. Birx was named the coronavirus response coordinator in March. The job has required her to manage the work of the White House coronavirus task force, tracking and orchestrating the government’s effort to contain the outbreak. In the early days of the pandemic, she projected a calm, authoritative presence — and a steady counterpoint to the mixed messages from Mr. Trump.

More recently, though, she has been eclipsed by Dr. Scott W. Atlas, Mr. Trump’s new pandemic adviser, who advocates allowing the virus to spread naturally among young people, while the government focuses its efforts on protecting the elderly and vulnerable. Many public health experts say such a strategy would lead to needless death and suffering.

A masked sculpture outside an art gallery in Coeur d’Alene, Idaho, on Thursday.Credit…Rajah Bose for The New York Times

The Mountain West region, in the throes of a coronavirus surge, appears to be headed for a long winter.

In Colorado, hospitalizations of Covid-19 patients have tripled since early September and could overwhelm the state’s intensive care units this winter, as new coronavirus cases set daily records.

On Monday in Utah, intensive care units were at over 71 percent capacity.

Idaho, where Gov. Brad Little has restored restrictions on large gatherings, is averaging about 850 new cases each day, more than triple the numbers seen just six weeks ago. In eastern Idaho, the Rexburg metro area has one of the highest rates of new cases per capita in the nation. In the north, Kootenai Health hospital has warned that the facility could exceed capacity and be forced to send patients to Seattle or Portland, Ore.

Hospitalizations in Wyoming have more than doubled in the past two weeks. Gov. Mark Gordon said on Monday that he was under a 14-day quarantine after attending a meeting with someone who tested positive for the virus.

Eastward, two battleground states that will play a pivotal role in tomorrow’s election set records for new cases Monday: Michigan and Pennsylvania.

And as the presidential race comes to a close, the outbreak in the key state of Wisconsin is only getting worse. More than 32,000 cases and more than 290 deaths have been announced in state over the last week. Ten of the 20 U.S. metro areas with the highest rates of recent cases are there.

And in Texas, now a fiercely competitive state, the El Paso area has the nation’s third-highest per capita rate for new cases. Deaths are surging beyond the area’s ability to handle the bodies, and El Paso County is setting up a fourth mobile morgue.

The tallies for the country as a whole tell an equally stunning story: The United States set records on Sunday for the average number of new virus cases over a seven-day period — more than 82,000 daily — and the total number of new cases over the same amount of time — more than 579,000 cases. On Monday, it tallied more than 93,000 cases, its second-highest daily total.

As the surge has quickened, it has also widened, reaching the Northeast, which bore the brunt of the nation’s first wave.

In Massachusetts, Gov. Charlie Baker issued a stay-at-home advisory for the hours of 10 p.m. to 5 a.m., beginning on Friday. The advisory urges people to “only leave home to go to work or school, or for essential needs,” like emergency medical care or going to the grocery store. It also discourages gatherings at home with “anybody outside of your household.”

The order will close businesses like movie theaters, casinos, gyms and pools at 9:30 p.m. The governor also put restrictions on private events, regardless of the time, limiting indoor gatherings to 10 people and outdoor gatherings to 25.

In Connecticut, where new cases have risen about 85 percent in two weeks, Gov. Ned Lamont announced similar restrictions amid a surge. Starting Friday, restaurants will be limited to eight people per table and must close for indoor dining at 9:30 p.m.

New Jersey, whose governor recently emerged from a self-quarantine, reported 1,379 new cases on Monday, the 16th straight day of more than 1,000 cases. Hospitalizations for confirmed or suspected cases exceeded 1,000 for the sixth consecutive day.

New cases per day in the state have increased by 92 percent over the past two weeks, according to a New York Times database. As of Sunday, there was an average of 1,306 new cases per day over the past week.

At a campaign rally on Monday, Mr. Trump repeated an assertion he has made several times in recent days: of the virus, “we’re rounding the corner.” Mr. Trump made the statement in Pennsylvania, a state both campaigns see as crucial to victory on Tuesday.

The state reported 2,749 new cases on Monday, a record.

With coronavirus rates in Colorado rising, many businesses must decide whether to stay open.Credit…Chancey Bush/The Gazette, via Associated Press

Colorado once looked like it had gotten a grip on the coronavirus. Gov. Jared Polis, a Democrat, is a zealous mask wearer who imposed a statewide mandate. Hospitalization levels stayed low for much of the summer and fall. The state even began dismantling two emergency field hospitals it set up early in the pandemic.

But that grip has slipped. Daily reports of new cases are soaring to record heights, and the number of patients hospitalized with Covid-19 has tripled since early September.

The Colorado Department of Public Health and Environment is now warning that hospitalizations in the state are likely to blast through the peaks of last April and could overwhelm the state’s intensive care units by January.

“It’s really a very scary rise,” Dr. Jonathan Samet, the dean of the Colorado School of Public Health, said in an interview. “Clearly, Coloradans have lapsed.”

Health officials said there was no single reason or particular hot spot fueling the increase in the state this time, unlike earlier spikes that were driven by outbreaks in long-term care homes and meatpacking plants or by students partying at the University of Colorado.

The state health department estimated that one in every 219 people in Colorado is infectious, making it likelier now than it was in the summer for uninfected people to catch the virus.

Colder weather and early snowstorms are starting to drive people back indoors. Mountain towns that rely on winter tourists are now torn: Do they accept the pain of shutting down the restaurants and bars that bring in the après-ski dollars, or do they let their communities become hubs of coronavirus transmission?

Denver, which reported a record 461 cases one day last week, has imposed tighter limits on retailers, offices and public gatherings and ordered people to wear face masks outdoors. A dozen counties across the state have also ratcheted restrictions back up.

Dr. Samet said pandemic fatigue and people’s yearning for normalcy after months of lockdown and mask wearing may be playing a part in the recent surge.

“Everybody’s impatient,” he said. “People want to have their lives back. But it’s too early to do that.”

“We are now saying pregnant women are at increased risk for severe illness. Previously we said they ‘might be’ at increased risk for severe illness,” said Sascha Ellington, a health scientist with the Centers for Disease Control and Prevention, and one of the authors of a new study.Credit…Jonathan Ernst/Reuters

Federal health officials on Monday added pregnancy to the list of conditions that put people with Covid-19 at increased risk of developing severe illness, including a heightened risk of death.

While most pregnant women infected with the coronavirus have not become severely ill, the new caution is based on a large study that looked at tens of thousands of pregnant women who had Covid-19 symptoms.

The study found they were significantly more likely to require intensive care, to be connected to a specialized heart-lung bypass machine, and to require mechanical ventilation than nonpregnant women of the same age who had Covid-19 symptoms. Most importantly, the pregnant women faced a 70 percent increased risk of death, when compared to nonpregnant women who were symptomatic.

The study from the Centers for Disease Control and Prevention examined the outcomes of 409,462 symptomatic women ages 15 to 44 who tested positive for the coronavirus, 23,434 of whom were pregnant.

“We are now saying pregnant women are at increased risk for severe illness. Previously we said they ‘might be’ at increased risk for severe illness,” said Sascha Ellington, a health scientist with the C.D.C., and one of the authors of the new study.

Still, Dr. Ellington emphasized that the overall risk of both complications and death was small.

“The absolute risk of these severe outcomes are low among women 15 to 44, regardless of pregnancy status, but what we do see is an increased risk associated with pregnancy,” she said.

An earlier study did not find a higher risk of dying among pregnant Covid-19 patients but the pregnant patients in the new study were 1.7 times more likely to die than nonpregnant patients. That amounted to a death rate of death of 1.5 per 1,000 cases among the symptomatic pregnant women, compared with 1.2 per 1,000 cases of symptomatic women who were not pregnant.

Even after adjustments were made for differences in age, race, ethnicity and underlying health conditions like diabetes and lung disease, the pregnant women were three times more likely than nonpregnant women to be admitted to an intensive care unit and 2.9 times more likely to receive mechanical ventilation.

Dr. Ellington emphasized the importance of taking precautions to avoid infection, saying pregnant women should not only wear masks, practice social distancing and wash their hands frequently, but also limit interactions to avoid people who may have been exposed.

“Pregnant women should be counseled about the importance of seeking prompt medical care if they have symptoms,” the authors wrote.

A smaller study, also released Monday from the C.D.C., reported that women who tested positive for the coronavirus were at increased risk for delivering their babies prematurely, finding that 12.9 percent of live births among a sample of 3,912 women were preterm births, compared with 10.2 percent in the general population. The sample was not nationally representative, but the finding echoes earlier reports that warned of a higher risk for preterm deliveries.

EDUCATION ROUNDUP

Muriel Bowser, the mayor of the District of Columbia, at a news briefing in September.Credit…Alex Brandon/Associated Press

The District of Columbia Public Schools said on Monday that it was canceling its plan to bring some elementary school students back to schools next week, after teachers staged a sickout to protest the plan.

Mayor Muriel Bowser announced in October that the district would bring back 7,000 students in prekindergarten through fifth grade on Nov. 9. Priority for in-person seats would be given to students who were homeless, disabled or learning English as a second language.

The plan had drawn opposition from not only teachers, but also some principals and parents, because of safety concerns, the way that students were chosen, and the fact that many students would have had to change teachers midyear.

Negotiations between the district and the teachers’ union fell apart over the weekend, with a major sticking point being the union’s insistence that no teacher should be forced to return to teaching in-person, the president of the Washington Teachers Union, Elizabeth A. Davis, said on Monday.

In a message to parents on Sunday, Ms. Davis asked them to join with teachers in opposing the mayor’s plan. “Tomorrow, Monday, November 2, many teachers across the District will be taking a ‘Mental Health Day,’” Ms. Davis wrote.

A number of principals informed parents on Sunday that teachers would be out on Monday and students could use the time to catch up on assignments.

Shortly before 10 a.m. on Monday, the district announced that it was reversing course and that all elementary school students would continue with remote learning.

At an appearance at a memorial to Covid-19 victims on Monday, Mayor Bowser was asked about why the district had withdrawn its plan.

“The teachers’ union has indicated that teachers won’t show up, so we have to make some adjustments to the timeline to ensure that the workforce is in place,” she said. She said the district was still working on plans under which some students could begin going to schools to engage in distance learning under supervision by non-teachers, possibly starting Nov. 16.

“As far as when teachers are going to return, we will continue to work with the teachers’ union,” Ms. Bowser said. “What we are unable to do is to say to parents and families and kids who need instruction in their school buildings that we’re going to write off the entire school year. I’m just not willing to do that.”

Experts are still divided on how much transmission schools may fuel, though there is increasing consensus that keeping elementary schools open does not pose a major risk, and that the potential for transmission in schools can be significantly reduced by safety measures such as mask requirements and adequate ventilation.

In other education news around the country:

More than one million parents in New York City must decide in the next two weeks whether to send their children into classrooms this school year or keep them learning from home, likely until at least next fall. The city had said parents could opt into the hybrid (part in-person, part online) program every few months, but the mayor changed course after only a quarter of the district’s 1.1 million students have shown up for in-person classes since September, far fewer than predicted.

Amid new restrictions on gatherings and businesses, Gov. Charlie Baker of Massachusetts suggested that he did not plan to order schools closed in an effort tamp down transmission of the virus. Schools “need to stay open,” he said, adding that in-person learning is “hugely important for the educational and social development of kids.”

A Connecticut judge on Monday denied a conservative group’s emergency request to block Gov. Ned Lamont’s requirement that students wear masks in school. The group, CT Freedom Alliance, had argued that the mask requirement posed an immediate danger to students. The judge said in his decision that “no emergency exists” and that “there is very little evidence of harm at all.”

VideoGermany entered a new partial lockdown on Monday amid skyrocketing coronavirus cases across Europe.CreditCredit…Filip Singer/EPA, via Shutterstock

Germany entered a new partial lockdown on Monday amid skyrocketing coronavirus cases across Europe, a specter that Chancellor Angela Merkel called a test not seen in her country since the end of World War II.

Under the new rules, labeled “lockdown light” by the German media, restaurants, bars and gyms will have to close for a month. The policy is designed to bring Germany’s per capita rate of new cases below 50 per 100,000 residents, from 128, so that health authorities can once again trace individual infections.

Ms. Merkel will meet with state governors in two weeks to gauge progress, and promised that if all goes well, Germans would be able to “allow ourselves more freedom at Christmas,” though wild New Year’s parties remain unimaginable.

Germany is still recording far fewer cases per capita than many other European nations, but there are grave fears that the second wave of infections could prove even more difficult than the spring.

Ms. Merkel pushed back against criticism of her government’s decision to focus on curtailing social life, saying it was the only way to keep schools and shops open, while still cutting back on interactions.

“Freedom is the possibility to decide from various options, but freedom is also freedom for everyone,” Ms. Merkel said. “That means, I don’t have endless freedom and everyone else has to live with my version of freedom.”

German orchestras, including the Munich Philharmonic, staged a protest on Monday, taking the stage and sitting in silence before walking away.

“There is still not enough aid to survive for so many people in the culture and event industry,” a statement posted to the Munich Philharmonic’s website said. Staatsoper Berlin — the Berlin State Opera’s orchestra — and the Berlin Philharmonic also posted on social media criticizing the lockdown.

“By letting silence speak we want to raise awareness for the painful gap that arises when opera, music, theatre, cinema and art are missing,” Staatsoper Berlin said in a tweet.

Europe as a whole surpassed 10 million confirmed cases and 268,000 Covid-19 deaths on Sunday, as many countries imposed tough new restrictions. France began a national lockdown on Sunday, and Britain is set to enter one on Thursday.

Prime Minister Boris Johnson of Britain laid out his lockdown plan before Parliament on Monday, and faced a mutiny from members of his Conservative Party, who said he went too far, and scalding criticism from Labour Party leaders, who said he waited too long to act. The measure is expected to be approved when it comes up for a vote on Wednesday.

Italy’s prime minister, Giuseppe Conte, told lawmakers on Monday that restrictions there would be tightened, but that there would not be a national lockdown. Some measures, though, will apply throughout the country, including a nighttime curfew and limiting travel between high-risk areas. Other restrictions would be applied depending on the perceived risk level in a specific territory.

“We are aware of the frustration, sense of disorientation and exhaustion on the part of citizens, as well as the anger that has been manifesting itself in recent days,” Mr. Conte said, a reference to the sporadic protests in various cities. He also acknowledged the significant impact that past restrictions have had on the national economy, adding that the government had sought to alleviate the hardships with aid.

Greece on Monday announced a full lockdown in the country’s second-largest city, Thessaloniki, and of the region of Serres, also in northern Greece. A government spokesman described the situation in those regions as “extremely serious,” as he announced the new measures, which go into effect on Tuesday for two weeks.

The restrictions include an overnight curfew and the reinstatement of a system requiring people to send a text message to the Greek government citing their reasons for venturing out — for work and health reasons only. All flights to and from Thessaloniki will be suspended. Schools will remain open.

The announcement came after Prime Minister Kyriakos Mitsotakis on Saturday heralded a new set of restrictions nationwide that are set to go into effect on Tuesday morning.

Portugal’s president said on Monday that he was considering a state of emergency that would give the government greater powers to impose lockdown restrictions to stop a second wave of Covid-19. Marcelo Rebelo de Sousa, Portugal’s president, sought to reassure citizens that the measures would be more limited than those imposed last spring. Portugal has registered in recent days a daily death toll of over 40, its highest since April.

An elderly couple in the town center of Rothbury, England. Deaths at nursing homes in Britain account for more than 20 percent of Covid-19 fatalities there.Credit…Mary Turner for The New York Times

The risk of death from Covid-19 in people under 65 is consistent across 45 countries in Europe, Asia and the Americas, but varies drastically for people above that age, according to a modeling study published on Monday in the journal Nature.

A measure called the infection fatality ratio — the portion of people who die among all infected individuals — is 0.001 percent in children ages 5 to 9 years, and rises by about 0.5 percent with each five-year increase in age, according to the model.

The I.F.R. averages 8.29 percent in those above 80, but ranges widely from 2.5 percent to 15.6 percent in different countries, the researchers reported. They did not give the specific numbers for each nation. The study also found that the risk of death is higher in men than in women, in line with results from other studies.

Large outbreaks in nursing homes and long-term care settings can skew a country’s I.F.R., the study found. Nursing homes account for more than 20 percent of deaths from Covid-19 in some countries, including Sweden and Britain, but much less in others, like South Korea and Singapore.

In France, a 22.25 percent I.F.R. in nursing homes bumps the country’s overall ratio to 1.1 percent from 0.74 percent in the general population. Because of this effect, data for people under 65 is likely to be more reliable and useful for studying the transmission of the virus in a population, the researchers said.

A study found that the Sofia rapid test detected 80 percent of infections in symptomatic people, but the results were poor when the test was given to people without symptoms.Credit…Quidel Corporation

A new study casts doubt on whether rapid coronavirus tests, widely hailed as a potential solution to the nation’s testing woes, perform as promised under real-world conditions, especially when used in people without symptoms.

In a head-to-head comparison, researchers at the University of Arizona found that, in symptomatic people, a rapid test made by Quidel could detect more than 80 percent of coronavirus infections found by a slower, lab-based P.C.R. test. But when the rapid test, called the Sofia, was used instead to randomly screen students and staff members who did not feel sick, it detected only 32 percent of the positive cases identified by the P.C.R. test.

“That’s worse than flipping a coin,” said Jennifer Dien Bard, the director of the clinical microbiology and virology laboratory at Children’s Hospital Los Angeles, who was not involved in the study.

When asked about the Sofia’s poorer performance in asymptomatic people, David Harris, an author on the study, said, “I think everybody expected that.”

But he and his colleagues argued in their manuscript that some of the asymptomatic people who tested positive with P.C.R., but negative with the rapid test, might have been missed for good reason: They were carrying too little of the coronavirus to spread it to others, based on data obtained by P.C.R.

Doug Bryant, Quidel’s president and chief executive, who received an early copy of the University of Arizona study, praised the results as “very, very good,” citing the Sofia’s ability to root out “people who are infectious.”

Other experts advised caution, however, noting that there is no definitive test for infectiousness.

For now, people with symptoms or known exposures to the coronavirus should still get the most precise and reliable tests available — those that use P.C.R., said Susan Butler-Wu, a clinical microbiologist at the University of Southern California who was not involved in the study. More data, she added, would be needed to figure out how rapid tests fit into the larger diagnostic landscape.

Global Roundup

Schools throughout Cambodia opened on Monday after months of closure to combat the spread of COVID-19.Credit…Heng Sinith/Associated Press

Cambodia on Monday announced that schools could reopen for the first time since March if they meet certain safety standards.

Like some of its regional neighbors, the Southeast Asian nation has avoided a large outbreak of the coronavirus. The country of over 16 million has reported no deaths and just 292 coronavirus cases total throughout the pandemic, most during March and July, according to data from Johns Hopkins University.

A poor country with underfunded schools, Cambodia has few resources to combat a major virus outbreak. Its highest daily case total was 31 new cases on March 22.

“We are also worried that the reopening will be risky,” Hang Chuon Naron, the minister of education, said on Monday. The education ministry said that the number of students in each classroom would be limited but did not specify whether students had to wear masks.

In other news around the world:

Over the weekend, Australia reported its first 24-hour period of no new coronavirus cases in nearly five months, paving the way for further easing of restrictions. Greg Hunt, the country’s health minister, told local media that Australia was on track for restrictions on travel between states to be removed by Christmas. Residents of New South Wales, where one case was reported late Saturday, and Victoria are barred from visiting some states and must quarantine for 14 days when entering other states.

At Mount Everest in Nepal, the trails snaking through the Himalayas are deserted. Fewer than 150 climbers have arrived this fall season, immigration officials said, down from thousands last year. Last year, the industry brought in more than $2 billion to Nepal, one of Asia’s poorest countries, and employed a million people, from porters to pilots.

Prince William contracted Covid-19 in England in April but kept his diagnosis a secret, the BBC and The Sun, England’s largest paper, have reported, citing information from sources within Kensington Palace. A person close to the palace confirmed the accuracy of the reports, but did not offer additional details. Prince William’s decision not to disclose his diagnosis raised questions about the palace’s secrecy since he is second in line for the throne. Buckingham Palace disclosed his father’s illness in March.

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Supporters Chant ‘Fire Fauci’ at Florida Trump RallyAt a late-night rally in Florida, President Trump suggested that he might fire Dr. Anthony S. Fauci, but that he would wait until “after the election.”

“But we’re going to have a safe vaccine that ends the pandemic. Without it, it’s rounding the turn. I say, it drives them crazy — it’s rounding the turn. Because all they want to do, you turn on the news, ‘Covid, Covid, Covid, Covid, Covid Covid.’ ‘We’d like to talk about Covid, and then next on —’ Here’s what happens: Nov. 4, you won’t hear too much about it. You won’t hear too much about it.” Crowd: “Fire Fauci! Fire Fauci! Fire Fauci! Fire Fauci! Fire Fauci! Fire Fauci! Fire Fauci! Fire Fauci! Fire Fauci! Fire Fauci!” “Don’t tell anybody — but let me wait till a little bit after the election, please. [cheering] I appreciate the advice. I appreciate the advice. Nah, he’s been wrong on a lot. He’s a nice man, though he’s been wrong on a lot.”

At a late-night rally in Florida, President Trump suggested that he might fire Dr. Anthony S. Fauci, but that he would wait until “after the election.”CreditCredit…Doug Mills/The New York Times

President Trump suggested at a rally early Monday morning that he might fire Dr. Anthony S. Fauci after Election Day, further escalating the tension between his administration and the nation’s top infectious disease expert as the number of new coronavirus cases in the United States reaches record highs.

Mr. Trump spoke well past midnight at the Miami-Opa Locka Executive Airport in Florida at his fifth and final rally on Sunday. At one point, he began reciting a familiar complaint about the news media’s continued coverage of the virus.

His grousing led the crowd to chant, “Fire Fauci! Fire Fauci!” Mr. Trump listened in silence for a few moments before remarking: “Don’t tell anybody, but let me wait until a little bit after the election. I appreciate the advice.”

Dr. Fauci, the longtime director of the National Institute of Allergy and Infectious Diseases, has civil service protections, and it would be extremely difficult for the president to have him removed. Under federal law, the president does not have authority to fire Dr. Fauci. Mr. Trump could try ordering his political appointees, such as Health Secretary Alex M. Azar II or Dr. Francis Collins, the director of the National Institutes of Health, to dismiss Dr. Fauci. But the process would be lengthy and arduous, because Dr. Fauci could appeal.

Dr. Fauci has run his institute since 1984; in years past, when he has been mentioned as a possible candidate for director of the N.I.H., he has demurred because that position is a political appointee, and he did not want his job to be tied to any president’s term.

The president’s remarks came toward the end of what was a whirlwind day of campaigning across five states — Michigan, Iowa, North Carolina, Georgia and Florida — and he spoke even as a local curfew aimed at curbing the spread of the coronavirus took effect at midnight. According to a New York Times database, the country set records on Sunday for the average number of new virus cases over a seven-day period — more than 82,000 daily — and the total number of new cases over the same amount of time — more than 579,000 cases.

Nonetheless, Mr. Trump has maintained without citing evidence that the United States has “turned the corner” in fighting the virus, a point he reiterated at the rally early Monday.

That assertion is strongly disputed by Dr. Fauci, who told the The Washington Post in an interview published on Saturday that the United States “could not possibly be positioned more poorly” as it heads into the winter. A White House spokesman later called Dr. Fauci’s comments “unacceptable.”

Former Vice President Joseph R. Biden Jr., the Democratic nominee, has said repeatedly that if he were to win the presidency, he is hopeful Dr. Fauci would remain in his role and serve in his administration.

In his interview with The Post, Dr. Fauci offered praise for the Biden campaign, saying it was taking the coronavirus “seriously from a public health perspective.”

Ordinarily circumspect, Dr. Fauci also took the opportunity to unload on another Trump pandemic adviser, Dr. Scott W. Atlas, who has won the president’s favor by questioning mask use and espousing a number of other contrarian views.

“I have real problems with that guy,” Dr. Fauci said, suggesting that Dr. Atlas, a neuroradiologist with no background in infectious disease, is out of his depth.

Dr. Atlas, on Saturday, appeared on RT, a Russian state-sponsored television network that has helped Moscow spread false health information about the pandemic. American intelligence agencies consider RT a propaganda arm for Russia, and it is registered in the United States as a foreign agent.

“The lockdowns will go down as an epic failure of public policy by people who refuse to accept they were wrong,” Dr. Atlas said in the interview. “The argument is undeniable, the lockdowns are killing people.”

The interview with RT was not approved by the White House press office, an administration official said, and Dr. Atlas apologized for giving it.

“I regret doing the interview and apologize for allowing myself to be taken advantage of,” he said in a tweet. “I especially apologize to the national security community who is working hard to defend us.”

The White House has had no public criticism of Dr. Atlas, though it did for Dr. Fauci.

In a statement to The Post, a White House spokesman, Judd Deere, said it was “unacceptable and breaking with all norms” for Dr. Fauci to “play politics” three days before the election. Dr. Fauci, he said, had made “his political leanings known by praising the president’s opponent, exactly what the American people have come to expect from the swamp.”

The death of an eighth grader from Covid-19 complications in Missouri over the weekend is rattling his community and may add to the already fraught debate over the risks and benefits of reopening schools in a pandemic.

The school district in Washington, Mo., about 35 miles west of St. Louis, said the student was 13 and attended Washington Middle School. It was not known whether he caught the virus in school or elsewhere, according to Julie Bell, an assistant to the district superintendent, Dr. Lori VanLeer.

Very few of the people who have died from the coronavirus around the world have been children, and the eighth grader may have been the first in Missouri. The state health department’s coronavirus data dashboard does not show any previous virus-related death of someone younger than 18.

Dr. VanLeer informed families in the school district about the boy’s death in an email on Sunday. She wrote that he had last attended school on Oct. 22 and had gone into quarantine on Oct. 26.

“Later, his family shared that he eventually began experiencing symptoms that required hospitalization, but he did not improve,” Dr. VanLeer wrote.

She said that the middle school would have extra counselors available on Wednesday, when students return to class after two days off for parent-teacher conferences and professional development.

The coronavirus has been surging in Missouri since late summer, and the state is now averaging more than 2,400 new cases a day. Franklin County, where Washington is located, is averaging more than 45 new cases a day per 100,000 population, according to a New York Times database, somewhat higher than the state average of 39 per 100,000 and well above the threshold at which some experts say that stay-at-home orders are necessary.

Skidmore College, a small liberal arts school in upstate New York, suspended 46 students this weekend, the majority of whom had violated rules meant to protect against the spread of the coronavirus, a college spokeswoman said. The college enrolls about 2,500 students, most of whom are back on campus this fall.

The spokeswoman, Sara Miga, said that some of the suspensions were connected to “unsanctioned parties” and that 31 students had been placed in a “precautionary quarantine” after on- and off-campus events. Ms. Miga said some of the suspensions involved rules pertaining to alcohol consumption. She did not immediately provide further details.

The quarantines were in response to potential exposure, Ms. Miga said, and whether any students had tested positive after the events was not immediately clear. It was also not clear how many of the 46 suspensions were not related to infractions regarding the coronavirus rules.

Ms. Miga said on Monday that the “health and safety of our entire community is our highest priority, and we have urged all students to follow the guidelines they agreed to in order to bring the semester to a successful close.”

She said the campus was investigating a report of a student who was attacked while trying to break up a party at the Case Campus Center on Saturday. The student was briefly hospitalized and has a concussion, said Mark Reyes, 20, a friend of the student, who was also present during the incident.

Mr. Reyes said that students had been regularly holding parties at the center in violation of social distancing guidelines, and had again gathered in a group of more than 50 people on Saturday night when he and his friend sought to intervene.

Ms. Miga said the school was “not aware of unsanctioned parties” in the center. She said a school safety coordinator makes sure students adhere to public health guidelines during campus-sanctioned events there.

Tedros Adhanom Ghebreyesus, left, the director general of the World Health Organization, met with China’s leader, Xi Jinping, in Beijing on Jan. 28.Credit…Naohiko Hatta/Agence France-Presse — Getty Images

On a cold weekend in mid-February, when the world still harbored hope that the coronavirus could be contained, a World Health Organization team arrived in Beijing to study the outbreak and investigate a critical question: How did the virus jump from animals to humans?

At that point, there were only three confirmed deaths from Covid-19 outside China, and scientists hoped that finding an animal source for the virus would unlock clues about how to stop it, treat it and prevent similar outbreaks.

“If we don’t know the source, then we’re equally vulnerable in the future to a similar outbreak,” Dr. Michael Ryan, the emergency director of the W.H.O., had said that week.

What the team members did not know was that they would not be allowed to investigate the source at all. Despite Dr. Ryan’s pronouncements, and against the advice of its emergency committee, the organization’s leadership had quietly negotiated terms that sidelined its own experts. They would not question China’s initial response or even visit the live-animal market in the city of Wuhan where the outbreak seemed to have originated.

Nine months and more than 1.1 million deaths later, there is still no transparent, independent investigation into the source of the virus. China has impeded the effort, while leaders of the W.H.O., if privately frustrated, have largely ceded control, even as the Trump administration has fumed.

From the earliest days of the outbreak, the W.H.O. — the only public health body with a global remit — has been both indispensable and impotent. The Geneva-based agency has delivered key information about testing, treatment and vaccine science. When the Trump administration decided to develop its own test kits, rather than rely on the W.H.O. blueprint, the botched result led to delays.

At the same time, the health organization pushed misleading and contradictory information about the risk of spread from symptomless carriers. Its experts were slow to accept that the virus could be airborne. Top health officials encouraged travel as usual, advice that was based on politics and economics, not science.

The W.H.O.’s staunchest defenders note that, by the nature of its constitution, it is beholden to the countries that finance it. And it is hardly the only international body bending to China’s might.

Now, as a new Covid-19 wave engulfs Europe and the United States, the organization is in the middle of a geopolitical standoff between the world’s two greatest powers, the United States and China.

China’s authoritarian leaders want to constrain the organization; President Trump, who formally withdrew the United States from the body in July, seems intent on destroying it; and European leaders are scrambling to reform and empower it.

CRITIC’S NOTEBOOK

Restaurants prepare for winter dining in Astoria, Queens.Credit…John Taggart for The New York Times

Covid-19 has changed New York City’s restaurant culture more than any event since Prohibition. The most obvious effect will be the death of hundreds and possibly thousands of small, independent businesses, each loss radiating out to employees, communities and suppliers. The crisis is so immediate and overwhelming that it is hard to imagine what life will be like after it’s over.

But when the pandemic is under control and restrictions on dining have been lifted, at least one emergency measure will remain. The outdoor dining program that allowed more than 10,000 restaurants to set out tables and chairs on the city’s sidewalks and streets is here to stay, according to Mayor Bill de Blasio and the City Council.

In the general calamity, it has been easy to overlook the enormous implications this move will have: The line between restaurant food and street food will disappear, street music will become as deeply woven into street life in New York as it is in New Orleans, and now that we have gotten used to enjoying dinner and a cocktail on a patch of blacktop that would otherwise be taken up by a RAV4, we might begin to wonder what else could sit in the street.

The stripped-down approval process that allows restaurants to set up sidewalk and street seating has turned out to be more fair than the former system. The whole city has benefited by encouraging restaurants, from the most well-off to the leanest and scrappiest, to lend their own flavor to public spaces. Our economy is struggling, but our street culture, after decades of changes that made it more boring, is interesting again.

As rapid coronavirus tests are becoming more widely available, delivering results in minutes, officials warn of a significant undercount, blurring the virus’s spread in the United States and in communities where such tests are more commonly used.

Public health officials say that antigen tests, which are faster than polymerase chain reaction (P.C.R.) tests but less able to detect low levels of the virus, are an important tool for limiting the spread of the virus. But they caution that with inconsistent public reporting, the case undercount may worsen as more “point-of-care” antigen tests, as well as D.I.Y. and home test kits, come on the market.

“We want to be sure that we’re not now saying, ‘there’s no disease,’ when there is lots of disease. All that’s happened is that the science with which we identify it has evolved,” said Janet Hamilton, the executive director of the Council of State and Territorial Epidemiologists, the group that helps the Centers for Disease Control and Prevention define cases of the coronavirus.

Despite C.D.C. guidance to report cases based on P.C.R. and antigen testing, Washington, D.C., and seven states don’t publicly share case counts for those with antigen positive tests, including California, New Jersey and Texas.

Another six states keep these tallies separate from their total counts, and most of these report them less frequently.

The differences among states are in part because of each state’s comfort level with the rapid tests, which aren’t “confirmatory” like P.C.R. tests because they can miss low levels of the virus. Yet most states treat antigen positive cases or “probable” cases the same as “confirmed” cases, by following up with interviews and contact tracing.

And a growing number of states, including New Mexico, Oregon and Utah, include individuals with positive antigen tests in their total confirmed case counts.

Scientists who follow the development of coronavirus tests say that rapid testing capacity — most of it antigen-based — could reach 200 million tests a month by early next year, and help the country reach recommended testing levels.

President Trump’s announcement of his nomination of Amy Coney Barrett to the Supreme Court, in late September, may have been a super-spreader event.Credit…Al Drago for The New York Times

President Trump’s illness from a coronavirus infection last month was the most significant health crisis for a sitting president in nearly 40 years. Yet little remains known about how the virus arrived at the White House and how it spread.

The administration did not take basic steps to track the outbreak, limiting contact tracing, keeping cases a secret and cutting out the Centers for Disease Control and Prevention.

One standard public health technique may still shed some light: tracking the cluster’s genetic fingerprints.

To better understand the outbreak, The New York Times worked with geneticists to determine the genetic sequence of viruses that infected two Times journalists believed to have been exposed as part of their work covering the White House.

The study reveals, for the first time, the genetic sequence of the virus that may have infected Mr. Trump and dozens of others, researchers said. That genome is a crucial clue that may allow researchers to identify where the outbreak originated and whether it went on to infect others across the country.

Additional sequencing could help establish the path of the virus through the White House, the role of a possible super-spreading event for Judge Amy Coney Barrett and the origin of an outbreak among the staff of Vice President Mike Pence.

The journalists, Michael D. Shear and Al Drago, both had significant, separate exposure to White House officials in late September, several days before they developed symptoms. They did not spend any time near each other in the weeks before their positive tests.

The viral genomes of the two journalists shared the same distinct pattern of mutations, the research found. The findings suggest that they were infected as part of the broader White House outbreak, said Trevor Bedford, a geneticist at the Fred Hutchinson Cancer Research Center and the University of Washington who led the research team.

The study, which has been posted online but not yet peer reviewed or published in a science journal, followed academic protocols that require genetic samples to be anonymous. Mr. Shear and Mr. Drago chose to disclose their identities for this article.



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