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For Biden, the start of the transition means his battle against the coronavirus begins.

Until now, President-elect Joseph R. Biden Jr.’s Covid-19 task force has had to prepare its battle plan without the keys to the government agencies leading the pandemic response.

That changes this week, when Mr. Biden can finally dispatch what are known as landing teams to the Department of Health and Human Services, the Centers for Disease Control and Prevention and the Food and Drug Administration.

They will have prepared the traditional welcome gift: enormous briefing books that detail nearly everything the agencies have been working on for the past four years; lists of friendly lawmakers, budgets, accomplishments, roadblocks; and suggested targets for the new administration.

The president-elect will also inherit something nobody would want: a national crisis that is accelerating by the day. The daily average of new cases in the United States over the past week is at record levels, a staggering 173,000, and growing. Forty-five states are recording sustained caseload increases, and nine are reporting more than twice as many new cases a day as they did two weeks ago.

In the weeks since Election Day, the dire outlook has been tempered by encouraging early results from three major vaccine developers. But Mr. Biden and his top aides have said their ability to effectively plan a pandemic response had been stymied by President Trump’s refusal to acknowledge his victory and the refusal of the head of the General Services Administration to formally authorize the transition process that would grant Mr. Biden’s transition team access to funds, equipment and government data. That argument has been seconded by a growing chorus of senior Republican lawmakers, business executives and other public figures.

On Monday, President Trump’s government finally authorized Mr. Biden to begin a formal transition process. It is supposed to be led by career staff, not political appointees — and the Biden team can expect to find a warm welcome from them, particularly scientists on the team who Mr. Trump has criticized for years.

But in a pandemic, there is no time to waste. The F.D.A. landing team will need to get up to speed on a planned vaccine roll out, as well as the most promising new vaccine candidates and therapeutics. It may also designate a career staff member to be the agency’s acting commissioner if the current one, Stephen M. Hahn, leaves before a replacement can be nominated and confirmed.

At the C.D.C., one of the most pressing issues will be taking over a public education campaign, now in development, to persuade the public to trust — and take — the vaccine.

In the absence of a formal transition, Mr. Biden had been left trying to signal to Americans that he is prepared to take charge of a disjointed federal virus response.

“It doesn’t matter who you voted for, where you stood before Election Day,” Mr. Biden said in Delaware in early November after announcing a coronavirus task force. “It doesn’t matter your party, your point of view. We can save tens of thousands of lives if everyone would just wear a mask for the next few months. Not Democratic or Republican lives — American lives.”

Sheila Kaplan and

An early mutation may have made the pandemic harder to stop.

As the coronavirus swept across the world, it picked up random alterations to its genetic sequence. Like meaningless typos in a script, most of those mutations made no difference in how the virus behaved.

But one mutation near the beginning of the pandemic did make a difference, multiple new findings suggest, helping the virus spread more easily from person to person and making the pandemic harder to stop.

The mutation, known as 614G, was first spotted in eastern China in January and then spread quickly throughout Europe and New York City. Within months, the variant took over much of the world, displacing other variants.

For months, scientists have been fiercely debating why. Researchers at Los Alamos National Laboratory argued in May that the variant had probably evolved the ability to infect people more efficiently. Many were skeptical, arguing that the variant may have been simply lucky, appearing more often by chance in large epidemics, like Northern Italy’s, that seeded outbreaks elsewhere.

But a host of new research — including close genetic analysis of outbreaks and lab work with hamsters and human lung tissue — has supported the view that the mutated virus did in fact have a distinct advantage, infecting people more easily than the original variant detected in Wuhan, China.

There is no evidence that viruses with the 614G mutation cause more severe symptoms, kill more people or complicate the development of vaccines. Nor do the findings change the reality that places that quickly and aggressively enacted lockdowns and encouraged measures like social distancing and masks have fared far better than the those that did not.

But if the findings hold up, they show that the mutation early this year played a key role in why the virus has been so hard to stop, said Dr. David Engelthaler, a geneticist at the Translational Genomics Research Institute in Arizona.

“When all is said and done, it could be that this mutation is what made the pandemic,” Dr. Engelthaler said.

What we know about AstraZeneca’s head-scratching vaccine results.

This month has seen a torrent of news about experimental vaccines to prevent Covid-19, with the latest development from AstraZeneca and the University of Oxford. On Monday they announced that a preliminary analysis showed their vaccine was effective — especially when the first dose was mistakenly cut in half.

Surprisingly, the vaccine combination in which the first dose was only at half strength was 90 percent effective at preventing Covid-19 in the trial. In contrast, the combination of two, full-dose shots led to just 62 percent efficacy.

Why would that be?

No one knows. The researchers speculated that the lower first dose did a better job of mimicking the experience of an infection, promoting a stronger immune response. But other factors, like the size and makeup of the groups that got different doses, may also be at play.

Why did the researchers test two different doses?

It was a lucky mistake. Researchers in Britain had been meaning to give volunteers the initial dose at full strength, but they made a miscalculation and accidentally gave it at half strength, Reuters reported. After discovering the error, the researchers gave each affected participant the full strength booster shot as planned about a month later.

Fewer than 2,800 volunteers got the half-strength initial dose, out of the more than 23,000 participants whose results were reported on Monday. That’s a pretty small number of participants on which to base the spectacular efficacy results — far fewer than in Pfizer’s and Moderna’s trials.


Coronavirus Vaccine Tracker

A look at all the vaccines that have reached trials in humans.


Carl Zimmer and

‘The escape route is in sight’: Boris Johnson outlines the end of Britain’s lockdown.

Buoyed by promising results for a British-led coronavirus vaccine and signs of a slowdown in the infection rate, Prime Minister Boris Johnson on Monday laid out a plan to lift England’s nationwide lockdown next week. But he warned of strict regional restrictions that would last until next spring.

Mr. Johnson’s “winter plan” is designed to give his exhausted country hope for better times ahead while preparing it for several more months of mostly shuttered pubs and restaurants, and limitations on social gatherings.

“We have turned a corner, and the escape route is in sight,” Mr. Johnson declared to the House of Commons via video from 10 Downing Street, where he was still isolating after being exposed to a Conservative lawmaker who tested positive for the virus. But he added, “the hard truth is we’re not there yet.”

Under the new plans, England will return to a system under which the country is divided into three tiers of restrictions, though the government has yet to announce which regions will be under the different sets of curbs.

When the current lockdown expires on Dec. 2, gyms, stores and hairdressers nationwide will be allowed to reopen, and religious services, weddings and outdoor sports can resume. But in the worst affected areas of the country, pubs and restaurants will stay closed except for takeout service.

For Mr. Johnson, whose popularity has suffered because of his government’s erratic handling of the pandemic, the announcement was yet another chance to regain his footing. He also expressed optimism about the vaccine developed by AstraZeneca and Oxford University, noting that it “has the makings of a wonderful British scientific achievement.” He said the government had ordered 100 million doses and 350 million vaccine doses overall, including two American-led vaccines.

On Tuesday, the British government said that people traveling to England would no longer have to quarantine for two weeks if they receive a negative test five days after arriving.

It’s not just the Midwest: The U.S. outbreak is accelerating all over the map.

When infections began rising sharply in the United States in September, the growth was driven largely by outbreaks in the Upper Midwest. States like North Dakota and Wisconsin soon became the hardest hit in the nation, relative to their size, and the region continues to struggle.

Now, though, with the whole country’s daily average of new cases is as high as it has ever been — over 173,000 — the most rapid growth is happening elsewhere. Nine states are reporting more than twice as many new cases a day as they did two weeks ago, and none of them are in the Midwest.

The surges in those states — Arizona, California, Delaware, Louisiana, Maryland, New Hampshire, New Mexico, Pennsylvania and Vermont — reflect a still-escalating national crisis. Officials warn that it will only get worse if people disregard warnings about travel and get-togethers for the approaching holidays.

“Let me be very clear: A Thanksgiving gathering this year may very well lead to a funeral,” said Gov. Michelle Lujan Grisham of New Mexico, whose state is home to five of the 10 metropolitan areas in the country where new case reports are rising the fastest. “The virus is at large,” the governor said. “Know the risks and respect them.”

Forty-five states are seeing sustained increases, and 17 states added more cases in the seven-day period that ended Sunday than in any other week of the pandemic. Major metropolitan areas that are reporting new cases at or near record levels are all across the country: Pittsburgh. Albuquerque. Baltimore. San Diego.

Some that have been bad for a while, like El Paso, are coping with the flood of hospitalizations that generally follow a couple of weeks behind a rising tide of new cases. A major hospital group in Arizona, Banner Health, began banning most visitors from its facilities Sunday night because of the worsening spread of the virus. And where the hospitals come under intense strain, officials are turning, however reluctantly, to impose or reimpose restrictions in the hope of flattening the curve. In Los Angeles County, Calif., which has been averaging more than 3,500 cases a day lately, officials said on Sunday that barring indoor restaurant dining was no longer sufficient, and that outdoor dining would have to shut down as well.

“Unfortunately, if our cases and hospitalizations continue to increase, we will need to issue further restrictions to protect our health care system and prevent more deaths,” said Barbara Ferrer, the county public health director.

New York City’s economy is in a downturn, but film production has been a bright spot.

With Broadway dark and concert halls closed, New York’s arts and entertainment industry has been devastated by the pandemic. But film production has been a bright spot, with television and streaming series again filling the city’s sound stages and, increasingly, the city’s streets.

The industry is not yet back to its old heights. Of the nearly 80 series that were filming or planning to film in New York City in the 2019-2020 season, 35 were back at work by early November, with another five expected by the end of the year.

A virus surge could threaten that recovery, particularly if Gov. Andrew M. Cuomo declares New York a “red zone” and orders nonessential businesses closed.

Still, in a pandemic-weary Manhattan, whose streetscapes are pockmarked by boarded-up storefronts and “for rent” signs, the sight of shiny production trucks and the hum of workers rolling equipment on and off film sets is giving the city a glimpse of its former self.

The major studios — Kaufman Astoria Studios in Queens, Steiner Studios in the Brooklyn Navy Yard and Silvercup Studios in Long Island City — all report that they are full, though each stage can function at only 50 percent of its regular occupancy under state rules.

The overlapping safety protocols of the industry’s labor unions, the Hollywood parent companies and the New York state and city government have led to robust safety protections, While near daily virus testing is turning up cases among the crew and actors, the productions, for the most part, have continued with few delays.

About one person every week or two test positive somewhere on the lot, said Doug Steiner, the chief executive of Steiner Studios. But so far, he said, the productions have managed to isolate cases and their contacts, and continue filming.


An Australian airline plans to make proof of vaccination compulsory for travelers, and other news from around the world.

Australia’s largest airline, Qantas, is planning to make coronavirus vaccines — when they become available — compulsory for passengers who want to fly internationally, and its chief executive predicted that other airlines would follow.

Alan Joyce, the head of Qantas, said on Monday that the airline was looking at changing its terms and conditions to make vaccines compulsory for those traveling into or out of Australia.

He also said he believed vaccinations as a condition for international air travel would be mandated by more airlines: “I’ve talked to my colleagues at other airlines across the globe, and I think it’s going to be a common theme across the board.”

He said airlines and governments around the world have considered developing an electronic vaccination passport that would certify if passengers were vaccinated and with what vaccine. Mr. Joyce’s comments coincided with an announcement by the International Air Transport Association that it was in the final stages of developing a digital health pass that would provide travelers’ testing and vaccine information to governments and airlines.

The Australian government has said that coronavirus vaccines will be “as mandatory as you can possibly make it.”

Qantas has not finalized any changes since no vaccines are predicted to be available in Australia until early next year, but one British travel company said it would stop selling Qantas flights.

In other news from around the world:

  • In an upcoming book, Pope Francis criticizes those who do not wear masks, saying, “It is all too easy for some to take an idea — in this case, for example, personal freedom — and turn it into an ideology.” The pope has himself been criticized for not wearing masks at his public appearances.

  • King Felipe VI of Spain has started a 10-day quarantine after coming into close contact with someone who later tested positive for Covid-19. The royal household did not disclose whom the king had met but said in a statement that all of his official activities had been canceled during the quarantine period. The king’s wife, Queen Letizia, and their two daughters have not been quarantined.

  • Prime Minister Johnny Briceño of Belize will isolate for two weeks after testing positive for Covid-19, Reuters reported. The country has recorded a total of 5,200 coronavirus cases, according to a New York Times database.

Hong Kong orders all bars and nightclubs to close as infections spike.

Facing a spike in coronavirus infections, the government in Hong Kong ordered all bars and nightclubs to shut starting on Thursday.

The city’s fourth wave of cases has emerged under cooler temperatures and what officials warned of as fatigue after months of social distancing. A cluster that began at a dance studio has since spread to similar venues across the city, bringing infections to another high since the summer.

Sophia Chan, Hong Kong’s health secretary, said that all bars, nightclubs, bathhouses and rented rooms for private parties must close, and that live performances and dancing would be banned. Banquets could have 10 tables at most, with each seating up to four people, she said.

The city’s authorities have toughened and relaxed its social-distancing rules with rises and falls in coronavirus cases. On Tuesday, Hong Kong reported 80 new cases, including 54 linked to the dancers, bringing the cluster that originated at Starlight Dance Club — a ballroom and Latin dance studio — to 187 cases, a health department spokeswoman said.

Also on Tuesday, Hong Kong’s leader, Carrie Lam, defended a plan to pay about $645 to those who test positive and who are in financial difficulty. Critics said the government was giving people an incentive to intentionally infect themselves, but officials have since clarified the eligibility requirements for the payments. Mrs. Lam said it was intended to help those who would lose income as a result of getting infected.

The pandemic is accelerating a change to change (the coin kind).

A funeral for cash has not yet been scheduled, but the pandemic has made it much easier to imagine a world without coins, and has already reinvigorated the movement to get rid of pennies.

For banks, credit card companies and some Bitcoin advocates, the demise of each unit of cash would be welcome news. For small businesses that rely on coins, it’s a slow-rolling earthquake. For archaeologists and collectors, it’s bittersweet at best and a tragedy at worst.

As the coin shortage reached its worst in June, trade groups for grocers, gas stations and convenience stores pleaded for help from the government, calling the coin shortage an emergency that threatened their ability to serve customers and stay in business.

The Federal Reserve started rationing coins, and the U.S. Mint kicked production into high gear, urging people to put spare change back in the economy. Major chains like Walmart and CVS asked customers to pay with cards or use exact change, and Chipotle was accused of keeping the change from customers who paid with cash.

While small businesses have had to adapt reluctantly to a cashless world, many tech firms, banks and credit card companies have pushed for one, said Jay Zagorsky, a professor at the Questrom School of Business at Boston University.

“The economy is bifurcating, sort of splitting in two parts, and there’s one part that’s taking a beating,” he said.

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