Covid-19: The U.S. Has Its Own New Worrisome Variants – The New York Times

Heres what you need to know:Genomic sequencing can detect and track virus variants, but the United States is sequencing relatively few coronavirus test samples. Lab technicians at Duke University prepared samples for sequencing earlier this month.Credit...Pete Kiehart for The New York Times

As Americans anxiously watch the spread of coronavirus variants that were first identified in Britain and South Africa, scientists are finding a number of new variants that seem to have originated in the United States and many of them may pose the same kind of extra-contagious threat.

In a study posted on Sunday, a team of researchers reported seven growing lineages of the coronavirus, spotted in states across the country. All have gained a mutation at the exact same spot in their genes.

Theres clearly something going on with this mutation, said Jeremy Kamil, a virologist at Louisiana State University Health Sciences Center and a co-author of the new study.

Its not clear yet whether this shared mutation makes the variants more contagious, but because it appears in a gene that influences how the virus enters human cells, the scientists are highly suspicious.

I think theres a clear signature of an evolutionary benefit, Dr. Kamil said.

Its not unusual for different genetic lineages to independently evolve in the same direction. Charles Darwin recognized convergent evolution in animals. Virologists have found that it happens with viruses, too. As the coronavirus branches into new variants, researchers are observing Darwins theory of evolution in action every day.

Its difficult to answer even basic questions about how prevalent the new variants are in the United States because the country sequences genomes from less than 1 percent of coronavirus test samples. The researchers found examples scattered across much of the country, but they cant tell where they first arose.

Its also hard to say whether the variants are spreading now because they are more contagious, or for some other reason, like holiday travel or superspreader events.

Scientists say the mutation could plausibly affect how easily the virus gets into human cells. But Jason McLellan, a structural biologist at the University of Texas at Austin who was not involved in the study, cautioned that the way that the coronavirus unleashes its harpoons was still fairly mysterious.

Its tough to know what these substitutions are doing, he said of the mutations. It really needs to be followed up with some additional experimental data.

Vaccinations are picking up pace. The spread of the coronavirus in the United States has slowed drastically. The Centers for Disease Control and Prevention is urging K-12 schools to reopen safely and as soon as possible.

But just as states are again lifting mask-wearing mandates and loosening restrictions, experts fear that more contagious variants could undo all that progress.

That threat seems only to grow as researchers learn more. British government scientists now believe the more contagious variant that is ravaging Britain is also likely to be deadlier than earlier versions of the virus, according to a document posted on a government website on Friday. An earlier assessment on a smaller scale warned last month that there was a realistic possibility the variant was more lethal.

The variant, also known as B.1.1.7, is spreading rapidly in the United States, doubling roughly every 10 days, another recent study found.

In line with an earlier warning from the C.D.C., the study predicted that by March the variant could become the dominant source of coronavirus infection in the United States, potentially bringing a surge of new cases and increased risk of death.

Beyond that, scientists reported on Sunday that they have begun to spot more new variants that seem to have emerged in the U.S. and are concerned that they may spread more readily than earlier versions.

Vaccine distribution is accelerating the U.S. is now averaging about 1.66 million doses a day, well above the Biden administrations target of 1.5 million but B.1.1.7 has a worrisome mutation that could make it harder to control with vaccines, a Public Health England study found this month.

The variant has spread to at least 82 countries, and is being transmitted 35 percent to 45 percent more easily than other variants in the United States, scientists recently estimated. Most people who catch the virus in Britain these days are being infected by that variant.

The British research on B.1.1.7s lethality did come with caveats, and the reasons for the variants apparently elevated death rate are not entirely clear. Some evidence suggests that people infected with the variant may have higher viral loads, a feature that could not only make the virus more contagious but also potentially undermine the effectiveness of certain treatments.

But government scientists were relying on studies that examined a small proportion of overall deaths. They also struggled to account for the presence of underlying illnesses in people infected with the new variant, and for whether the cases originated in nursing homes.

Bill Hanage, an epidemiologist at Harvard University, said that although we do need to have a degree of caution in looking at the findings, its perfectly reasonable to think that this is something serious I am certainly taking it seriously.

Its pretty clear we have something which is both more transmissible and is more worrying if people become infected, he said.

Angela Rasmussen, a virologist at Georgetown University, said relaxing restrictions now would be courting disaster. She urged Americans to be extra vigilant about mask wearing, distancing and avoiding enclosed spaces.

You dont want to get any variant, Dr. Rasmussen said, but you really dont want to get B.1.1.7.

The United States confirmed its first case of the B.1.1.7 variant on Dec. 29. Unlike Britain, it has been conducting little of the genomic sequencing necessary to track the spread of new variants that have caused concern, though the Biden administration has vowed to do more.

On Friday, for the fifth time in six days, the number of new virus cases reported in the United States dipped below 100,000 far less than the countrys peak of more than 300,000 reported on Jan. 8.

As the number of virus cases and hospitalizations has fallen, the Republican governors of Montana, Iowa, North Dakota and Mississippi have recently ended statewide mask-wearing mandates. In New York, Gov. Andrew M. Cuomo, a Democrat, has allowed indoor dining to resume at 25 percent capacity, though experts have repeatedly warned that maskless activities, such as eating, in enclosed spaces are high-risk.

Although virus case numbers are moving in the right direction, the loosening of restrictions has unnerved experts like Saskia Popescu, an epidemiologist at George Mason University in Virginia.

Now more than ever, with novel variants, we need to be strategic with these reopening efforts and be slow and not rush things, she said.

The director of the Centers for Disease Control, Dr. Rochelle Walensky, tried on Sunday to build support for reopening schools, even in districts with high infection rates and before vaccinating teachers, political sticking points for the Biden administration.

In a round of appearances on the morning news shows, Dr. Walensky promoted her agencys new guidelines for schools, seeking to build confidence that the Biden administrations strategy could satisfy teachers and parents alike and fulfill the new presidents promise to reopen schools by his 100th day in office.

We hadnt previously had the science in order to inform how to open safely, Dr. Walensky said on Fox News Sunday. We didnt have the data, and prior we didnt have any guidance as to how to do it safely, so we are really anticipating with this guidance emerging, that schools will be able to start reopening.

She reiterated her earlier, controversial statement at a news briefing that scientific data supported the idea of reopening schools before teachers were vaccinated but she also noted that the C.D.C.s advisory panel on vaccines recommended that states consider teachers to be essential workers, placing them high on the priority list.

The Biden administration is juggling demands to open schools as soon as possible with teachers concerns about safety. Earlier this month, teachers unions objected to Dr. Walenskys comment about teachers not needing to be vaccinated before schools reopened. The comment also drew a rebuke from the White House press secretary, Jen Psaki, who said Dr. Walenskys remark was made in her personal capacity.

The guidelines issued on Friday offered a chance for a reset, by outlining strict and expensive safety measures, like cleaning, mask wearing, contact tracing, frequent testing and social distancing.

But on Sunday, Dr. Walensky acknowledged that few schools were currently up to the task, without a significant infusion of federal funds.

Not all schools are able to do all of those things right now, she said on CNN, and many of those schools are in red zones, referring to communities with high infection rates. We need to do the work to get all of those mitigation strategies up and running in all of the schools.

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Its a very important day for us, weve been waiting for it, this pandemic took a great toll. Weve had a lot of cases, a lot of fatalities in Lebanon. So were really looking forward to the vaccine to hopefully see some light at the end of the tunnel. Privileged. Excited. Happy that this is happening, that it is happening to Lebanon. A good thing for once. Its working. And I look forward to everybody being able to get the chance to get it too.

BEIRUT, Lebanon Lebanon began vaccinating its citizens against Covid-19 on Sunday, offering a rare glimmer of hope in a country suffering badly from several overlapping crises, just one of which is the pandemic.

The first shot was administered to the director of the intensive care unit at the lead government hospital fighting the pandemic. The second was given to a famous 93-year-old comedian.

The vaccination drive began after Lebanon received its first batch of 28,500 doses of the Pfizer-BioNTech vaccine. Using $34 million in financing from the World Bank, Lebanon is buying enough doses to vaccinate about two million people, roughly one-third of its population. Millions more doses are expected to arrive in the spring and summer through a United Nations program and commercial sources.

Lebanons worst coronavirus surge peaked in mid-January, when the country was averaging more than 4,800 newly reported cases a day, according to a New York Times database; the average has since fallen somewhat, to about 2,700 a day. Some 337,000 people in Lebanon almost 5 percent of the population are now known to have had the virus, and more than 3,900 have died.

To try to drive the numbers down, the government imposed a very strict lockdown in mid-January, with a 24-hour curfew and widespread shop closures. It eased the restrictions slightly last week, but the curfew largely remains in effect.

The suffering caused by the pandemic has been compounded by a political crisis that has left Lebanon without an effective government for six months, and a financial crisis that has drastically weakened the local currency, making imported medicines, food and other products more expensive.

A huge explosion in the port of Beirut last August also made matters worse, heavily damaging four hospitals, killing 200 people and leaving thousands more wounded.

global roundup

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These new cases pose questions our public health staff are working around the clock to answer. We dont yet have a complete picture of the potential source of the infection and spread, if any, beyond one household. And we are waiting for the genome sequencing and serology, both of which will provide important pieces of this puzzle. As of 11:59 p.m. tonight, Sunday, Feb. 14, Aukland will move to Level 3 for a period of three days, until midnight on Wednesday. The rest of New Zealand will move to Level 2 for the same period of time. The main thing we are asking people in Auckland to do is to stay home to avoid any risk of spread. That means staying in your bubble other than for essential personal movement. People should work from home unless that is not possible. If you go outside your home, please maintain physical distancing of two meters outside. Or if youre in a controlled environment where you know others present, one meter. Im asking New Zealanders to continue to be strong and be kind. I know we all feel the same way when this happens. We all get that sense of, not again. But remember, we have been here before. That means we know how to get out of this again. And that is together. If you know someone in Auckland, reach out, please check on them. And if youre in Auckland, please check on your neighbors, ensure theyre looked after and supported. And finally, as Ive said all the way through this, ultimately, please remember, we are going to be OK.

AUCKLAND, New Zealand Faced with the creeping threat of more infectious coronavirus variants, Australia and New Zealand have responded to a small number of cases with near-immediate regional lockdowns.

On Sunday night, as couples celebrating Valentines Day strolled arm-in-arm through central Auckland, Prime Minister Jacinda Ardern of New Zealand announced that the city would begin a three-day lockdown at midnight because of three unexplained positive test results in a single family. The rest of New Zealand would be subject to increased physical distancing requirements over the same period, she said.

Ms. Ardern said Monday that all three cases were the variant first detected in Britain, and that its higher transmissibility meant the government had been absolutely right to order the lockdown. Australia has also suspended quarantine-free travel with New Zealand for at least 72 hours over the new cases.

Separately, both countries said Monday that they had received their first shipments of the Pfizer vaccine.

New Zealand has had almost no virus-related restrictions since the fall, when it successfully eliminated the virus for a second time. Over all, the country has reported 2,330 coronavirus cases and 25 deaths, far fewer in proportion to its population than most other developed nations.

The Australian state of Victoria has also been placed in a short-term lockdown in response to a small outbreak, which began at a quarantine hotel and has grown to 16 cases. During the lockdown, which began at 11:59 p.m. Friday and is intended to last five days, most of Victorias six million people are not allowed to leave home except for limited periods of outdoor exercise or shopping. Professional tennis players who are in Melbourne, the state capital, for the Australian Open are considered essential workers and have been allowed to continue playing their matches, albeit without fans in attendance.

Like New Zealand, Australia has had relatively few infections and deaths, and acts aggressively at the first sign of new outbreaks. Similar snap lockdowns in the Australian cities of Perth and Brisbane were successful recently at quashing transmission.

Announcing the Auckland lockdown on Sunday, Ms. Ardern said, Our view is, youll have less regret if you move early and hard than if you leave it and it gets out of control.

In other news around the world:

The start of ski season in Italy is delayed, the health minister Roberto Speranza announced. Citing the spread of a coronavirus variant, Mr. Speranza said amateur skiing was forbidden through at least March 5, The Associated Press reported. Italys last ski season was halted as the country became a coronavirus epicenter last spring, and it hasnt restarted since then. This years closure is another blow to an industry that generates 1.2 billion euros, or $1.5 billion, in annual revenues.

Portugal, which until the last few days had been enduring one of the worlds worst coronavirus surges, has prolonged its Covid-19 state of emergency. The extension, until at least March 1, comes as new daily cases fell over the weekend to their lowest level since late December, while the latest daily death toll, 138, is the lowest since Jan. 11. Still, Portugals Covid-19 death toll now stands at 15,321. By comparison, Greece, which has a roughly equal population of about 10 million, has recorded 6,126 deaths.

Japan issued its first approval for a vaccine against the coronavirus on Sunday, saying that it would use the Pfizer-BioNTech vaccine to begin inoculating frontline health care workers this week. Japan has been slower than the United States and Europe to authorize any coronavirus vaccines, but it has also had the luxury of time. Public health measures have successfully kept case rates low and the countrys economy has suffered less than others. It showed a sharp rebound, growing 3 percent, in the last three months of 2020. But the growth was fragile and could easily be disrupted, analysts cautioned.

New Yorkers with chronic health conditions that made them newly eligible for the Covid-19 vaccine flooded a state website and call center Sunday morning, leaving many unable to immediately schedule appointments at mass vaccination centers.

State officials said on Sunday that 73,000 appointments had been scheduled as of 11:30 a.m., while 500,000 people went through an online eligibility screening tool needed to make appointments. Thousands were in virtual waiting rooms that can hold up to 8,000 people per vaccination site. Once those waiting rooms are full, people attempting to schedule appointments are told to try again later.

Richard Azzopardi, a senior adviser to Gov. Andrew M. Cuomo, said demand was high, but our infrastructure has remained up and intact. He said that the states ability to make appointments depended on the vaccine supply, which is steadily increasing.

Officials said the new criteria, which include chronic health conditions like obesity and hypertension, made four million more New Yorkers eligible for the Covid-19 vaccine. They join a growing number of people in the state who are eligible for the vaccine despite a shortage in supply.

Those who are now eligible include adults who have certain health conditions that may increase their risk of severe illness or death from the coronavirus. Aside from obesity and hypertension, other conditions that would qualify New Yorkers for the vaccine include pulmonary diseases and cancer, Mr. Cuomo announced this month. He also made pregnancy a qualifying condition.

Appointments for people who are in this group can be scheduled for as early as Monday, though most people will probably face a long wait because vaccine doses are scarce now. New Yorkers must provide proof of their condition with a doctors note, signed certification or medical documentation, Mr. Cuomo said.

While this is a great step forward in ensuring the most vulnerable among us have access to this lifesaving vaccine, its no secret that any time youre dealing with a resource this scarce, there are going to be attempts to commit fraud and game the systems, Mr. Cuomo said in a statement.

In New York State, about 10 percent of the population has received its first dose, according to data gathered by The New York Times. With the new criteria, about 11 million people are now eligible in the state, including people ages 65 and older, health care workers and teachers over half the state population.

New York City recently opened mass vaccination sites at Yankee Stadium in the Bronx and Citi Field in Queens to better reach communities hit hard by the virus. The state and federal government also announced last week that the Federal Emergency Management Agency would open vaccination sites at Medgar Evers College in Brooklyn and York College in Queens.

To check on eligibility and schedule an appointment, New Yorkers can complete a prescreening on the states website. They can also call the states vaccination hotline at 1-833-NYS-4VAX (1-833-697-4829) for more information about vaccine appointments.

Phila Lachaux, a 22-year-old business student in France, dreamed of striking out on her own in the live music industry. But the pandemic led to the loss of her part-time job as a waitress, and sent her back to live at her family home.

Now, struggling to envision a future after months of restrictions, Ms. Lachaux says that loneliness and despair seep in at night. I look at the ceiling, I feel a lump in my throat, she said. Ive never had so many suicidal thoughts.

With curfews, closures and lockdowns in Europe set to drag into the spring or even the summer, mental health professionals are growing increasingly alarmed about the deteriorating mental state of young people.

Last in line for vaccines and with schools and universities shuttered, young adults have borne many of the sacrifices made largely to protect older people, who are more at risk from severe infections.

Across the world, the young have lost economic opportunities, missed traditional milestones and forfeited relationships at a pivotal time for forming identity.

Many feel theyre paying the price not of the pandemic, but of the measures taken against the pandemic, said Dr. Nicolas Franck, the head of a psychiatric network in Lyon, France. In a survey of 30,000 people that he conducted last spring, young people ranked the lowest in psychological well-being, he said.

In Italy and in the Netherlands, some youth psychiatric wards have filled to record capacity. In France, professionals have urged the authorities to consider reopening schools to fight loneliness. And in Britain, some therapists said that they had counseled patients to break lockdown guidelines to cope.

In the United States, a quarter of 18- to 24-year-olds said they had seriously considered suicide, one report said. In Latin America and the Caribbean, a survey conducted by UNICEF of 8,000 young people found that more than a quarter had experienced anxiety and 15 percent depression.

We are in the midst of a mental health pandemic, and I dont think its treated with near enough respect, said Arkadius Kyllendahl, a psychotherapist in London who has seen the number of younger clients double in recent months.

If you are having thoughts of suicide, the following organizations can help.

In Britain, call Papyrus at +44 800 068 4141 (9am to midnight), or message Young Minds: text YM to 85258. You can also find a list of additional resources on Mind.org.

In France, call SOS Amiti at +33 9 72 39 40 50 (24/7) or Fil Sant Jeunes at +33 800 235 236 (9am to 11pm). Ameli has a list of additional resources.

In Italy, call Telefono Amico at +39 2 2327 2327 (10am to midnight) or Telefono Azzurro at +39 19696 (a webchat is also available).

A team of experts selected by the World Health Organization to investigate the origins of the coronavirus returned last week from Wuhan, China, site of the worlds first outbreak. Having broken the ice with Chinese scientists, the team plans to produce a joint report on the possible origins of the virus.

The two groups of scientists agreed to pursue some ideas that the Chinese government has been promoting, like the possibility that the virus was transported on frozen food. But the W.H.O. team also became frustrated by Chinas refusal to turn over raw data for analysis.

Peter Daszak, a member of the W.H.O. team and the president of EcoHealth Alliance in New York, is primarily concerned with the animal origins of the virus. A specialist in animal diseases and their spread to humans, Dr. Daszak has worked with the Wuhan Virology Institute, a collaboration that last year prompted the Trump administration to cancel a grant to his organization.

In an interview after his return to New York, he said that the visit had provided some new clues, which all of the scientists, Chinese and international, agreed most likely pointed to an animal origin within China or Southeast Asia. The scientists have largely discounted claims that the virus originated in a lab, saying that possibility was so unlikely that it was not worth further investigation.

He reflected on the atmosphere in Wuhan and his first glimpse of the seafood market where the initial outbreak occurred last year, although it was not the site of the first cases. He also said the path ahead would be straightforward scientifically, but not politically.

The W.H.O. investigation was the subject of a sharp exchange over the weekend between the U.S. and Chinese governments. Jake Sullivan, the national security adviser, said Saturday that the Biden administration had deep concerns about its early findings and how they were communicated.

It is imperative that this report be independent, with expert findings free from intervention or alteration by the Chinese government, he said in a statement.

In response, the Chinese government asked whether the United States could be considered a credible partner in the matter, having only recently rejoined the W.H.O. after withdrawing during the Trump administration.

What the U.S. has done in recent years has severely undermined multilateral institutions, including the W.H.O., and gravely damaged international cooperation on Covid-19, the Chinese Embassy in Washington said in a statement.

But the U.S., acting as if none of this had ever happened, is pointing fingers at other countries who have been faithfully supporting the W.H.O. and at the W.H.O. itself, it continued. With such a track record, how can it win the confidence of the whole world?

Austin Ramzy contributed reporting.

WHEELING, W.Va. After nearly a year in lockdown for the residents of Good Shepherd Nursing Home eating meals in their rooms, playing bingo through their television sets and isolating themselves almost entirely from the outside world their coronavirus vaccinations were finished and the hallways were slowly beginning to reawaken.

In a first, tentative glimpse at what the other side of the pandemic might look like, Betty Lou Leech, 97, arrived to the dining room early, a mask on her face, her hair freshly curled.

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Covid-19: The U.S. Has Its Own New Worrisome Variants - The New York Times