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These Virus Sequences That Have been Abruptly Deleted? They’re Again

Those Virus Sequences That Were Suddenly Deleted? They’re Back

A pile of early coronavirus data that was missing for a year has emerged from its hiding place.

In June, an American scientist discovered that more than 200 genetic sequences from Covid-19 patient samples isolated in China at the beginning of the pandemic had been mysteriously removed from an online database. Jesse Bloom, a virologist at the Fred Hutchinson Cancer Center in Seattle, used digital research to find 13 of the sequences in Google Cloud.

When Dr. Bloom, sharing his experience in a report published online, wrote that “it seems likely that the sequences were deleted to obscure their existence”.

But now a strange explanation has emerged from an editorial oversight of a scientific journal. And the sequences were uploaded to another database monitored by the Chinese government.

The story began in early 2020 when researchers from Wuhan University explored a new way to test for the deadly coronavirus that is sweeping the country. They sequenced a short section of genetic material from virus samples taken from 34 patients at a Wuhan hospital.

The researchers published their results online in March 2020. That month they also uploaded the sequences to an online database called the Sequence Read Archive, maintained by the National Institutes of Health, and submitted a publication of their results to a scientific journal called. a small one. The paper was published in June 2020.

Dr. Bloom became aware of the Wuhan sequences this spring while researching the origin of Covid-19. While reading a May 2020 report on coronavirus early genetic sequences, he came across a table that noted their presence in the Sequence Read Archive.

But dr. Bloom couldn’t find it in the database. On June 6th, he emailed the Chinese scientists to ask where the data was going, but received no response. On June 22nd, he published his report, which was covered by the New York Times and other media outlets.

At the time, a spokeswoman for the NIH said the study’s authors requested in June 2020 that the sequences be removed from the database. The authors informed the agency that the sequences would be updated and included in a different database. (The authors did not respond to inquiries from The Times.)

But a year later, Dr. Bloom couldn’t find the sequences in any database.

On July 5, more than a year after the researchers removed the sequences from the Sequence Read Archive and two weeks after Dr. Bloom’s report was published online, the sequences were quietly uploaded to a database of the China National Center for Bioinformation by Ben Hu. a researcher at Wuhan University and co-author of the small paper.

On July 21, the disappearance of the sequences was raised during a press conference in Beijing at which Chinese officials denied claims that the pandemic began as a laboratory leak.

According to a translation of the press conference by a journalist from the state-controlled Xinhua News Agency, Vice Minister of China’s National Health Commission Dr. Zeng Yixin that the problems arose when the editors of Small deleted a paragraph in which the scientists described the sequences in the Sequence Read Archive.

“Therefore, the researchers thought that it was no longer necessary to save the data in the NCBI database,” said Dr. Zeng, referring to the Sequence Read Archive published by the NIH. is operated

An editor at Small, who specializes in micro and nano science and is based in Germany, confirmed his presentation. “The data availability declaration was mistakenly deleted,” wrote editor Plamena Dogandzhiyski in an email. “We will shortly issue a fix that will clear up the error and contain a link to the depot where the data is now hosted.”

The Journal published a formal correction to this effect on Thursday.

It is not clear why the authors did not mention the journal’s error when they requested to remove the sequences from the Sequence Read Archive, or why they notified the NIH that the sequences would be updated. It’s also not clear why they waited a year to upload it to another database. Dr. Hu did not respond to an email asking for comment.

Dr. Bloom was also unable to provide an explanation for the conflicting accounts. “I am unable to judge between them,” he said in an interview.

These sequences alone cannot solve the open questions about the origin of the pandemic, be it through contact with a wild animal, a leak from a laboratory or otherwise.

In their first reports, the Wuhan researchers wrote that they extracted genetic material from “samples from outpatients suspected of having Covid-19” at the beginning of the epidemic. But the entries in the Chinese database now suggest they were taken from the Renmin Hospital at Wuhan University on Jan. 30 – almost two months after the earliest reports of Covid-19 in China.

While the disappearance of the sequences appears to be the result of an editorial error, it was Dr. Bloom still worth looking for other coronavirus sequences that might be lurking online. “That definitely means we should keep looking,” he said.

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Vaccinated Folks Could Unfold the Virus, Although Hardly ever, C.D.C. Reviews

Vaccinated People May Spread the Virus, Though Rarely, C.D.C. Reports

In another unexpected and unwelcome twist in the pandemic, the Centers for Disease Control and Prevention released a report on Friday strongly suggesting that fully immunized people with so-called breakthrough Delta variant infections can pass the virus on to others as easily as unvaccinated people People.

The vaccines remain highly effective against serious illness and death, and the agency said infections are comparatively rare in people who have been vaccinated. But the reveal follows a number of other recent discoveries about the Delta variant that have turned scientists’ understanding of the coronavirus on its head.

In the new report, which should explain the agency’s sudden revision of its masking recommendations for vaccinated Americans, the CDC described an outbreak in Provincetown, Massachusetts this month that rose rapidly to 470 cases in Massachusetts alone by Thursday.

Three quarters of those infected were fully immunized, and the Delta variant was found in most of the genetically analyzed samples. Vaccinated and unvaccinated people who were infected carried high levels of the virus, the agency reported.

“High viral loads indicate an increased risk of transmission and raised concerns that, unlike other variants, people infected with Delta can transmit the virus,” said Dr. Rochelle Walensky, director of the CDC, on Friday.

The viral load data shows that even fully vaccinated people can spread the virus just as easily as unvaccinated people who become infected. “We believe this can be done on an individual level, which is why we have updated our recommendation,” said Dr. Walensky in an email to the New York Times earlier this week.

An internal agency document the Times received Thursday evening indicated even greater concern among CDC scientists, raising harrowing questions about the virus and its trajectory.

The delta variant is about as contagious as chickenpox, the document says, and universal masking may be necessary. Nevertheless, according to the agency, breakthrough infections are rare overall.

On Friday, the Kaiser Family Foundation reported that the breakthrough rate among fully vaccinated people in states that store such data is less than 1 percent.

The accumulated research on the variant messes up the country’s plans to return to offices and schools this fall, and enlivens tough questions about masking, testing, and other precautions that Americans had hoped were behind them.

Government officials and scientists alike are seriously concerned that the results could shake confidence in the vaccines and shake the nation’s delayed vaccination campaign if Americans mistakenly conclude that the vaccinations are not effective.

Concerned about the delayed campaign, President Biden has ordered all federal employees to be vaccinated or tested for viruses on a weekly basis. Support for vaccination regulations is growing at some companies and in some parts of the country.

Developing research into the Delta variant has humiliated scientists around the world who are now asking themselves new questions about the virus that they had not considered.

They do not understand the circumstances that can increase the likelihood of a breakthrough infection, nor who is most at risk. They don’t know for sure that the Delta variant causes more severe illness in unvaccinated people who become infected, although early data suggests it.

“We spent so much time, energy, and treasure last year trying to figure out this damn virus and how it works and what it does,” said Dr. Robert Wachter, chairman of the Department of Medicine at the University of California. San Francisco.

To learn how differently the Delta variant differs from the original virus is “just plain staggering,” he added. “The brain doesn’t like being pushed around like that.”

While breakthrough infections are rare, the new data suggest that those who were vaccinated may contribute to an increase in new infections – albeit likely to a far lesser extent than those who were not. Breakthrough infections have always been reckoned with, but until the arrival of the Delta variant, vaccinated Americans were not seen as drivers of its spread in the community.

“Delta teaches us to expect the unexpected,” said John Moore, a virologist at Weill Cornell Medicine in New York. “There are aspects of what we now know that we don’t see coming.”

Updated

July 30, 2021, 7:36 p.m. ET

The finding is frightening, but vaccines remain the only reliable shield against the virus in whatever form. Even with the Delta variant, the vaccines largely prevent infection and significantly reduce the likelihood of serious illness or death in the event of an infection.

Nationwide, about 97 percent of people hospitalized with Covid-19 are unvaccinated, according to the CDC.

“Full vaccination is very protective, even against Delta,” said Angela Rasmussen, researcher at the Organization for Vaccines and Infectious Diseases at the University of Saskatchewan in Canada.

“Masks are a wise precaution, but most of the transmission occurs among the unvaccinated and that is still the most at risk,” she added.

The accumulated research underscores the urgency to accelerate the rate of vaccination in the United States and reduce the number of people susceptible to serious illnesses. This week, the vaccination rate in the European Union exceeded that in the US for the first time.

About 58 percent of Americans 12 years and older are fully vaccinated. The rate of vaccination has slowed to just over 500,000 people a day, although it has swung up slightly in recent weeks as infections pick up again.

In the UK, where the variant seems to have subsided after an increase, vaccinations have been introduced by age and a much higher proportion of people over 50 are vaccinated than in the United States.

Understand the state of vaccine mandates in the United States

Vaccination rates are much more inconsistent across the United States, said Bill Hanage, an epidemiologist at Harvard TH Chan School of Public Health. “The result is that what Delta is doing in the UK is not necessarily what it will be doing in places with very different vaccinations,” he said.

“Things are getting worse than they would have been,” without the variant, he added. “But they will be much better than they would have been without the vaccination.”

In its report on Friday, the CDC urged local and state officials in jurisdictions with even lower virus concentrations to consider precautions such as masking and restricting gatherings. The CDC internal document sounded more urgent, recommending that the agency “recognize that the war has changed”.

Indeed, the questions Americans now face seem almost inexhaustible, almost insoluble. Should companies allow employees to return to work when vaccinated people could occasionally spread the variant? What does this mean for shops, restaurants and schools? Are unmasked family celebrations off the table again?

With the number of daily cases averaging nearly 72,000 on Friday, the new data suggests vaccinated people with young children, aging parents, or friends and family with weak immune systems may need to wear masks to protect those around them – even in Communities with lower infection rates.

The Provincetown, Massachusetts outbreak germinated this month after more than 60,000 revelers celebrated the July 4th gathering in crowded bars, restaurants, guest houses and rental apartments, often indoors.

On July 3, there were no cases in the city or the surrounding district. By July 10, officials saw an increase and by July 17 there were 177 cases per 100,000 people. The outbreak has since spread to nearly 900 people across the country.

“Vaccines are like waders,” said Dr. Rasmussen. “They keep you dry when you wade through a river, but when you get too deep, water starts flowing over it. That seems to have happened with the Massachusetts eruption. “

Three-quarters of citizens linked to the outbreak reported a cough, headache, sore throat, or fever – symptoms of an upper respiratory tract infection – and 74 percent were known to be fully immunized.

Of the five people hospitalized, four were fully vaccinated – one with the Pfizer BioNTech vaccine and three with the Johnson & Johnson vaccine. Two of the vaccinated patients had previous illnesses. The genetic analysis of 133 cases identified the delta variant in 119 cases and a closely related virus in another case.

Scientists even warned last year that the vaccines may not completely prevent infection or transmission. However, experts didn’t expect these infections to play a significant role in the fight against the virus, nor did they anticipate how quickly the Delta variant would rip across the country.

“Two months ago I thought we were over the top,” said Dr. Guardian. In San Francisco, the most heavily vaccinated city in the country, 77 percent of people over the age of 12 are vaccinated.

And yet the hospital he works in has grown significantly, from a Covid-19 case on June 1 to 40 now. 15 of the patients are in intensive care.

“When a 70 or 75 percent immunity doesn’t protect the community, I think it’s very difficult to extrapolate what happens to a place that is 30 percent vaccinated,” said Dr. Guardian. “Humility is perhaps the most important thing here.”

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Behind the Masks, a Thriller: How Usually Do the Vaccinated Unfold the Virus?

Behind the Masks, a Mystery: How Often Do the Vaccinated Spread the Virus?

The recommendation that vaccinated people dust their masks off in some parts of the country was based, according to Dr. Rochelle Walensky, director of the Centers for Disease Control and Prevention, is largely based on a problematic finding.

New research showed that vaccinated people infected with the Delta variant carry tremendous amounts of the virus in their noses and throats, she said in an email in response to questions from the New York Times.

The finding contradicts what scientists had observed in vaccinated people who were infected with previous versions of the virus and who mostly appeared unable to infect others.

This conclusion dealt a severe blow to Americans: people with what are known as breakthrough infections – cases that occur despite being fully vaccinated – of the Delta variant can be just as contagious as unvaccinated people, even if they have no symptoms.

This means that fully vaccinated people with young children, aging parents, or friends and family with weak immune systems need to renew their vigilance, especially in communities with high transmission. Vaccinated Americans may need to wear masks not only to protect themselves but everyone around them.

In the US, there are an average of 67,000 new cases per day as of Thursday. If vaccinated people transmit the Delta variant, they can contribute to the increases – albeit likely to a far lesser extent than those who were not vaccinated.

The CDC has not yet released its data, frustrating experts who want to understand the basis for the change of heart with masks. But four scientists familiar with the research said it was imperative, and based the CDC’s advice, that those vaccinated again wear masks in public indoor spaces.

The study was conducted by a group outside the CDC, the scientists said, and the agency is working quickly to analyze and publish the results.

It is still unclear how common breakthrough infections are and how long the virus stays in the body in these cases, said Dr. Walensky. Breakthroughs are rare and unvaccinated people are responsible for the majority of virus transmission, she said.

Regardless, the data the CDC is reviewing suggests that even fully immunized people can be unwilling vectors for the virus. “We believe this can be done on an individual level, which is why we have updated our recommendation,” said Dr. Walensky in her email to the Times.

The conclusion also suggests that vaccinated people exposed to the virus should get tested even if they feel fine. (In the UK, vaccinated individuals who come into contact with a known case are required to isolate themselves for 10 days.)

The new data doesn’t mean the vaccines are ineffective. The vaccines are still effective in preventing serious illness and death as they were intended, and people with breakthrough infections very rarely end up in hospital.

Updated

July 29, 2021, 5:53 p.m. ET

According to data from the CDC, around 97 percent of people hospitalized with Covid-19 are unvaccinated. (Immunity to a natural infection can offer even less protection.)

Earlier versions of the virus rarely broke the immunization barrier, prompting the CDC to advise in May that vaccinated people could go mask-free indoors. But the usual rules don’t seem to apply to the delta variant.

The variant is twice as contagious as the original virus, and one study found that the amount of virus in unvaccinated people infected with Delta could be a thousand times higher than in people infected with the original version of the virus. The CDC data support this finding, said an expert familiar with the results.

Anecdotes of clusters of breakthrough infections are becoming more common, with groups of those vaccinated reporting runny nose, headache, sore throat, or loss of taste or smell – symptoms of an upper respiratory infection.

The overwhelming majority, however, do not need intensive care because the immune system created by the vaccine destroys the virus before it can reach the lungs.

Understand the state of vaccine mandates in the United States

“We’re still going to see a huge, huge impact on disease severity and hospitalization,” said Michal Tal, an immunologist at Stanford University. “That’s what the vaccine was really made for.”

The coronavirus vaccines are injected into the muscle, and most of the antibodies produced in response remain in the blood. Some antibodies can get into the nose, the main entry point for the virus, but not enough to block it.

“The vaccines – they’re beautiful, they work, they’re amazing,” said Frances Lund, a viral immunologist at the University of Alabama in Birmingham. “But they won’t give you that local immunity.”

When people are exposed to a respiratory pathogen, it can gain a foothold in the lining of the nose – without causing any further damage. “If you walked down the street and wiped people, you’d find people with viruses in their lining that were asymptomatic,” said Dr. Michael Marks, epidemiologist at the London School of Hygiene and Tropical Medicine. “Our immune systems fight these things most of the time.”

But the Delta variant seems to thrive in the nose, and its abundance could explain why more people than scientists expected are experiencing breakthrough infections and cold-like symptoms.

However, when the virus tries to snake its way into the lungs, the immune cells in vaccinated people are fired up and quickly clear the infection before it does any major damage. That means vaccinated people should be infected and contagious for a much shorter period of time than unvaccinated people, said Dr. Lund.

“But that doesn’t mean they can’t pass it on to someone else for the first few days when they’re infected,” she added.

To stop the virus right where it enters, some experts have recommended nasal spray vaccines that would prevent the intruder from entering the upper respiratory tract. “Vaccine 1.0 is designed to prevent death and hospitalization. Vaccine 2.0 should prevent transmission, ”said Dr. Valley. “We just need one more iteration.”

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As Virus Instances Rise, One other Contagion Spreads Among the many Vaccinated: Anger

As Virus Cases Rise, Another Contagion Spreads Among the Vaccinated: Anger

As coronavirus cases resurface across the country, many vaccine Americans are losing patience with vaccine holdouts who they believe neglect a civic duty or cling to conspiracy theories and misinformation, even as new patients arrive in emergency rooms and the nation renews mask recommendations.

The pandemic appeared to be leaving the country; Almost a month ago there was a feeling of celebration. Now many of the vaccinated fear for their unvaccinated children and fear that they themselves are at risk for breakthrough infections. Rising case numbers are turning plans to reopen schools and workplaces upside down and threaten another wave of infections that could overwhelm hospitals in many communities.

“It’s like the morning sun came up and everyone was arguing about it,” said Jim Taylor, 66, a retired civil servant in Baton Rouge, LA, a state where fewer than half of adults are fully vaccinated.

“The virus is here and killing people, and we have a proven way to stop it – and we’re not going to. That is rude.”

The rising sentiment adds support for further coercive measures. Scientists, business leaders, and government officials are demanding vaccine mandates – if not from the federal government, then from local jurisdictions, schools, employers, and corporations.

“I’ve gotten angrier over time,” said Doug Robertson, 39, a teacher who lives outside of Portland, Oregon and has three children too young to be vaccinated, including a toddler with serious health.

“Now there’s a vaccine and a light at the end of the tunnel and some people choose not to go to it,” he said. “You are making it darker for my family and others like mine by making this decision.”

On Monday, New York City Mayor Bill de Blasio ordered all city workers to be vaccinated against Covid-19 or subjected to weekly tests until schools reopen in mid-September. Officials in California followed hours later with a similar mandate that covered all government employees and health care workers.

The Department of Veterans Affairs on Monday called for 115,000 local health care workers to be vaccinated over the next two months, becoming the first federal agency to mandate a mandate. Nearly 60 major medical organizations, including the American Medical Association and the American Nurses Association, called for mandatory vaccination of all health care workers on Monday.

“It is time to blame the unvaccinated people, not the ordinary people,” a frustrated Governor Kay Ivey, Republican of Alabama, told reporters last week. “It’s the unvaccinated people who fail us.”

There is no doubt that the United States has reached a turning point. According to a New York Times database, 57 percent of Americans 12 and older are fully vaccinated. Eligible Americans receive an average of 537,000 doses per day, down 84 percent from the high of 3.38 million in early April.

Infections are on the rise as a result of delayed vaccinations and lifted restrictions. As of Sunday, the country recorded 52,000 new cases a day, an average of 170 percent more than the previous two weeks. Hospital stays and death rates are also increasing, though not as rapidly.

Communities from San Francisco to Austin, Texas recommend that people who have been vaccinated wear masks again in public indoor spaces. Citing the spread of the more contagious Delta variant of the virus, Los Angeles and St. Louis, Missouri counties have mandated indoor masking.

For many Americans who were vaccinated months ago, the future looks bleak. Frustration strains relationships even within close-knit families.

Josh Perldeiner, 36, a Connecticut public defender who has a 2-year-old son, was fully vaccinated in mid-May. But a close relative who visits frequently refused to get the syringes, even though he and other family members urged them to do so.

She recently tested positive for the virus after traveling to Florida, where hospitals are filling up with Covid-19 patients. Now Mr Perldeiner is concerned that his son, too young to have a vaccine, might be exposed.

“It’s beyond risk,” he said. “People with privileges are opposed to the vaccine, and it affects our economies and continues the cycle.” As infections rise, he added, “I feel like we are on the same precipice as we were a year ago, when People don’t care if more people die. “

Hospitals have become a particular focus. Vaccination remains voluntary in most facilities and is not required for nursing staff in most hospitals and nursing homes. Many large hospital chains are just beginning to require their employees to be vaccinated.

A city stirs

As New York begins its post-pandemic life, we are investigating the ongoing effects of Covid on the city.

Despite being fully vaccinated, Aimee McLean, a nurse case manager at the University of Utah Hospital in Salt Lake City, is concerned that she will contract the virus in a patient and accidentally pass it on to her father, who has a severe chronic condition Suffers from lung disease. Less than half of Utah’s population is fully vaccinated.

“The longer we get near that number, the more it feels like there is a decent percentage of the population that honestly doesn’t care about us as healthcare workers,” said Ms. McLean, 46.

She suggested that health insurers link hospital bills to vaccination. “If you choose not to be part of the solution, you should be responsible for the consequences,” she said.

Many schools and universities will resume classroom teaching as early as next month. With the increase in the number of infections, the tensions between vaccinated and unvaccinated people have also risen in these settings.

Recommendations from the Centers for Disease Control and Prevention to reopen K-12 schools are tied to community virus transmission rates. In communities where vaccination is delayed, these rates are rising and vaccinated parents are again concerned about school outbreaks. The vaccines are not yet approved for children under 12 years of age.

The American Academy of Pediatrics has recommended that children wear masks in class when schools reopen. School districts from Chicago to Washington began enacting mandates on Friday.

Universities, on the other hand, can often require students and staff to be vaccinated. But many don’t have what frustrates the vaccinated.

“If we respect the rights and freedoms of the unvaccinated, what happens to the rights and freedoms of the vaccinated?” Said Elif Akcali, 49, who teaches engineering at the University of Florida at Gainesville. The university doesn’t require students to be vaccinated, and as rates rise in Florida, it worries about exposure to the virus.

Some even wonder how much sympathy they should have for fellow citizens who are not acting in their own interests. “I feel like if you decide not to have a vaccination and now you get sick, it’s kind of bad,” said Lia Hockett, 21, the manager of Thunderbolt Spiritual Books in Santa Monica, California.

Understand the state of vaccine mandates in the United States

As the virus spreads again, some vaccinated people believe the federal government should start using sticks instead of carrots, like lottery tickets.

Carol Meyer, 65, of Ulster County, NY, suggested withholding incentive payments or tax credits from vaccine objectors. “I have a feeling that in this country we have a social contract with our neighbors, and people who can get vaccinated and choose not to get vaccinated are breaking it,” said Meyer.

Bill Alsstrom, 74, a retired innkeeper in Acton, Massachusetts, said he would not support measures that would directly affect individual families and children, but asked if states that do not meet vaccination goals are withholding federal government funding should be.

Perhaps the federal government should require employees and contractors to be vaccinated, he thought. Why shouldn’t federal funding be withheld from states that don’t meet vaccination goals?

Although it is often viewed as a conservative phenomenon, hesitant and refused vaccination occurs in the United States for a variety of reasons across the political and cultural spectrum. No argument can address all of these concerns, and rethinking is often a slow, individual process.

Pastor Shon Neyland, who regularly pleads with members of his Portland, Oregon church to get Covid-19 vaccines, estimates that only about half of the members of the Highland Christian Center church have been injected. There was tension in the community over vaccination.

“It is disappointing because I was trying to show them that their life is in danger and that this is a serious threat to humanity,” he said.

Shareese Harris, 26, who works in the Grace Cathedral International office in Uniondale, NY, has not been vaccinated and is “taking my time” with it. She fears that the vaccines may have long-term side effects and that they have been brought to market.

“I shouldn’t be convicted or forced into a decision,” said Ms. Harris. “Society will just have to wait for us.”

Rising resentment among vaccinated people may well lead the public to support stronger coercive action, including mandates, but experts warn that punitive action and social exclusion can backfire and end dialogue and outreach.

Elected officials in several communities in Los Angeles County, for example, are already refusing to enforce the county’s new mask mandate.

“Anything that limits the opportunity for honest dialogue and persuasion is not a good thing,” said Stephen Thomas, professor of health policy and management at the University of Maryland School of Public Health. “We are already in isolated, isolated information systems where people are in their own echo chambers.”

Gentle persuasion and persistent urging convinced Dorrett Denton, a 62-year-old home nurse in Queens, to get vaccinated in February. Her employer repeatedly urged Ms. Denton to get vaccinated, but in the end it was her doctor who persuaded her.

“She says to me: ‘You have been coming to me since 1999. How many times have I operated on you and your life was in my hands? You trust me with your life, don’t you? ”Ms. Denton recalled.

“I said, ‘Yes, Doctor.’ She said, ‘Well, trust me on this.’ “

Giulia Heyward contributed the coverage from Miami, Sophie Kasakove from New York and Livia Albeck-Ripka from Los Angeles.

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On England’s ‘Freedom Day,’ Rising Virus Instances and a Prime Minister in Isolation

On England’s ‘Freedom Day,’ Rising Virus Cases and a Prime Minister in Isolation

Freedom Day arrived in England on Monday, with its chief architect, Prime Minister Boris Johnson, in quarantine, millions of Britons who might join it there and countless people more concerned about the risks of liberation.

Those were the inconsistencies on the long-awaited day the government lifted all but a few remaining coronavirus restrictions – a day the virus infected 39,950 people and carried away tens of thousands more, from the National Health Service’s cell phone app were notified after they were in contact with an infected person.

Mr Johnson defended the decision to reopen Checkers from his country estate, where he has been in self-isolation since Sunday after the NHS notified or “pinged” him for contact with his Health Secretary, Sajid Javid. who on Saturday said he had mild symptoms of Covid-19.

“If we don’t open up now, conditions are even tougher in the coming months, if the virus has a natural advantage,” Johnson told a video feed at a press conference in a slightly hushed voice and a slightly blurry image. “We have to ask ourselves: ‘If not now, then when?'”

“It is right to be as careful as we are,” he added. “It is also right to acknowledge that this pandemic is far from over.”

Mr Johnson’s safe tone captured the sharp shift in sentiment since the Prime Minister first announced and then withdrew the date for most restrictions to be lifted. British newspapers quickly dubbed Monday “Freedom Day” and celebrated it as a symbolic end to the country’s 16-month ordeal with the pandemic.

But as new cases have skyrocketed and hospital admissions started, the plan to open the economy instead looks like a likely prescription for a massive third wave – a wave of infections that Mr Johnson believes is inevitable and worthwhile with while of summer when the warmer weather and school holidays reduce the key chains of transmission.

The government’s decision represents a staggering gamble that a country with relatively widespread vaccines can learn to live with the coronavirus in its adult population. Much will depend on the resilience of vaccines and the ability of the country’s health system to deal with those who actually get sick.

“The government is basically saying, ‘We have done all we can. Now it’s up to you, ‘”said Devi Sridhar, director of the global public health program at the University of Edinburgh. “You are the first country to surrender.”

Keeping some restrictions in place for a while, Professor Sridhar argued, would allow vaccines to roll out further and hospitals to develop better treatments. “You’re devaluing time,” she said.

According to the new rules, pubs and restaurants can operate at full capacity and night clubs are allowed to reopen. The restrictions on the number of people who can meet indoors, generally limited to six, have also been lifted. The legal requirement to wear face masks has been dropped, despite the government urging people to continue wearing them on public transport. (They are compulsory to stay on London Undergrounds and buses.)

Mr Johnson initially hoped to avoid self-isolation by participating in a program that would have allowed him to continue working in the office had he been tested daily. But after being accused of breaking the rules, he reversed course and said he was self-isolating like everyone else.

Updated

July 19, 2021, 2:50 p.m. ET

The Prime Minister warned young people that they would likely need to show a full vaccination card to enter nightclubs and other crowded places. He said the flood of people ordered to isolate was an inevitable side effect of reopening. And he refused to rule out the reintroduction of restrictions, as the Netherlands recently did when hospital admissions rise catastrophically.

Almost 70 percent of adults in the UK have received both doses of a vaccine. That leaves a large pool of unvaccinated people, especially younger people, through which the highly transmissible delta variant is spreading rapidly. While these people are less likely to get seriously ill, they can transmit the virus to unvaccinated older people who remain vulnerable.

To add to uncertainty, the government said it would only offer vaccines to children ages 12-18 if they have pre-existing health conditions that make them particularly susceptible to the virus. Some scientists questioned the decision, saying the long-term effects of Covid-19 on children were unclear and that if they were not vaccinated they could speed up the infections when schools start next month.

In London, where the lifting of restrictions coincided with the mildest weather of the summer, sunbathers near Liverpool train station expressed a mixture of relief and concern as the country broke new ground.

“I don’t think it’s the right time, but we can’t hold up our lives for long,” said Silvia Andonova, dentist, 43. “There will never be a right time.”

She said she intends to continue wearing masks on public transport and in crowded places, but the instructions are not clear enough. “The government put it confusing,” she said. “What should I do?”

After long months of restrictions, there were signs of a serene mood and many restaurants wrote “Happy Freedom Day” on their signs. Still, many people said they felt conflicted over the government’s decision to relax the restrictions.

“No matter what the politicians say, I will wear my face covering in the transport,” says Saj Sangha, assistant to a law firm. Still, Mr Sangha, 52, said he looked forward to ordering a beer in a pub without the inconvenience of having to reserve a table in advance.

Not all young people believe that returning to nightclubs is safe. “The deaths are a little lower with the vaccination, but people still have Corona – we still have high numbers,” said Simone Papi, 24, cook.

In the northern city of Bradford, 26-year-old Kasim Khan stood in line to receive his first vaccination. “I am hopeful,” said Mr. Khan. “I hope to go to where my family is from, Pakistan,” he said, adding that it could be some time before this could happen as the government is currently requiring travelers from Pakistan to arrive in the UK upon arrival Quarantine hotels.

Another Bradford resident, Kirsty Mcguire, 33, said she plans to continue taking some precautions, like wearing a face mask, despite the new freedom.

“It’s out of respect for the elders and I have children,” said Ms. Mcguire, “I’m afraid something will happen to them, so I hope that people still hold on to what they were.” “

Isabella Kwai provided coverage from London and Aina Jabeen Khan from Bradford, England.

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As Virus Instances Pace Up, Seoul Tells Fitness center Customers to Sluggish Down

As Virus Cases Speed Up, Seoul Tells Gym Users to Slow Down

Kang Seung Hyun, a teacher and former rugby player preparing for a fitness photo shoot, said his gym decided to turn off the treadmills instead of imposing the slow pace. However, the bikes remained open for reasons he did not understand.

“So we can’t run or use the treadmills, but we can ride bikes? It seems strange to me, ”he said.

Ralph Yun, a CrossFit instructor who has been teaching for five months, said listening to music at a pace similar to your heart rate can improve performance, but it doesn’t necessarily make you harder.

“You could listen to slow music and train just as intensely,” he said.

Costas Karageorghis, a professor at Brunel University in London who has studied the effects of music on training for 30 years, was amused by the recommendations and called them “ridiculous”.

“If people are motivated enough to train at high intensity, the music can’t stop them,” he said.

However, research has shown that music can make significant changes to exercise even if it wasn’t what the Korean authorities intended.

Dr. Karageorghis said the sweet spot for aerobic exercise, like running on a treadmill or cycling, is 120 to 140 beats per minute. Music can distract the mind from feelings of fatigue, diminish your perception of how hard your body is working, and improve your mood. Loud music above 75 decibels can make a workout more intense, although very loud music carries the risk of hearing problems such as tinnitus.

He said he was not surprised that health officials chose 120 strokes, as research has shown that this was, in some ways, a “key break.” It’s about twice the lower end of a healthy resting heart rate, and 120 steps per minute is a common walking pace, he said. Wedding DJs have told him they’ll use a 120-beat song to get people onto the dance floor (Whitney Houston’s “I Wanna Dance With Somebody” checks in at around 120).

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Health

Birthday Events as Virus Vector

Birthday Parties as Virus Vector

KJ Seung, the director of strategy and policy for Partners in Health’s response to Covid in Massachusetts, who helped set up the contact tracing system, said it had been difficult for contact tracing authorities to clearly demonstrate that people were interacting with the in small private gatherings Virus infected.

Public revelations, like those at a factory or a wedding, were easier for her to follow. People often didn’t share the evenings when they had a cousin for dinner or drove a friend home from work, be it out of shame or forgetfulness – and when they did, they were reluctant to give names.

“Small social gatherings are the hardest places to keep track of,” he said. But “when we spoke to tracers across the country, they said, yes, people get infected at these little gatherings.”

So much of the pandemic-related behavior – including using masks and taking vaccines – seems to vary across people’s political party. However, the study found that birthdays in Republican and Democratic areas of the country resulted in similar increases in Covid infections. This suggests that while Democratic households were more likely to wear a mask when going for a walk, they may have been less different than Republicans in visiting a trusted friend.

“This element of your home is definitely a safe place and when you have your friends and family at home it just doesn’t feel risky,” said Dr. Ashish Jha, the dean of the School of Public Health at Brown University, who called the paper “creative” for finding an unusual way to capture disease transmissions that are otherwise difficult to measure.

For many Americans, birthday celebrations have become a lot safer in the past few months. The Centers for Disease Control and Prevention say it is safe for fully vaccinated individuals to gather indoors without wearing face coverings.

But for those who remain unvaccinated, the study is a reminder that even activities that feel safest pose a risk of infection. In many parts of the country, unvaccinated people are grouped by region or social group, which means birthday parties – and other such festive, private occasions – can still be risky.

Categories
Health

Birthday Events as Virus Vector

Birthday Parties as Virus Vector

At the height of the pandemic, it was easy to worry that strangers would transmit the virus to you. But a new study of what happens after people’s birthdays suggests that people we trust were also a common source of virus spreading.

Private gatherings were harder to measure for researchers than large public events – after all, they are private. And there has been heated debate among epidemiologists for months about what influence they have on how the coronavirus has moved from person to person.

But a team of Harvard researchers used a creative method to find them: Using damage data from health insurers, they examined the Covid rates of families in the two weeks after one of them had a birthday. Overall, their paper, published in Jama Internal Medicine, found that a recent family birthday increased the risk of Covid by almost a third.

Their theory is that the increased risk is almost certainly explained by birthday parties. Although the insurance claims don’t show whether a single Covid patient actually hosted a birthday party, several aspects of the data strongly suggest a connection. When researchers looked at other days of the year by randomly assigning birthdays instead of using actual birthdays, or looking at diagnoses in weeks prior to birthdays, they found no such pattern. But, perhaps more importantly, they found the greatest risk of infection in the weeks following a child’s birthday.

“My wife and I certainly didn’t see the need to gather indoors for our birthdays,” said Anupam Jena, professor of health policy at Harvard Medical School and a co-author of the article, who said the study was inspired by Birthday of his own daughter. “Our children could be more disappointed.”

At birthday parties, of course, groups often huddle together in a small space, perhaps to watch a child blowing out candles on a cake.

With birthdays happening across the country and spread out throughout the calendar year, the researchers were able to study the effects where Covid was widespread and less common. Other infections followed on a broad front after birthdays.

The study took into account data from last year when Covid was much more common and fewer Americans were vaccinated. But his conclusions are still relevant to Americans who are unvaccinated today – a group that includes all children under 12. That may be especially true since the new, more contagious Delta variant is circulating in more states.

Much political debates about managing the pandemic have centered on what to do with public spaces – such as whether restaurants are allowed to open or whether masks are required. Officials have a harder time monitoring people’s behavior at home. They also struggled to measure the impact.

KJ Seung, the director of strategy and policy for Partners in Health’s response to Covid in Massachusetts, who helped set up the contact tracing system, said it had been difficult for contact tracing authorities to clearly demonstrate that people were interacting with the in small private gatherings Virus infected. Public revelations, like those at a factory or a wedding, were easier for her to follow. People often didn’t share the evenings when they had a cousin for dinner or drove a friend home from work, be it out of shame or forgetfulness – and when they did, they were reluctant to give names.

“Small social gatherings are the hardest places to keep track of,” he said. But “when we spoke to tracers across the country, they said, yes, people get infected at these little gatherings.”

So much of the pandemic-related behavior – including using masks and taking vaccines – seems to vary across people’s political party. However, the study found that birthdays in Republican and Democratic areas of the country resulted in similar increases in Covid infections. This suggests that while Democratic households were more likely to wear a mask when going for a walk, they may have been less different than Republicans in visiting a trusted friend.

“This element of your home is definitely a safe place and when you have your friends and family at home it just doesn’t feel risky,” said Dr. Ashish Jha, the dean of the School of Public Health at Brown University, who called the paper “creative” for finding an unusual way to capture disease transmissions that are otherwise difficult to measure.

For many Americans, birthday celebrations have become a lot safer in the past few months. The Centers for Disease Control and Prevention say it is safe for fully vaccinated individuals to gather indoors without wearing face coverings. But for those who remain unvaccinated, the study is a reminder that even activities that feel safest pose a risk of infection. In many parts of the country, unvaccinated people are grouped by region or social group, which means birthday parties – and other such festive, private occasions – can still be risky.

Categories
Health

Greater than 600,000 folks have died from the virus within the U.S.

More than 600,000 people have died from the virus in the U.S.

A woman looks at the “Naming the Lost Memorials,” as US deaths from coronavirus disease (COVID-19) are expected to exceed 600,000, in Green Wood Cemetery in Brooklyn, New York, the United States, June 10, 2021 .

Brendan McDermid | Reuters

The US hit another dire milestone in the pandemic on Monday, hitting more than 600,000 Covid deaths, while the nation is delivering at least one vaccine by July 4th, which is given to 70% of adult Americans.

According to data from Johns Hopkins University, deaths in the US have been slowing for months, largely due to an aggressive campaign to vaccinate the elderly and medically vulnerable in the country who are most at risk of dying from Covid. About 76% of Americans 65 and older, who made up the majority of deaths from pandemics, were fully vaccinated, according to the Centers for Disease Control and Prevention.

Health workers perform CPR on a patient at a coronavirus disease (COVID-19) unit at the United Memorial Medical Center as the United States approaches 300,000 COVID-19 deaths on December 12, 2020 in Houston, Texas, United States. Image from December 12, 2020 2020.

Callaghan O’Hare | Reuters

Covid deaths in the US, which peaked in January with a daily average of more than 3,000 deaths, fell to a daily average of about 360 by Sunday, according to a seven-day average based on data from Johns Hopkins University based. The number of deaths has gradually decreased as vaccination rates have increased.

Pfizer-BioNTech and Moderna Covid vaccines were approved for emergency use by the Food and Drug Administration in December, followed by Johnson & Johnson in February.

Pfizer and Moderna’s vaccines, administered to nearly 300 million people, have shown greater than 90% effectiveness against the original “wild-type” covid strain. Studies have shown that the vaccines are still effective against some of the new variants that emerged last year, including the Delta variant first identified in India, but less so.

Johnson & Johnson has administered approximately 9 million doses of its single-use vaccine in the United States. The company’s vaccination was suspended by the FDA for 10 days in April after reports of rare blood clots surfaced in several patients.

The US has registered more Covid cases than any other country in the world – about 33.5 million cases, according to John Hopkins University. More than 176 million cases and more than 3.8 million deaths have been recorded worldwide.

As new varieties emerge that are more communicable and could potentially lead to more serious illnesses, federal health officials have been pushing young adults to get their vaccines too. Pfizer’s Covid vaccine received emergency youth approval last month.

President Joe Biden, his wife Jill Biden, U.S. Vice President Kamala Harris, and second gentleman Doug Emhoff attend a minute of silence and a candle-lighting ceremony to commemorate the grim milestone of 500,000 deaths in the U.S. from coronavirus disease (COVID-19) at the White House in Washington, USA, February 22, 2021.

Jonathan Ernst | Reuters

The effects of the pandemic were deeply felt in the United States. The national unemployment rate rose to 14.8% in April 2020, the highest since data collection began in 1948, when states across the country put lockdowns to control the outbreak, according to the Congressional Research Service.

Black, Hispanic and young workers were disproportionately affected by the bans. Throughout the pandemic, black workers had a peak unemployment rate of 16.7%, while Hispanic workers had a peak unemployment rate of 18.5%. Among white workers, the number peaked at 14.1%. As of May 2021, unemployment rates for black and Hispanic workers are still higher than those for white workers.

In February 2020, before most of the lockdowns, the US unemployment rate was 3.5%. Unemployment has improved but is still stubbornly high compared to previous years and stood at 5.8% in May.

Currently, more than half of the U.S. population, 174.2 million people, have received at least one shot of a Covid-19 vaccine, and about 44% of the population is fully vaccinated, according to the Centers for Disease Control and Prevention.

More than 64% of adults in the US have received at least one dose of vaccine, which is closer to an optimistic goal of at least partially immunizing 70% of all adults in the country by July 4th.

Correction: This story has been updated to correct the day the US exceeded 600,000 deaths in a bullet point at the beginning of the article. It was tuesday.

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Politics

Virus Scientist Kristian Andersen On Fauci Electronic mail and Lab-Leak Principle

Virus Scientist Kristian Andersen On Fauci Email and Lab-Leak Theory

Among the thousands of pages of Dr. Anthony S. Fauci’s emails released recently by BuzzFeed News, a short note from Kristian Andersen, a virologist at the Scripps Research Institute in La Jolla, Calif., has garnered a lot of attention.

Over the past year, Dr. Andersen has been one of the most outspoken proponents of the theory that the coronavirus originated from a natural spillover from an animal to humans outside of a lab. But in the email to Dr. Fauci in January 2020, Dr. Andersen hadn’t yet come to that conclusion. He told Dr. Fauci, the government’s top infectious disease expert, that some features of the virus made him wonder whether it had been engineered, and noted that he and his colleagues were planning to investigate further by analyzing the virus’s genome.

The researchers published those results in a paper in the scientific journal Nature Medicine on March 17, 2020, concluding that a laboratory origin was very unlikely. Dr. Andersen has reiterated this point of view in interviews and on Twitter over the past year, putting him at the center of the continuing controversy over whether the virus could have leaked from a Chinese lab.

When his early email to Dr. Fauci was released, the media storm around Dr. Andersen intensified, and he deactivated his Twitter account. He answered written questions from The New York Times about the email and the fracas. The exchange has been lightly edited for length.

Much has been made of your email to Dr. Fauci in late January 2020, shortly after the coronavirus genome was first sequenced. You said, “The unusual features of the virus make up a really small part of the genome (<0.1%) so one has to look really closely at all the sequences to see that some of the features (potentially) look engineered.”

Can you explain what you meant?

Kristian Andersen At the time, based on limited data and preliminary analyses, we observed features that appeared to potentially be unique to SARS-CoV-2. We had not yet seen these features in other related viruses from natural sources, and thus were exploring whether they had been engineered into the virus.

Those features included a structure known as the furin cleavage site that allows the SARS-CoV-2 spike protein to be cleaved by furin, an enzyme found in human cells, and another structure, known as the receptor binding domain, that allowed the virus to anchor to the outside of human cells via a cell-surface protein known as ACE2.

Credit…Scripps Research Institute

You also said you found the virus’s genome to be “inconsistent with expectations from evolutionary theory.”

Andersen This was a reference to the features of SARS-CoV-2 that we identified based on early analyses that didn’t appear to have an obvious immediate evolutionary precursor. We hadn’t yet performed more in-depth analyses to reach a conclusion, rather were sharing our preliminary observations.

I cautioned in that same email that we would need to look at the question much more closely and that our opinions could change within a few days based on new data and analyses — which they did.

In March, you and other scientists published the Nature Medicine paper saying that “we do not believe that any type of laboratory-based scenario is plausible.” Can you explain how the research changed your view?

Andersen The features in SARS-CoV-2 that initially suggested possible engineering were identified in related coronaviruses, meaning that features that initially looked unusual to us weren’t.

Many of these analyses were completed in a matter of days, while we worked around the clock, which allowed us to reject our preliminary hypothesis that SARS-CoV-2 might have been engineered, while other “lab”-based scenarios were still on the table.

Yet more extensive analyses, significant additional data and thorough investigations to compare genomic diversity more broadly across coronaviruses led to the peer-reviewed study published in Nature Medicine. For example, we looked at data from coronaviruses found in other species, such as bats and pangolins, which demonstrated that the features that first appeared unique to SARS-CoV-2 were in fact found in other, related viruses.

Overall, this is a textbook example of the scientific method where a preliminary hypothesis is rejected in favor of a competing hypothesis after more data become available and analyses are completed.

As you know, there has been a lot of speculation and hype over the past few weeks about a particular protein in the coronavirus: the furin cleavage site. Some people, including virologist David Baltimore, say the presence of this protein could be a sign of human manipulation of the virus, whereas you and other virologists have said it naturally evolved. Can you explain for readers why you don’t think it is proof of an engineered virus?

Andersen Furin cleavage sites are found all across the coronavirus family, including in the betacoronavirus genus that SARS-CoV-2 belongs to. There has been much speculation that patterns found in the virus’s RNA that are responsible for certain portions of the furin cleavage site represent evidence of engineering. Specifically, people are pointing to two “CGG” sequences that code for the amino acid arginine in the furin cleavage site as strong evidence that the virus was made in the lab. Such statements are factually incorrect.

While it’s true that CGG is less common than other patterns that code for arginine, the CGG codon is found elsewhere in the SARS-CoV-2 genome and the genetic sequence[s] that include the CGG codon found in SARS-CoV-2 are also found in other coronaviruses. These findings, together with many other technical features of the site, strongly suggest that it evolved naturally and there is very little chance somebody engineered it.

Do you still believe that all laboratory scenarios are implausible? If not an engineered virus, what about an accidental leak from the Wuhan lab?

Andersen As we stated in our article last March, it is currently impossible to prove or disprove specific hypotheses of SARS-CoV-2 origin. However, while both lab and natural scenarios are possible, they are not equally likely — precedence, data and other evidence strongly favor natural emergence as a highly likely scientific theory for the emergence of SARS-CoV-2, while the lab leak remains a speculative hypothesis based on conjecture.

Based on detailed analyses of the virus conducted to date by researchers around the world, it is extremely unlikely that the virus was engineered. The scenario in which the virus was found in nature, brought to the lab and then accidentally release[d] is similarly unlikely, based on current evidence.

In contrast, the scientific theory about the natural emergence of SARS-CoV-2 presents a far simpler and more likely scenario. The emergence of SARS-CoV-2 is very similar to that of SARS-CoV-1, including its seasonal timing, location and association with the human food chain.

Some people have pointed to your email to Dr. Fauci, suggesting that it raises questions about whether scientists and government officials gave more credence to the lab-leak theory than they let on to the public. And some recent reports have suggested that certain government officials didn’t want to talk about the lab-leak theory because it would draw attention to the government’s support of so-called gain-of-function research.

What is your response to these suggestions? Were you worried in the spring of 2020 about the public latching on to a lab-leak theory?

Andersen My primary concern last spring, which is true to this day, is to perform research to discern exactly how SARS-CoV-2 emerged in the human population.

I won’t speak to what government officials and other scientists did or didn’t say or think. My comments and conclusions are strictly driven by scientific inquiry, and I strongly believe that careful, well-supported public messaging around complex topics is paramount.

Many scientists have now expressed an openness to the possibility that a lab leak occurred. Looking back over the past year, do you have any regrets about the way you or the broader scientific community have communicated with the public about the lab-leak idea?

Andersen First, it is important to say that the scientific community has made tremendous inroads in understanding Covid-19 in a remarkably short amount of time. Vigorous debate is integral to science and that’s what we have seen regarding the origins of SARS-CoV-2.

It can be difficult at times for the public, I think, to observe the debate and discern the likelihood of the various hypotheses. That is particularly true where science becomes politicized, and the current vilification of scientists and subject matter experts sets a dangerous precedent. We saw that with the climate change debate and now we’re seeing it with the debate around various facets of the Covid-19 pandemic.

Throughout this pandemic, I have made my best efforts to help explain what the scientific evidence is and suggests, and I have no regrets about that.

Do you support President Biden’s call for U.S. intelligence agencies to further investigate these various possibilities? Could they find anything that would change your mind?

Andersen I have always supported further inquiries into the origin of SARS-CoV-2, including President Biden’s recent call, as it is important that we more fully understand how the virus emerged.

As is true for any scientific process, there are several things that would lend credence to the lab-leak hypothesis that would make me change my mind. For example, any credible evidence of SARS-CoV-2 having been at the Wuhan Institute of Virology prior to the pandemic — whether in a freezer, in tissue culture or in animals, or epidemiological evidence of very early confirmed Covid-19 cases associated with the institute.

Other evidence, were it to emerge, could lend further weight to the natural origin hypothesis. That includes the identification of an intermediate [animal] host (if one exists). Also, now that we know that live animals were sold at markets across Wuhan, further understanding of the flow of animals and connected supply lines could lend additional credence to natural emergence.

It seems that you’ve shut down your Twitter account. Why? Will you come back?

Andersen I have always seen Twitter as a way to interact with other scientists and the general public to encourage open and transparent dialogue about science.

Increasingly, however, I found that information and comments I posted were being taken out of context or misrepresented to push false narratives, in particular about the origins of SARS-CoV-2. Daily attacks against scientists and the scientific method have also become common, and much of the conversation has steered far away from the science.

For those reasons, I felt that at present, I could no longer productively contribute to the platform, and I decided it would be more productive for me to invest more of my time into our infectious disease research, including that on Covid-19.