Daily Archives: October 15, 2021

As the virus spread, more mutations sprang up, giving rise to even more transmissible variants. First came Alpha, which was about 50 percent more infectious than the original virus, and soon Delta, which was, in turn, roughly 50 percent more infectious than Alpha.

Now were basically in a Delta pandemic, said Robert Garry, a virologist at Tulane University. So another surge, another spread of a slightly better variant.

Although some experts were surprised to see the hyperinfectious variant, which has more than a dozen notable mutations, emerge so quickly, the appearance of more transmissible variants is textbook viral evolution.

Its hard to imagine that the virus is going to pop into a new species perfectly formed for that species, said Andrew Read, an evolutionary microbiologist at Penn State University. Its bound to do some adaptation.

But scientists dont expect this process to continue forever.

There are likely to be some basic biological limits on just how infectious a particular virus can become, based on its intrinsic properties. Viruses that are well adapted to humans, such as measles and the seasonal influenza, are not constantly becoming more infectious, Dr. Bloom noted.

It is not entirely clear what the constraints on transmissibility are, he added, but at the very least, the new coronavirus cannot replicate infinitely fast or travel infinitely far.

Transmission requires one person to somehow exhale or cough or breathe out the virus, and it to land in someone elses airway and infect them, Dr. Bloom said. There are just limits to that process. Its never going to be the case that Im sitting here in my office, and Im giving it to someone on the other side of Seattle, right?

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What the Future May Hold for the Coronavirus and Us - The New York Times

Tedros Adhanom Ghebreyesus, director general of the World Health Organization (WHO), speaks during a news conference on the COVID-19 coronavirus outbreak in Geneva, in March 2020. Stefan Wermuth/Bloomberg via Getty Images hide caption

Tedros Adhanom Ghebreyesus, director general of the World Health Organization (WHO), speaks during a news conference on the COVID-19 coronavirus outbreak in Geneva, in March 2020.

The World Health Organization has announced the establishment of a scientific advisory group aimed at identifying the origin of COVID-19 and to better prepare for future outbreaks of other deadly pathogens.

The WHO's Scientific Advisory Group for the Origins on Novel Pathogens, or SAGO, will include scientists from the U.S., China and about two dozen other countries. It will be charged with answering the question of how the novel coronavirus first infected humans a mystery that continues to elude experts more than 18 months into the crisis. The group will also be responsible for establishing a framework to combat future pandemics

Maria Van Kerkhove, the head of WHO's emerging disease unit, called the establishment of the new group "a real opportunity right now to get rid of all the noise, all the politics surrounding this and focus on what we know, what we don't know."

The team will be selected from more than 700 applications from experts in fields including epidemiology, animal health, ecology, clinical medicine, virology, genomics, molecular epidemiology, molecular biology, biology, food safety, biosafety, biosecurity and public health, the WHO said in a statement.

"The emergence of new viruses with the potential to spark epidemics and pandemics is a fact of nature, and while SARS-CoV-2 is the latest such virus, it will not be the last," WHO Director-General Dr. Tedros Adhanom Ghebreyesus said. "Understanding where new pathogens come from is essential for preventing future outbreaks with epidemic and pandemic potential, and requires a broad range of expertise."

The establishment of the group comes as China has continued to resist efforts to study the possible origin of the virus there. After an initial investigation by the WHO, Beijing rejected a plan for a second phase of the probe in July that might delve into various hypotheses about the origin of the virus, including that it escaped from a Chinese government lab in the city of Wuhan.

The so-called "lab-leak theory" was initially dismissed by WHO, but has nonetheless gained traction in recent months, fueled in part by Beijing's secrecy. Many scientists contend that a lab leak is much less likely than the alternative that the novel coronavirus has a natural origin.

Beijing did not immediately react to the announcement of the new task force.

Despite the WHO's initial findings, Tedros has called for audits of Wuhan laboratories, including the Wuhan Institute of Virology, which some scientists believe may be the source of the virus that caused the first infections in China.

Some of the proposed SAGO members were on the original 10-person WHO team that studied possible origins in China, including Chinese scientist Yungui Yang of the Beijing Institute of Genomics at the Chinese Academy of Sciences.

An editorial co-authored by Tedros that was published in Science on Wednesday said SAGO would "quickly assess the status of SARS-CoV-2 origin studies and advise WHO on what is known, the outstanding gaps, and next steps."

It said that "[all] hypotheses must continue to be examined," including the "studies of wildlife sold in markets in and around Wuhan, China (where cases of COVID-19 were first reported in December 2019); studies of SARS-like coronaviruses circulating in bats in China and Southeast Asia; studies on prepandemic biological sampling around the world; and other animal susceptibility studies."

"As well, laboratory hypotheses must be examined carefully, with a focus on labs in the location where the first reports of human infections emerged in Wuhan," it said, adding, "A lab accident cannot be ruled out until there is sufficient evidence to do so and those results are openly shared."

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WHO launches a new group to study the origins of the coronavirus - NPR

After a brutal summer surge, driven by the highly contagious Delta variant, the coronavirus is again in retreat.

The United States is recording roughly 90,000 new infections a day, down more than 40 percent since August. Hospitalizations and deaths are falling, too.

The crisis is not over everywhere the situation in Alaska is particularly dire but nationally, the trend is clear, and hopes are rising that the worst is finally behind us.

Again.

Over the past two years, the pandemic has crashed over the country in waves, inundating hospitals and then receding, only to return after Americans let their guard down.

It is difficult to tease apart the reasons that the virus ebbs and flows in this way, and harder still to predict the future.

But as winter looms, there are real reasons for optimism. Nearly 70 percent of adults are fully vaccinated, and many children under 12 are likely to be eligible for their shots in a matter of weeks. Federal regulators could soon authorize the first antiviral pill for Covid-19.

We are definitely, without a doubt, hands-down in a better place this year than we were last year, said Dr. Nahid Bhadelia, director of the Center for Emerging Infectious Diseases Policy and Research at Boston University.

But the pandemic is not over yet, scientists cautioned. Nearly 2,000 Americans are still dying every day, and another winter surge is plausible. Given how many Americans remain unvaccinated, and how much remains unknown, it is too soon to abandon basic precautions, they said.

Weve done this again and again, where we let the foot off the pedal too early, Dr. Bhadelia said. It behooves us to be a bit more cautious as were trying to get to that finish line.

When the first wave of cases hit the United States in early 2020, there was no Covid vaccine, and essentially no one was immune to the virus. The only way to flatten the proverbial curve was to change individual behavior.

That is what the first round of stay-at-home orders, business closures, mask mandates and bans on large gatherings aimed to do. There is still debate over which of these measures were most effective, but numerous studies suggest that, collectively, they made a difference, keeping people at home and curbing the growth of case numbers.

These policies, combined with voluntary social distancing, most likely helped bring the early surges to an end, researchers said.

And then the measures would be lifted, maybe memories would fade, said Jennifer Nuzzo, an epidemiologist at Johns Hopkins University.

Eventually, cases would rise again, and similar patterns would play out. Businesses and local governments would reimplement restrictions, while people who had begun venturing out into the world again would hunker down and mask up.

During last winters surge, for instance, the percentage of Americans who reported going to bars or restaurants or attending large events declined, according to the U.S. Covid-19 Trends and Impact Survey, which has surveyed an average of 44,000 Facebook users daily since April 2020.

The curve is shaped by public awareness, Dr. Nuzzo said. Were sort of lurching between crisis and complacency.

Delta arrived during a period of deep pandemic fatigue, and at a moment when many vaccinated Americans felt as though they could finally relax. Data suggests that the new variant prompted less profound behavioral change than previous waves.

In mid-July, just 23 percent of Americans said that they always wore a mask in public, the lowest percentage since March 2020, according to the Institute for Health Metrics and Evaluation at the University of Washington, which compiles data from several sources.

By Aug. 31, the peak of the Delta wave, that figure had risen to 41 percent, although it remained far below the 77 percent of people who reported wearing masks during the winter surge.

If you just look around, people are much more living a normal life or a pre-Covid life, said Dr. Christopher Murray, director of the institute.

Still, even modest changes in behavior can help slow transmission, especially in combination, and Delta prompted changes at both the individual and organizational levels. Schools adopted new precautions, companies postponed reopenings, and organizations canceled events, giving the virus fewer opportunities to spread.

Meanwhile, more temperate autumn weather arrived, making it possible for Americans in many regions of the country to socialize outside, where the virus is less likely to spread.

Oct. 15, 2021, 5:21 p.m. ET

Were in a shoulder season, where its cooler in the South than it is in the middle of the summer and its warmer in the North than it is in the middle of the winter, said David OConnor, a virologist at the University of Wisconsin-Madison.

Indeed, many of the current virus hot spots are in the northernmost parts of the country, from Alaska to Minnesota, where even cooler temperatures may be sending people back inside.

Behavioral change is a temporary, short-term way to drive cases down. The true end to the pandemic will come through immunity.

The Delta wave was the first major, national surge to occur after vaccines had become widely available, providing many adults with substantial protection against the virus. (Delta also probably led more Americans to get vaccinated.)

At the same time, the variant was so infectious that it spread rapidly through vulnerable populations, conferring natural immunity on many unvaccinated Americans.

Although neither vaccination nor prior infection provides perfect protection against the virus, they dramatically reduce the odds of catching it. So by September, the virus had a substantially harder time finding hospitable hosts.

Delta is running out of people to infect, said Jeffrey Shaman, an infectious disease epidemiologist at Columbia University.

The fact that case numbers are falling does not mean that the country has reached herd immunity, a goal that many scientists now believe is unattainable. But the rising levels of vaccination and infection, combined with more modest behavioral changes, may have been enough to bring the surge to an end.

Its a combination of immunity, but also people being careful, said Joshua Salomon, an infectious disease expert and modeler at Stanford University.

Indeed, scientists said that a combination of factors, which might be different in different parts of the country, would ultimately determine when and why the virus waxed and waned.

The different surges and waves depend on how big were the waves before that one, how many people have been vaccinated, when the schools reopened, the different variants, said Alessandro Vespignani, director of the Network Science Institute at Northeastern University in Boston.

There is some randomness involved, too, especially because small numbers of superspreaders seem to play a disproportionate role in setting off outbreaks. About 10 to 20 percent of the people are responsible for 80 to 90 percent of the infections, said Christina Ramirez, a biostatistician at the University of California, Los Angeles.

That means that two similar communities might find themselves on radically different trajectories simply because one highly infectious person happened to attend a crowded indoor event, fueling a major outbreak.

Some patterns still defy explanation. In March and April, for instance, Michigan was hit hard by the Alpha variant, Deltas slightly less infectious predecessor.

Other states were largely spared, for reasons that remain unclear, Dr. Murray said. Why was Michigan the only state with a large Alpha surge in spring? he said. We have no idea.

What comes next is hard to predict, but cases may not necessarily continue their steady decline, scientists warned.

Britain and Israel, which both have higher vaccination rates than the United States, are still struggling with outbreaks.

That should be a wake-up call, said Michael Osterholm, director of the Center for Infectious Disease Research and Policy at the University of Minnesota. Do not go back into the pre-Fourth-of-July mind-set again, where everybody thought it was done and over with.

Most experts said they would not be surprised to see at least a small increase in cases later this fall or this winter as people begin spending more time indoors and traveling for the holidays.

But because the vaccines remain highly effective at preventing hospitalization and death, any coming winter spikes may be less catastrophic than last years.

Its not likely that it will be as deadly as the surge we had last winter, unless we get really unlucky with respect to a new variant, Dr. Salomon said.

The emergence of a new variant remains a wild card, as does the possibility that the protection afforded by vaccination could start to wane more substantially.

Our own behavior is another source of uncertainty.

Predicting an outbreak is not like predicting the weather, because youre dealing with human behavior, said Nicholas Reich, a biostatistician at the University of Massachusetts, Amherst. And thats a fundamentally really hard thing to predict: new policies that would come into force, peoples reactions to them, new trends on social media, you know the list goes on and on.

But our behavior is, at least, under our control, and it remains a critical variable as we head into the winter, scientists said. By and large, they did not recommend canceling holiday plans; many said they themselves would be celebrating with friends and relatives. But they did suggest taking sensible precautions.

There is still time to be vaccinated or encourage loved ones to be vaccinated before Thanksgiving. Wearing masks in certain high-risk settings, hosting events outdoors when the weather is nice and taking rapid Covid tests before holiday gatherings are all common-sense strategies for reducing risk, experts said.

It doesnt mean Lockdown Christmas No. 2, said Angela Rasmussen, a virologist at the Vaccine and Infectious Disease Organization at the University of Saskatchewan. But it does mean that we should all just be mindful that this is not completely over yet.

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Lurching Between Crisis and Complacency: Was This Our Last Covid Surge? - The New York Times

In the summer of 2020, half a year into the coronavirus pandemic, scientists traveled into the forests of northern Laos to catch bats that might harbor close cousins of the pathogen.

In the dead of night, they used mist nets and canvas traps to snag the animals as they emerged from nearby caves, gathered samples of saliva, urine and feces, then released them back into the darkness.

The fecal samples turned out to contain coronaviruses, which the scientists studied in high security biosafety labs, known as BSL-3, using specialized protective gear and air filters.

Three of the Laos coronaviruses were unusual: They carried a molecular hook on their surface that was very similar to the hook on the virus that causes Covid-19, called SARS-CoV-2. Like SARS-CoV-2, their hook allowed them to latch onto human cells.

It is even better than early strains of SARS-CoV-2, said Marc Eloit, a virologist at the Pasteur Institute in Paris who led the study, referring to how well the hook on the Laos coronaviruses binds to human cells. The study was posted online last month and has not yet been published in a scientific journal.

Virus experts are buzzing about the discovery. Some suspect that these SARS-CoV-2-like viruses may already be infecting people from time to time, causing only mild and limited outbreaks. But under the right circumstances, the pathogens could give rise to a Covid-19-like pandemic, they say.

The findings also have significant implications for the charged debate over Covids origins, experts say. Some people have speculated that SARS-CoV-2s impressive ability to infect human cells could not have evolved through a natural spillover from an animal. But the new findings seem to suggest otherwise.

That really puts to bed any notion that this virus had to have been concocted, or somehow manipulated in a lab, to be so good at infecting humans, said Michael Worobey, a University of Arizona virologist who was not involved in the work.

These bat viruses, along with more than a dozen others discovered in recent months in Laos, Cambodia, China and Thailand, may also help researchers better anticipate future pandemics. The viruses family trees offer hints about where potentially dangerous strains are lurking, and which animals scientists should look at to find them.

Last week, the U.S. government announced a $125 million project to identify thousands of wild viruses in Asia, Latin America and Africa to determine their risk of spillover. Dr. Eloit predicted that there were many more relatives of SARS-CoV-2 left to find.

I am a fly fisherman, he said. When I am unable to catch a trout, that doesnt mean there are no trout in the river.

When SARS-CoV-2 first came to light, its closest known relative was a bat coronavirus that Chinese researchers found in 2016 in a mine in southern Chinas Yunnan Province. RaTG13, as it is known, shares 96 percent of its genome with SARS-CoV-2. Based on the mutations carried by each virus, scientists have estimated that RaTG13 and SARS-CoV-2 share a common ancestor that infected bats about 40 years ago.

Both viruses infect cells by using a molecular hook, called the receptor-binding domain, to latch on to their surface. RaTG13s hook, adapted for attaching to bat cells, can only cling weakly to human cells. SARS-CoV-2s hook, by contrast, can clasp cells in the human airway, the first step toward a potentially lethal case of Covid-19.

To find other close relatives of SARS-CoV-2, wildlife virus experts checked their freezers full of old samples from across the world. They identified several similar coronaviruses from southern China, Cambodia, and Thailand. Most came from bats, while a few came from scaly mammals known as pangolins. None was a closer relative than RaTG13.

Oct. 15, 2021, 5:21 p.m. ET

Dr. Eloit and his colleagues instead set out to find new coronaviruses.

They traveled to northern Laos, about 150 miles from the mine where Chinese researchers had found RaTG13. Over six months they caught 645 bats, belonging to 45 different species. The bats harbored two dozen kinds of coronaviruses, three of which were strikingly similar to SARS-CoV-2 especially in the receptor-binding domain.

In RaTG13, 11 of the 17 key building blocks of the domain are identical to those of SARS-CoV-2. But in the three viruses from Laos, as many as 16 were identical the closest match to date.

Dr. Eloit speculated that one or more of the coronaviruses might be able to infect humans and cause mild disease. In a separate study, he and colleagues took blood samples from people in Laos who collect bat guano for a living. Although the Laotians did not show signs of having been infected with SARS-CoV-2, they carried immune markers, called antibodies, that appeared to be caused by a similar virus.

Linfa Wang, a molecular virologist at the Duke-NUS Medical School in Singapore who was not involved in the study, agreed that such an infection was possible, since the newly discovered viruses can attach tightly to a protein on human cells called ACE2.

If the receptor binding domain is ready to use ACE2, these guys are dangerous, Dr. Wang said.

Paradoxically, some other genes in the three Laotian viruses are more distantly related to SARS-CoV-2 than other bat viruses. The cause of this genetic patchwork is the complex evolution of coronaviruses.

If a bat infected with one coronavirus catches a second one, the two different viruses may end up in a single cell at once. As that cell begins to replicate each of those viruses, their genes get shuffled together, producing new virus hybrids.

In the Laotian coronaviruses, this gene shuffling has given them a receptor-binding domain thats very similar to that of SARS-CoV-2. The original genetic swap took place about a decade ago, according to a preliminary analysis by Spyros Lytras, a graduate student at the University of Glasgow in Scotland.

Mr. Lytras and his colleagues are now comparing SARS-CoV-2 not just to the new viruses from Laos, but to other close relatives that have been found in recent months. Theyre finding even more evidence of gene shuffling. This process known as recombination may be reshaping the viruses from year to year.

Its becoming more and more obvious how important recombination is, Mr. Lytras said.

He and his colleagues are now drawing the messy evolutionary trees of SARS-CoV-2-like viruses based on these new insights. Finding more viruses could help clear up the picture. But scientists are divided as to where to look for them.

Dr. Eloit believes the best bet is a zone of Southeast Asia that includes the site where his colleagues found their coronaviruses, as well as the nearby mine in Yunnan where RaTG13 was found.

I think the main landscape corresponds to north Vietnam, north Laos and south China, Dr. Eloit said.

The U.S. governments new virus-hunting project, called DEEP VZN, may turn up one or more SARS-CoV-2-like viruses in that region. A spokesman for USAID, the agency funding the effort, named Vietnam as one of the countries where researchers will be searching, and said that new coronaviruses are one of their top priorities.

Other scientists think its worth looking for relatives of SARS-CoV-2 further afield. Dr. Worobey of the University of Arizona said that some bat coronaviruses carrying SARS-CoV-2-like segments have been found in eastern China and Thailand.

Clearly the recombination is showing us that these viruses are part of a single gene pool over hundreds and hundreds of miles, if not thousands of miles, Dr. Worobey said.

Colin Carlson, a biologist at Georgetown University, suspects that a virus capable of producing a Covid-like outbreak might be lurking even further away. Bats as far east as Indonesia and as far west as India, he noted, share many biological features with the animals known to carry SARS-CoV-2-like viruses.

This is not just a Southeast Asia problem, Dr. Carlson said. These viruses are diverse, and they are more cosmopolitan than we have thought.

The interest in the origins of the pandemic has put renewed attention on the safety measures researchers are using when studying potentially dangerous viruses. To win DEEP VZN grants, scientists will have to provide a biosafety and biosecurity plan, according to a USAID spokesman, including training for staff, guidelines on protective equipment to be worn in the field and safety measures for lab work.

If scientists find more close cousins of SARS-CoV-2, it doesnt necessarily mean they pose a deadly threat. They might fail to spread in humans or, as some scientists speculate, cause only small outbreaks. Just seven coronaviruses are known to have jumped the species barrier to become well-established human pathogens.

Theres probably a vast range of other coronaviruses that end up going nowhere, said Jessica Metcalf, an evolutionary ecologist at Princeton University.

Still, recombination may be able to turn a virus going nowhere into a new threat. In May, researchers reported that two coronaviruses in dogs recombined in Malaysia. The result was a hybrid that infected eight children.

When a coronavirus that we have monitored for decades, that we think of as just something our pets can get, can make the jump we should have seen that coming, right? Dr. Carlson said.

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Newly Discovered Bat Viruses Give Hints to Covids Origins - The New York Times