Science
New genetic research points to Wuhan animal market as origin of COVID pandemic, study says
A new analysis of genetic material gathered from a live-animal market in Wuhan in the early weeks of the COVID-19 pandemic strengthens the case that the outbreak originated there when the coronavirus jumped from infected animals to humans, scientists said.
The findings, reported the journal Cell, do not identify any specific infected animal that brought the SARS-CoV-2 virus to a Chinese city inhabited by more than 11 million people. Nor do they definitively prove that the Huanan Seafood Wholesale Market was Ground Zero for a pandemic that has resulted in more than 7 million deaths.
But the genetic evidence shows the market met the conditions necessary to spark an outbreak and makes it increasingly difficult to explain how the coronavirus could have emerged from a laboratory, a farm or even from another of the city’s four live-animal markets, the study authors said.
“It’s like if a gorilla virus emerged in San Diego and first hit people who worked at the San Diego Zoo and lived nearby, then spread later more widely,” said Michael Worobey, an evolutionary biologist at the University of Arizona who worked on the study. “It would not be difficult to reason that it very likely came from the gorillas at the zoo.”
The root cause of the pandemic has been hotly debated since its early days. Wuhan is home to a government laboratory where scientists study coronaviruses similar to SARS-CoV-2, a fact that prompted politicians, national security experts, late-night talk show hosts and many scientists — including Worobey — to question whether the virus had leaked from the lab.
Compelling though the argument may be, hard evidence to support the leak hypothesis has been lacking. Meanwhile, more information has come to light that has persuaded scientists with expertise in relevant fields that the virus that causes COVID-19 originated in animals, just like the viruses that cause SARS, MERS and influenza.
The new results continue that trend, said Dr. Dominic Dwyer, a member of the international task force that investigated the pandemic’s origins for the World Health Organization.
“You put all of these origin hypotheses on the table, and then some of them become stronger as you get evidence,” said Dwyer, a medical virologist at the University of Sydney and Westmead Hospital in Australia who wasn’t involved in the latest work. “This paper has more evidence that supports the animal origin through the Huanan market.”
The analysis published Thursday was based on genetic data gleaned from hundreds of samples gathered in and around the Huanan market collected by researchers from the Chinese Center for Disease Control and Prevention soon after the market was shut down on Jan. 1, 2020. The Chinese team detected the coronavirus in 74 of the environmental samples they tested, according to their report last year in the journal Nature.
Worobey and his colleagues dug deeper into that data. Using two distinct gene-sequencing techniques, they looked for pieces of SARS-CoV-2 as well as for DNA from animals and people.
Then they plotted what they found on a map of the sprawling market, allowing the team to reconstruct how a few initial infections could have ballooned into a global health emergency.
Among 585 samples gathered in early January 2020, the ones that contained the coronavirus were clustered in the southwestern section of the market. That happened to be the area where wild animals were held in cages for sale.
“The market covers a couple of acres, and this comes down to one corner of the market, and to a couple of stalls,” Dwyer said. “That fits with an animal origin. If it was coming from people wandering around the market, you’d find it everywhere.”
One market stall “stood out,” the study authors wrote. It had evidence of SARS-CoV-2 in multiple places: on at least one cart, on an iron container, on the ground, and on a machine used to remove hair and feathers. The researchers dubbed it “wildlife stall A.”
Another 60 samples were taken from the market’s drainage system at the end of January 2020. The researchers found genetic evidence of the coronavirus in four of them, including one in front of wildlife stall A.
That drain was still testing positive for SARS-CoV-2 in mid-February. So were two drains downstream from it that could have been contaminated by runoff from wildlife stall A, the researchers wrote.
The samples from the stall that contained the coronavirus also contained DNA from a variety of animals, including dogs, rabbits, hoary bamboo rats, Malayan porcupines and masked palm civets. The most abundant DNA was from raccoon dogs, and some was detected in a nearby garbage cart that also tested positive for the virus.
The closest-known relatives to SARS-CoV-2 that exist in the wild are coronaviruses that circulate in horseshoe bats in southern China, Laos and Vietnam and in pangolins from southern China. But no DNA from bats or pangolins turned up in any of the Huanan market samples.
Raccoon dogs, masked palm civets, hoary bamboo rats and Malayan porcupines have transmitted bat coronaviruses before, the study authors noted. Could they have done so in Wuhan, they wondered?
It is unclear whether bamboo rats or Malayan porcupines can be infected with SARS-CoV-2, the study authors wrote. There is no hard evidence that masked palm civets can catch the virus, but cell lines from the animals were susceptible in laboratory experiments.
Raccoon dogs, on the other hand, are known to catch and transmit SARS-CoV-2. And they were the most abundant animal in wildlife stall A.
The researchers dug into the raccoon dog DNA to see if they could have come from southern China, where they might have crossed paths with bats. They couldn’t tell, but they were able to rule out a connection to raccoon dogs that lived on fur farms in northern China.
Worobey and his colleagues also studied non-SARS-CoV-2 animal viruses that were detected in wildlife stalls to see if they offered clues about where the infected animals had come from.
A kobuvirus that infected civets in the Huanan market was closely related to a virus detected in animals sold in Sichuan and Guangxi provinces, which are closer to the territory of horseshoe bats and pangolins. And a betacoronavirus that infected bamboo rats had a close relative on a bamboo rat farm in Guangxi, one of two southern provinces where market vendors were known to have sourced the animals.
“These findings suggest some movement of infected animals from southern China to Wuhan, a trade conduit that could have also led to the emergence of SARS-CoV-2,” the study authors wrote.
Nailing this down will require more sleuthing, including field work to collect samples from animals in China, said Florence Débarre, an evolutionary biologist at the French National Centre for Scientific Research in Paris and the study’s senior author. Worobey said he plans to continue this line of inquiry.
Dwyer praised the effort to determine where the animals in the market had come from — and by extension, how the virus could have gotten to the market.
A second line of evidence also supports the hypothesis that the pandemic had a so-called zoonotic origin, scientists said.
Among the samples collected at the Huanan market on Jan. 1, 2020, the researchers were able to identify four nearly complete SARS-CoV-2 genomes. One of them was from so-called lineage A, and the other three were from the closely related lineage B.
The researchers weren’t able to tell whether those viruses were shed by animals or people, but the lineage A sample came from a stall where a worker sought medical attention in mid-December 2019. Although that was weeks before COVID-19 had been recognized as a disease, a report from the World Health Organization later described the worker as a suspected early patient.
Confirming the presence of both lineages in the market allowed the team to compare their genomes and work backward to figure out when the two strains diverged, and what their most recent common ancestor looked like. They came up with six candidates, some of them more plausible than others.
There was a 99% probability that one of the four most likely candidates was correct, and those four all had something important in common: They were “equivalent or identical” to the most recent common ancestor for the pandemic as a whole, said study leader Alexander Crits-Christoph, an independent computational microbiologist.
That’s what they would expect to find if the outbreak began at the Huanan market, the study authors said. In that scenario, an animal or animals infected with the virus arrived at the market in November or early December. The virus then spread among animals held in close quarters indoors, as well as to their human handlers. Those conditions would have given the virus the multiple chances it needed to establish itself in people and begin spreading among its new hosts in a densely populated city.
On the other hand, it’s getting more difficult to fit all of this evidence into a coherent story that has the coronavirus entering China via imported frozen food (as the Chinese government has claimed) or escaping from a virology lab with lax biosecurity protocols (as some members of the U.S. intelligence community have proposed), Dwyer said.
“We’ve had nothing added to support the lab leak or the frozen food theories,” he said. “It just continues to strengthen the animal and market hypothesis.”
Considering that the pandemic began in a city with a virology lab where scientists study coronaviruses, it makes sense to ask whether that’s more than a coincidence and to wonder whether incriminating evidence is being covered up, DéBarre said.
“Many of us were extremely open to this idea,” she said. “But then data have accumulated, and they all go in the same direction — they all point to the market.”
“In science you very rarely have final answers,” she added. “You say, ‘Given all the data we have, this looks like the most likely interpretation.’”
Science
Political stress: Can you stay engaged without sacrificing your mental health?
It’s been two weeks since Donald Trump won the presidential election, but Stacey Lamirand’s brain hasn’t stopped churning.
“I still think about the election all the time,” said the 60-year-old Bay Area resident, who wanted a Kamala Harris victory so badly that she flew to Pennsylvania and knocked on voters’ doors in the final days of the campaign. “I honestly don’t know what to do about that.”
Neither do the psychologists and political scientists who have been tracking the country’s slide toward toxic levels of partisanship.
Fully 69% of U.S. adults found the presidential election a significant source of stress in their lives, the American Psychological Assn. said in its latest Stress in America report.
The distress was present across the political spectrum, with 80% of Republicans, 79% of Democrats and 73% of independents surveyed saying they were stressed about the country’s future.
That’s unhealthy for the body politic — and for voters themselves. Stress can cause muscle tension, headaches, sleep problems and loss of appetite. Chronic stress can inflict more serious damage to the immune system and make people more vulnerable to heart attacks, strokes, diabetes, infertility, clinical anxiety, depression and other ailments.
In most circumstances, the sound medical advice is to disengage from the source of stress, therapists said. But when stress is coming from politics, that prescription pits the health of the individual against the health of the nation.
“I’m worried about people totally withdrawing from politics because it’s unpleasant,” said Aaron Weinschenk, a political scientist at the University of Wisconsin–Green Bay who studies political behavior and elections. “We don’t want them to do that. But we also don’t want them to feel sick.”
Modern life is full of stressors of all kinds: paying bills, pleasing difficult bosses, getting along with frenemies, caring for children or aging parents (or both).
The stress that stems from politics isn’t fundamentally different from other kinds of stress. What’s unique about it is the way it encompasses and enhances other sources of stress, said Brett Ford, a social psychologist at the University of Toronto who studies the link between emotions and political engagement.
For instance, she said, elections have the potential to make everyday stressors like money and health concerns more difficult to manage as candidates debate policies that could raise the price of gas or cut off access to certain kinds of medical care.
Layered on top of that is the fact that political disagreements have morphed into moral conflicts that are perceived as pitting good against evil.
“When someone comes into power who is not on the same page as you morally, that can hit very deeply,” Ford said.
Partisanship and polarization have raised the stakes as well. Voters who feel a strong connection to a political party become more invested in its success. That can make a loss at the ballot box feel like a personal defeat, she said.
There’s also the fact that we have limited control over the outcome of an election. A patient with heart disease can improve their prognosis by taking medicine, changing their diet, getting more exercise or quitting smoking. But a person with political stress is largely at the mercy of others.
“Politics is many forms of stress all rolled into one,” Ford said.
Weinschenk observed this firsthand the day after the election.
“I could feel it when I went into my classroom,” said the professor, whose research has found that people with political anxiety aren’t necessarily anxious in general. “I have a student who’s transgender and a couple of students who are gay. Their emotional state was so closed down.”
That’s almost to be expected in a place like Wisconsin, whose swing-state status caused residents to be bombarded with political messages. The more campaign ads a person is exposed to, the greater the risk of being diagnosed with anxiety, depression or another psychological ailment, according to a 2022 study in the journal PLOS One.
Political messages seem designed to keep voters “emotionally on edge,” said Vaile Wright, a licensed psychologist in Villa Park, Ill., and a member of the APA’s Stress in America team.
“It encourages emotion to drive our decision-making behavior, as opposed to logic,” Wright said. “When we’re really emotionally stimulated, it makes it so much more challenging to have civil conversation. For politicians, I think that’s powerful, because emotions can be very easily manipulated.”
Making voters feel anxious is a tried-and-true way to grab their attention, said Christopher Ojeda, a political scientist at UC Merced who studies mental health and politics.
“Feelings of anxiety can be mobilizing, definitely,” he said. “That’s why politicians make fear appeals — they want people to get engaged.”
On the other hand, “feelings of depression are demobilizing and take you out of the political system,” said Ojeda, author of “The Sad Citizen: How Politics is Depressing and Why it Matters.”
“What [these feelings] can tell you is, ‘Things aren’t going the way I want them to. Maybe I need to step back,’” he said.
Genessa Krasnow has been seeing a lot of that since the election.
The Seattle entrepreneur, who also campaigned for Harris, said it grates on her to see people laughing in restaurants “as if nothing had happened.” At a recent book club meeting, her fellow group members were willing to let her vent about politics for five minutes, but they weren’t interested in discussing ways they could counteract the incoming president.
“They’re in a state of disengagement,” said Krasnow, who is 56. She, meanwhile, is looking for new ways to reach young voters.
“I am exhausted. I am so sad,” she said. “But I don’t believe that disengaging is the answer.”
That’s the fundamental trade-off, Ojeda said, and there’s no one-size-fits-all solution.
“Everyone has to make a decision about how much engagement they can tolerate without undermining their psychological well-being,” he said.
Lamirand took steps to protect her mental health by cutting social media ties with people whose values aren’t aligned with hers. But she will remain politically active and expects to volunteer for phone-banking duty soon.
“Doing something is the only thing that allows me to feel better,” Lamirand said. “It allows me to feel some level of control.”
Ideally, Ford said, people would not have to choose between being politically active and preserving their mental health. She is investigating ways to help people feel hopeful, inspired and compassionate about political challenges, since these emotions can motivate action without triggering stress and anxiety.
“We want to counteract this pattern where the more involved you are, the worse you are,” Ford said.
The benefits would be felt across the political spectrum. In the APA survey, similar shares of Democrats, Republicans and independents agreed with statements like, “It causes me stress that politicians aren’t talking about the things that are most important to me,” and, “The political climate has caused strain between my family members and me.”
“Both sides are very invested in this country, and that is a good thing,” Wright said. “Antipathy and hopelessness really doesn’t serve us in the long run.”
Science
Video: SpaceX Unable to Recover Booster Stage During Sixth Test Flight
President-elect Donald Trump joined Elon Musk in Texas and watched the launch from a nearby location on Tuesday. While the Starship’s giant booster stage was unable to repeat a “chopsticks” landing, the vehicle’s upper stage successfully splashed down in the Indian Ocean.
Science
Alameda County child believed to be latest case of bird flu; source unknown
California health officials reported Tuesday that a child in Alameda County tested positive for H5 bird flu last week.
The source of infection is not known — although health officials are looking into possible contact with wild birds — and the child is recovering at home with mild upper respiratory symptoms.
Health officials have confirmed the “H5” part of the virus, not the “N1.” There is no human “H5” flu; it is only associated with birds.
The child was treated with antiviral medication, and the sample was sent to the U.S. Centers for Disease Control and Prevention for confirmatory testing.
The initial test showed low levels of the virus and, according to the state health agency, testing four days later showed no virus.
“The more cases we find that have no known exposure make it difficult to prevent additional” infections, said Jennifer Nuzzo, professor of epidemiology and director of the Brown University School of Public Health’s Pandemic Center. “It worries me greatly that this virus is popping up in more and more places and that we keep being surprised by infections in people whom we wouldn’t think would be at high risk of being exposed to the virus.”
A statement from the California Department of Public Health said that none of the child’s family members have the virus, although they, too, had mild respiratory symptoms. They are also being treated with antiviral medication.
The child attended a day care while displaying symptoms. People the child may have had contact with have been notified and are being offered preventative antiviral medication and testing.
“It’s natural for people to be concerned, and we want to reinforce for parents, caregivers and families that based on the information and data we have, we don’t think the child was infectious — and no human-to-human spread of bird flu has been documented in any country for more than 15 years,” said CDPH Director and State Public Health Officer Dr. Tomás Aragón.
The case comes days after the state health agency announced the discovery of six new bird flu cases, all in dairy workers. The total number of confirmed human cases in California is 27. This new case will bring it to 28, if confirmed. This is the first human case in California that is not associated with the dairy industry.
The total number of confirmed human cases in the U.S., including the Alameda County child, now stands at 54. Thirty-one are associated with dairy industry, 21 with the poultry industry, and now two with unknown sources.
In Canada, a teenager is in critical condition with the disease. The source of that child’s infection is also unknown.
Genetic sequencing of the Canadian teenager’s virus shows mutations that may make it more efficient at moving between people. The Canadian virus is also a variant of H5N1 that has been associated with migrating wild birds, not cattle.
Genetic sequencing of the California child’s virus has not been released, so it is unclear if it is of wild bird origin, or the one moving through the state’s dairy herds.
In addition, WastewaterScan — an infectious disease monitoring network led by researchers from Stanford University and Emory University, with laboratory support from Verily, Alphabet Inc.’s life sciences organization — follows 28 wastewater sites in California. All but six have shown detectable amounts of H5 in the last couple of weeks.
There are no monitoring sites in Alameda Co., but positive hits have been found in several Bay Area wastewater districts, including San Francisco, Redwood City, Sunnyvale, San Jose and Napa.
“This just makes the work of protecting people from this virus and preventing it from mutating to cause a pandemic that much harder,” said Nuzzo.
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