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
FDA sets limits for lead in many baby foods as California disclosure law takes effect
The U.S. Food and Drug Administration this week set maximum levels for lead in baby foods such as jarred fruits and vegetables, yogurts and dry cereal, part of an effort to cut young kids’ exposure to the toxic metal that causes developmental and neurological problems.
The agency issued final guidance that it estimated could reduce lead exposure from processed baby foods by about 20% to 30%. The limits are voluntary, not mandatory, for food manufacturers, but they allow the FDA to take enforcement action if foods exceed the levels.
It’s part of the FDA’s ongoing effort to “reduce dietary exposure to contaminants, including lead, in foods to as low as possible over time, while maintaining access to nutritious foods,” the agency said in a statement.
Consumer advocates, who have long sought limits on lead in children’s foods, welcomed the guidance first proposed two years ago, but said it didn’t go far enough.
“FDA’s actions today are a step forward and will help protect children,” said Thomas Galligan, a scientist with the Center for Science in the Public Interest. “However, the agency took too long to act and ignored important public input that could have strengthened these standards.”
The new limits on lead for children younger than 2 don’t cover grain-based snacks such as puffs and teething biscuits, which some research has shown contain higher levels of lead. And they don’t limit other metals such as cadmium that have been detected in baby foods.
The FDA’s announcement comes just one week after a new California law took effect that requires baby food makers selling products in California to provide a QR code on their packaging to take consumers to monthly test results for the presence in their product of four heavy metals: lead, mercury, arsenic and cadmium.
The change, required under a law passed by the California Legislature in 2023, will affect consumers nationwide. Because companies are unlikely to create separate packaging for the California market, QR codes are likely to appear on products sold across the country, and consumers everywhere will be able to view the heavy metal concentrations.
Although companies are required to start printing new packaging and publishing test results of products manufactured beginning in January, it may take time for the products to hit grocery shelves.
The law was inspired by a 2021 congressional investigation that found dangerously high levels of heavy metals in packaged foods marketed for babies and toddlers. Baby foods and their ingredients had up to 91 times the arsenic level, up to 177 times the lead level, up to 69 times the cadmium level, and up to five times the mercury level that the U.S. allows to be present in bottled or drinking water, the investigation found.
There’s no safe level of lead exposure for children, according to the U.S. Centers for Disease Control and Prevention. The metal causes “well-documented health effects,” including brain and nervous system damage and slowed growth and development. However, lead occurs naturally in some foods and comes from pollutants in air, water and soil, which can make it impossible to eliminate entirely.
The FDA guidance sets a lead limit of 10 parts per billion for fruits, most vegetables, grain and meat mixtures, yogurts, custards and puddings and single-ingredient meats. It sets a limit of 20 parts per billion for single-ingredient root vegetables and for dry infant cereals. The guidance covers packaged processed foods sold in jars, pouches, tubs or boxes.
Jaclyn Bowen, executive director of the Clean Label Project, an organization that certifies baby foods as having low levels of toxic substances, said consumers can use the new FDA guidance in tandem with the new California law: The FDA, she said, has provided parents a “hard and fast number” to consider a benchmark when looking at the new monthly test results.
But Brian Ronholm, director of food policy for Consumer Reports, called the FDA limits “virtually meaningless because they’re based more on industry feasibility and not on what would best protect public health.” A product with a lead level of 10 parts per billion is “still too high for baby food. What we’ve heard from a lot of these manufacturers is they are testing well below that number.”
The new FDA guidance comes more than a year after lead-tainted pouches of apple cinnamon puree sickened more than 560 children in the U.S. between October 2023 and April 2024, according to the CDC.
The levels of lead detected in those products were more than 2,000 times higher than the FDA’s maximum. Officials stressed that the agency doesn’t need guidance to take action on foods that violate the law.
Aleccia writes for the Associated Press. Gold reports for The Times’ early childhood education initiative, focusing on the learning and development of California children from birth to age 5. For more information about the initiative and its philanthropic funders, go to latimes.com/earlyed.
Science
NASA punts Mars Sample Return decision to the next administration
Anyone hoping for a clear path forward this year for NASA’s imperiled Mars Sample Return mission will have to wait a little longer.
The agency has settled on two potential strategies for the first effort to bring rock and soil from another planet back to Earth for study, NASA Administrator Bill Nelson said Tuesday: It can either leverage existing technology into a simpler, cheaper craft or turn to a commercial partner for a new design.
But the final decision on the mission’s structure — or whether it should proceed at all — “is going to be a function of the new administration,” Nelson said. President-elect Donald Trump will take office Jan. 20.
“I don’t think we want the only [Mars] sample return coming back on a Chinese spacecraft,” Nelson said, referencing a rival mission that Beijing has in the works. “I think that the [Trump] administration will certainly conclude that they want to proceed. So what we wanted to do was to give them the best possible options so that they can go from there.”
The call also contained words of encouragement for NASA’s Jet Propulsion Laboratory in La Cañada Flintridge, which leads the embattled mission’s engineering efforts.
“To put it really bluntly, JPL is our Mars center in NASA science,” said Nicky Fox, associate administrator of the Science Mission Directorate. “They are the people who landed us on Mars, together with our industry partners. So they will be moving forward, regardless of which path, with a key role in the Mars Sample Return.”
In April, after an independent review found “near zero probability” of Mars Sample Return making its proposed 2028 launch date, NASA put out a request for alternative proposals to all of its centers and the private sector. JPL was forced to compete for what had been its own project.
The independent review board determined that the original design would probably cost up to $11 billion and not return samples to Earth until at least 2040.
“That was just simply unacceptable,” said Nelson, who paused the mission in late 2023 to review its chances of success.
Ensuing cuts to the mission’s budget forced a series of layoffs at JPL, which let go of 855 employees and 100 on-site contractors in 2024.
The NASA-led option that Nelson suggested Tuesday includes several elements from the JPL proposal, according to a person who reviewed the documents. This leaner, simpler alternative will cost between $6.6 billion and $7.7 billion, and will return the samples by 2039, he said. A commercial alternative would probably cost $5.8 billion to $7.1 billion.
Nelson, a former Democratic U.S. senator from Florida, will step down as head of the space agency when Trump takes office. Trump has nominated as his successor Jared Isaacman, a tech billionaire who performed the first private space walk, who must be confirmed by the Senate.
NASA has not had any conversations with Trump’s transition team about Mars Sample Return, Nelson said. How the new administration will prioritize the project is not yet clear.
“It’s very uncertain how the new administration will go forward,” said Casey Dreier, chief of space policy for the Planetary Society, a Pasadena nonprofit that promotes space research. “Cancellation is obviously still on the table. … It’s hard to game this out.”
Planetary scientists have identified Mars Sample Return as their field’s highest priority in the last three decadal surveys, reports that the National Academies of Sciences, Engineering, and Medicine prepare every 10 years in order to advise NASA.
Successfully completing the mission is “key for the nation’s leadership in space science,” said Bethany L. Ehlmann, a planetary scientist at Caltech in Pasadena. “I hope the incoming administrator moves forward decisively to select a plan and execute. There are extraordinary engineers at JPL and NASA industry partners eager and able to get to work to make it happen.”
Science
Panama Canal’s Expansion Opened Routes for Fish to Relocate
Night fell as the two scientists got to work, unfurling long nets off the end of their boat. The jungle struck up its evening symphony: the sweet chittering of insects, the distant bellowing of monkeys, the occasional screech of a kite. Crocodiles lounged in the shallows, their eyes glinting when headlamps were shined their way.
Across the water, cargo ships made dark shapes as they slid between the seas.
The Panama Canal has for more than a century connected far-flung peoples and economies, making it an essential artery for global trade — and, in recent weeks, a target of President-elect Donald J. Trump’s expansionist designs.
But of late the canal has been linking something else, too: the immense ecosystems of the Atlantic and the Pacific.
The two oceans have been separated for some three million years, ever since the isthmus of Panama rose out of the water and split them. The canal cut a path through the continent, yet for decades only a handful of marine fish species managed to migrate through the waterway and the freshwater reservoir, Lake Gatún, that feeds its locks.
Then, in 2016, Panama expanded the canal to allow supersize ships, and all that started to change.
In less than a decade, fish from both oceans — snooks, jacks, snappers and more — have almost entirely displaced the freshwater species that were in the canal system before, scientists with the Smithsonian Tropical Research Institute in Panama have found. Fishermen around Lake Gatún who rely on those species, chiefly peacock bass and tilapia, say their catches are growing scarce.
Researchers now worry that more fish could start making their way through from one ocean to the other. And no potential invader causes more concern than the venomous, candy-striped lionfish. They are known to inhabit Panama’s Caribbean coast, but not the eastern Pacific. If they made it there through the canal, they could ravage the defenseless local fish, just as they’ve done in the Gulf of Mexico and the Caribbean.
Already, marine species are more than occasional visitors in Lake Gatún, said Phillip Sanchez, a fisheries ecologist with the Smithsonian. They’re “becoming the dominant community,” he said. They’re “pushing everything else out.”
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