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New genetic research points to Wuhan animal market as origin of COVID pandemic, study says

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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.

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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.

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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.

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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?

Security guards stand in front of the closed Huanan Seafood Wholesale Market in Wuhan on Jan. 11, 2020.

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(Noel Celis / AFP via Getty Images)

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.

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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.

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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.

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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.”

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“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.’”

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Flu is hitting California early. Why doctors worry this year will be especially hard on kids

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Flu is hitting California early. Why doctors worry this year will be especially hard on kids

Fueled by a new viral strain, flu is hitting California early — and doctors are warning they expect the season may be particularly tough on young children.

Concentrations of flu detected in wastewater have surged in the San Francisco Bay Area, and the test positivity rate is rising in Los Angeles County and Orange County, according to state and county data. Hospitalizations and emergency room visits for flu are also rising in L.A. and Orange counties.

“We are at the point now where we’re starting to see a sharp rise in flu cases. This is a few weeks earlier than we usually experience, but very much akin to what was seen in the Southern Hemisphere’s experience with flu during their winter,” said Dr. Elizabeth Hudson, regional physician director of infectious diseases at Kaiser Permanente Southern California.

At Kaiser, flu cases are primarily being seen in clinics so far, but hospitalizations typically rise after Christmas. “We expect to see the same this year, too,” Hudson said.

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“The number of cases appears to be higher at an earlier time in the usual flu season than we’ve seen in years past,” she added.

Flu levels are high in San Francisco’s sewage as well as in wastewater across San José, Sunnyvale and Palo Alto, according to WastewaterSCAN and the Santa Clara County Public Health Department.

One area of concern this winter has been the rise of a relatively new flu subvariant, known as H3N2 Flu A subclade K, which appeared toward the end of summer. That was months after officials decided which strains this fall’s flu vaccine would target.

Subclade K “is causing an active, early flu season, with more cases occurring in some countries within the Northern Hemisphere,” the California Department of Public Health said.

It remains unclear whether subclade K will reduce the efficacy of this year’s flu shot. Data recently released in Britain showed this season’s vaccines were 70% to 75% effective against hospitalization for children from the flu, and 30% to 40% effective in adults, which is within expectations, the U.S. Centers for Disease Control and Prevention noted.

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This suggests “that influenza vaccination remains an effective tool in preventing influenza-related hospitalizations this season,” according to the agency.

However, the intended effectiveness of the flu vaccine against symptomatic disease caused by the new subvariant remains uncertain, the World Health Organization said.

Overall, flu rates in L.A. County remain relatively low, but are on the rise. Across California, flu hospitalizations are likewise low but increasing.

On a national level, severity indicators remain low, according to the CDC.

But the experience in other nations have led some experts to worry another severe flu season could be on deck for California.

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Australia’s flu season, which is seasonally opposite from California’s, came far earlier than usual, hit with record strength and was particularly hard on the nation’s children.

Japan, Taiwan and Britain have also reported early spikes to their flu seasons.

“Whether or not this season will be more severe, only time will tell,” Hudson said of California. “We know that we have a mutation … which may make the flu vaccine work less well. But the vaccine still offers excellent protection against hospitalization and death, even with the mutated strain in circulation.”

Based on what happened in the Southern Hemisphere — particularly in Australia — “we are expecting this season to have a disproportionate impact on children under the age of 10,” Hudson said.

Already, three flu-associated pediatric deaths have been reported nationally this season, including two Friday.

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During the flu season that ended in September, 280 children died from flu — the most since the swine flu pandemic season of 2009-10.

Overall, the 2024-25 season was considered the worst flu season since 2017-18, and hit adults hard as well. At least 38,000 people died from the flu last season, health authorities estimate.

Only a little more than half of the children who died from flu had an underlying medical condition, and 89% of those who died were not vaccinated, according to the CDC’s National Center for Immunization and Respiratory Diseases.

Among the children who died from flu last season, the most common complications experienced before death were shock or sepsis, pneumonia, acute respiratory distress syndrome, seizures and damage to the brain.

Early diagnosis of flu can help stave off the worst by giving those who are sick time to take antiviral medications like Tamiflu. Three out of five children who died from the flu during the 2024-25 season never received antiviral medication.

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Emergency warning signs of flu complications in children include trouble breathing; bluish lips or face; ribs pulling in with each breath; chest pain; severe muscle pain, in which a child may refuse to walk; dehydration, signs of which include no urine for eight hours or no tears when crying; seizures; fevers above 104 degrees that are not controlled by medication; fever or cough that improve but return or worsen; and any fever in newborns younger than 12 weeks.

Since the official start of the respiratory virus season Oct. 1, the CDC estimates there have been at least 1,900 flu-related deaths, 49,000 hospitalizations and 4.6 million illnesses nationwide.

Doctors have been urging everybody to get the flu vaccine — the CDC recommends it for everyone age 6 months and up.

But vaccination rates have been lagging. Among children age 6 months to 17 years, an estimated 40.8% had been vaccinated as of the first week of December, according to the National Immunization Survey. In the last season before the COVID-19 pandemic, flu vaccination rates were notably higher by this time of year, at 51.2%.

At the end of last flu season, only 49.8% of children and teens had been vaccinated, the survey estimated, down from the 62.4% who had gotten their shots by the end of the 2019-20 flu season.

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The decline in flu vaccinations has been seen locally, too. “Notably, fewer influenza vaccines have been administered this year compared to the same period last year,” the Orange County Health Care Agency said.

It takes about two weeks for protection to build, but getting vaccinated as soon as possible before travel or seeing friends and family “helps keep you and your loved ones safer,” the L.A. County Department of Public Health said in a statement to The Times.

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Why California’s milk cartons may lose their coveted recycling symbol

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Why California’s milk cartons may lose their coveted recycling symbol

California milk cartons may lose their coveted recycling symbol, the one with the chasing arrows, potentially threatening the existence of the ubiquitous beverage containers.

In a letter Dec. 15, Waste Management, one of the nation’s largest waste companies, told the state the company would no longer sort cartons out of the waste stream for recycling at its Sacramento facility. Instead, it will send the milk- and food-encrusted packaging to the landfill.

Marcus Nettz, Waste Management’s director of recycling for Northern California and Nevada, cited concerns from buyers and overseas regulators that cartons — even in small amounts — could contaminate valuable material, such as paper, leading them to reject the imports.

The company decision means the number of Californians with access to beverage carton recycling falls below the threshold in the state’s “Truth in Recycling” law, or Senate Bill 343.

And according to the law, that means the label has to come off.

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The recycling label is critical for product and packaging companies to keep selling cartons in California as the state’s single-use packaging law goes fully into effect. That law, Senate Bill 54, calls for all single-use packaging to be recyclable or compostable by 2032. If it isn’t, it can’t be sold or distributed in the state.

The labels also provide a feel-good marketing symbol suggesting to consumers the cartons won’t end up in a landfill when they’re discarded, or find their way into the ocean where plastic debris is a large and growing problem.

On Tuesday, the state agency in charge of waste, CalRecycle, acknowledged Waste Management’s change.

In updated guidelines for the Truth in Recycling law, recycling rates for carton material have fallen below the state threshold.

It’s a setback for carton manufacturers and their customers, including soup- and juice-makers. Their trade group, the National Carton Council, has been lobbying the state, providing evidence that Waste Management’s Sacramento Recycling and Transfer Station successfully combines cartons with mixed paper and ships it to Malaysia and other Asian countries including Vietnam, proving that there is a market. The Carton Council persuaded CalRecycle to reverse a decision it made earlier this year that beverage cartons did not meet the recycling requirements of the Truth in Recycling law.

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Brendon Holland, a spokesman for the trade group, said in an email that his organization is aware of Waste Management’s decision, but its understanding is that the company will now sort the cartons into their own dedicated waste stream “once a local end market is available.”

He added that even with “this temporary local adjustment,” food and beverage cartons are collected and sorted in most of California, and said this is just a “temporary end market adjustment — not a long-term shift away from historical momentum.”

In 2022, Malaysia and Vietnam banned imports of mixed paper bales — which include colored paper, newspapers, magazines and other paper products — from the U.S. because they were so often contaminated with non-paper products and plastic, such as beverage cartons. Waste Management told The Times on Dec. 5 that it has a “Certificate of Approval” by Malaysia’s customs agency to export “sorted paper material.” CalRecycle said it has no regulatory authority on “what materials may or may not be exported.”

Adding the Sacramento facility to the list of waste companies that were recycling cartons meant that the threshold required by the state had been met: More than 60% of the state’s counties had access to carton recycling.

At the time, CalRecycle’s decision to give the recycling stamp to beverage cartons was controversial. Many in the environmental, anti-plastic and no-waste sectors saw it as a sign that CalRecycle was doing the bidding of the plastic and packaging industry, as opposed to trying to rid the state of non-recyclable, polluting waste — which is not only required by law, but is something state Atty. Gen. Rob Bonta is investigating.

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Others said it was a sign that the Truth in Recycling law was working: Markets were being discovered and in some cases, created, to provide recycling.

“Recyclability isn’t static, it depends on a complicated system of sorting, transportation, processing, and, ultimately, manufacturers buying the recycled material to make a new product,” said Nick Lapis, director of advocacy for Californians Against Waste.

He said this new information, which will likely remove the recycling label from the cartons, also underscores the effectiveness of the law.

“By prohibiting recyclability claims on products that don’t get recycled, SB 343 doesn’t just protect consumers. It forces manufacturers to either use recyclable materials or come to the table to work with recyclers, local governments and policymakers to develop widespread sustainable and resilient markets,” he said.

Beverage and food cartons — despite their papery appearance — are composed of layers of paper, plastic and sometimes aluminum. The sandwiched blend extends product shelf life, making it attractive to food and beverage companies.

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But the companies and municipalities that receive cartons as waste say the packaging is problematic. They say recycling markets for the material are few and far between.

California, with its roughly 40 million residents, has some of the strictest waste laws in the nation. In 1989, the state passed legislation requiring cities, towns and municipalities to divert at least 50% of their residential waste away from landfills. The idea was to incentivize recycling and reuse. However an increasing number of products have since entered the commercial market and waste stream — such as single use plastics, polystyrene and beverage cartons — that have limited (if any) recycling potential, can’t be reused, and are growing in number every year.

Fines for municipalities that fail to achieve the required diversion rates can run $10,000 a day.

As a result, garbage haulers often look for creative ways to deal with the waste, including shipping trash products overseas or across the border. For years, China was the primary destination for California’s plastic, contaminated paper and other waste. But in 2018, China closed its doors to foreign garbage, so U.S. exporters began dumping their waste in smaller southeast Asian countries, including Malaysia and Vietnam.

They too have now tried to close the doors to foreign trash as reports of polluted waterways, chokingly toxic air, and illness grows — and as they struggle with inadequate infrastructure to deal with their own domestic waste.

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Jan Dell, the founder and CEO of Last Beach Cleanup, released a report with the Basel Action Network, an anti-plastic organization, earlier this month showing that the Sacramento facility and other California waste companies were sending bales of carton-contaminated paper to Malaysia, Vietnam and other Asian nations.

According to export data, public records searches and photographic evidence collected by Dell and her co-authors at the Basel Action Network, more than 117,000 tons or 4,126 shipping containers worth of mixed paper bales were sent by California waste companies to Malaysia between January and July of this year.

Dell said these exports violate international law. A spokesman for Waste Management said the material they were sending was not illegal — and that they had received approval from Malaysia.

However, the Dec. 15 letter suggests they were receiving more pushback from their export markets than they’d previously disclosed.

“While certain end users maintain … that paper mills are able to process and recycle cartons,” some of them “have also shared concerns … that the inclusion of cartons … may result in rejection,” wrote Nettz.

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Dell said she was “pleased” that Waste Management “stopped the illegal sortation of cartons into mixed paper bales. Now we ask them and other waste companies to stop illegally exporting mixed paper waste to countries that have banned it.”

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Video: Why Scientists Are Performing Brain Surgery on Monarchs

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Video: Why Scientists Are Performing Brain Surgery on Monarchs

new video loaded: Why Scientists Are Performing Brain Surgery on Monarchs

Scientists in Texas are studying monarch butterflies to understand how they navigate thousands of miles, possibly by sensing Earth’s magnetic field. Alexa Robles-Gil explains how researchers are examining the butterflies’ brains to find answers.

By Alexa Robles-Gil, Leila Medina, Joey Sendaydiego and Mark Felix

December 23, 2025

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