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?
Security guards stand in front of the closed Huanan Seafood Wholesale Market in Wuhan on Jan. 11, 2020.
(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.
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
Social media users in the Central Valley are freaking out about unusual fog, and what might be in it
A 400-mile blanket of fog has socked in California’s Central Valley for weeks. Scientists and meteorologists say the conditions for such persistent cloud cover are ripe: an early wet season, cold temperatures and a stable, unmoving high pressure system.
But take a stroll through X, Instagram or TikTok, and you’ll see not everyone is so sanguine.
People are reporting that the fog has a strange consistency and that it’s nefariously littered with black and white particles that don’t seem normal. They’re calling it “mysterious” and underscoring the name “radiation” fog, which is the scientific descriptor for such natural fog events — not an indication that they carry radioactive material.
An X user with the handle Wall Street Apes posted a video of a man who said he is from Northern California drawing his finger along fog condensate on the grill of his truck. His finger comes up covered in white.
“What is this s— right here?” the man says as the camera zooms in on his finger. “There’s something in the fog that I can’t explain … Check y’all … y’all crazy … What’s going on? They got asbestos in there.”
Another user, @wesleybrennan87, posted a photo of two airplane contrails crisscrossing the sky through a break in the fog.
“For anyone following the dense Tule (Radiation) fog in the California Valley, it lifted for a moment today, just to see they’ve been pretty active over our heads …” the user posted.
Scientists confirm there is stuff in the fog. But what it is and where it comes from, they say, is disappointingly mundane.
The Central Valley is known to have some of the worst air pollution in the country.
And “fog is highly susceptible to pollutants,” said Peter Weiss-Penzias, a fog researcher at UC Santa Cruz.
Fog “droplets have a lot of surface area and are suspended in the air for quite a long time — days or weeks even — so during that time the water droplets can absorb a disproportionate quantity of gasses and particles, which are otherwise known as pollutants,” he said.
He said while he hasn’t done any analyses of the Central Valley fog during this latest event, it’s not hard to imagine what could be lurking in the droplets.
“It could be a whole alphabet soup of different things. With all the agriculture in this area, industry, automobiles, wood smoke, there’s a whole bunch” of contenders, Weiss-Penzias said.
Reports of the fog becoming a gelatinous goo when left to sit are also not entirely surprising, he said, considering all the airborne biological material — fungal spores, nutrients and algae — floating around that can also adhere to the Velcro-like drops of water.
He said the good news is that while the primary route of exposure for people of this material is inhalation, the fog droplets are relatively big. That means when they are breathed in, they won’t go too deep into the lungs — not like the particulate matter we inhale during sunny, dry days. That stuff can get way down into lung tissue.
The bigger concern is ingestion, as the fog covers plants or open water cisterns, he said.
So make sure you’re washing your vegetables, and anything you leave outside that you might nosh on later.
Dennis Baldocchi, a UC Berkeley fog researcher, agreed with Weiss-Penzias’ assessment, and said the storm system predicted to move in this weekend will likely push the fog out and free the valley of its chilly, dirty shawl.
But, if a high pressure system returns in the coming weeks, he wouldn’t be surprised to see the region encased in fog once again.
Science
Trump administration, Congress move to cut off transgender care for children
The Trump administration and House Republicans advanced measures this week to end gender-affirming care for transgender children and some young adults, drawing outrage and resistance from LGBTQ+ advocacy organizations, families with transgender kids, medical providers and some of California’s liberal leaders.
The latest efforts — which seek to ban such care nationwide, strip funding from hospitals that provide it and punish doctors and parents who perform or support it — follow earlier executive orders from President Trump and work by the Justice Department to rein in such care.
Many hospitals, including in California, have already curtailed such care or shuttered their gender-affirming care programs as a result.
Abigail Jones, a 17-year-old transgender activist from Riverside, called the moves “ridiculous” and dangerous, as such care “saves lives.”
She also called them a purely political act by Republicans intent on making transgender people into a “monster” to rally their base against, and one that is “going to backfire on them because they’re not focusing on what the people want,” such as affordability and lower healthcare costs.
On Wednesday, the House passed a sweeping ban on gender-affirming care for youth that was put forward by Rep. Marjorie Taylor Greene (R-Ga.), largely along party lines.
The bill — which faces a tougher road in the U.S. Senate — bars already rare gender-affirming surgeries but also more common treatments such as hormone therapies and puberty blockers for anyone under 18. It also calls for the criminal prosecution of doctors and other healthcare workers who provide such care, and for penalties for parents who facilitate or consent to it being performed on their children.
“Children are not old enough to vote, drive, or get a tattoo and they are certainly not old enough to be chemically castrated or permanently mutilated!!!” Greene posted on X.
“The tide is turning and I’m so grateful that congress is taking measurable steps to end this practice that destroyed my childhood,” posted Chloe Cole, a prominent “detransitioner” who campaigns against gender-affirming care for children, which she received and now regrets.
Queer rights groups denounced the measure as a dangerous threat to medical providers and parents, and one that mischaracterizes legitimate care backed by major U.S. medical associations. They also called it a threat to LGBTQ+ rights more broadly.
“Should this bill become law, doctors could face the threat of prison simply for doing their jobs and providing the care they were trained to deliver. Parents could be criminalized and even imprisoned for supporting their children and ensuring they receive prescribed medication,” said Kelley Robinson, president of the Human Rights Campaign, one of the nation’s leading LGBTQ+ rights groups.
On Thursday, the U.S. Department of Health and Human Services announced that the Centers for Medicare & Medicaid Services are proposing new rules that would ban such care by medical providers that participate in its programs — which includes nearly all U.S. hospitals. The health department said the move is “designed to ensure that the U.S. government will not be in business with organizations that intentionally or unintentionally inflict permanent harm on children.”
The department said officials will propose additional rules to prohibit Medicaid or federal Children’s Health Insurance Program funding from being used for gender-affirming care for children or for young adults under the age of 19, and that its Office of Civil Rights would be proposing a rule to exclude gender dysphoria as a covered disability.
The U.S. Food and Drug Administration, meanwhile, issued warning letters to manufacturers of certain medical devices, including breast binders, that marketing their products to transgender youth is illegal.
“Under my leadership, and answering President Trump’s call to action, the federal government will do everything in its power to stop unsafe, irreversible practices that put our children at risk,” Health and Human Services Secretary Robert F. Kennedy Jr. said in a statement. “Our children deserve better — and we are delivering on that promise.”
The proposed rule changes are subject to public comment, and the Human Rights Campaign and other LGBTQ+ organizations, including the Los Angeles LGBT Center, urged their supporters to voice their opposition.
Joe Hollendoner, the center’s chief executive, said the proposed changes “cruelly target transgender youth” and will “destabilize safety-net hospitals” and other critical care providers.
“Hospitals should never be forced to choose between providing lifesaving care to transgender young people and delivering critical services like cancer treatment to other patients,” Hollendoner said. “Yet this is exactly the division and harm these rules are designed to create.”
Hollendoner noted that California hospitals such as Children’s Hospital Los Angeles have already curtailed their gender-affirming services in the face of earlier threats from the Trump administration, and thousands of transgender youth have already lost access to care.
Gov. Gavin Newsom issued a statement contrasting the Trump administration’s moves with California’s new partnership with The Trevor Project, to improve training for the state’s 988 crisis and suicide hotline for vulnerable youth, including LGBTQ+ kids at disproportionately high risk of suicide and mental health issues.
“As the Trump administration abandons the well-being of LGBTQ youth, California is putting more resources toward providing vulnerable kids with the mental health support they deserve,” Newsom said.
California Atty. Gen. Rob Bonta’s office is already suing the Trump administration for its efforts to curtail gender-affirming care and target providers of such care in California, where it is protected and supported by state law. His office has also resisted Trump administration efforts to roll back other transgender rights, including in youth sports.
On Thursday, Bonta said the proposed rules were “the Trump Administration’s latest attempt to strip Americans of the care they need to live as their authentic selves.” He also said they are “unlawful,” and that his office will fight them.
“If the Trump Administration puts forth final rules similar to these proposals, we stand ready to use every tool in our toolbox to prevent them from ever going into effect,” Bonta said — adding that “medically necessary gender-affirming care remains protected by California law.”
Arne Johnson, a Bay Area father of a transgender child who helps run a group of similar families called Rainbow Families Action, said there has been “a lot of hate spewed” toward them in recent days, but they are focused on fighting back — and asking hospital networks to “not panic and shut down care” based on proposed rules that have not been finalized.
Johnson said Republicans and Trump administration officials are “weirdly obsessed” with transgender kids’ bodies, are “breaking the trust between us and our doctors,” and are putting politics in between families and their healthcare providers in dangerous ways.
He said parents of transgender kids are “used to being hurt and upset and sad and worried about their kids, and also doing everything in their power to make sure that nothing bad happens to them,” and aren’t about to stop fighting now.
But resisting such medical interference isn’t just about gender-affirming care. Next it could be over vaccines being blocked for kids, he said — which should get all parents upset and vocal.
“If our kids don’t get care, they’re coming for your kids next,” Johnson said. “Pretty soon all of us are going to be going into hospital rooms wondering whether that doctor across from us can be trusted to give our kid the best care — or if their hands are going to be tied.”
Science
His computer simulations help communities survive disasters. Can they design a Palisades that never burns?
In what used to be a dry cleaner’s on Sunset Boulevard, Robert Lempert listened, hands clasped behind his back, as his neighbors finally took a moment to step away from recovery’s endless stream of paperwork, permits, bills and bureaucracy to, instead, envision a fire-resilient Pacific Palisades in 2035.
As a researcher at RAND, Lempert has spent decades studying how communities, corporations and governments can use computer simulations to understand complex problems with huge uncertainties — from how an Alaska town can better warn its residents about landslides to how climate change is worsening disasters and what strategies the United Nations can support to address them.
In January, one such complex problem ran straight through his neighborhood and burned down his house.
As Lempert and his wife process their own trauma forged by flames, Lempert has become fixated on capturing the flickers of insights from fellow survivors and, hopefully, eventually, transforming them into computer programs that could help the community rebuild the Palisades into a global leader in wildfire resilience.
“Otherwise, we won’t end up with a functional community that anybody wants to — or can — live in,” he said. “You can spin out all sorts of disaster scenarios” for the Pacific Palisades of 2035. If the community fails to confront them in rebuilding, “you make them a hell of a lot more likely.”
Lempert doesn’t see a mass exodus from high-fire-hazard areas as a viable solution. Out of the more than 12 million buildings the climate risk modeling company First Street studies in California, 4 in 10 have at least a 5% chance of facing a wildfire in the next 30 years. (Out of the nearly 10,000 buildings First Street studies in the Palisades, 82% carry that level of risk.) And the areas without significant fire risk have their own environmental challenges: flooding, earthquakes, landslides, hurricanes, tornadoes, droughts. Learning to live with these risks, consequently, is part of the practice of living in California — and really, in most of the places humans have settled on Earth.
After two of the most destructive fires in the state’s history, The Times takes a critical look at the past year and the steps taken — or not taken — to prevent this from happening again in all future fires.
So, Lempert has taken to the modus operandi he helped develop at RAND:
Identify the problem. In this case, living in Pacific Palisades carries a nonzero risk you lose your house or life to fire.
Define the goals. Perhaps it is that, in the next fire, the Palisades doesn’t lose any homes or lives (and, ideally, accomplishes this without spending billions).
Then, the real work: Code up a bunch of proposed solutions from all of the groups with wildly disparate views on how the system (i.e., Southern California wildfires) works.
Stress-test those solutions against a wide range of environmental conditions in the computer. Extreme winds, downed communication systems, closed evacuation routes — the list goes on.
Finally, sit back, and see what insights the computer spits out.
It’s easy enough to agree on the problem, goals and environmental factors. For the proposed solutions, Lempert set out to collect data.
Poster paper with residents’ handwritten ideas now fills the walls of the former dry cleaner’s, now the headquarters of the grassroots organization Palisades Recovery Coalition. It’s through these “visioning charrettes” that Lempert hopes his community can develop a magic solution capable of beating the computer’s trials.
Lempert holds a photo of his home as it looked before it was destroyed by the Palisades fire.
The streets could be lined with next-generation homes of concrete and steel where even the tiniest gaps are meticulously sealed up to keep embers from breaching the exterior. Each home could be equipped with rain-capture cisterns, hooked up to a neighborhood-wide system of sensors and autonomous fire hoses that intelligently target blazes in real time. One or two shiny new fire stations — maybe even serving as full-blown fire shelters for residents, equipped with food and oxygen to combat the smoke — might sit atop one of the neighborhood’s main thoroughfares, Palisades Drive. The street, formerly a bottleneck during evacuations, might now have a dedicated emergency lane.
Every year, the community could practice a Palisades-wide evacuation drill so the procedures are fresh in the mind. Community brigades might even train with the local fire departments so, during emergencies, they can effectively put out spot fires and ensure their elderly neighbors get out safely.
Lempert, who now lives in a Santa Monica apartment with his wife, doesn’t entertain speculation about whether the Palisades will ever reach this optimistic vision — even though his own decision to move back someday, in part, hinges on the answer.
Right now, all that matters is that change is possible.
He pointed to an anecdote he heard once from the fire historian Stephen Pyne: American cities used to burn down — from within — all the time in the 19th century. Portland, Maine, burned in 1866 thanks to a Fourth of July firecracker. Chicago in 1871, after a blaze somehow broke out in a barn. Boston the following year, this time starting in a warehouse basement. Eventually, we got fed up with our cities burning down, so we created professional fire departments, stopped building downtowns out of wood and bolstered public water systems with larger water mains and standardized fire hydrants. Then, it stopped happening.
Now we face a new fire threat — this time, from the outside. Maybe we’re fed up enough to do something about it.
“Cities shouldn’t burn down,” Lempert said with a chuckle, amused by the simplicity of his own words. “So let’s just design them so they don’t.”
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