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Coronavirus: How dangerous a threat?

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New Data Links Pandemic’s Origins to Raccoon Dogs at Wuhan Market
Genetic samples from the market were recently uploaded to an international database and then removed after scientists asked China about them.

March 16, 2023

An international team of virus experts said on Thursday that they had found genetic data from a market in Wuhan, China, linking the coronavirus with raccoon dogs for sale there, adding evidence to the case that the worst pandemic in a century could have been ignited by an infected animal that was being dealt through the illegal wildlife trade.
The genetic data was drawn from swabs taken from in and around the Huanan Seafood Wholesale Market starting in January 2020, shortly after the Chinese authorities had shut down the market because of suspicions that it was linked to the outbreak of a new virus. By then, the animals had been cleared out, but researchers swabbed walls, floors, metal cages and carts often used for transporting animal cages.
In samples that came back positive for the coronavirus, the international research team found genetic material belonging to animals, including large amounts that were a match for the raccoon dog, three scientists involved in the analysis said.
The jumbling together of genetic material from the virus and the animal does not prove that a raccoon dog itself was infected. And even if a raccoon dog had been infected, it would not be clear that the animal had spread the virus to people. Another animal could have passed the virus to people, or someone infected with the virus could have spread the virus to a raccoon dog.

But the analysis did establish that raccoon dogs — fluffy animals that are related to foxes and are known to be able to transmit the coronavirus — deposited genetic signatures in the same place where genetic material from the virus was left, the three scientists said. That evidence, they said, was consistent with a scenario in which the virus had spilled into humans from a wild animal.

A report with the full details of the international research team’s findings has not yet been published. Their analysis was first reported by The Atlantic.

The new evidence is sure to provide a jolt to the debate over the pandemic’s origins, even if it does not resolve the question of how it began.
In recent weeks, the so-called lab leak theory, which posits that the coronavirus emerged from a research lab in Wuhan, has gained traction thanks to a new intelligence assessment from the U.S. Department of Energy and hearings led by the new Republican House leadership.

But the genetic data from the market offers some of the most tangible evidence yet of how the virus could have spilled into people from wild animals outside a lab. It also suggests that Chinese scientists have given an incomplete account of evidence that could fill in details about how the virus was spreading at the Huanan market.
Jeremy Kamil, a virologist at Louisiana State University Health Sciences Center Shreveport who was not involved in the study, said the findings showed that “the samples from the market that had early Covid lineages in them were contaminated with DNA reads of wild animals.”
Dr. Kamil said that fell short of conclusive evidence that an infected animal had set off the pandemic. But, he said, “it really puts the spotlight on the illegal animal trade in an intimate way.”
Chinese scientists had released a study looking at the same market samples in February 2022. That study had reported that samples were positive for the coronavirus but suggested that the virus had come from infected people who were shopping or working in the market, rather than from animals being sold there.
At some point, those same researchers, including some affiliated with the Chinese Center for Disease Control and Prevention, posted the raw data from swabs around the market to GISAID, an international repository of genetic sequences of viruses. (Attempts to reach the Chinese scientists by phone on Thursday were not successful.)

On March 4, Florence Débarre, an evolutionary biologist at the French National Center for Scientific Research, happened to be searching that database for information related to the Huanan market when, she said in an interview, she noticed more sequences than usual popping up. Confused at first about whether they contained new data, Dr. Débarre put them aside, only to log in again last week and discover that they held a trove of raw data.
Virus experts had been awaiting that raw sequence data from the market since they learned of its existence in the Chinese report from February 2022. Dr. Débarre said she had alerted other scientists, including the leaders of a team that had published a set of studies last year pointing to the market as the origin.
An international team — which included Michael Worobey, an evolutionary biologist at the University of Arizona; Kristian Andersen, a virologist at the Scripps Research Institute in California; and Edward Holmes, a biologist at the University of Sydney — started mining the new genetic data last week.
One sample in particular caught their attention. It had been taken from a cart linked to a specific stall at the Huanan market that Dr. Holmes had visited in 2014, scientists involved in the analysis said. That stall, Dr. Holmes found, contained caged raccoon dogs on top of a separate cage holding birds, exactly the sort of environment conducive to the transmission of new viruses.
The swab taken from a cart there in early 2020, the research team found, contained genetic material from the virus and a raccoon dog.

“We were able to figure out relatively quickly that at least in one of these samples, there was a lot of raccoon dog nucleic acid, along with virus nucleic acid,” said Stephen Goldstein, a virologist at the University of Utah who worked on the new analysis. (Nucleic acids are the chemical building blocks that carry genetic information.)
After the international team stumbled upon the new data, they reached out to the Chinese researchers who had uploaded the files with an offer to collaborate, hewing to rules of the online repository, scientists involved with the new analysis said. After that, the sequences disappeared from GISAID.
It is not clear who removed them or why they were taken down.
Dr. Débarre said the research team was seeking more data, including some from market samples that were never made public. “What’s important is there’s still more data,” she said.
Scientists involved with the analysis said that some of the samples had also contained genetic material from other animals and from humans. Angela Rasmussen, a virologist at the Vaccine and Infectious Disease Organization at the University of Saskatchewan in Canada, who worked on the analysis, said that the human genetic material was to be expected given that people were shopping and working there and that human Covid cases had been linked to the market.
Dr. Goldstein, too, cautioned that “we don’t have an infected animal, and we can’t prove definitively there was an infected animal at that stall.” Genetic material from the virus is stable enough, he said, that it is not clear when exactly it was deposited at the market. He said that the team was still analyzing the data and that it had not intended for its analysis to become public before it had released a report.
“But,” he said, “given that the animals that were present in the market were not sampled at the time, this is as good as we can hope to get.”
View: https://twitter.com/jbloom_lab/status/1651428639676960769

"More broadly, what can we conclude about COVID-19 origins from all this?

Probably not much.

@DrTedros of @WHO had correct interpretation: we should analyze everything, but these data don’t tell us how pandemic began"
I'll have to read that a least one more time...too much for my brain to digest in one read.

Interesting IMO:

View: https://twitter.com/jbloom_lab/status/1651428687362035712?s=20

View: https://twitter.com/jbloom_lab/status/1651428691438895106?s=20
Interesting interview with immunology professor at Yale School of Medicine, Akiko Iwasaki
In December, China abruptly abandoned its draconian “Zero Covid” policies, battered by a surge of infections and rising public anger against lockdowns. Half a year on, Covid cases again are on the rise, but this time the nation appears to be determined to press on with normal life as the government focuses on reigniting economic growth.
Though other countries have long settled into such a pattern, it is a shift for China. Until late last year, its national leadership was still ready to lock down whole neighborhoods and districts, even cities, in a bid to stamp out what were sometimes just small clusters of cases.
The Chinese health authorities have reported a rise in Covid cases since April, especially from newer subvariants that are spreading across the world. Dr. Zhong Nanshan, a prominent doctor who was among the first to openly confirm in early 2020 that Covid could easily spread among people, estimated on Monday that by late June as many as 65 million people a week could become infected with the coronavirus across China. (That would be up from what he estimated at 40 million infections a week in late May. China no longer publishes regular official nationwide estimates of infections.)
By comparison, after “Zero Covid” controls were set aside in December, new infections reached 37 million a day in China at their peak, according to estimates cited by Bloomberg.

Based on China alone it is nowhere close to being done.................
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Is it covid so marginal nowdays or is it lack of interest in testing and reporting? 58 000 cases worldwide last week and "only" 508 deaths. Society is prepandemic right now I dont know about any particular rules except maybe mask mandates somewhere. When I remember whole lockdown rules it seems already distant to me. And pretty crazy we live it some time ago.
Is it covid so marginal nowdays or is it lack of interest in testing and reporting? 58 000 cases worldwide last week and "only" 508 deaths. Society is prepandemic right now I dont know about any particular rules except maybe mask mandates somewhere. When I remember whole lockdown rules it seems already distant to me. And pretty crazy we live it some time ago.
There is very little testing now, and even less reporting so case numbers don't tell us much.
There are still about 300-400 deaths per week (continuing downward).
--I'm not sure how there were "only" 508 deaths worldwide because that wouldn't be many outside of the USA.
---I just did a quick peek and Brazil reported 320 and the USA 393 so just those two countries are over 700 deaths. There are a lot of zeros on -----the chart so that makes me wonder if reporting is even less reliable now (not an emergency).
I don't know of any public restrictions (other than ie: oncology units at the hospital).

Its crazy how 2020-2022 seemed like a time warp, and now seems like some weird gap in time.
Biden declassified (most) of the of the SC2 origin 'intelligence'.

Whatever. 99% of people won't even bother to read it, and most who do won't be able to make sense of it. Most will still just go with what their shock jock tells them...so nothing new to see.
I watch all the Jordan Klepper videos, all are meant to be funny, but soon after I smile a little sadness washes over me. And on a cycling finish.. TDF is over.. Sagan out with not even a twinkle.. Remco eating Pizza Hut and so many other victims, sure not extreme, not life threatening but still the after effects of Covid. If you watch Klepper talking to people about Covid you will hide under your bed
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sample of one:

I ran into the young adult daughter of someone I used to work with, and asked how she and her mom were doing. Mostly all good, but her mom got covid in April of 2020, and still has no sense of taste and very little smell. She said that her mom didn't even really get that sick, just a couple of days of being tired. Obviously that is way better than some of the other long-term symptoms, but that still sucks, IMO!
Biden declassified (most) of the of the SC2 origin 'intelligence'.

Whatever. 99% of people won't even bother to read it, and most who do won't be able to make sense of it. Most will still just go with what their shock jock tells them...so nothing new to see.
Maybe it will shut Rand up. We can hope.
On more news....another wave has hit our neighborhood with a handful of co workers afflicted around my wife. I'm hoping I don't get it again, dammit.
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