COVID-19 Coronavirus current events

Agreed apart from the future tense "will give". From the outset there have been two distinct questions about COVID viz:
(1) How did it start? and
(2) How best to prevent or minimise its spreading impact?
These questions are linked. For example, the knowledge that MERS comes from dromedary camels is very helpful in keeping it from spreading in the future.
Can you explain in more detail, I am not following here.
If a virus lab collects a virus in the wild and keeps it secret, and then that virus escapes, all they have to do is send another expedition to the same place, collect that virus again, and then present proof of the zoonotic origin of the virus, exhonorating themselves.

Wuhan has had 3 years to do this, but they didn't.
 
If a virus lab collects a virus in the wild and keeps it secret, and then that virus escapes, all they have to do is send another expedition to the same place, collect that virus again, and then present proof of the zoonotic origin of the virus, exhonorating themselves.

Wuhan has had 3 years to do this, but they didn't.
Thanks, I follow you now.
Gotta cogitate on that a bit...
 
These questions are linked. For example, the knowledge that MERS comes from dromedary camels is very helpful in keeping it from spreading in the future.

If a virus lab collects a virus in the wild and keeps it secret, and then that virus escapes, all they have to do is send another expedition to the same place, collect that virus again, and then present proof of the zoonotic origin of the virus, exhonorating themselves.

Wuhan has had 3 years to do this, but they didn't.

But "keeps it secret" is not what people are accusing the Wuhan lab of, it's performing gain of function reaseach. A pathogen that had had gain of function research performed on it, and that escaped, would not be able to be matched with its zoonotic origin - therefore their lack of finding its zoonotic origin for three years reinforces the narrative that GoF was performed.
 
What should we make of the original WHO expedition, which included Peter Daszak, and found that:

In March 2021, the WHO published a written report with the results of the study.[133] The joint team stated that there are four scenarios for introduction:[56]

  • direct zoonotic transmission to humans (spillover), assessed as "possible to likely"
  • introduction through an intermediate host followed by a spillover, assessed as "likely to very likely"
  • introduction through the (cold) food chain, assessed as "possible"
  • introduction through a laboratory incident, assessed as "extremely unlikely"
https://en.wikipedia.org/wiki/Investigations_into_the_origin_of_COVID-19#Findings

And now both the DoE and FBI have determined that lab leak is more likely. Were they just straight up lying? Is the WHO compromised?
 
But "keeps it secret" is not what people are accusing the Wuhan lab of, it's performing gain of function reaseach. A pathogen that had had gain of function research performed on it, and that escaped, would not be able to be matched with its zoonotic origin - therefore their lack of finding its zoonotic origin for three years reinforces the narrative that GoF was performed.
yes, but there's even less evidence for that, AFAIK. The one that gets cited where the WIV was involved was actually performed at Chapel Hill. And then both the research and the origin viruses have to match the "escaped" virus, there's no "magic" that suddenly makes the RaTG13 RNA match SARS-CoV-2 RNA.
 
Here's what I'm moderately confident of:

1. There's a SARS-CoV-2 precursor somewhere in the wild in southeast Asia. If you look at the map below, the further South you go, the closer the match is.
SmartSelect_20230302-144757_Samsung Notes.jpg

2. The virus easily jumps from bats to pangolins. Look for the pangolin silhouttes in this phylogenetic tree:
Article:
SmartSelect_20230302-145416_Samsung Internet.jpg


3. Somewhere in the SE Asian jungle, there's an illegal pangolin farm, or a village of pangolin hunters, where the virus migeates back and forth between humans and pangolins, selecting for efficient human infection. I'm positing this to explain the origin of the furin cleavage site, but this point is actually pure speculation. (This infection cycle does happen to bat hunters.)

4. "Pangolin Zero" gets traded to China, via Vietnam.
Article:
Our phylogenetic trees based on two fragments of the RdRp gene revealed that the Sarbecoviruses identified in these pangolins were closely related to pangolin coronaviruses detected in pangolins confiscated from the illegal wildlife trade in Yunnan and Guangxi provinces, China. Our curated data collection of media reports of wildlife confiscation events involving pangolins in Viet Nam between January 2016 and December 2020, reflected what is known about pangolin trafficking globally. Pangolins confiscated in Viet Nam were largely in transit, moving toward downstream consumers in China. Confiscations included pangolin scales sourced originally from Africa (and African species of pangolins), or pangolin carcasses and live pangolins native to Southeast Asia (predominately the Sunda pangolin) sourced from neighboring range countries and moving through Viet Nam toward provinces bordering China.


5. Pangolin Zero ends up at the Wuhan seafood market, and the rest is history.

What are the odds of that pangolin ending up in the city with the bat virus institute? Wuhan is the 8th largest city in China, so if pangolin trade is limited to big cities and follows population density, the chance might be 1:20 or 5%. (It'd be better than that if pangolins are not traded into other big cities like Beijing.)

Is my chain of events plausible? Yes. Is it proven? No.

But it's much more plausible and has better odds than any lab leak theory, none of which can plausibly explain how the virus came to be in the lab in the first place, and that have to contend with miniscule odds of the seafood market being ground zero for a lab-originating outbreak in a city of 8+ million inhabitants.
 
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You could think of the probability globally, though... Because presumably, a natural spillover could happen just about anywhere. SARS started in another part of China, MERS was first detected in Saudi Arabia. There's bats with all kinds of viruses all over the globe. So with that in mind, what are the chances that a spillover would happen a few miles away from a coronavirus laboratory, rather than anywhere else?
 
There's bats with all kinds of viruses all over the globe.
That's why there's virology labs all over the globe, as well.

Also, I notice your argument is dropping the comparison: if you conclude a natural spillover seems unlikely, you shouldn't then turn around and champion an even more unlikely hypothesis uncritically.
 
So with that in mind, what are the chances that a spillover would happen a few miles away from a coronavirus laboratory, rather than anywhere else?
let's look at this paper, "Novel sarbecovirus bispecific neutralizing antibodies with exceptional breadth and potency against currently circulating SARS-CoV-2 variants and sarbecoviruses", https://pubmed.ncbi.nlm.nih.gov/35443747/ . the authors' institutions are located in Shanghai, Wuhan, Beijing, Hangzhou, and Guangzhou. According to https://en.m.wikipedia.org/wiki/List_of_cities_in_China_by_population , these cities have approximately 25, 9, 21, 8 and 19 million inhabitants, sum total 82 million, representing ~6% of the Chinese population — just from that one paper.

Germany exceeds that (just by taking Hamburg and Berlin), other places (Africa? South America?) might not, but most countries have something like the CDC located in a big city.

you are not going to depress this chance substantially by looking globally. if we just take the 82 million from that one study from China and relate it to a global population of 7.8 billion, we're already exceeding 1%, which means the global chance cannot be lower than this. 1% is already 200 times more likely than the chance of the first cluster in Wuhan being at the seafood market and not anywhere else in the city if it was a lab leak.
 
Article:
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.)

[...]

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.”


The idea that raccoon dogs can transmit SARS is not new: back in 2009, the WIV published a study titled "Angiotensin-converting enzyme 2 (ACE2) from raccoon dog can serve as an efficient receptor for the spike protein of severe acute respiratory syndrome coronavirus".

This was confirmed in 2020:
Article:
Raccoon dogs might have been intermediate hosts for severe acute respiratory syndrome–associated coronavirus in 2002–2004. We demonstrated susceptibility of raccoon dogs to severe acute respiratory syndrome coronavirus 2 infection and transmission to in-contact animals. Infected animals had no signs of illness.


A 2021 study:
Article:
Prof. Markus Pfenninger, molecular ecologist at LOEWE TBG and SBiK-F, and Professor of Molecular Ecology at University of Mainz: “The genetic information showed that raccoon dogs are likely susceptible to SARS-COV-2 and that they can potentially transmit it to other animals.“ The data also show that one of the raccoon dog’s membrane proteins binds with higher affinity to the spike protein of SARS-CoV-2 than membrane proteins in their relatives such as foxes and wolves, but also than bats, or Asian pangolins.

“Recently, bats and pangolins have been regarded as potential direct vectors of SARS-CoV-2 to humans,” Klimpel says. “Which animal host transferred the coronavirus ultimately to humans is still unresolved. However, our study shows that the raccoon dog is a suitable reservoir host for the coronavirus.”


The new finding has given more strength to this idea.

We know that raccoon dogs can get SARS-CoV-2 infections and not look sick; that the virus is better adapted to them than to other animals; that they can transmit it; and that the virus was found in raccoon dog cages at the Wuhan market where the outbreak started.
 
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and that the virus was found in raccoon dog cages at the Wuhan market where the outbreak started.
a cart.
The swab taken from a cart there in early 2020, the research team found, contained genetic material from the virus and a raccoon dog.
" By then, the animals had been cleared out, but researchers swabbed walls, floors, metal cages and carts often used for transporting animal cages." https://www.nytimes.com/2023/03/16/science/covid-wuhan-market-raccoon-dogs-lab-leak.html
 
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