On the Origins of Covid

lol

ETA: WAIT WUT

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This post makes me wonder what weā€™re even doing here. The ā€˜blog postā€™ is on the edge of what I can conclusively say I understand, and you just casually dismiss a major expert in virology as a ā€˜blog postā€™. You obviously donā€™t understand whatā€™s going on in that post. He addresses your concern directly btw:

Proponents of the Lab Leak theory will point out that none of the animals sold at the Huanan Market tested positive for SARS-CoV-2 (WHO, 2021). Although mentioned in the WHO Report, but not discussed in detail, several independent sources indicate that wildlife species susceptible to SARS-CoV-2, including civets and raccoon dogs, were sold at the Huanan market (Stout, 2020; Yee, 2020; Zhang and Holmes, 2020). Similar species were likely to have been available to purchase at other wildlife markets in Wuhan. Certain species of animals may have been removed after the appearance of the first COVID-19 cases and the linkage of COVID-19 cases to the market, but prior to the closure of the Market on January 1, 2020. It should also be noted that environmental samples that did test positive were associated with the portion of the market where wildlife or wildlife products were sold. A temporal analysis of the early human cases at the Huanan market confirms the pattern of spread from the areas of the market where wildlife products were sold to other parts of the market. (WHO, 2021).

Now I suppose I donā€™t know if this is actually Dr Garry, but you should take a look at his resume before flippantly dismissing him. His work on ebola was especially interesting.

As for a cliffs version, what Trolly said. The lack of a positive test does not rule anything out.

I think itā€™s also useful to compare the WSJ report (which is not new) about 3 lab workers who got sick (but never tested positive for covid) versus

Among the first 168 diagnosed cases of COVID-19 in Wuhan with onset date prior to December 31, 2019 and a known history of exposure to wildlife markets 55.4% (93/168) reported such exposures. Of the 168 cases, 28% (47/168) had only been to the Huanan market, 22% (38/168) had exposure to another wildlife market and 4.7% (8/168) had exposure to the Huanan market and another market (Annex E2, Table 1 of WHO, 2021).

Garry doesnā€™t claim that it rules lab leak out, it just adds another uncommon thing to get to the lab leak result. His point is that not only do have to overcome how people who worked in and around wet markets were vastly overrepresented in the initially sick, but you would need for covid to diverge genetically early on.

That means that if there was a lab leak, there would have had to be a leak of two different lineages of covid at the same time or that there was a near immediate divergence of a lab leaked covid.

Both of those are very improbable. It makes far more sense that this came from a natural reservoir.

Iā€™m not sure exactly how I want to address this because both of these things are true:

  1. This is the third major coronavirus outbreak with a significant amount of death, all likely from a bat as a source, in the past 20 or so years. Itā€™s the second in China. So your premise is completely wrong from a longer term point of view.

  2. On a shorter term, itā€™s very difficult for viruses to jump from species to species. Itā€™s more difficult for it to spread efficiently after the jump. Itā€™s more difficult for it to be clinically significant. This is a common mechanism for how a pandemic happens. SARS, MERS, H1N1, swine flu and more all happened this way, yet didnā€™t happen over and over again immediately.

https://mobile.twitter.com/ChrisMegerian/status/1397599252013060097

I think the paper is somewhat convincing but very speculative still.

Right, but the alternative explanation is this:

In one possible scenario divergence of SARS-CoV-2 to lineages A and B occurred prior to the transport of infected animals to Wuhan and the infected animals were subsequently distributed to different wildlife markets.

But if a large population of animals were infected we might expect to see more than two points of initial spread, while if a small population is infected I donā€™t see why itā€™s more probable for this divergence to occur in animal hosts rather than human. Itā€™s not clear to me that divergence within an animal population followed by exactly two transmissions of different lineages to humans is more probable than one transmission to humans followed by divergence; the paper just asserts this is so. If we had two confirmed outbreaks in wet markets the case would be a lot stronger, but the paper doesnā€™t even identify a specific second site, itā€™s just wet markets in general:

Among the first 168 diagnosed cases of COVID-19 in Wuhan with onset date prior to December 31, 2019 and a known history of exposure to wildlife markets 55.4% (93/168) reported such exposures. Of the 168 cases, 28% (47/168) had only been to the Huanan market, 22% (38/168) had exposure to another wildlife market and 4.7% (8/168) had exposure to the Huanan market and another market (Annex E2, Table 1 of WHO, 2021).

This is kind of meaningless because it lacks base-rate information on how probable it is for people to have attended one of these markets. I donā€™t know what percentage of people in these areas of Wuhan regularly visit such places. Like if you looked at a Western outbreak and were like ā€œomg a lot of these people have been to supermarkets recentlyā€ thatā€™s obviously meaningless. Thatā€™s before we get into bobmanā€™s point about possibly biased sampling of people who had attended known sites of COVID outbreaks, or people who had attended wet markets in general.

The conclusion of which is that exactly two jumps of two different lineages into humans is an improbable event. Less improbable than a divergence almost immediately after jumping into humans? I donā€™t know. It seems like weā€™re looking at an improbable sequence of events either way. The paper just asserts that it knows which is these sequences is more improbable. Maybe that is obvious to an experienced virologist, but Iā€™d like to see a bit more detail backing this up.

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I was poking around that virologist site Lawnmower_Man linked to yesterday and found this thread by a professor of microbiology, immunology & parasitology where his findings were eventually published in a journal. The subject is about whether the closest publicly known relative to CoV2 could conceivably have been engineered or gain-of-functioned or whatevered into our current plague. His conclusion, like many others, was no, and Iā€™m certainly not qualified to question the science there (although others have).

However, he made some other observations along the way I found interesting.

So the definitive source of the pandemic is a mixed infection of viruses similar to SARS-CoV-2 and Bat HKU9 ā€“ copy choice error resulting in an insert in SARS-CoV-2. Could occur in bats, intermediate animal or human.

Human in incubation with SARS-CoV-2 could hop a max speed train, direct line from Kunming in Yunnan Province and disembark in Wuhan train station 6.5-8 hours later, sometime last fall. The line began service in 2017.

Infected in Yunnan, does not spread it there, but goes to Wuhan, where he/she either falls ill or spreads it asymptomatically to another person, initiating the pandemic there. The initial outbreak occurs a short distance from the Wuhan train station for good reason ā€“ that is where it arrived.

This accidental mixed infection in the wild, and infection of a human by some form of bush meat or bat guano, who carries it by high speed train to Wuhan ā€“ this is the most likely series of events leading to the pandemic.

We have too ample evidence now that the animal that can transport SARS-CoV-2 from point A to point B, and spread it the fastest is a human being. Caged animals of any kind need not apply ā€“ and no animal reservoir for the virus has been found, now several months into the investigation. It is not for lack of the Chinese looking - they are far more motivated to understand the genesis of this than anyone.

The "pangolin hypothesisā€™ was based on faulty molecular analysis of sequence similarity, which turned out to not be that similar at all. That explanation was debunked 2.5 months ago.

I am not a fan of ā€œgain of functionā€ experiments at all, but the work of Zhengli and colleagues has shown that direct bat to human Coronavirus infection is possible. We are certain of it for Ebola.

The overall sequence of SARS-CoV-2 is closest to Yunnan isolates ā€“ only a bit appears to come from a virus that is HKU9-like. So it most likely came from Yunnan ā€“ but the outbreak occurred 700 miles away in Wuhan, not in Yunnan. Not along the way there either. The sole human traveler on high speed train while still in incubation is the best fit to the known information, in my view.

So for this to be true we need people traveling to Yunnan where they engage in risky behavior that could lead to infection, and then promptly returning to Wuhan. Turns out we have a large pool of people who frequently did just that - the researchers and their assistants from the Wuhan Institute of Virology. They have been making repeated trips several times each year to area bat caves, collecting 15,000 samples and finding around 400 novel coronaviruses so far.

How were the safety protocols, you may wonder?

From 4:45 to 4:56, a scientist can be seen holding a bat with his bare hands. Team members from 7:44 to 7:50 can be seen collecting potentially highly infectious bat feces while wearing short sleeves and shorts and with no noticeable personal protective equipment (PPE) other than gloves.

From 8:31 to 8:34, some team members can be seen wearing complete hazmat suits while many others are interacting with them in ordinary clothing and scrub caps and still others have no head covering at all. The camera then cuts to a container full of live, thrashing bats.

From the 8:42-8:47 mark, one team member is wearing full scrubs, mask, and scrub cap, while another is in street clothes, scrub cap, and mask, and the third person, possibly Shi, is handing samples with her bare hands.

Virus researcher Cui Jie (å“”ę°) relates his experiences of being bitten from 8:47 to 8:50.

Again, a scientist is seen holding and touching a live wild bat from the 8:51-9:06 mark. The video cuts back to the interior of the lab, where Hu Ben (胔ēŠ‡) is shown overseeing a woman as she handles specimens from 10:26 to 10:33. Neither is wearing a mask.

From 10:45 to 10:50, a team member in a camouflage shirt and without any PPE can be seen at the entrance of a cave in Yunnan, where many coronaviruses originate, with bats flying all around him. From 10:51 to 11:12, the video cuts to three lab technicians handling samples as the narrator describes ā€œthree live virusesā€ collected from Yunan. None are wearing masks.

Oh, you want to see the video itself? OK.

But surely things were much more secure back in Wuhan, under Shiā€™s careful leadership.

Google translation of the third to last paragraph on this page about her (archive.org in case it gets deleted):

Zhang Huajun said: ā€œThe research team captured a few bats from the wild to be used as experimental animals. They need to be fed every day. This Spring Festival, the students went home for a holiday, and Teacher Shi silently undertook the task of raising bats.ā€ Regarding this matter, many No one knows until now.

Great, thatā€™s great. She kept bats as pets.


So, how about those market origin theories? According to both NPR and the Kaiser Foundation, the two most high profile scientists pushing the animal origin theories - Peter Daszak and Robert Garry - have long-standing ties to and a close working relationship with the Wuhan Institute of Virology. Gee, I wonder if they have any biases or conflicts of interest?

Whatever and wherever the point of transmission ends up being, if found at all, it seems beyond obvious that there is a fairly high probability the Wuhan Institute played some key role in the initial outbreak.

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using my window to grunch and say

WERE U ABSENT THE DAY THEY TAUGHT LAW AT LAW SCHOOL

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Iā€™m using my 24 hour post to call you guys dumb for whatever drama this thread spawned. Told you it was a good idea to split it off from the main thread.

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US President Joe Biden has ordered intelligence officials to ā€œredoubleā€ efforts to investigate the origins of Covid-19, including the theory that it came from a laboratory in China.

He said the US intelligence community was split on whether it was the result of a lab accident, or emerged from human contact with an infected animal.

Mr Biden asked the groups to report back to him within 90 days.

Assume virus escaped China lab after gain of function research, what implication? International oversight of Chinese labs, sanctions, war? Good luck with those.

I submit that thereā€™s basically no practical difference with wet market vs lab (and obv lab probably wouldnā€™t mean human influence, just that they did field work and some samples were ā€œhitsā€). In either case the CCP has likely already taken major steps to limit future events. As vaccine development and deployment shows viruses are a bigger threat to China than US/EU.

China will continue to be a much bigger factor in global warming than the US (same with India). What international pressure works with regard to covid but not the more significant issue of global warming? Global warming is a much more certain if slow moving disaster than covid but the US, thanks to incoherent politics, canā€™t even offer de minimis international leadership or pressure.

China lab theory being practically meaningless, its only useful to gin up racists and thus help people like Cotton, which is a strong basis for skepticism, because his interest is in making the accusation, regardless of truth. Would I like to know the 100% accurate story? Sure. Does it matter? Not at all.

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It makes sense as I understand it (I could be misreading things). You have an area outside Wuhan with many animals in close contact, some variant is more effective at spreading in one population of animals and becomes variant B. You ship some animals to one market and other animals to another and boom, two lineages blow up at the same time. Itā€™s harder (but not impossible) to square how this happens with a lab leak of one variant. There could certainly have been more than one animal-human transmission at each location. Given how slowly this mutates and how little we know about the specifics Iā€™m not sure how many variants weā€™d expect to see on this animal farm.

Yeah, it fucking matters if weā€™ve spent the past year demonizing people who are actually doing incredibly important research. If we ever rule out a lab leak* we ought to send them a Hallmark apology card or something. ā€œSorry we called you guys cartoon supervillains and tried to defund your work, weā€™re just really bad at using Occamā€™s Razor,ā€ something like that.

  • ā€“ Which we havenā€™t done yet. Which I have to say explicitly every time now because people seem to get confused about what Iā€™m actually saying.

Are you on team Facebook?

Itā€™s exactly these things, i.e., an opportunistic tactical play by states aligned against China. This recent ā€œdeepening debateā€ fake news tour is coming from U.S. (and aligned) intelligence, hawkish think tanks, and rags that operate as mouthpieces for those groups like the WSJ. This guy Metzl from the Atlantic Council, the neocon hawk media influencer, is a lab leak cheerleader getting a lot of airplay. Hereā€™s what he wrote on his personal website:

Let me be clear. While I do believe that a lab incident is the most likely origin of the pandemic, this is only a hypothesis. That this pandemic might stem from a zoonotic jump in the wild is also a hypothesis, even though very little evidence supporting that hypothesis has so far emerged. When comparing the evidence for each possibility, the case for a lab incident origin seems significantly stronger to me.

Lolk but WSJ has been pumping this shit the whole time.

Like Keeed, he was a lab leaker from the very beginning, so weā€™re left wondering if heā€™s actually this kooky or just trying to influence shit, but itā€™s obviously the latter because thatā€™s what the marionnette Atlantic Council does. Notice what he says here too: a lab accident followed by a criminal cover up. Brah loudly calling for FuLl iNvEsTiGaTiOnS (read: espionage, defunding, and sanctions) is balls deep into the criminal fucking conspiracy angle as the most likely explanation and openly accusing China of massive criminal activity. Also notice that the puppets doing this reboot are saying we should now ask intelligence agencies for the correct answers.

Facebook has a public partnership with the Atlantic Council and is one of their largest donors.

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yeah Iā€™m wondering the same thing. people are talking about this like ā€œlab leakā€ and ā€œcame from an animalā€ are mutually exclusive but even if this had been in a lab at some point, it almost certainly came from animal before it got into the lab, right? Thereā€™s nothing so far to suggest this is a fabricated, engineered virus, correct?

but yeah, in a bigger sense, what difference does it make (other than maybe getting people to realize their lab procedures are deficient)? It doesnā€™t seem that the US response (from a health perspective, at least) would need to be different if the answer to this is one or the other (Trump loved to peddle this because he thinks it gets him off the hook somehow but ā€¦ it doesnā€™t). Like, if anything itā€™s worse, china unleashed a bioweapon and trump did nothing and let them kill half a million americans is somehow good for him???

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https://twitter.com/NateSilver538/status/1397869883585708034

https://twitter.com/NateSilver538/status/1397876974434066432

It is not some contrarian position to suggest there is considerable uncertainty about it. It is the mainstream position, rather.

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You do realize that this is exactly what happened with SARS right? The source was found after a decade+ of research, and the outbreak was in Guangdong. Pointing to the distance as if itā€™s inconceivable when it literally already happened is nonsense. Ignoring how those same bats are used in bush meat and ignoring basic facts how the market was the epicenter of the beginning of the outbreak is just ludicrous.

Weā€™ll skip over how this is climate denier style impugning of credibility, because why bother honestly. Nothing in either article actually demonstrates any conflict of interest or bias. Feel free to actually quote something specifically if you feel differently. The market theory isnā€™t some thing supported mainly by these two guys. Itā€™s the overwhelming consensus.

ā€˜fairly high probabilityā€™. Yikes, the whole 1% thing is gone now. Based on some YouTube videos and an essay from an author that definitely states it comes from bats in a cave, a scenario thatā€™s literally happened twice in the past 20 years?

This post is a perfect example of what gets my jimmies rustled. You get to just throw whatever nonsense against the wall, and itā€™s up to me and others to disprove your completely unsupported assertions. Itā€™s especially bad when your main point is a link that directly contradicts your point and you try to frame it as plausibly supporting your theory. Your evidence is literally nothing more than that someone has been studying coronaviruses since theyā€™ve been responsible for two major outbreaks. Itā€™s utter shit level of evidence.

Meanwhile, I like this thread:

https://twitter.com/MoNscience/status/1396240581651742724

Highlights, because no one reads anything:

Taking down Wade:

https://twitter.com/MoNscience/status/1396243452099170305

Studies as evidence for natural origin:

https://twitter.com/MoNscience/status/1396247184635539466

Furin site stuff:

https://twitter.com/MoNscience/status/1396249523668795394

Nice little take about the ā€˜BUT WE DONā€™T KNOW THE SOURCEā€™ with talking about how we donā€™t know the source of ebolaā€¦ after 40+ years:

https://twitter.com/MoNscience/status/1396252396842541057

Canā€™t be ruled out you say?

https://twitter.com/MoNscience/status/1396253057508421632

Calls out ZikZakā€™s conspiracy theory:

https://twitter.com/MoNscience/status/1396254969699962887

Also Nate can fuck right off. Experts on both sidesā€¦ no, thatā€™s not true. Thereā€™s a clear consensus. His twitter feed is hilarious. Biden is investigating so it must be a lab! Yair Rosenberg got push back after saying Trump could win in 2016! Notably, zero experts backing his assertion of >50%. I like his work more than most, but heā€™s such a fucking idiot sometimes.

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Long post just to say natural origin is most likely. Iā€™m pretty sure that has been the consensus here the whole time.

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Iā€™m using todayā€™s post to say that while this happened a while ago, whoever changed the original original thread title to ā€œthe oranges of covidā€ was a genius and whoever changed it back was a silly.

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ZZ is saying that thereā€™s a fairly high probability with next to nothing backing it. Silver is positing it at >50%. Consensus doesnā€™t seem to actually be there.