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New DNA analysis adds strong evidence for natural origin of COVID-19 virus

The Atlantic reports today that three researchers have performed a re-analysis of swabs taken at the Huanan Market in Wuhan early in the COVID-19 pandemic. The original analysis, done last year by a Chinese team, drew no conclusions about the origin of the virus, but the new analysis strongly suggests that the virus developed naturally and then jumped to humans from raccoon dogs:

A new analysis of genetic sequences collected from the market shows that raccoon dogs being illegally sold at the venue could have been carrying and possibly shedding the virus at the end of 2019....The genetic sequences were pulled out of swabs taken in and near market stalls around the pandemic’s start. They represent the first bits of raw data that researchers outside of China’s academic institutions and their direct collaborators have had access to.

....Within about half a day of downloading the data from GISAID, [the researchers] discovered that several market samples that tested positive for SARS-CoV-2 were also coming back chock-full of animal genetic material—much of which was a match for the common raccoon dog. Because of how the samples were gathered, and because viruses can’t persist by themselves in the environment, the scientists think that their findings could indicate the presence of a coronavirus-infected raccoon dog in the spots where the swabs were taken.

“This is a really strong indication that animals at the market were infected,” said Seema Lakdawala, a virologist at Emory University who wasn’t involved in the research. “There’s really no other explanation that makes any sense.”

So that's the latest science. Here's the latest polling:

Sigh.

32 thoughts on “New DNA analysis adds strong evidence for natural origin of COVID-19 virus

    1. George Salt

      Speaking of faked evidence, this week marks the 20th anniversary of the invasion of Iraq.

      The lack of introspection in the US media is telling.

    2. Lounsbury

      Given the history of the data (not posted to attract attention, see below), and the PRC pretence that in fact Covid originated outside of China, it is frankly 100 per cent incoherent to even think it's fake to show Hunan market origin given if PRC Gov wanted to fake genetic data they would clearly choose something that would fit their preferred narrative.

      Not fake data that pointed the finger at PRC incompetence in suppressing mixed wild-and-domestic live-animal markets that are not supposed to be extent... as doubly not in their narrative (re markets, re health controls in PRC, re origin of virus)

      Of course frankly the idea of lab origin is silly when a large unregulated wet-market mixing in uncontrolled fashion wild animals and domestic is and was the veritable perfect breeding ground for virus species jumping .

      Rather than engage in pseudo-scientific American Action Movie conspiracy mongering, rather better to point the finger at PRC lying about health risks from unregulated (effectively) live animal markets in extremely dense population areas, which are veritable open-air labs for next pandemic.

      Science.org linked below
      Unearthed genetic sequences from China market may point to animal origin of COVID-19
      French scientist finds previously undisclosed data from Chinese research team
      https://www.science.org/content/article/covid-19-origins-missing-sequences

      1. D_Ohrk_E1

        From the last paragraph of that Science article:

        “You can’t observe the zoonotic transmission of a novel virus from animals to humans,” Wertheim says. “We’re just never going to get that level of data.”

        It should be technically possible to find the source reservoir and track the lineage back to a common ancestor, even after a period of time past the spillover event. The exceptions include a one-off infected animal or the reservoir died off.

        Civet SARS-CoV and Tanuki SARS-CoV were 99.9% match for human SARS-CoV.

        That's what we should be looking for. The closest known relative to SARS-CoV-2 is RaTG13 (the infamous WIV horseshoe bat sample from Yunnan), which matched 96.1% of the total genome of SARS-CoV-2 and 92.9% of the S protein. By comparison, RaTG13 is only a 79% match to SARS-CoV, highlighting two very distant lineages.

        What Worobey is apparently showing (unknowable since they haven't actually published yet), on account that they've cited commingled DNA, is proof of proximity of Tanuki to humans. They're not, again because of the DNA being commingled, showing that the virus likely came from Tanuki.

    3. Solar

      And what type analysis would you find sufficient or convincing?

      From what I've seen, for the lab leak conspiracy theorists, Xi publicly admitting the virus came from the lab is the only "analysis" they are willing to believe.

  1. MattBallAZ

    I just hope it is far enough from the lockdowns that there isn't violence against people of Asian descent. (And poor Fauci. 🙁 )

  2. cmayo

    To me, that poll is just another example of the phenomenon that nudges people into conspiracism - because it's more comforting to believe that someone somewhere caused the awful events than it is to know that the world is just random and sometimes bad shit happens at random.

    Perhaps magnified a bit by the extraordinarily low-disease environment of the last 90+ years. Yes, we had some pretty bad diseases and a bad flu pandemic at the end of WW1, but compared to the historical record when epidemics/pandemics were more frequent and more deadly...

  3. Richard

    Could you please post a link to the article itself? The Atlantic story is not accessible to those of us who aren't subscribers.

    1. golack

      hard to find....
      Here's a NewsHour report:
      https://www.ket.org/program/pbs-newshour/new-evidence-tracks-covids-origin-to-wuhan-m

      And here's a write up on the Science website (not the article):
      https://www.science.org/content/article/covid-19-origins-missing-sequences

      From what I can tell, the Chinese loaded their genomic data onto a database used by the viral community, no announcement, others saw it, quickly analyzed it, came up with a report for WHO and/or preprints, the the Chinese withdrew the data. Oops. It seems that the official Chinese position is that Covid originated elsewhere (not China), and was introduced into the wet market in Hunan (not that it was actually a wet market).

    2. D_Ohrk_E1

      You can access the article if you do one of two things:

      1) Dump your site-specific cookies, which will reset the number of articles you're allowed to view for free, then refresh.
      2) Turn off javascript and refresh.

  4. George Salt

    The lab leak hypothesis has become this century's JFK assassination. The conspiracy theories will never die.

    1. D_Ohrk_E1

      We have found the source of zoonosis: Tanuki (Tanooki) Mario. After skinning a racoon dog, he'd contracted SARS-CoV-2 and became patient zero, quickly infecting his brother Luigi, Baby Mario, and Baby Luigi.

        1. iamr4man

          A while back I saw a news story about how a lot of Chinese made supposed faux fur clothing items sold in the US were actually tanuki fur. In the story they showed a wet market vendor killing a tanuki by swinging the live animal by its hind legs and smacking its head on to a concrete slab.
          It’s humans who are the monsters.

    2. iamr4man

      One of my favorite Studio Ghibli films is Heisei Tanuki Gassen Pom Poko, (Heisei era tanuki war boom boom) directed by Isao Takahata. In Japan tanuki are shape shifters who battle warriors using their gigantic scrotums as clubs. In the movie, humans are going to build a housing project that will destroy the tanuki’s habitat and the tanuki use their powers to try to stop them. It’s a fun movie that’s better if you know a little bit about Japanese folklore.
      Takahata directed probably one of the greatest of all anime films, Grave of the Fireflies. I very highly recommend that film, but be prepared to cry. It is one of the most heart wrenching films you will ever see.

      1. cld

        Heisei Tanuki Gassen Pom Poko is on HBO under the title Pom Poko, so now I have to something to do this evening!

        I only managed to see half of Grave of the Fireflies before I couldn't take it anymore.

        I've wanted to watch it again for [insert shocking length of time] but I can never bring myself to.

  5. D_Ohrk_E1

    You would be one of those people who would have convicted Amanda Knox for murder, I think.

    Her DNA was found in the same location where a murder occurred, so clearly, she committed the murder, right?

    All of the researchers and Wu herself state that all of the samples of surfaces had commingled bits of DNA. The coincidence of a set of samples with higher bits of raccoon dog DNA in a stall where there had previously been raccoon dogs is proof of what, exactly?

    It's proof of confirmation bias.

    1. jdubs

      Youre an expert in this field? Or only an expert when it comes to the specific data related to covid origins? Or not enough of an expert to engage with the data, but enough of an expert to be certain that the experts are wrong?

      Are you projecting your own confirmation bias here?

      Fascinating.

      1. Jasper_in_Boston

        Or not enough of an expert to engage with the data, but enough of an expert to be certain that the experts are wrong?

        This. For guidance on the likely source of the novel coronavirus, we definitely should all embrace the ramblings of the lab leak conspiracy buffs who regularly chime in on these threads.

        The actual PhD-level virologists willing to go on record and explain why natural zoonotic spillover is the likely culprit? Those guys we should write off. Because Commies.

      2. D_Ohrk_E1

        Science sometimes requires experts of a field to accept the prevailing narrative in order to get funding or to be heard. Skeptics become heretics.

        For nearly two decades, ALZ has focused amyloid beta. Drug research in reducing amyloids in the brain got all the funding and air time. They were wrong. Some still believe that amyloid drives ALZ, and while they surely play some part, it's not the whole picture, as people full of amyloid never show signs of ALZ.

        The point is, you shouldn't be so dogmatic to claim, as many are doing in the comment section of this blog, to know with great certainty of the source of SARS-CoV-2. Labeling people as kooks or conspiracists when they point out the obvious flaws of a claim, is just trolling.

        If you cannot provide a counter-claim because you don't know enough to have a discussion, why resort to name-calling?

  6. jdubs

    Everyone knows that the lab routinely hired racoon dogs as interns. Lab dog was probably out on a smoke break, cut his finger when he dropped the virus beaker he was carrying around town.

    Viva la conspiracy!!

  7. Justin

    I would always answer a pollsters question in the most extreme way possible. It's much more fun that way.

    Clearly this was a Chinese bioweapon that "leaked" out. Or probably intentionally since the Chinese are soulless bastards.

  8. Toofbew

    What does polling have to do with the origin of Covid-19? Science writers Matt Ridley and Nicholas Wade in separate books both conclude it was a lab leak. Why is that less probable than raccoon dog zoonosis? The fact that the Chinese government has obstructed scientific investigation of this outbreak suggests they know it began with some sort of contamination via bio lab staff. Weird Chinese food and medicine preferences seem to have mesmerized many Americans into believing (without any scientific basis) that this was a natural spillover event even though one of the most active SARS research labs in the world happens to be in Wuhan. We don’t yet know. We may never know.

    1. aldoushickman

      "The fact that the Chinese government has obstructed scientific investigation of this outbreak suggests they know it began with some sort of contamination via bio lab staff. "

      No, it just suggests that the Chinese government, like all lousy authoritarian governments, is not forthcoming about subjects that it doesn't like. China would not be 100% open and transparent in the event of a zoonotic pandemic that started on their soil because (a) they don't care about the Truth, and (b) they don't care whether some dude named Toofbew on the internets believes them.

      You're engaging in silly conspiracy theory mongery, in which you're aligning evidence to support what you think are the most fun/interesting conclusions, not the most likely.

  9. Citizen99

    Well, as with so much polling, the QUESTION is stupid! Note that it asks if the pandemic was "caused by a laboratory leak OR by a natural transmission from animals to humans." Whatever stoned intern wrote that question didn't understand that even the lab leak hypothesis was based on prior transmission from animal to human. The "lab leak" presumes that someone in the lab who was RESEARCHING the virus may have gotten infected.
    So the form of the question reinforces the implied right-wing narrative that the virus was a nefarious bioweapon developed by the Chinese and deliberately leaked out into the world to kill Americans. And now 64% of Americans have bought that storyline, which has 0% chance of being correct.
    This is why I am so disgusted with the mainstream media, and polling houses most of all.

  10. D_Ohrk_E1

    Feel free to watch WHO explain it (since none of you believe in what I've written) here: https://twitter.com/WHO/status/1636700787702403072

    Tedros: "This data do not prove a definitive answer to the question of how the pandemic began."
    Kerkhove: "...and what they presented to us is that they found molecular evidence that animals were sold at that market...and some of the animals that were there were susceptible to SARS-CoV-2 infection...unfortunately this does not give us the answer of how this pandemic began."

    We already had photographic evidence from late 2019 that this same area previously had civets and racoon dogs.

    Also Kerkhove: "We have repeatedly asked for studies to be done in other markets in Wuhan and in Hubei and across China...studies to trace those animals back to their source farms...serology to be conducted of people who worked in the markets."

    Do you think China conducted those studies (and are hiding the results) or not?

    See, here's the thing. If the do these studies, the location of mutations and number of mutations could provide a timeline of where, when, and how the spillover occurred. I'm not saying anything new here; this is how we can trace SARS-CoV-2 to China, after all.

    But therein lies the rub, right? China's official narrative is that the source of SARS-CoV-2 was foreign. To trace it back to a Chinese source is to lay blame on CCP for its failures to maintain strict regulation of its wildlife trade at wet markets.

  11. shapeofsociety

    How do they know that the raccoon dogs didn't get the virus from the humans who were handling them?

    And how do you explain the fact that the closest known wild relatives of Covid are all bat coronaviruses in Yunnan province? How did a Yunnanese bat virus make it into raccoon dogs being sold at a market in Wuhan?

    Yeah... I'm not 100% convinced of lab leak but I don't find this convincing either.

  12. Gilgit

    I really appreciate Kevin making these posts about the origin of the pandemic. Until now I was aware that the evidence pointed to natural origin instead of a lab leak, but I hadn’t realized just how strong the evidence was. It isn’t just that there's evidence from the wet market, it's the many different strands that all point the same way. And none of them pointing the other way.

    Of course, none of the conspiracy guys will change their minds. But to any of you that read this and wonder if the lab leak theory has any credibility, who think, “Maybe there is some massive cover up by the Chinese,” I will simply compare it with other stupid, fake ideas that have come out in the last few years. 1st would be the US weapons labs in Ukraine. Basically, the Russians just pointed out that the US has had dealings with labs in Ukraine and then claimed that that proved that the US was developing magical bio-weapons there. No weapons were produced to prove it. No workers describing the evil deeds. Nothing. Just some talking heads saying that if there was any contact for any reason then it was proven to be bio-weapons.

    Another good one was the 2020 election. They’d make a million claims and then go before a judge and be unable to show even the simplest fraud. I’d also point to the Uyghurs in China. The Chinese say they are being treated great, but even the simplest investigation would show the abuses.

    But somehow with Covid many, many separate investigative teams managed to find 100s of documents, interviews, and scientific analyses that all point in the same direction and confirm each other's findings. It wasn’t just different, it was an order of magnitude different and also involved highly experienced scientists around the world.

    Yes the lab leak guys will all claim they can’t see the difference, but odds are you can.

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