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Both of your points are directly and conclusively addressed in the post.. > First, because viruses travel easily – so even if 100% of early cases were around t

Both of your points are directly and conclusively addressed in the post.. > First, because viruses travel easily – so even if 100% of early cases were around the market, it could have reached the market via a lab worker There were two distinct lineages at the market with a cluster of positive environmental samples in the wild animal section. I would love to hear a plausible theory on how two unrelated lineages came to be present there after human-human transmission. > And second, early overemphasis on the market cluster caused authorities to search for every case there, and ignore cases elsewhere – just as in the US, authorities missed early community spread because they didn't even consider/test people who hadn't recently returned from China. Not remotely true. I'd encourage you to read this paper: https://zenodo.org/record/6299600#.YjSWqDUxmUk https://zenodo.org/record/6299600#.YjSWqDUxmUk

gojomo 4y ago
The prior linked post is a gish-gallop of overconfident motivated reasoning. "Two lineages" in rapid-succession is weird - but no better explained by two zoonoses (that left no hints in any animal population) than two lab-leaks. Worobey et al's analysis is at the mercy of Chinese data sources, and even if all early cases were exclusively in the market, and even the live-animal section, that doesn't disprove lab origin. It might slant things slightly against it - but when no other animals, anywhere from Laos to Wuhan, have revealed any of these supposed intermediate forms – that somehow zoonosed twice, only after reaching Wuhan, with a dangerous new viral feature Wuhan researchers had proposed splicing into bat viruses?!? – the slant remains very much in the other direction. But you don't have to trust me; even the WHO now wants a better investigation of the prematurely-suppressed lab-origin possibility: https://www.washingtonpost.com/world/2022/06/09/who-sago-covid-origins/ https://www.washingtonpost.com/world/2022/06/09/who-sago-cov... There's a field-wide omerta about gain-of-function risks – who wants to ruin their relationship with the NIH, & admit research that's pretty typical across many leaky labs worldwide, may have killed 20 million people (and counting)?
- mikeyouse 4y ago
  > "Two lineages" in rapid-succession is weird - but no better explained by two zoonoses (that left no hints in any animal population) than two lab-leaks. I mean, everyone can stop reading here... This is patently false. Multiple Spillover is a readily reproducible phenomenon that perfectly explains the dual lineages. Again, spell out specifically the route how two distinct lineages would be present at the market under the lab leak scenario. > It might slant things slightly against it - but when no other animals, anywhere from Laos to Wuhan, have revealed any of these supposed intermediate forms – that somehow zoonosed twice, only after reaching Wuhan You literally only need one animal shedding virus - it's how literally every other pandemic started. The market was shut down weeks after it was clear that a pandemic was underway and only after that did the authorities start looking for infected animals. Absence of evidence here isn't remotely a substitution for evidence of the absence. > with a dangerous new viral feature Wuhan researchers had proposed splicing into bat viruses?!? – the slant remains very much in the other direction. This part is just false and belies your lack of understanding of the science and the direction of causality. The reason scientists proposed studying the FCS is because it was identified a decade+ ago as both dangerous for zoonosis and readily possible with natural mutation. All of these virologists studying coronaviruses weren't doing it out of the blue, but because everyone knew that it was the single greatest zoonotic risk we faced.
  - gojomo 4y ago
    A lab worker who was careless (if not depressed/malicious) could just as easily carry out two variants as one. One animal shedded... two variants of virus? How did the animal get it, when no other nearby wild or market animals in the (lackluster) investigation around Wuhan, or since elsewhere, have shown candidate SARS-CoV2/precursor viruses? They proposed adding the FCS to existing viruses where FCS hadn't been seen before – and yes, the motivation was because that was considered a potential natural risk. But that doesn't mean it was a natural inevitability. Isn't the proximity of the proposal, "add FCS to a bat coronavirus to see how much worse it makes it", to the appearance of SARS-CoV2 at least a little suspicious? They & others have published lots of work that specifically made existing viruses more transmissable, or more severe – often in labs with a history of leaks. This can be done via evolutionary pressures – serial passage forced-evolution – or via explicit engineering of new chimeric viruses. Coronavirus crossover was theorized to be a major risk, after SARS/MERS. That didn't mean that actually outracing nature to make the hypothesized worse viruses in accelerated lab processes was a good risk-reducing idea!
- epistasis 4y ago
  > There's a field-wide omerta about gain-of-function risks – who wants to ruin their relationship with the NIH, & admit research that's pretty typical across many leaky labs worldwide, may have killed 20 million people (and counting)? Claims like this, without evidence, reallt detract from any other point you want to make. Because it seems that your thumb is pretty heavy in the scale, without any evidence.
  - pbreit 4y ago
    No heavier than your thumb on the zoonosis scale.
    - epistasis 4y ago
      Where have I put my thumb on the zoonosis scale?
  - gojomo 4y ago
    When there are massive institutional incentives to proclaim X, it is only wise to discount, somewhat, proclamations of X. In Vanity Fair's lab-leak theory story, there was an illustrative detail: *> Inside the NIH, which funded such research, the P3CO ["Potential Pandemic Pathogen Care and Oversight"] framework was largely met with shrugs and eye rolls, said a longtime agency official: “If you ban gain-of-function research, you ban all of virology.” He added, “Ever since the moratorium, everyone’s gone wink-wink and just done gain-of-function research anyway.” A whole field wants certain research to happen, with minimal limits. They don't want to admit, or even let themselves believe, that their peers' accident killed 20 million people. It's a hard pill to swallow!
    - epistasis 4y ago
      That's reading an awful lot into an unattributed quote, which includes a direct refutation attributed quotes right above it. It's clear that there have been moratoriums on GoF without stopping "all of virology," so whatever was meant by this "wink wink nudge nudge" is really unclear. Also, in the prior paragraph, the reporter talks about "details of proposed experiments being secret" but that's just standard practice for literally all government funding of science. As if they shouldn't be secret for some reason in this case. If this the sort of weak sauce, I mean, come on. Just a bunch of weird insinuations, and having read more, saying there's "omerta" on this seems even less likely. How about at least a little bit of real meat?
lamontcg 4y ago
> There were two distinct lineages at the market No there were two distinct lineages in two separate crossover events, the market was just one of them. Which is even worse for the lab-leak hypothesis.
- tripletao 4y ago
  They're literally just two SNPs apart, per my reply to the grandparent and link to Jesse Bloom's Twitter. What do you think excludes the possibility that those arose during human-to-human transmission, whether at the market or during cryptic spread before that?
  - deleted 4y ago
    [deleted]
- kaitaincps 4y ago
  No, we don’t know there were two separate crossover events. The two lineages are more likely to be the result of a minor mutation having occurred during human-human transmission, i.e. subsequent to the initial (single) crossover event.
pbreit 4y ago
Two lineages do not preclude lab origin. And the data collection was absolutely biased to the market.
tripletao 4y ago
These "two distinct lineages" are separated by exactly two single-nucleotide polymorphisms (SNPs). For comparison, omicron differs from the original Wuhan virus by more than fifty SNPs. SARS-CoV-2 averages something around a third of an SNP per human-to-human transition. https://mobile.twitter.com/jbloom_lab/status/1534630607220711425 https://mobile.twitter.com/jbloom_lab/status/153463060722071... It's overwhelmingly likely that something around two months of cryptic spread occurred before the market super-spreader event, regardless of whether the origin was natural or research-related. That's plenty of time for these "two distinct lineages" to develop. They could also have developed at the market, either in a single transmission with two mutations, or in two transmissions with an intermediate lineage that died out before it could be sampled. Were you previously aware that the two lineages were just two SNPs apart? It's bizarre to me that the "two lineages" have received so much press as evidence of natural zoonosis, when they could have arisen so easily in human-to-human transmission.
- mikeyouse 4y ago
  > Were you previously aware. Yes, of course. > It's overwhelmingly likely that something around two months of cryptic spread occurred before the market super-spreader event, regardless of whether the origin was natural or research-related. That's plenty of time for these "two distinct lineages" to develop. They could also have developed at the market, either in a single transmission with two mutations, or in two transmissions with an intermediate lineage that died out before it could be sampled. Two points - if there were months of cryptic spread, that essentially rules out 95% of the lab leak hypotheses and further reduces the importance of the WIV proximity. Secondly, Twitter is an obnoxious interface but Pekar who wrote the paper highlighting the divergent sequences has a good thread explaining why it’s such an important data point: https://mobile.twitter.com/jepekar/status/1499843269500407808 https://mobile.twitter.com/jepekar/status/149984326950040780... Since the multiple lineages were present in the very first patients as compared to say January 2020, it narrows the dates and source of the first virus considerably. The very first identified cases had two distinct viruses and were all present at the market. That’s not at all what you would see if the virus had been spreading for a longer period (we’d have intermediate samples) or if someone from the WIV went to the market and infected people (they’d all show the common lineage that all other transmission chains show).
kaitaincps 4y ago
I would be much more fascinated to know how two separate lineages both made their first leap to humans at the same market. The odds on THAT occurring are much, MUCH smaller than those of two lineages that had already made the leap to humans (or two branches descended from the first human leap) being found at the same market during the first few months of an epidemic.
deleted 4y ago
[deleted]

gojomo 4y ago

The prior linked post is a gish-gallop of overconfident motivated reasoning. "Two lineages" in rapid-succession is weird - but no better explained by two zoonoses (that left no hints in any animal population) than two lab-leaks. Worobey et al's analysis is at the mercy of Chinese data sources, and even if all early cases were exclusively in the market, and even the live-animal section, that doesn't disprove lab origin. It might slant things slightly against it - but when no other animals, anywhere from Laos to Wuhan, have revealed any of these supposed intermediate forms – that somehow zoonosed twice, only after reaching Wuhan, with a dangerous new viral feature Wuhan researchers had proposed splicing into bat viruses?!? – the slant remains very much in the other direction. But you don't have to trust me; even the WHO now wants a better investigation of the prematurely-suppressed lab-origin possibility: https://www.washingtonpost.com/world/2022/06/09/who-sago-covid-origins/ https://www.washingtonpost.com/world/2022/06/09/who-sago-cov... There's a field-wide omerta about gain-of-function risks – who wants to ruin their relationship with the NIH, & admit research that's pretty typical across many leaky labs worldwide, may have killed 20 million people (and counting)?

mikeyouse 4y ago
> "Two lineages" in rapid-succession is weird - but no better explained by two zoonoses (that left no hints in any animal population) than two lab-leaks. I mean, everyone can stop reading here... This is patently false. Multiple Spillover is a readily reproducible phenomenon that perfectly explains the dual lineages. Again, spell out specifically the route how two distinct lineages would be present at the market under the lab leak scenario. > It might slant things slightly against it - but when no other animals, anywhere from Laos to Wuhan, have revealed any of these supposed intermediate forms – that somehow zoonosed twice, only after reaching Wuhan You literally only need one animal shedding virus - it's how literally every other pandemic started. The market was shut down weeks after it was clear that a pandemic was underway and only after that did the authorities start looking for infected animals. Absence of evidence here isn't remotely a substitution for evidence of the absence. > with a dangerous new viral feature Wuhan researchers had proposed splicing into bat viruses?!? – the slant remains very much in the other direction. This part is just false and belies your lack of understanding of the science and the direction of causality. The reason scientists proposed studying the FCS is because it was identified a decade+ ago as both dangerous for zoonosis and readily possible with natural mutation. All of these virologists studying coronaviruses weren't doing it out of the blue, but because everyone knew that it was the single greatest zoonotic risk we faced.
- gojomo 4y ago
  A lab worker who was careless (if not depressed/malicious) could just as easily carry out two variants as one. One animal shedded... two variants of virus? How did the animal get it, when no other nearby wild or market animals in the (lackluster) investigation around Wuhan, or since elsewhere, have shown candidate SARS-CoV2/precursor viruses? They proposed adding the FCS to existing viruses where FCS hadn't been seen before – and yes, the motivation was because that was considered a potential natural risk. But that doesn't mean it was a natural inevitability. Isn't the proximity of the proposal, "add FCS to a bat coronavirus to see how much worse it makes it", to the appearance of SARS-CoV2 at least a little suspicious? They & others have published lots of work that specifically made existing viruses more transmissable, or more severe – often in labs with a history of leaks. This can be done via evolutionary pressures – serial passage forced-evolution – or via explicit engineering of new chimeric viruses. Coronavirus crossover was theorized to be a major risk, after SARS/MERS. That didn't mean that actually outracing nature to make the hypothesized worse viruses in accelerated lab processes was a good risk-reducing idea!
epistasis 4y ago
> There's a field-wide omerta about gain-of-function risks – who wants to ruin their relationship with the NIH, & admit research that's pretty typical across many leaky labs worldwide, may have killed 20 million people (and counting)? Claims like this, without evidence, reallt detract from any other point you want to make. Because it seems that your thumb is pretty heavy in the scale, without any evidence.
- pbreit 4y ago
  No heavier than your thumb on the zoonosis scale.
  - epistasis 4y ago
    Where have I put my thumb on the zoonosis scale?
- gojomo 4y ago
  When there are massive institutional incentives to proclaim X, it is only wise to discount, somewhat, proclamations of X. In Vanity Fair's lab-leak theory story, there was an illustrative detail: *> Inside the NIH, which funded such research, the P3CO ["Potential Pandemic Pathogen Care and Oversight"] framework was largely met with shrugs and eye rolls, said a longtime agency official: “If you ban gain-of-function research, you ban all of virology.” He added, “Ever since the moratorium, everyone’s gone wink-wink and just done gain-of-function research anyway.” A whole field wants certain research to happen, with minimal limits. They don't want to admit, or even let themselves believe, that their peers' accident killed 20 million people. It's a hard pill to swallow!
  - epistasis 4y ago
    That's reading an awful lot into an unattributed quote, which includes a direct refutation attributed quotes right above it. It's clear that there have been moratoriums on GoF without stopping "all of virology," so whatever was meant by this "wink wink nudge nudge" is really unclear. Also, in the prior paragraph, the reporter talks about "details of proposed experiments being secret" but that's just standard practice for literally all government funding of science. As if they shouldn't be secret for some reason in this case. If this the sort of weak sauce, I mean, come on. Just a bunch of weird insinuations, and having read more, saying there's "omerta" on this seems even less likely. How about at least a little bit of real meat?

lamontcg 4y ago

> There were two distinct lineages at the market No there were two distinct lineages in two separate crossover events, the market was just one of them. Which is even worse for the lab-leak hypothesis.

tripletao 4y ago
They're literally just two SNPs apart, per my reply to the grandparent and link to Jesse Bloom's Twitter. What do you think excludes the possibility that those arose during human-to-human transmission, whether at the market or during cryptic spread before that?
- deleted 4y ago
  [deleted]
kaitaincps 4y ago
No, we don’t know there were two separate crossover events. The two lineages are more likely to be the result of a minor mutation having occurred during human-human transmission, i.e. subsequent to the initial (single) crossover event.

pbreit 4y ago

Two lineages do not preclude lab origin. And the data collection was absolutely biased to the market.

tripletao 4y ago

These "two distinct lineages" are separated by exactly two single-nucleotide polymorphisms (SNPs). For comparison, omicron differs from the original Wuhan virus by more than fifty SNPs. SARS-CoV-2 averages something around a third of an SNP per human-to-human transition. https://mobile.twitter.com/jbloom_lab/status/1534630607220711425 https://mobile.twitter.com/jbloom_lab/status/153463060722071... It's overwhelmingly likely that something around two months of cryptic spread occurred before the market super-spreader event, regardless of whether the origin was natural or research-related. That's plenty of time for these "two distinct lineages" to develop. They could also have developed at the market, either in a single transmission with two mutations, or in two transmissions with an intermediate lineage that died out before it could be sampled. Were you previously aware that the two lineages were just two SNPs apart? It's bizarre to me that the "two lineages" have received so much press as evidence of natural zoonosis, when they could have arisen so easily in human-to-human transmission.

mikeyouse 4y ago
> Were you previously aware. Yes, of course. > It's overwhelmingly likely that something around two months of cryptic spread occurred before the market super-spreader event, regardless of whether the origin was natural or research-related. That's plenty of time for these "two distinct lineages" to develop. They could also have developed at the market, either in a single transmission with two mutations, or in two transmissions with an intermediate lineage that died out before it could be sampled. Two points - if there were months of cryptic spread, that essentially rules out 95% of the lab leak hypotheses and further reduces the importance of the WIV proximity. Secondly, Twitter is an obnoxious interface but Pekar who wrote the paper highlighting the divergent sequences has a good thread explaining why it’s such an important data point: https://mobile.twitter.com/jepekar/status/1499843269500407808 https://mobile.twitter.com/jepekar/status/149984326950040780... Since the multiple lineages were present in the very first patients as compared to say January 2020, it narrows the dates and source of the first virus considerably. The very first identified cases had two distinct viruses and were all present at the market. That’s not at all what you would see if the virus had been spreading for a longer period (we’d have intermediate samples) or if someone from the WIV went to the market and infected people (they’d all show the common lineage that all other transmission chains show).

kaitaincps 4y ago

I would be much more fascinated to know how two separate lineages both made their first leap to humans at the same market. The odds on THAT occurring are much, MUCH smaller than those of two lineages that had already made the leap to humans (or two branches descended from the first human leap) being found at the same market during the first few months of an epidemic.

deleted 4y ago

[deleted]