5 ms·

> Aside from the contact-tracing, investigators were able to get positive PCR recovery of sars-cov-2 from -environmental samples- at the wet markets, indicating

by timr 5y ago

> Aside from the contact-tracing, investigators were able to get positive PCR recovery of sars-cov-2 from -environmental samples- at the wet markets, indicating an incredible degree of contamination there. So? It's a market. People go there, in large numbers. Is it really surprising that you'd find traces of a widely circulating respiratory virus in a place where large numbers of people congregate? > By natural standards the Laos samples are extremely close RaTG13 is closer than the BANAL viruses, and we already knew about it. You have to look at specific genes and squint and make hand-wavy arguments about how SARS-CoV2 evolved from recombination of ~5 different viruses to make any sort of claim that this is strong evidence of natural evolution. I'll give you this: the RBD of BANAL-20-52 is the closest match yet for the RBD of SARS-CoV2. Still no furin cleavage site, though. https://assets.researchsquare.com/files/rs-871965/v1/986c09ca-d494-4a7c-a65b-9eec9c0a06b8.pdf https://assets.researchsquare.com/files/rs-871965/v1/986c09c... > the evolutionary "risk surface area" of zoonosis is many orders of magnitude larger than this nutty lab-leak idea I love this. The evolutionary story is too complicated and improbable to imagine, but sure, the idea of making a few relatively simple additions to a known virus is "nutty". And hey...it's not like there was a lab in Wuhan writing grants about similar transformations or anything. You have to be kidding. Look, I don't have a strong opinion one way or the other, but you're simply in love with a theory and dismissing all evidence to the contrary.

dnautics 5y ago
The furin cleavage site looks suspiciously like a hallmark cut-and-paste operation that is exactly what I would do as a genetic engineer.
- hcknwscommenter 5y ago
  Really? I'd like to hear more about this. What exactly looks so "suspicious" that it can't be explained by typical recombination events that are known to occur naturally in RNA viral genomes?
  - dnautics 5y ago
    The beta coronavirus class has a paucity of naturally occurring furin cleavage sites relative to the other coronavirus clades. I'm just saying that copying sequence from genomes a few species over is very common strategy for engineering projects. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7836551/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7836551/ Irony is that this paper is highly doctored to make it look (from the figures) like the opposite point, without outright lying, like they loaded the dendrogram of beta coronaviruses with a ton of sequences that are distinct but "basically from the same collection", to make the pie slice of betas with furin cleavage sites look much much bigger than it should be. Also, the betas are excerpted from the dendrogram of all coronaviruses... Do you believe the DRASTIC leaked document? https://drasticresearch.files.wordpress.com/2021/09/main-document-preempt-volume-1-no-ess-hr00118s0017-ecohealth-alliance.pdf https://drasticresearch.files.wordpress.com/2021/09/main-doc... It's pretty complete, and exactly like what I would expect a DARPA/NIH grant to look like, having helped prepare one in my career (and one DOE grant). I can't imagine a group of nonexperts drafting this document - correctly - just to make up a conspiracy theory - I'm not a virologist but I am a molecular biologist and biochemist and skimming the leaked document all of the technobabble looks correct to my understanding of science.
    - hcknwscommenter 5y ago
      umm. a paucity. So like, you admit that betacoronaviruses naturally do indeed sometimes have furin cleavage sites? I have no opinion on DRASTIC.
      - dnautics 5y ago
        > you admit that betacoronaviruses naturally do indeed sometimes have furin cleavage sites? Never claimed otherwise. They are rare. The DRASTIC leak talks specifically about engineering cleavage sites into bat coronaviruses. (P. 11)
- alevskaya 5y ago
  The trouble with the synthetic furin hypothesis and all this DRASTIC stuff on that grant, etc. is that all of this work would certainly be done in known viral vectors... you would never go messing around testing spike proteins in some totally random virus backbone whose in-vitro behavior hadn't been worked out before in your assay cell lines. So, maybe I missed something, but none of the experimental designs I've seen in those grants would ever plausibly lead to the SARS-COV-2 sequence. Again, pre-pandemic there was no reason to be sneaky about this stuff if it were actually being done... I don't know why anyone would waste their time on some uncharacterized, completely markerless viral vector for these RBD and proteolysis tests. Sigh... maybe if we -had- been doing those experiments earlier we would have discovered this new clade and been more ready for it. That grant looks spooky to some people precisely because it was so prophetic.
  - dnautics 5y ago
    I don't think those grants would have led to the SARS-CoV-2 sequence either, because the base strain is different. BUT let's be real here. You don't ask for money and do the experiment. You do the experiment and then ask for continuation money. So it is a "generally accepted grantsmanship strategy" that WIV would have been working on viruses adjacent to that in the grant with the same techniques, and adjacent techniques that would lead to the natural next step. If that natural next step infected a postdoc that was careless that one time when he/she was pulling a 9-9-6 workweek... It's all so terrifyingly plausible to anyone who has been there on the front lines doing lab work.
    - alevskaya 5y ago
      You're really into stacking these hypotheticals. Why would anyone bother developing a pile of fiddly new vectors? cui bono? Vector development sucks, I've done it in simpler virus families. And why do it completely markerless? Remember that the other odd thing about this grant was that a lot of the genetic work was supposed to be done in the US. If it were already being done we'd probably have had those sequences in -our- databases!
      - 5y ago
alevskaya 5y ago
Per the CCDC 33 of 585 environmental samples taken early Jan. were positive, and 31 of those were concentrated near the live-animal region of the Huanan market. Environmental PCRs aren't magic, they have a finite level-of-detection, RNA viruses don't survive very long in the wild... There's no handwaving and I'm not positing a particular evolutionary history - the sarbecoronaviruses are clearly understudied and we don't have a good survey of what's out there, we just know about a few close relatives. These are known to be highly mosaic viruses! "few relatively simple additions to a known virus" Which additions and which known virus? There are a huge number of random mutations between the above mentioned strains and SARS-COV-2, there's no plausible story for lab manipulation here from those strains. ...have you ever worked with viruses before? There are billions of animals in the chinese markets, each a test tube... this is the cauldron of evolution, not a few dinky petri dishes in one lab, man. I'm in love with parsimony, and the history of human disease is the history of zoonosis. If extraordinary claims are going to be made, the burden is on those with the radical new theory to offer up a shred of molecular or epidemiological evidence, not just stories about conspiracies. Recent work re-evaluating timelines has only -strengthened- the case for Huanan market and a possible link to a racoon-dog intermediate. https://www.science.org/doi/10.1126/science.abm4454 https://www.science.org/doi/10.1126/science.abm4454
- neffy 5y ago
  The trouble with that piece, is that it is contradicted by this: https://www.reddit.com/r/China_Flu/comments/es21aq/wuhan_pneumonia_survivor_my_22_day_battle_against/ https://www.reddit.com/r/China_Flu/comments/es21aq/wuhan_pne... (Chinese original has been deleted, but I remember seeing it at the time and running it through google, scroll down for English translation in the comments) which reports a case with symptoms starting 24th December, and reports of the hospitals in Wuhan already having multiple cases. Patient didn't visit the market, but did work near. With what we now know of disease progression, and infectiousness, this pushes the initial date back at least a month, probably two or more.
  - alevskaya 5y ago
    ...but that report doesn't contradict anything. The current earliest known case is a Huanan market seafood vendor who contracted the disease on Dec -11-. Dec 24 is way late in the existing epidemiological timeline. (And no one is saying the above is the provable first case, just the first recorded case.)
deleted 5y ago
[deleted]

by timr 5y ago

dnautics 5y ago

The furin cleavage site looks suspiciously like a hallmark cut-and-paste operation that is exactly what I would do as a genetic engineer.

hcknwscommenter 5y ago
Really? I'd like to hear more about this. What exactly looks so "suspicious" that it can't be explained by typical recombination events that are known to occur naturally in RNA viral genomes?
- dnautics 5y ago
  The beta coronavirus class has a paucity of naturally occurring furin cleavage sites relative to the other coronavirus clades. I'm just saying that copying sequence from genomes a few species over is very common strategy for engineering projects. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7836551/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7836551/ Irony is that this paper is highly doctored to make it look (from the figures) like the opposite point, without outright lying, like they loaded the dendrogram of beta coronaviruses with a ton of sequences that are distinct but "basically from the same collection", to make the pie slice of betas with furin cleavage sites look much much bigger than it should be. Also, the betas are excerpted from the dendrogram of all coronaviruses... Do you believe the DRASTIC leaked document? https://drasticresearch.files.wordpress.com/2021/09/main-document-preempt-volume-1-no-ess-hr00118s0017-ecohealth-alliance.pdf https://drasticresearch.files.wordpress.com/2021/09/main-doc... It's pretty complete, and exactly like what I would expect a DARPA/NIH grant to look like, having helped prepare one in my career (and one DOE grant). I can't imagine a group of nonexperts drafting this document - correctly - just to make up a conspiracy theory - I'm not a virologist but I am a molecular biologist and biochemist and skimming the leaked document all of the technobabble looks correct to my understanding of science.
  - hcknwscommenter 5y ago
    umm. a paucity. So like, you admit that betacoronaviruses naturally do indeed sometimes have furin cleavage sites? I have no opinion on DRASTIC.
    - dnautics 5y ago
      > you admit that betacoronaviruses naturally do indeed sometimes have furin cleavage sites? Never claimed otherwise. They are rare. The DRASTIC leak talks specifically about engineering cleavage sites into bat coronaviruses. (P. 11)
alevskaya 5y ago
The trouble with the synthetic furin hypothesis and all this DRASTIC stuff on that grant, etc. is that all of this work would certainly be done in known viral vectors... you would never go messing around testing spike proteins in some totally random virus backbone whose in-vitro behavior hadn't been worked out before in your assay cell lines. So, maybe I missed something, but none of the experimental designs I've seen in those grants would ever plausibly lead to the SARS-COV-2 sequence. Again, pre-pandemic there was no reason to be sneaky about this stuff if it were actually being done... I don't know why anyone would waste their time on some uncharacterized, completely markerless viral vector for these RBD and proteolysis tests. Sigh... maybe if we -had- been doing those experiments earlier we would have discovered this new clade and been more ready for it. That grant looks spooky to some people precisely because it was so prophetic.
- dnautics 5y ago
  I don't think those grants would have led to the SARS-CoV-2 sequence either, because the base strain is different. BUT let's be real here. You don't ask for money and do the experiment. You do the experiment and then ask for continuation money. So it is a "generally accepted grantsmanship strategy" that WIV would have been working on viruses adjacent to that in the grant with the same techniques, and adjacent techniques that would lead to the natural next step. If that natural next step infected a postdoc that was careless that one time when he/she was pulling a 9-9-6 workweek... It's all so terrifyingly plausible to anyone who has been there on the front lines doing lab work.
  - alevskaya 5y ago
    You're really into stacking these hypotheticals. Why would anyone bother developing a pile of fiddly new vectors? cui bono? Vector development sucks, I've done it in simpler virus families. And why do it completely markerless? Remember that the other odd thing about this grant was that a lot of the genetic work was supposed to be done in the US. If it were already being done we'd probably have had those sequences in -our- databases!
    - 5y ago

alevskaya 5y ago

Per the CCDC 33 of 585 environmental samples taken early Jan. were positive, and 31 of those were concentrated near the live-animal region of the Huanan market. Environmental PCRs aren't magic, they have a finite level-of-detection, RNA viruses don't survive very long in the wild... There's no handwaving and I'm not positing a particular evolutionary history - the sarbecoronaviruses are clearly understudied and we don't have a good survey of what's out there, we just know about a few close relatives. These are known to be highly mosaic viruses! "few relatively simple additions to a known virus" Which additions and which known virus? There are a huge number of random mutations between the above mentioned strains and SARS-COV-2, there's no plausible story for lab manipulation here from those strains. ...have you ever worked with viruses before? There are billions of animals in the chinese markets, each a test tube... this is the cauldron of evolution, not a few dinky petri dishes in one lab, man. I'm in love with parsimony, and the history of human disease is the history of zoonosis. If extraordinary claims are going to be made, the burden is on those with the radical new theory to offer up a shred of molecular or epidemiological evidence, not just stories about conspiracies. Recent work re-evaluating timelines has only -strengthened- the case for Huanan market and a possible link to a racoon-dog intermediate. https://www.science.org/doi/10.1126/science.abm4454 https://www.science.org/doi/10.1126/science.abm4454

neffy 5y ago
The trouble with that piece, is that it is contradicted by this: https://www.reddit.com/r/China_Flu/comments/es21aq/wuhan_pneumonia_survivor_my_22_day_battle_against/ https://www.reddit.com/r/China_Flu/comments/es21aq/wuhan_pne... (Chinese original has been deleted, but I remember seeing it at the time and running it through google, scroll down for English translation in the comments) which reports a case with symptoms starting 24th December, and reports of the hospitals in Wuhan already having multiple cases. Patient didn't visit the market, but did work near. With what we now know of disease progression, and infectiousness, this pushes the initial date back at least a month, probably two or more.
- alevskaya 5y ago
  ...but that report doesn't contradict anything. The current earliest known case is a Huanan market seafood vendor who contracted the disease on Dec -11-. Dec 24 is way late in the existing epidemiological timeline. (And no one is saying the above is the provable first case, just the first recorded case.)

deleted 5y ago

[deleted]