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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.

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.)
  - timr 5y ago
    No, you're wrong. The earliest cases were at least in November, and quite probably earlier. The earliest case identified in the market was on December 11. There's simply no way that was the first actual case. https://twitter.com/BallouxFrancois/status/1462173243247407111 https://twitter.com/BallouxFrancois/status/14621732432474071...
- rjzzleep 5y ago
  If you want to argue like that there's also this publication from Italy claiming that the first antibodies were detected in September 2019. The comment above says I would just do X, and bringing up RaTG13 and BANAL-52 as an argument as if it's all trivial. They share 96.2% and 96.9% similarity with sars-cov-2. There are seemingly unrelated animals sharing that much. The linked study also doesn't mention any of that. I'm not going to argue one way or the other, but I'm starting to get really annoyed at people posting random studies they half understand to argue one way or the other. Covid-19 discussions hackernews(or reddit for that matter) are like the Joe Rogan of nerds. It's ridiculous, people here should know or act better. https://pubmed.ncbi.nlm.nih.gov/33176598/ https://pubmed.ncbi.nlm.nih.gov/33176598/
  - timr 5y ago
    One strain of BANAL (52) has a high DNA sequence similarity to SARS-CoV2. Nonetheless, RaTG13 is closer overall (as you can see in the phylogenetic analysis in the paper I posted), and there are enough differences that you have to make complex assumptions about how multiple viruses crossed over evolutionary time. Possible? Yes. Parsimonious? Not necessarily. Also, nobody reasonable is arguing that BANAL-52 is not evolutionarily related to SARS-CoV2. Of course it is. But that could be true even if it were a precursor of some virus that was later engineered in a lab. To fully convince me of a natural origin hypothesis, you'd have to find a virus in an animal reservoir that had a highly similar RBD with a furin cleavage site -- or something within a few point mutations of a furin cleavage site. Also, a high degree of homology across the remainder of the genome.
timr 5y ago
> Per the CCDC 33 of 585 environmental samples taken early Jan. were positive, The first cases were at least in November, and quite probably earlier. The virus was in circulation in Northern Italy by December. We know this from multiple lines of evidence. https://twitter.com/BallouxFrancois/status/1462173243247407111 https://twitter.com/BallouxFrancois/status/14621732432474071...
- alevskaya 5y ago
  Are you seriously posting a link to a one-off phylogenetic molecular clock estimate as experimental evidence of italian priority? The other Italian claims of priority are highly disputed by basically everyone - but have I missed anything - are there any actual sequenced, dated samples from Italy in December? That's the standard of evidence here, not some crappy antigen test or unsequenced amplification hit. No one believes the Dec 11 case to be "the first", just the first well attested case.
  - timr 5y ago
    No. I'm seriously posting a paper by the director of the University College of London Genetics Institute. The same twitter thread (again, same person: director of UCL UGI) shows a Lancet article placing the first documented hospitalization on December 1, and a different source documenting a case in China in mid-November: https://www.scmp.com/news/china/society/article/3074991/coronavirus-chinas-first-confirmed-covid-19-case-traced-back https://www.scmp.com/news/china/society/article/3074991/coro... So yes, there are multiple lines of evidence. This isn't even remotely controversial. You're arguing that the sky is red, and your only counter-argument to the evidence otherwise is incredulity. > are there any actual sequenced, dated samples from Italy in December? That's the standard of evidence here, not some crappy antigen test or unsequenced amplification hit. I mean, you're inventing "standards of evidence" here, but as long as you're asking: yes. Dated, PCR-confirmed wastewater samples in Italy were purified by gel electrophoresis and sequenced. https://twitter.com/BallouxFrancois/status/1328058402052968448 https://twitter.com/BallouxFrancois/status/13280584020529684... https://www.medrxiv.org/content/10.1101/2020.06.25.20140061v1.full.pdf https://www.medrxiv.org/content/10.1101/2020.06.25.20140061v...
prox 5y ago
Then why did the Chinese shut down access to the covid database for instance if there is nothing there? Edit : You can downvote this, but that doesn’t answer this question that I am seriously curious about?
- kuhewa 5y ago
  The same reason they surpressed all evidence of widespread wildlife trade in the city in 2019 and lied to the WHO about it?
emmelaich 5y ago
> If extraordinary claims are going to be made ... I don't think any claim here is extraordinary, and none with very good evidence. So pursuit of parsimony doesn't help much.

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.)
- timr 5y ago
  No, you're wrong. The earliest cases were at least in November, and quite probably earlier. The earliest case identified in the market was on December 11. There's simply no way that was the first actual case. https://twitter.com/BallouxFrancois/status/1462173243247407111 https://twitter.com/BallouxFrancois/status/14621732432474071...
rjzzleep 5y ago
If you want to argue like that there's also this publication from Italy claiming that the first antibodies were detected in September 2019. The comment above says I would just do X, and bringing up RaTG13 and BANAL-52 as an argument as if it's all trivial. They share 96.2% and 96.9% similarity with sars-cov-2. There are seemingly unrelated animals sharing that much. The linked study also doesn't mention any of that. I'm not going to argue one way or the other, but I'm starting to get really annoyed at people posting random studies they half understand to argue one way or the other. Covid-19 discussions hackernews(or reddit for that matter) are like the Joe Rogan of nerds. It's ridiculous, people here should know or act better. https://pubmed.ncbi.nlm.nih.gov/33176598/ https://pubmed.ncbi.nlm.nih.gov/33176598/
- timr 5y ago
  One strain of BANAL (52) has a high DNA sequence similarity to SARS-CoV2. Nonetheless, RaTG13 is closer overall (as you can see in the phylogenetic analysis in the paper I posted), and there are enough differences that you have to make complex assumptions about how multiple viruses crossed over evolutionary time. Possible? Yes. Parsimonious? Not necessarily. Also, nobody reasonable is arguing that BANAL-52 is not evolutionarily related to SARS-CoV2. Of course it is. But that could be true even if it were a precursor of some virus that was later engineered in a lab. To fully convince me of a natural origin hypothesis, you'd have to find a virus in an animal reservoir that had a highly similar RBD with a furin cleavage site -- or something within a few point mutations of a furin cleavage site. Also, a high degree of homology across the remainder of the genome.

timr 5y ago

> Per the CCDC 33 of 585 environmental samples taken early Jan. were positive, The first cases were at least in November, and quite probably earlier. The virus was in circulation in Northern Italy by December. We know this from multiple lines of evidence. https://twitter.com/BallouxFrancois/status/1462173243247407111 https://twitter.com/BallouxFrancois/status/14621732432474071...

alevskaya 5y ago
Are you seriously posting a link to a one-off phylogenetic molecular clock estimate as experimental evidence of italian priority? The other Italian claims of priority are highly disputed by basically everyone - but have I missed anything - are there any actual sequenced, dated samples from Italy in December? That's the standard of evidence here, not some crappy antigen test or unsequenced amplification hit. No one believes the Dec 11 case to be "the first", just the first well attested case.
- timr 5y ago
  No. I'm seriously posting a paper by the director of the University College of London Genetics Institute. The same twitter thread (again, same person: director of UCL UGI) shows a Lancet article placing the first documented hospitalization on December 1, and a different source documenting a case in China in mid-November: https://www.scmp.com/news/china/society/article/3074991/coronavirus-chinas-first-confirmed-covid-19-case-traced-back https://www.scmp.com/news/china/society/article/3074991/coro... So yes, there are multiple lines of evidence. This isn't even remotely controversial. You're arguing that the sky is red, and your only counter-argument to the evidence otherwise is incredulity. > are there any actual sequenced, dated samples from Italy in December? That's the standard of evidence here, not some crappy antigen test or unsequenced amplification hit. I mean, you're inventing "standards of evidence" here, but as long as you're asking: yes. Dated, PCR-confirmed wastewater samples in Italy were purified by gel electrophoresis and sequenced. https://twitter.com/BallouxFrancois/status/1328058402052968448 https://twitter.com/BallouxFrancois/status/13280584020529684... https://www.medrxiv.org/content/10.1101/2020.06.25.20140061v1.full.pdf https://www.medrxiv.org/content/10.1101/2020.06.25.20140061v...

prox 5y ago

Then why did the Chinese shut down access to the covid database for instance if there is nothing there? Edit : You can downvote this, but that doesn’t answer this question that I am seriously curious about?

kuhewa 5y ago
The same reason they surpressed all evidence of widespread wildlife trade in the city in 2019 and lied to the WHO about it?

emmelaich 5y ago

> If extraordinary claims are going to be made ... I don't think any claim here is extraordinary, and none with very good evidence. So pursuit of parsimony doesn't help much.