Comment by alevskaya | Hacker News Reader

Comment by alevskaya | Hacker News Reader

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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. 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

> 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/14621732432474071...

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.

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/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/13280584020529684...

https://www.medrxiv.org/content/10.1101/2020.06.25.20140061v...

I'm not a huge fan of "appeal to authority", but I'm curious what your credentials and experience in this area are?

The person you are arguing with claims to have direct experience working with viruses in a lab setting.

Is this another of HN's all too frequent, "computer science major arguing with expert in field completely unrelated to computer science"?

Reasoning doesn't require credentials, please let's keep it that way.

One of the parties did an appeal to authority as a way to _prove_ they entered _relevant_ evidence.

This is obviously entirely misguided, and if you start making such basic logical mistakes it is expedient to inquire about the posters background to know if they've reached the limit to their ability to create reasoned arguments.

There are nuances, but at it's core either it was valid for them to make that appeal and it is valid for us to request their credentials (which is essentially an appeal to authority--"who has the better credentials?"), or it was not valid for them to make that appeal and it is not valid for us to request their credentials. I lean towards the latter view.

Logical mistakes don't weaken a person's entire argument (we don't want to just see who's "winning"), or even weaken the line of reasoning they were invoked to support -- they just fail to provide evidence.

One of the parties called into question the validity of a paper the other party posted, and the other party rebutted by implying that as the director of an established institution, the paper's author has something to lose. I find that argument weak, but the initial questioning of validity also provided no evidence or made any strong arguments as to why the paper was not valid.

Appeals to authority are useful not as logical arguments but as a way to avoid wasting time on drivel, and I don't believe that to be the case here.

No one is arguing that the earliest known case on Dec 11 is when sars-cov-2 "began". We know it must be older than that. More recent reviews of chinese epidemiology don't mention the hubei patient, the Dec 11 case seems to be consensus earliest verified case.

And yes, for a data point of this importance a random environmental sewage PCR handled over half a year later is of dubious provenance. If you've never done a ton of environmental PCR work you'd be amazed how easy it is to contaminate everything, but whatever. Given how contagious sars-cov-2 is, if it really were present in Italy in early December... we'd probably have more definitive proof of it's presence much earlier than Jan 31.

Ok, fine. We're agreed then: the virus was obviously circulating widely by December, which means in all likelihood, it could have been found in pubic places in Wuhan China. Like, say...a public market.

I'm not saying it had to happen that way, just that finding shreds of viral RNA in a market, in December, in Wuhan, is in no way dispositive evidence of the market being the origin of the virus -- any more than finding flu virus in the ball pit at a McDonalds means that the flu came from Ronald McDonald.

> And yes, for a data point of this importance a random environmental sewage PCR handled over half a year later is of dubious provenance. If you've never done a ton of environmental PCR work you'd be amazed how easy it is to contaminate everything, but whatever.

"They could have made a mistake, so I'm going to ignore all evidence which disagrees with my prior beliefs."

Millions of old people in dense cities turn out to be a fantastically sensitive instrument for detecting the presence of sars-cov-2 in a population. You’d have to explain nearly two months of cryptic transmission that left no hospital reports or verifiable samples…

You do realize these papers pointing to an international nov-dec timeline only -weaken- any link to WIV at all, and have in fact been heavily leaned upon by Chinese conspiracy theorists as evidence this disease has -western- origins?

> You do realize these papers pointing to an international nov-dec timeline only -weaken- any link to WIV at all, and have in fact been heavily leaned upon by Chinese conspiracy theorists as evidence this disease has -western- origins?

Chairman Pooh? Is that you?

The CCP can fuck right off with this idiocy. Seriously. Nobody with half a brain is falling for it.

You don't get to suppress information and/or not look for it in the first place, then claim that the lack of information is indicative of something.

The trouble with that piece, is that it is contradicted by this:

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.

...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.)

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/14621732432474071...

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/

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.

I'm fine with people posting random studies that I can read and form my own opinion on. This isn't ridiculous. This is the process of science.

I’m actually not fine with people posting random studies and then also making random claims from undereducated interpretation. That’s not the process of science, mostly because in the process of science you’re expected to be educated first before you can enter a discussion, otherwise you’re not discussing heavily niche subjects with peers you’re just introducing noise and that drowns out the actually useful educated niche. As a layman that is trying to find what the actual, educated in virus research and virus forensics folks are discussing and saying, this sort of undereducated claim is more noise for me to try and sift. It’s very annoying and a waste of my time.

"Chinese original has been deleted"

Wait that never happens...

> 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.

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?

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

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