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Comment by drtillberg | Hacker News Reader

Since we already know the virus shared up to 96% of the same DNA as horseshoe bat virus collected by Wuhan Institute of Virology in 2003 from a cave 600 miles away ... why are researchers still agonizing over all these alternative theories? The only place near Wuhan the virus existed prior to the outbreak was at the institute of virology. And the first places the outbreak occurred were in the immediate neighborhood of the institute. I'm really genuinely curious why bigtime news outlets keep talking about Vietnamese pangolins.

[1] E.g., https://metro.co.uk/2020/02/17/coronavirus-start-chinese-lab...

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> why are researchers still agonizing over all these alternative theories?

The evidence currently implicates a virus that jumped from pangolins to bats and then bats to humans (EDIT: bats to pangolins and then pangolins to humans [1]).

Understanding that transmission mechanism is crucial to reducing the odds of it happening again.

[1] https://www.cell.com/pb-assets/journals/research/current-bio...

It could also help curtail the sales of specific animals in wet markets that are higher risk. Although as usual, this is looking back rather than looking forward.

This depends on the will of the Chinese government. They instituted bans on exotic wildlife selling and farming shortly after SARS, but then rolled it back when the furor died down.

Exotic animals in wet markets are not consumed by the majority of the population; this is mostly driven by the Chinese rich. The industry has survived creating its first pandemic due to its lobbying power; let's see how it rides out the second one.

I thought it was bats to pangolins to humans. Same as the first sars coronavirus being bats to civets (paradoxurinae) to humans.

The theory being, bats are natures reservoir of the parent virus, and SARS-CoV and SARS-CoV-2 both descended from it, through an intermediate host.

> I thought it was bats to pangolins to humans

You’re correct [1]. Thank you.

[1] https://www.cell.com/pb-assets/journals/research/current-bio...

Either way, AFAICT we know for certain that it didn’t come from a lab somewhere and that narrative needs to stop spreading.

Please don't parrot conspiracy theories. The virus shares almost 100% of its identity with known pangolin viruses.

> The discovery of multiple lineages of pangolin coronavirus and their similarity to SARS-CoV-2 suggests that pangolins should be considered as possible hosts in the emergence of novel coronaviruses and should be removed from wet markets to prevent zoonotic transmission.

https://www.nature.com/articles/s41586-020-2169-0

Edit: To clarify, these viruses have approximately 90% identity but in the (oft-suspected and brought up) ACE2-binding spike protein there is a ~97% sequence identity.

> In particular, SARS-CoV-2 exhibits very high sequence similarity to the Guangdong pangolin coronaviruses in the receptor-binding domain (RBD; 97.4%) ... Indeed, the Guangdong pangolin coronaviruses and SARS-CoV-2 possess identical amino acids at the five critical residues of the RBD.

There is another preprint that details more about betacoronavirus recombination.

https://www.biorxiv.org/content/10.1101/2020.02.10.942748v1....

It's almost certainly the product of a recombination event between a pangolin and bat betacoronavirus, since recombination aggressively involves the spike protein in betacoronaviruses. Since we already have a bat virus with high identity (96%) and now a spike protein with very high identity (97%), both in the same phylogenetic tree with origins to SARS-CoV-2, it's reasonably to assume that this is the product of natural recombinant evolution.

Now, it might be the case that it's guided evolution in a Wuhan lab somewhere, but I don't really buy it. Nature is staggeringly good at producing new and innovating viruses, and I believe we will soon find more closely related ancestors to this virus.

We know, from published scientific research in well-respected journals, that "guided evolution in a Wuhan lab somewhere" has been happening for many years.

We also know that China has previously had several terrifying biocontainment failures with virus labs. Things got out, including coronaviruses, but were stopped before spreading far and wide.

By the way, the very original conspiracy theory was eventually proven correct. Calling it a conspiracy theory was a great way to mock people who were pointing out the truth.

This seems pretty outdated -- The Wuhan market and (proximity to the Disease Research center) has been IDed as the primary place where it spread, but is no longer considered the place where it originated. That's why we're still looking into the origins of this thing.

The first case IDed by the Lancet had no exposure to the seafood market, but many later cases did (pg 499):

https://www.thelancet.com/action/showPdf?pii=S0140-6736%2820...

A decent preprint from the US looking at the genetic origins:

http://virological.org/t/the-proximal-origin-of-sars-cov-2/3...

> It is improbable that SARS-CoV-2 emerged through laboratory manipulation of an existing SARS-related coronavirus. As noted above, the RBD of SARS-CoV-2 is optimized for human ACE2 receptor binding with an efficient binding solution different to that which would have been predicted. Further, if genetic manipulation had been performed, one would expect that one of the several reverse genetic systems available for betacoronaviruses would have been used. However, this is not the case as the genetic data shows that SARS-CoV-2 is not derived from any previously used virus backbone17. Instead, we propose two scenarios that can plausibly explain the origin of SARS-CoV-2: (i) natural selection in a non-human animal host prior to zoonotic transfer, and (ii) natural selection in humans following zoonotic transfer. We also discuss whether selection during passage in culture could have given rise to the same observed features.

It "is not derived from any previously used virus backbone 17". That is supposed to prove anything?

isn't 4% difference in DNA pretty significant? that's comparable to the genetic difference between a human and a mouse, iirc.

Human and chimp DNA is 96% the same according to [0]. I'm not a biologist so I have no idea if this logic is applicable to viruses.

[0]: https://www.nationalgeographic.com/news/2005/8/chimps-humans...

It’s not DNA, it’s an RNA virus. More changes happen with them.

There's also a lot less genetic information in a typical virus than in a human, so each mutation represents a much larger percentage change.

For context: The entire SARS-COV-2 genome is 29,811 nucleotides long. The human genome is around 3 billion base pairs.

Quantifying differences is really difficult and the commonly cited numbers are kinda iffy as a rigorous measurement (https://www.smithsonianmag.com/smart-news/what-does-being-99...) in the sense that the public interprets them - 99% comes from looking at single base pair changes only. For the coronavirus, it's an RNA virus so it'll mutate a lot faster than DNA viruses or organisms like us. And the generation time is gong to be a lot faster to allow for a lot more divergence more quickly than longer generation times in mammals.

Because good science is humble enough to humor and analyze reasonable alternate possibilities.

I think "we already know" is a little strong. Here's the only place I can find the paper they refer to: https://gofile.io/?c=D4zfxD

It is one page long, not peer reviewed, and says "96% or 89% identical". If I were a journalist, I think I would at least want to have an expert review the citations for those numbers, and the evidence that this particular virus was present at those labs.

Why would you? Posting nonsense is generating clicks and “Engagement“ just fine....

It wouldn't be the first time something like this happened, either. Russia accidentally released Anthrax[1] from one of their facilities in the late 70's, and it killed over 100 people in the neighboring town. Of course they tried to cover it up, and the truth did not come out until much later.

[1] https://en.wikipedia.org/wiki/Sverdlovsk_anthrax_leak

It wouldn't be the first time something like this has happened in China: https://www.scidev.net/global/disease/news/chinese-lab-accid...

China seems to be looking to change the narrative and the history on where this started.

_96% of the same DNA_

Humans and chimpanzees also share 96% of the same DNA – that's not as similar as it sounds.

I think it kind of is when it comes to spreading diseases, that's why us humans eating great apes has had disastrous consequences for our health as a species in the past (the same goes for us eating pig brains)

It would be like if a global pandemic was traced back to the U.S. 300 yards from Fort Detrick. Any rational person would take notice of this but instead it's labeled a conspiracy theory.

What is more crazy is that there is no international pressure for China to at least temporarily close down that research institute. The international community should have also demanded for immediate inspections on the institute's premises as soon as this virus started going worldwide, for crying out loud, we've had wars started because of some aerial photos of some metal tubes in the Iraqi desert but instead this is treated like "super-power business as usual".

> What is more crazy is that there is no international pressure for China to at least temporarily close down that research institute.

Why is that crazy? Unless you're suspecting the Chinese of designing a fairly dull viral weapon that they first released on their own people, I'm not sure why anyone would care to go through the doors.

Sweet jungle meat from a wet market is the likely source, as with many of these kinds of virii over the centuries.

> Sweet jungle meat from a wet market is the likely source

There are numerous reports of the wet market source not being the actual source. I've never said that the Chinese have released this virus on purpose, I did in fact imply though that the Chinese created this virus on purpose (how it got out in the wild is anybody's guess). Having countries creating bio-weapons in 2020 should be grounds for war, no matter if they release it or not.

Later edit: Now I saw that you said "dull viral weapon", what do you find so "dull" about a virus that has put the whole world economy on its knees in a matter of 4-5 weeks? Yes, it's not as gore-y as Ebola but it's an order of magnitude (at least) more effective in bringing us down as a species.

> I've never said that the Chinese have released this virus on purpose, I did in fact imply though that the Chinese created this virus on purpose

There is zero credible evidence that this virus was engineered in any way. What we do have is detailed genomic analysis done by actual virologists, comparing it with coronavirii from the vast pools in animal populations, that can trace its natural evolution [1]. This analysis and ongoing surveillance is how virologists and epidemiologists hope to predict future epidemics.

1 - https://www.nature.com/articles/s41591-020-0820-9

No one (in this thread at least) is claiming it's a weapon. The point is that the research lab at the center of this pandemic has, and continues to, research and collect viruses just like SARS-CoV-2. The authorities in Wuhan also tried to cover up the outbreak before it became too severe to deny. It may be a coincidence, but it also may not.

The coverup stuff seems suspicious. Also

>Chinese Ministry of Science and Technology released a new directive titled: “Instructions on strengthening biosecurity management in microbiology labs that handle advanced viruses like the novel coronavirus.” https://nypost.com/2020/02/22/dont-buy-chinas-story-the-coro...

shortly after.

> weapon that they first released on their own people

I don't think anyone suspects that it was a weapon. A totally non-selective weapon like this would be extremely stupid. But it still could have come from that lab, and such a theory should not be discarded for the time being.

That the Wuhan Institute of Virology was doing research on engineered coronaviruses isn't in dispute. They have published several research papers describing their work over the last 10 years.

It wouldn't have had to have been a deliberate release for SARS-CoV-2 to have come from there. Accidents happen, and there have been several accidental releases of the original SARS-CoV from Chinese labs. It's also not beyond the realm of possibilities that someone tasked with destroying animals that were research subjects decided to make a few extra yuan selling them to the wet market across the street instead.

> there have been several accidental releases of the original SARS-CoV from Chinese labs.

I've never heard of any accidental escapes of SARS. Do you have a source for this claim?

https://nationalpost.com/news/a-brief-terrifying-history-of-...

> SARS has not re-emerged naturally, but there have been six escapes from virology labs: one each in Singapore and Taiwan, and four separate escapes at the same laboratory in Beijing.

Perfect, thank you. The links in that article don't work for me, but they do in the original essay from the Bulletin of the Atomic Scientists:

https://thebulletin.org/2014/03/threatened-pandemics-and-lab...

Those accidents are fucking terrifying. I'm not sure whether to be more scared of that, or of wet markets and antibiotic-soaked factory swine/cattle/poultry farms. Humanity certainly isn't taking any of this seriously enough.

I think that when you look at both the properties of the virus (fairly long-tailed inhibition period, large proportion of carriers not displaying any symptoms, being infectious even after becoming healthy yourself, life-long consequences even for people who survive, aerosol spread and so on) and the results so far (the human lives + medicine systems of so far only a few countries + The Next Big Depression), it is not 'a fairly dull viral weapon'.

Sure, if you think of it in terms of being a weapon, it's not an armageddon weapon, but very few madmen want those anyway.

Shutting down virology labs would be the stupidest, most self destructive thing we could do right now. The Wuhan Institute of Virology has probably the best equipped and most experienced coronavirus researchers in the world. Within weeks of the start of the outbreak, they had sequenced the virus' genome, published it widely and publicly, and immediately started investigating antivirals. They remain on the forefront of the fight.

The virologists there are very active publishers, and by all accounts among the very best in their field. And now they're pissed off. Here's a snippet from the institute's coronavirus lead, defending them from an onslaught of insane and stupid conspiracy theories:

> [Shi Zhengli] said on her social media account that she “guaranteed with her own life” that the outbreak had nothing to do with the lab but was a “nemesis for the barbaric habits and lifestyle of some people – like eating wild game including bats.”

Chinese researchers and doctors have generally been among those most willing to push back against the CCP's misinformation and censorship. Of all people, why in the FUCK would we want to muzzle these guys?

Imagine taking someone in that position at their word.

Also worth noting is that the term conspiracy theory is itself traceable to psyops.

I think they found a Pangolin virus that matched 99% so that beats 96%. The source is still unproven.

https://www.sciencenews.org/article/coronavirus-covid-19-not...

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