The proximal origin of SARS-CoV-2 | Hacker News Reader

The proximal origin of SARS-CoV-2

nature.com

64 pointsKarlKemp46 comments

To summarize, this paper's argument is that SARS-COV-2 can't be lab grown because: 1. It uses a different method of binding to ACE 2 than has previously been found to be most efficient 2. It has several mutations that are of unknown consequence 3. It doesn't have any retrovirus (tool for manipulating virus) backbone

The paper then concludes that SARS-COV-2 must be a result of natural selection. While I think this is possible, they ignore the possibility that the virus is a result of artificial selection. If a laboratory were studying how SARS-COV-2 could pass to humans, they might serially pass the virus between mammals (like pangolins) in order to artificially select for mutations.

That is, in fact, exactly what previous scientists did in a 2012 experiment with bird flu. They wanted to make it transmissible between mammals, so they serially passed genetically modified bird flu between ferrets until it was. I wrote this up on my blog:https://get21stnight.com/2020/04/14/why-do-some-viruses-cros... . The result of this is that bird flu acquired previously unknown mutations in order to pass between mammals.

I'm not saying this is what happened, and there are some key differences (i.e. in the bird flu experiment, scientists had to start off with a genetically modified virus). Still, I disagree that we can definitively conclude this was a result of natural selection.

Yes, this virus definitely could be the result of artificial selection, negating the whole argument of this nature medicine paper. That said, I agree that the virus likely emerged as a natural phenomena. Both SARS and MERS emerged as natural phenomena, so there's no reason to believe that SARS-Cov-2 is unnatural.

I don't think they negate it. They state that it is unlikely, and then they note that the debate is not settled:

"More scientific data could swing the balance of evidence to favor one hypothesis over another. Obtaining related viral sequences from animal sources would be the most definitive way of revealing viral origins. For example, a future observation of an intermediate or fully formed polybasic cleavage site in a SARS-CoV-2-like virus from animals would lend even further support to the natural-selection hypotheses."

Isn't it unlikely that a naturally emerged virus would have both high virality and mortality rate? I have read that viruses usually have one or the other, which would indicate that both is more rare. Combining the rare odd with the odds that the host happens to infect a human would make it even less likely to happen. I'm not very familiar with the topic so I could be mistaken.

I don't think it's very interesting if it was a naturally or artificially selected virus. The more interesting question is was the infected specimen a research subject or not.

Like Spanish Flu? Smallpox? Tuberculosis? SARS was both as well, we just caught it early.

You can't prove it was not engineered or bred/selected (an ancient method of genetic engineering!). But... the burden of proof is on anyone asserting that it was intentionally created to provide evidence.

So far I have only seen innuendo and the weakest sort of circumstantial evidence, but if someone can produce something stronger I'd be willing to consider it.

Perhaps, though in this case I'd put that burden as relatively weak. That is, we know that in principle it could have been made, even if we don't (publicly) know how that would have been done in 2019.

An additional important point is that there's a middle scenario where a natural virus being studies could have been accidentally mutated and accidentally released. This might be all but impossible to distinguish between origin in the wild.

I'd guess intentional manufacture as very unlikely, but sloppy lab practices as not likely but much more likely than that.

There was a spike in non-influenza related pneumonia cases prior to the outbreak, particularly in Australia where it's not flu season. My wife caught it in early March and developed mild bacterial pneumonia but tested negative for flu and Covid-19.

Part of the argument for natural evolution is that there are mutations that most likely occured in a human host as they indicated adaption to an immune response.

My personal theory is that an individual infected with this unknown virus that was going around came into contact with the bat originated coronavirus in Wuhan (which may or may not have originated in the lab). RNA was exchanged and a novel variation emerged that was now both highly contagious and deadly. But I am not an epidemiologist.

Can you help me understand why scientists would intentionally take a virus that can’t transmit in humans and go to lengths to make it transmissible in humans? Just at a gut level that seems reckless and irresponsible to me, but people talk about it like it’s normal and no big deal... so, help me understand?

Also, if it was somehow proven that the virus did come from a Chinese lab, what does that mean? Will the world hold China liable for this mess? That seems unlikely to me, rather I assume it would come down to “big stick diplomacy” and China carries a pretty big stick. But is there any precedent for a disease being leaked from a lab and the lab being held responsible for the consequences?

> if it was somehow proven that the virus did come from a Chinese lab? Will the world hold China liable for this mess?

Why necessarily Chinese? There are people that like to hypothesize that perhaps this was a misjudged attempt at biowarfare against China.

Powerful people can be very religious.

https://wearethene.ws/notable/95575

Can you please stop posting flamebait to HN?

Historically, what I illuded to is almost a law of nature. I could have elaborated, but is it really necessary? People dont need stuff spelled out, and pointing that out didnt start a flame. That's the founder of CNN... his opinions effect people; it shouldn't be off limits to discuss. Parent ultimately was asking about the def of irresponsible is, and might not have considered that other people have other definitions.

https://news.ycombinator.com/item?id=17781131

>Will the world hold China liable for this mess?

Likely but not in a military invasion type of way. No one wants a nuclear exchange with China and most other military option are unproductive for everyone involved. My guess is that individuals will be allowed to make financial claims against China for decades to come. Chinese assets around the world will be seized as necessary to pay off the claims. Logistics systems will be reconfigured to avoid China, further harming their economy. But it will be a long process because everyone is dependent on China for something or the other. The leadership of China could try to be defiant but they are going to have plenty of internal conflict to deal with so they'll be distracted on both ends. Nothing about this is going to be easy or over quickly.

It's natural. The lab only existed because everyone knew this could happen. There's absolutely nothing point at that lab, except the very existence of that lab. Zero. Nada.

That being said: what would happen if it were?

Again: nothing. Only the bottom feeders among conspiracy nuts are alleging intent here, and there's neither a legal nor a moral framework to hold states accountable for errors of negligence. We'd hopefully get a mea culpa from China, but don't hold your breath. Welcome to the community of lesser countries. There are thousands of Iraqis still waiting for a "sorry, my bad" for their brother's wedding being bombed.

This narrative is only being discussed because someone is looking for scapegoat. Realistically, it doesn't even matter. The Federal Government is supposed to protect citizens from threads irregardless of their origin. They were first warned by China itself on January 3rd. Two weeks later, the outbreak and resulting shutdown was public knowledge. Its genesis is completely irrelevant for anything that happened after New Year's.

Do you really think bioweapons research is not a thing?

The problem with artificial selections on virus like SARS-COV-2 is that human do selection much less efficient than our mother nature. Virus that is already spreading in the nature is of far larger quantity than any lab or labs could ever possible achieve. That is, if a natural mutation is going to happen in the lab, it could almsot always be said it has already happened in the nature.

On the other hand, unless they are experimenting with humans, current technology simply doesn't allow us to produce a virus that is not fatal to many other animals but human.

It is not really a viable theory, unless the ground is that the Chinese biologist are way ahead of us in understanding the DNA, which is quite frankly extremely unlikely as a tiny bit of that would be a nature-worthy paper.

They address this -- there's a discussion of the likelihood of laboratory evolution, and their conclusion is that it's unlikely because the progenitor virus has never been described, and the selection system has never been described.

I don't think this is the strongest argument they could have made. To me, the strongest counterargument is that the large insertion (4 amino acids; 12 nucleotides) is statistically unlikely. Even highly efficient laboratory selection systems don't produce those kinds of mutations very often.

Maybe you could do it by passing the virus between pangolins or bats over and over again, but that would be an immense amount of work.

Is it possible? Sure. Likely? No. The parsimonious answer is that it's been circulating in nature.

>While the analyses above suggest that SARS-CoV-2 may bind human ACE2 with high affinity, computational analyses predict that the interaction is not ideal and that the RBD sequence is different from those shown in SARS-CoV to be optimal for receptor binding

Sounds like it could evolve to be more transmissible in humans. The more people it infects, the more likely that is to happen.

With that in mind, "flattening the curve" is even more essential.

Most viruses will start very harmful but tend to mutate into less lethal stains causing them to spread further.

The Oxford study talks about the S and L strains. The L strain is the more deadly one, but it's likely not made it very far.

Source on the first claim?

The S/L strain study has been heavily challenged, see commentary at https://nextstrain.org/help/coronavirus/FAQ#is-one-strain-of...

I do remember this phenomenon being mentioned quite a few times in my genetics classes. Don’t remember the name, unfortunately. But the logic is fairly obvious:a virus wants you to die just as little as humans want the earth to die.

As I remember it, it probably wouldn’t make much of a difference here. The classic case mentioned were extremely fast & lethal viruses such as Ebola & Marburg: When a virus kills you within two or three days of infection, any small change can easily double that time and thereby gain significantly better chances of transmission. But for Covid (and, before that, HIV) the infectious period is pretty long already and any improvements would matter less in relative terms.

Pathogens can definitely evolve to improve fitness and settle into an ecological balance with their hosts. I more meant to contest that most start out very harmful. I don't think we have data to support that, or to be able to separate virus vs. host adaptations that would cause the appearance of lessened severity, given that most viruses circulating today have ancient origins.

Only four dupes ranging from a month ago: https://hn.algolia.com/?q=proximal+origin

I'm fairly convinced it wasn't designed or engineered, but I do think it escaped from the Wuhan virus lab. That they had invited american scientists to the lab and asked for advice in securing it satisfies me that they weren't doing biological weapons research, the fact that they were studying coronaviruses in a facility where the outbreak happened and americans were sounding the alarm on security months before hand is too much of a coincidence for me to believe the story that it came from a wet market.

I agree, they were most likely studying SARS like viruses to prevent future outbreaks, but due to employee negligence it got out.

I'm torn between not being able to entirely dismiss this theory, and the harm it could cause putting this out there whether true or not.

Even more geopolitical distrust is the last thing we need right now, but how do you look the other way?

Edit: look the other way referring specifically to any cover up done, fwiw.

Its gossip. Don't spread gossip.

Welp, cats outta the bag on that one.

The OP indicated natural origin. The rest is speculation/gossip.

So? People speculate on hacker news all the time. It’s a plausible theory for what happened.

Its a conspiracy theory. And bigoted one.

If there was a viral outbreak at a grocery store within a mile of a CDC infectious diseases lab, no one would assume its bigoted to speculate a containment breach as a possible origin.

Its actually less bigoted than the assumption the media pushed before which was that someone ate a bat or because of unsanitary health practices regarding the handling of wild animals.

This at least assumes someone was doing scientific research and accidental exposure occurred and no one noticed until it was too late.

It’s fair to be skeptical when there’s a laboratory that studies SARS-like coronaviruses in the area where the outbreak occurred.

People are conflating ‘engineered’ with ‘lab leak’.

It would actually be pretty irresponsible not to fully audit the lab’s practices — determine whether such a leak was possible, etc.

It's barely gossip when the web site advertised research into coronaviruses and was looking to hire more researchers and the head researcher is missing.

http://www.whiov.cas.cn/105341/

http://www.whiov.cas.cn/105341/201911/t20191118_5438006.html

http://www.whiov.cas.cn/105341/201912/t20191224_5471634.html

http://gd.whiov.cas.cn/zxpy/yjsswgg/201409/t20140923_258008....

http://www.rfi.fr/cn/%E4%B8%AD%E5%9B%BD/20200216-%E6%AD%A6%E...

http://www.rfi.fr/cn/%E4%B8%AD%E5%9B%BD/20200217-%E6%AD%A6%E...

http://gd.whiov.cas.cn/tzgg/201111/t20111104_151377.html

http://www.whiov.ac.cn/tzgg_105342/202002/t20200216_5500201....

http://blog.creaders.net/u/3027/202002/366239.html

https://www.backchina.com/blog/261460/article-314718.html

http://www.bjnews.com.cn/news/2020/02/26/695325.html

https://bbs.pku.edu.cn/v2/post-read.php?bid=1465&threadid=17...

Run these through Google Translate, see what you find.

Geopolitical mistrust is healthy when things are being done in bad faith.

There's a lot of circumstantial evidence, this lab housed bats, did research on these diseases and was in the proximity of the initial out break zone, everyone seems fine with accepting someone ate a bat as a likely cause. Whenever the lab is mentioned by anyone, a lot of effort is being put into calling it a conspiracy theory using strawman arguments against bioengineering, etc. That's just going to make people more suspicious something is being hidden and create a Streisand effect. It's already been well established that the existence of the disease was hidden at first, its ability to spread was hidden, then the idea of it becoming worse than the flu and a pandemic, why not the origins?

It's not so hard to suspect this isn't due to malice, or bio-engineering, but research into a naturally occurring virus, and a lack of good safety procedures or enforcement of safety protocols.

This has happened at least twice before with a Chinese lab with SARS so it's not unknown.

https://www.the-scientist.com/news-analysis/sars-escaped-bei...

However the cases before, the virus was not new and the spread was quickly stopped.

There were state department cables warning about safety issues with this lab.

https://www.washingtonpost.com/opinions/2020/04/14/state-dep...

The laboratory in Wuhan posted a job before the outbreak for a person who will study "pathogenic biology of bats carrying important viruses". [1]

If NBA players can be forced to not speak out about Hong Kong, how far of a stretch do you think it is that China told US media companies to not cover the lab connection story?

[1] https://www.nationalreview.com/2020/04/coronavirus-china-tra...

See this Aussie news program showing the the lockdown in Wuhan. Clearly the authorities were terrified. https://www.youtube.com/watch?v=ycrqXJYf1SU

Why is this one-month-old paper reposted now that the lab leak theory is regaining traction in media outlets?

Here is the conclusion of the paper: “[…] we do not believe that any type of laboratory-based scenario is plausible”.

Here is the title of Scripps Research Institute press release about their publication: “The COVID-19 coronavirus epidemic has a natural origin, scientists say”.

Here are some links to Scripps Research press releases of multi-million dollars deals with chinese labs:

https://www.scripps.edu/news-and-events/press-room/2017/2017...

https://www.scripps.edu/news-and-events/press-room/2019/2019...

https://www.biospace.com/article/releases/yisheng-biopharma-...

I am not going to address the china-praising statements and political stances from main researcher twitter account at a time when CCP cover-up was already known worldwide.

At the time this paper was published, moderators on social networks deleted any possible discussion on the topic. Copy-paste op's link in reddit search bar and see how many comments were deleted from related discussion.

Are you suggesting that .. China is going to engineer a virus and release it in its own population?

And then shut the whole country down and pray that it would spread fast and worse elsewhere?

Let's just say that back in early February nobody even in China thought that other countries are going to be affected. It is a disaster for the CCP at the time that had popular opinion on the internet swing suddenly and violently against the government.

Now, seeing how other countries reacted, that suddenly was not the case anymore. And the CCP have no ability to control other countries action.

The theory that it escaped from the lab does not imply that it was engineered -- they could very well have been doing legitimate medical research and made a mistake.

"China is going to engineer a virus..."

Yes, that is part of what they were doing at their labs in Wuhan. That is not a conspiracy theory, they have research papers, conferences, press releases and job offers about this very topic.

"release it in its own population?"

Could you point out where I wrote that they "released it"?

I only suspect it was a potential accidental leak from one of their labs in Wuhan. It happened already twice in the past, including SARS lab leak in Beijing lab for which Chinese CDC officials were punished at the time:

https://www.chinadaily.com.cn/english/doc/2004-07/02/content...

Not to mention researchers who warned us years ago about dangers of engineered bat virus leak scenario in an article from Nature Research Journal.

> Let's just say that back in early February nobody even in China thought that other countries are going to be affected.

This is ridiculous. If you mean Nov. or early Dec., maybe. But by Jan. corona was nation-wide. Amd Wuhan has an international airport.

Mid-Jan. documented widely-known pandemic at latest:

https://www.cnn.com/2020/04/16/asia/china-wuhan-coronavirus-...

Disney world Shanghai was closed Jan. 24 (Disney should have told the US CDC it was that bad in China.)

Known to be contagious? early Dec.

> Known to be contagious? early Dec.

Source?

Reply on news.ycombinator.com