
Unusual Features of SARS-CoV-2 Genome Suggesting Sophisticated Lab Modification - ycombonator
https://zenodo.org/record/4028830#.X1_8aRb3bDu
======
djaque
The author affiliations are listed as "Rule of Law Society". A quick google
search shows that it is a political non-profit dedicated to "investigating
Chinese corruption" and is led by Steve Bannon of all people [1].

Given the extraordinary nature of the claims, the fact that this didn't see
any peer review and isn't published in a real journal as well as the clear
political motivations of the money behind the study, my BS meter is going off
the charts. Even the name of the document "The Yan Report" makes it sound like
a political hit piece cosplaying as a scientific article.

[1] [https://www.washingtonpost.com/politics/steve-bannon-guo-
wen...](https://www.washingtonpost.com/politics/steve-bannon-guo-
wengui/2020/09/13/8b43cd06-e964-11ea-bc79-834454439a44_story.html)

~~~
ttflee
Putting the Bannon label aside, this paper seems to be well written and
proofread. The claims fell into the range of educated guess and reasonable
doubts.

EDIT:

You may like or dislike Bannon and/or Trump, but I judged this paper using my
only knowledge in biochemistry/molecular cloning from when I was trained
during undergraduate.

~~~
simonh
I think knowing that this comes from people with a long and well established
track record of intentional deception, propagating misinformation and
exaggeration is useful background knowledge.

As for knowledge of biochemistry, there is no new research here. None. It's
pasted together from other sources. For example the discussion of the proteins
ZXC21 and ZC45 comes form this article [1], which also presents evidence that
the virus can infect and therefore could have passed to humans from mammals
other than bats. In other words it's closest viral relatives might be in a
mammal species other than bats, so in focusing on bats for the virus's nearest
relative we might be looking in the wrong place. That blows a hole in this
paper's thesis that the virus not being almost identical to the bat viruses
means it must be engineered, so of course it isn't mentioned in the article at
all. Nice cherries they're picking!

[1][https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6135831/](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6135831/)

~~~
hajile
Yet somehow, it's a _very_ close match (96%) for a bat coronavirus.

[https://www.nature.com/articles/s41586-020-2012-7](https://www.nature.com/articles/s41586-020-2012-7)

Magically, that virus was allegedly discovered in 2013, but despite their
claim that it killed 3 out of 6 infected people, they somehow "forgot" to
mention it to anyone anywhere or enter the genome into any public databases.

[https://www.thetimes.co.uk/article/seven-year-covid-trail-
re...](https://www.thetimes.co.uk/article/seven-year-covid-trail-
revealed-l5vxt7jqp)

Even when you move away from politically-funded research, the story still
stinks (well, CCP-sponsored research is still political).

~~~
simonh
These viruses circulate between mammal species. I said it's nearest relative
might not be in bats, not that it has no relatives in bats.

------
dannykwells
Not to ad hom the piece, but Miles Guo, funder of this work, is a
controversial Steve Bannon associate and Chinese billionaire in exile. So, you
know, might have an axe to grind.

Also, for a different, and published, perspective, see this piece:

[https://www.nature.com/articles/s41591-020-0820-9](https://www.nature.com/articles/s41591-020-0820-9)

~~~
mathw
I'll definitely take the paper from Nature Medicine over the article by
someone associated with Steve Bannon. I simply do not believe it is plausible
that this many scientists are in on the massive cover-up that would be
required to hide such evidence.

~~~
chrisco255
Wait, you don't think people in China would be afraid of outing their
government's nefarious deeds? Even in the U.S. our whistleblowers like Snowden
have to run to Russia and face exile at best. How many people work in the NSA
that could have said something but didn't? Now add that China isn't afraid to
jail hundreds of thousands of people if it has to to get compliance. It's not
afraid to harvest the organs of prisoners either. Add that they literally
control all communication in the country behind a tightly controlled firewall.

~~~
roca
The conspiracy theory presented in this paper is that mainstream medical
journals _around the world_ are "strictly censoring" evidence that COVID19 was
developed in a lab.

~~~
drran
Yep. It's strictly censored by everybody around the globe. Nobody wants to see
scientists hanging on trees.

------
thinkingemote
Science 2004:
[https://www.researchgate.net/publication/8587412_Infectious_...](https://www.researchgate.net/publication/8587412_Infectious_diseases_Mounting_lab_accidents_raise_SARS_fears)

"For the third time in less than a year, an outbreak of SARS seems to have
originated from a failure in laboratory containment. This latest incident,
revealed in China late last week, is the most serious."

2019 Journal of Biosafety and Biosecurity: Inaugural editorial: Towards
evidence-based biosafety and biosecurity
[https://www.researchgate.net/publication/331229899_Inaugural...](https://www.researchgate.net/publication/331229899_Inaugural_editorial_Towards_evidence-
based_biosafety_and_biosecurity)

"In 2004, a case of laboratory-acquired SARS infection was reported, and a
number of containment failures occurred in high-security laboratories in
Singapore, Taiwan, and mainland China. The 2004 SARS outbreak in North China
resulted from a series of flaws in the biosafety protocol at a national
institute in Beijing, resulting in infection of four laboratory workers. This
has been the most serious biosafety event to date."

~~~
simonh
Oh I think it's entirely plausible this was an inadvertent escapee from a
research facility, either of a naturally occurring virus under study or a bio-
weapon. Neither possibility can be entirely discounted and I'd like to see a
thorough investigation into the origins of the virus.

That doesn't mean this paper is any use whatsoever. It's evidence is sketch,
pasted together from snippets of other articles. There is no new research here
at all, and it comes from sponsors with a long and well established track
record of peddling disinformation. So sure, please do keep an open mind, but
that goes both ways on theories like this.

~~~
jkhdigital
Sketchy evidence? Tell me more. I look forward to your thoroughly-cited
refutation of the paper’s main claims.

~~~
simonh
I described some of my criticisms in another post, basically they cherry
picked only the evidence they wanted to from the papers they sourced their
ideas from. This is not research. There is nothing new or original in this
paper, it's just taking things from elsewhere, stripping off the context and
stitching it together into their own narrative. There's nothing original or
substantive there to refute.

~~~
jkhdigital
Since this paper is making what amounts to a forensic argument, there will
inevitably be some "cherry picking" of evidence since much of the available
evidence is not relevant and will necessarily be omitted. Just because the
authors did not present new data from original experiments does not mean this
doesn't count as "research"; synthesizing knowledge from across prior research
is an important and effective tool for advancing any field.

If you want to refute the claims of the paper by arguing that they cherry-
picked evidence, you need to provide specific evidence that was omitted from
the paper and show how it contradicts their claims. Your other comments on
this thread provide only the slightest hint of an argument and do not
constitute anything resembling a true refutation.

I completely understand if you don't have the time or energy to compose a more
thorough argument--after all, this is basically a flame war on an anonymous
Internet forum. But if you find another source which presents a properly
composed refutation of these claims, I'd appreciate it if you post a link
here. I'll also be on the lookout for such arguments and post anything I find.

~~~
simonh
They took the protein sequences as evidence the virus didn't come directly
from bats and concluded that therefore it must have been engineered. However
the paper that did the research on that also showed that the virus is well
adapted to mammals other than bats and humans, so it's very likely it cam to
us from another mammal species other than bats.

This blows a big hole in their bat -> engineering -> humans thesis and so they
completely omitted any mention of it even though they must have read it and
known all about it.

I'm not refuting the claim that it might have been engineered. I'm still open
minded on that question. I'm refuting their claim that the evidence
demonstrates that it was engineered. The evidence does not demonstrate what
they claim it does. That's what I'm refuting.

------
DoingIsLearning
If the root-cause was anything more than a zoonotic event then there will
never be an independent and serious investigation on it.

Personally there are so many inconsistences with the timeline and location
that I am much more inclined to believe the hypothesis of a "Gain-of-function"
experiment that negligently escaped the lab, more so than a 'designed' virus
or an unfortunate zoonotic event.

I don't want to be controversial or go into arguments on facts versus
'circunstancial' evidence but I would like to point out that the last time I
linked a url about this on reddit, my comments got silently shawdowbanned. I
tried multiple variations and unless I obsfuscated the url the comment would
always get shadowbanned.

This is the link in question: [https://project-
evidence.github.io](https://project-evidence.github.io)

~~~
gridlockd
People need to understand that this scenario is entirely plausible and could
have happened _even in the US_ and many research labs around the world.

Gain-of-function experiments and engineered viruses are not the stuff of James
Bond stories, they are ordinary scientific work. They aren't necessarily that
dangerous, but even extremely dangerous pathogens have leaked from labs
numerous times.

The origin of the virus is unproven, yet somehow the "lab origin" story is a
conspiracy theory while "zoonotic transfer through multiple hosts in an
unlikely area (Wuhan)" is the dominant narrative. Either hypothesis has, at
best, circumstantial evidence going for it.

~~~
neuronic
The problem isn't even that it happened, since accidents and issues are an
unfortunate part of research and life.

It's the way some entities deal with it for political reasons that screws
everything up and leads to huge public distrust and poisoning of discourse.

The Coronavirus talk points are clear and to be adhered to. While I agree with
the majority of the talk points (wear a mask etc.) I find it highly suspicious
how some things evolved and changed over time.

Before April 7th, apparently no research existed in the world which proved
that even simple textile masks are highly efficient at reducing transmission
of viruses like SARS-CoV-2 simply because they reduce droplets you spread. The
virus needs droplets so its own size is irrelevant and the only leftover thing
to check are fine aerosols which outside of artificial conditions rarely
occur.

Then suddenly, mask was everything as if somebody flipped a switch. People
somewhere came together to flip the rhetoric which means that at some point,
regarding the masks, it wasn't science-based but messages of control. Yea,
maybe the mask supply was to be protected for medical personnel. Ok. But
spreading the message that masks are not required is the wrong way to go about
it.

Case in point:

> By contrast, surgical masks — those cheap, disposable, gauzy masks that
> often come in blue or green — are less uncomfortable. But Schaffner says the
> scientific evidence that "there might be a benefit for people in the
> community wearing [surgical] face masks is _very, very meager_. The general
> sense is perhaps, but they're certainly not an absolute protection." In
> other words, they do provide some benefit but they're far from foolproof.
> [1]

This is NPR! It's January 29th, 2020 and they spread the message that simple
disposable surgical masks have VERY VERY MEAGER BENEFIT. I can only say: what
the fuck?! Why?

This reads as if masks are not _really_ helping so forget them anyways. As
opposed to: there is significant reduction in transmission, even if not 100%,
so wear them!

But research has long since existed proving effectiveness of surgical masks
spreading airborne pathogens [2, 2013!]. It was abundantly clear that they
help. But WHO and media told us a different story. RKI in Germany lied as well
until early April.

[1]
[https://www.npr.org/sections/goatsandsoda/2020/01/29/8005317...](https://www.npr.org/sections/goatsandsoda/2020/01/29/800531753/face-
masks-what-doctors-say-about-their-role-in-containing-
coronavirus?t=1600164447562)

[2]
[https://journals.plos.org/plospathogens/article?id=10.1371/j...](https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1003205)

~~~
gridlockd
> But research has long since existed proving effectiveness of surgical masks
> spreading airborne pathogens...

No it hasn't! The claim that the evidence is "very meager" has been correct
and is still correct. The study that you linked only shows a reduction in
viral particles, but it also shows that coarse droplets contain less virus.

It stands to reason that reduced particle counts imply reduced viral load, and
that reduced viral load implies fewer or less severe infections. However, that
is hypothetical and _not scientific proof_.

In my view, the narrative has changed because of political pressure. If
scientists were asked "Do masks work?", the honest answer would be "I don't
know".

However, that's not what people want to hear from the experts. So you rephrase
the question to "Could masks confer a benefit?" and then the honest answer is
"That is plausible". Now politicians have something that they can _tell people
to do_ , to give the impression that something _can be done_ and that
something _has been done_.

That is not to say people shouldn't wear masks. However, it bothers me that
this one scientifically plausible but unproven intervention gets a lot of
attention, but many others don't. For instance, take vitamin D or zinc
supplementation. Somehow, we need gold-standard double-blind placebo-
controlled trials on 100,000 subjects before officially declaring those as
potentially beneficial interventions.

------
schrodingersCat
PhD in molecular biophysics here (did virology rotation in grad school also).
There's not enough time to go into how bad the "science" is in this paper.
Evidence is cherry-picked, and circumstantial at best. Lots of non-sequitors
presented that are unconnected to the actual science. I've read earlier claims
that are similar to this and basically they see low alignment similarity to
commercially available vectors and claim "AHA it must be engineered". But
anyone who has studied molecular biology knows that vectors are almost always
derived from natural viruses. Also, while viral linkages are normally linear,
crossover between viri in hosts is well documented and does occur "rarely".
That's say it's rare compared to normal genetic drift, but common enough that
it's not particularly surprising to see genetic material from another "vector"
in the wild. It does not have to be lab derived to see the mutations observed.
Once you call into question this fundamental premise, everything else looks
like the scientific trash that it is.

------
hyperbovine
For an opposing viewpoint written by actual experts in this field, please see:

[https://www.nature.com/articles/s41591-020-0820-9](https://www.nature.com/articles/s41591-020-0820-9)

------
jkhdigital
I posted what appears to be the top comment on the previous submission of a
similar paper describing the probable laboratory origins of SARS-CoV-2
([https://news.ycombinator.com/item?id=23875758](https://news.ycombinator.com/item?id=23875758)),
so I'll try and do another quick summary here. (Caveat: I have no particular
expertise in this area, I just read a lot of scientific research)

The lead author here is an immunologist who, unlike the authors of prior
papers alleging laboratory origin, is Chinese and was trained in Chinese
institutions. At the time of the outbreak Dr. Li-Meng Yan was working in a
public health lab at Hong Kong University and was asked to investigate. She
claims that she fled to the US after realizing that there was a cover-up going
on and she knew too much already.

The most striking and novel claim made here is that the bat coronavirus
RaTG13, which is a 96% genetic match to the novel coronarivus, is a _total
fabrication_. This argument is based upon a few key observations:

1\. RaTG13 was supposedly discovered in 2013 but not publicly reported until
after the outbreak already started, in a paper (published by researchers
closely affiliated with the WIV) that claimed it as evidence SARS-CoV-2 likely
originated from bats.

2\. A number of independent preprint papers raise significant concerns about
the veracity of RaTG13, and one published paper indicates that the RaTG13
spike protein is actually ineffective at binding to ACE2 receptors in
horseshoe bats (the supposed reservoir).

3\. After excluding RaTG13, the next closest relatives are two bat
coronaviruses (ZC45/ZXC21) that were discovered and characterized by Chinese
military research labs. A Chinese lab published research near the start of the
outbreak which identified these viruses as the closest relatives, and that
same lab was apparently closed for "rectification" shortly thereafter.

The paper goes on under the assumption that ZC45 or ZXC21 was the backbone for
engineering the SARS-CoV-2 virus, noting how the particular characteristics of
the genomic match (100% E protein, 94% Orf8 protein) align with what one would
expect after the gain-of-function modifications that produced the unusual RBM
and furin cleavage site which were also identified in the Sørensen paper. This
paper goes into much more detail on those two points, and provides
counterfactuals to describe how unlikely these observations would be in a
naturally-evolved virus.

In the second half of the paper the authors describe in detail how a lab with
sufficient technical acumen could engineer a virus like SARS-CoV-2 through a
sequence of well-defined steps, with references to published research
demonstrating these capabilities. Then they postulate the exact components
involved in engineering the actual SARS-CoV-2, along with a projected timeline
of six months for the whole process.

~~~
drran
There is very few labs in the world, which can do synthesis of the virus from
the published paper. One of them had major incident[0] (equipment was stolen
from the lab by rescue team after blast and fire in the lab) right before
epidemic.

[0] [https://edition.cnn.com/2019/09/17/health/russia-lab-
explosi...](https://edition.cnn.com/2019/09/17/health/russia-lab-explosion-
smallpox-intl-hnk/index.html)

------
ttflee
> In fact, a Chinese BSL-3 lab (the Shanghai Public Health Clinical Centre),
> which published a Nature article reporting a conflicting close phylogenetic
> relationship between SARS-CoV-2 and ZC45/ZXC21 rather than with RaTG13, was
> quickly shut down for “rectification”.

~~~
4684499
I think that's misinterpretd, the ref link in the paper is
[https://globalbiodefense.com/headlines/chinese-lab-that-
firs...](https://globalbiodefense.com/headlines/chinese-lab-that-first-shared-
novel-coronavirus-genome-shut-down/) , which leads to SCMP's
[https://www.scmp.com/news/china/society/article/3052966/chin...](https://www.scmp.com/news/china/society/article/3052966/chinese-
laboratory-first-shared-coronavirus-genome-world-ordered)

SCMP's piece also mentioned that "It also obtained the required credentials to
conduct research on the coronavirus on January 24." That indicates the Centre
actually gained more access.

And if you search Shanghai Public Health Clinical Centre on Google, you can
see it's still actively doing COVID-19 related research.
[https://jamanetwork.com/journals/jamainternalmedicine/fullar...](https://jamanetwork.com/journals/jamainternalmedicine/fullarticle/2769741)

------
dependenttypes
There is a wikipedia article about the 1st author
[https://en.wikipedia.org/wiki/Li-Meng_Yan](https://en.wikipedia.org/wiki/Li-
Meng_Yan)

------
zug_zug
Worth reading Li Meng Yan's wikidedia page as a first stab at untangling this
mess.

She is a Chinese[1] viral researcher who published on covid[1], who fled to
America when she felt her life was in jeopardy[1] for saying that China knew
about human-to-human transmission of covid much earlier [1].

And lead author of this paper.

1 - [https://en.wikipedia.org/wiki/Li-
Meng_Yan](https://en.wikipedia.org/wiki/Li-Meng_Yan)

------
jlbooker
Other commentary on this paper: [https://www.thedailybeast.com/steve-bannon-
linked-groups-pus...](https://www.thedailybeast.com/steve-bannon-linked-
groups-push-study-claiming-china-manufactured-covid)

Bannon clearly has a narrative he wants to push, and this is just part of that
play. This is far from objective science. The authors and funding clearly have
huge conflicts of interest. The claims made are extraordinary compared with
most other experts in the field. Those two facts alone are enough to
significantly discount any claims made in the paper.

------
pella
flagged in other threads :
[https://news.ycombinator.com/item?id=24477162](https://news.ycombinator.com/item?id=24477162)

~~~
gridlockd
Why should it be flagged?

~~~
ttflee
People don't learn molecular cloning, phylogenetics, or how to perform a PCR
before they upvote/downvote. People just hate its rhetoric.

------
Zycloparadoxus
Is this article already available in German?

------
White_Wolf
So any country could do this (and even some rich private individuals if they
are motivated enough). Keeping in mind that this virus showed up a lot earlier
in other countries I'd say there is no way to prove who let the dogs out
anyway.

------
biolurker1
I really don't get why people were so resistant to the idea. We knew
experiments went on at that lab. We knew they had coronaviruses.

------
hitsetute
I have now flagged this particular bullshit misinformation FIVE TIMES on HN.

There is a group here on HN repeatedly posting this drivel and related
nonsense. I would have thought that Trump-style lies and propaganda would be
beneath HN, but here we are.

So what’s up OP? Care to explain why you’re engaged in lies?

~~~
jkhdigital
This is a scientific research paper. If you think it’s BS then I eagerly await
your point-by-point refutation of the scientific evidence presented therein.

~~~
dekhn
This isn't a scientific research paper; it's propaganda masequerading as a
science paper. I know it's hard to tell the difference, especially if the
authors were skilled.

~~~
SomeoneFromCA
Have you actually read it?

~~~
dekhn
I skimmed it, like most "articles" about articles that suggest that SARS was
either intentionally or inadvertently released from a lab, and after a bit
determined it was propaganda, not legitimate science, and did not continue.

~~~
SomeoneFromCA
Each and every claim they make is substantiated by links to some other
research, by unrelated and independent research. Most of people here are not
virologist, molecular biologists etc, and probably have no say in determining
if it is propaganda or not.

~~~
dekhn
Sure, but it's probably not in anybody's best interest for those of us with
molecular biology (biophysics in my case) PhDs to do rebuttals of papers like
this in an ELI5 way, so that hackers can understand how to recognize
propaganda.

~~~
SomeoneFromCA
Baseless statements like it is "I skimmed it, and it is just propaganda" are
not welcome in any educated conversation. If you cannot give a good
explanation why it is "a propaganda", it is probably better to not say
anything.

~~~
dekhn
OK. This sentence in the abstract: The alternative theory that the virus may
have come from a research laboratory is, however, strictly censored on peer-
reviewed scientific journals.

that's not true. If you wrote a good article that was completely defensible
and submitted it to a top journal, it wouldn't be censored. It's not like the
editors of nature are just sitting around stomping on papers they don't agree
with. The problem is that if you wanted to convince peer reviewers and editors
to publish such an article, it would need to be absolute perfect- not a single
detail wrong, not a single bit of politics, totalyl consistent with the
observed evidence, and more likely than natural origin (which is a very
reasonable hypothesis to start with). Very few of the articles I've seen that
claim lab origin pass the basic technical tests.

The editors of nature, science, etc, would love to receive a paper that
actually made a good enough argument that there was a lab origin. that would
be the scoop of a century.

~~~
SomeoneFromCA
Please, let's not focus on some political points of the article (my personal
experience actually confirms that going against the established consensus will
hurt you carrier; there is a plenty of evidence in the history of science,
when the scientists were ridiculed for being contrarian; check Zemmelweis,
Cantor etc.). Please focus on scientific points.

------
AnnoyingSwede
As many i started reading the paper from a non biologist perspective, then hit
the comment section here to see the Steve Bannon references. That man has a
whole carddeck up his sleeve. Question: Is it illegal to release misleading
material like this?

~~~
dekhn
No, it is not illegal to release known factually incorrect propaganda
masequerading as scientific literature. If it was, large numbers of professors
would be violating the law constantly.

