
Scientists claim to find HIV virus-like insertions in the 2019-nCov [pdf] - ronalbarbaren
https://www.biorxiv.org/content/10.1101/2020.01.30.927871v1.full.pdf
======
folli
Sorry, but it's very easy to verify that these claims are crap by replicating
their study, i.e. doing a simple blast search of the insert sequence against
the virus database. Here's the result of the first insert:
[https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=398N4CS...](https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=398N4CSR01R)

Although, there are some hits against HIV, there are also equally matching
hits against bacteriophages; viruses that only target bacterias, they are
completely unrelated to any viruses that target humans and animals.
Furthermore, the E value is around 170, that means that matches are
statistically completely insignificant, meaning they happened by chance only.
Such a high E value corresponds to a p-value of very, very close to 1
([https://www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html](https://www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html)).

These guys that published such a paper are either completely clueless or
nefarious in trying to stir up conspiracy theories.

~~~
Palptine
What's the chance of hitting all 4 of them though? This is a good step in
verification but you are awfully too quick to reject their claim.

~~~
folli
Read the paper, they actually only match 2 inserts, the other two inserts are
modified by the authors in such a way that they are made to match (Table 1).

Both inserts 1 and 2 also match to Streptococcus phage, but a bacteriophage
would of course not be such a bold claim as HIV matches are.

Also, be aware that because of the scientific interest in HIV, there are
hundreds of HIV strains sequenced, a virus known for its mutation rate
(especially in these two proteins gp120 and gag, as they are under pressure to
mutate in order to evade the immunesystem). So in such a large library of
protein sequences one is bound to find a match of a short 6 letter (amino
acid) sequence. That's why E values exist to make a statement about the
statistical significance.

~~~
folli
For posteriority, here's the link to the Blast results for the second insert:
[https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=39ACRKV...](https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=39ACRKV3014)

~~~
im3w1l
Hello posteriority here! I wanted to reference these comments in a discussion
but the links expired :/

------
hirenj
This looks like a whole lot of rubbish to me. They're excited they managed to
get blast hits for these short inserts.

But in the spirit of open-mindedness, what do I need to be convinced this is
even interesting? First I want to see where on gp120 these inserts align to.
Are they receptor/carbohydrate binding regions? Where do they map to on the
coronavirus? These structures are known, so I don't know why this isn't in
this manuscript.

If somehow this is engineered, I am honestly impressed that someone could take
features from one protein and estimate how to engineer those same features in
another protein altogether, with little homology. It's like engineering a
monkey tail onto an elephant and somehow getting the elephant to swing through
the trees.

~~~
fapjacks
I appreciate your skepticism (and your sense of humor) but for the benefit of
other readers, it is not like engineering a monkey tail onto an elephant and
expecting the elephant to swing through the trees.

------
jszymborski
I think the important things to know here are:

1\. A group of scientist have submitted a manuscript for review with a number
of exceptionally (and uncharacteristically) bold claims.

2\. A huge amount of scrutiny and additional reproducibility will necessarily
need to be conducted before conclusions of this nature can be drawn.

3\. This manuscript hasn't even passed the normal muster... a biorxiv post
isn't much different than a Medium post. Claims like these require many eyes.

EDIT: My sentiment echoed by someone who know more than I
[https://twitter.com/DrEricDing/status/1223325141364592640?s=...](https://twitter.com/DrEricDing/status/1223325141364592640?s=20)

~~~
cs702
As regards #3, I agree: the more eyes who see this _unconfirmed_ claim, the
better. That's the main reason I upvoted the OP.

A great outcome would be if reputable scientists see this on HN or Twitter or
learn about it through colleagues, and subsequently refute it or dismiss it as
bad science.

~~~
im3w1l
> the more eyes who see this unconfirmed claim, the better.

Isn't it a waste of those eyes' time if it turns out to be false? When there
are plenty of _confirmed_ things they could be reading?

------
thorum
This is especially interesting since there have been reports that China was
testing HIV treatments on patients with the coronavirus:

[https://www.reuters.com/article/us-china-health-abbvie-
hiv/c...](https://www.reuters.com/article/us-china-health-abbvie-hiv/china-
testing-hiv-drug-as-treatment-for-new-coronavirus-abbvie-says-idUSKBN1ZP0QK)

~~~
Arete314159
Yes they are BUT it's my understanding those HIV drugs had already been used
against SARS and found helpful in an anecdotal way. So it would be an obvious
first go-to drug.

------
ajna91
A thread by an epidemiologist on the new results:

[https://twitter.com/DrEricDing/status/1223305946723704832](https://twitter.com/DrEricDing/status/1223305946723704832)

~~~
chadmeister
This has been pointed out in previous threads, but this Twitter is full of
alarmist unscientific BS and it appears to be spammed with some regularity on
HN recently.

~~~
WillPostForFood
Alarmist, yes. Unscientific BS, not really. He’s got the background to make
comments from a position of legitimacy. If we can’t trust this guy, even with
some healthy skepticism, who should we trust?

[https://scholar.harvard.edu/ericding/home](https://scholar.harvard.edu/ericding/home)

Edit: by trust, I don’t mean blindly believe, but mean one should consider his
comments seriously.

~~~
MiroF
From that link, it seems like he is commenting far outside of his expertise in
"behavioral interventions" to improve things like "medicare cost."

Don't trust anyone, just weigh their claims and their background. In this
case, I have yet to see people with serious credentials in genomics make this
claim (outside of the original scientists who published the paper relating it
to HIV - IIT is impressive, but I don't really know how to assess their
credentials writ large)

~~~
WillPostForFood
How is this outside his area of expertise? He has a doctorate in epidemiology.

 _He graduated from The Johns Hopkins University with Honors in Public Health
and Phi Beta Kappa. He then completed his dual doctorate in epidemiology and
doctorate in nutrition, as the youngest graduate to complete his dual program
at age 23 from Harvard SPH. Teaching at Harvard for over 15 years, he has
advised and mentored 2 dozen students, and lectured in more than a dozen
graduate and undergraduate courses, for which he received the Derek Bok
Distinction in Teaching Award from Harvard College._

------
Tenoke
Why was this submission suddenly so heavily penalized by the mod(s)?

~~~
akamaka
Users can press the “flag” button for content that is off-topic. I flagged
this article because it is an unreviewed pre-print paper that has been rushed
out by its authors, who clearly have not investigated any of the most obvious
follow-up questions, such as “what is the probability of this occurring
naturally?”

~~~
ctoth
Okay so we definitely need to flag any machine learning papers from Arxiv
because hey preprint.

Further, do you assume that other members cannot read the preprint warning and
decide for themselves? This strikes me as some sort of bizarre way to
patronize the entire community.

~~~
akamaka
I’m not a biologist, so I’m really not interested in this type of paper, and I
expressed my opinion through the voting mechanism.

Also, there are thousands of researchers studying this new virus. If this
turns out to be an important finding, I can wait until it is validated. At
this point, this paper looks poor quality, and it was a waste of time for me
to click on it and read it.

~~~
Tenoke
There are no post downvotes on HN for a reason (or at least normal users dont
have them) - flag doesn't and shouldn't mean the same thing as a downvote.

~~~
akamaka
I don’t flag things often, as one might downvote a comment they disagree with.
The flag mechanism is for off-topic or spam content, and I consider this way
off-topic for this site. There have already been hundreds of published
articles about this virus, and if I was interested in seeing them, I would use
a site like PubMed to see them.

~~~
ngcc_hk
Need summary otherwise bad coin drive away good coins. What are the good one?

------
aqme28
"...unlikely to be fortuitous."

Ignoring the odd word-choice, this ties in to the conspiracy theory that this
was a Wuhan biolab containment leak.

I have been writing it off as a crackpot conspiracy until now, depending on
peer review.

------
hnarn
I'm not saying I believe the conspiracies, but it would be a pretty scary
future if a totalitarian nation decided to quietly immunize their population
(or just a selected elite) from a pathogen designed by themselves, and if push
comes to shove you have a bioweapon that will do the job for you, which you
know the people you care about can't contract. It's like a smart nuke.

~~~
mcantelon
Given historical experimentation by the military and intelligence agencies it
seems pretty likely that this sort of research is happening.

------
jakewins
So what is the probability that a lab that works with HIV normally, now
working under extreme pressure, contaminated or mixed up a sample?

And what is the probability that this is not just a third type of major
coronavirus, but in fact a secret bioweapon?

Knowing how commonly there are arguments about mixed up samples in the biolabs
friends work in, I know where I would place my bets.

~~~
xvector
It would be a pretty lame bioweapon given how few people it’s killed.

~~~
fapjacks
Be advised that there are many posts on Chinese social media claiming the
crematoriums are backlogged with people whose listed cause of death is "viral
pneumonia" (or just "pneumonia") because hospitals are turning away so many
and diagnostics are not catching up. Do not take statistical reporting for
granted: The numbers are a best case scenario of definitive knowns. Also,
bioweapons have as diverse a variety of use cases as any other class of
weapon: They don't need to kill half of a population to be effective weapons.

~~~
xvector
While I think China is hiding the number of infected, it'd be pretty hard to
hide the proportion of dead to infected as the virus has already escaped
Wuhan.

~~~
ngcc_hk
The question is not hard but no one really know. Would you test a body died
recently?

China is not very reliable in gdp (one top guy told us to look at the
electricity and we look at pollution). It is very hard to get stat.

So far touch wood no one died outside of China. The death rate should not be
high unless the alternative saying hiv death rate after 1 month is 0%.

The conspiracy theory in a proper sense is accidentally leaked for an
experiment, like sars virus leaked (later and during study) by Beijing level 3
lab.

------
charliemil4
Does anyone know the extent of the symptoms of 2019-nCoV? Does the virus get
fully expelled from a person when they are recovered? Or is there a secondary
effect / reemergence?

------
rafaelm
Some comments on this Biorxiv site from an epidemiologist:
[https://twitter.com/aetiology/status/1223328143647236097](https://twitter.com/aetiology/status/1223328143647236097)

"For non-scientists, if you see something posted from a site called BioRxiv,
have some skepticism. It could be a fantastic paper! (I've used it!)--but. The
site is for preprints, which means they haven't undergone peer review yet."

------
tomrod
That's very, very disturbing.

If this is an engineered virus, why as a race do we keep doing these things to
ourselves? Do we _really_ think that weapons of mass destruction won't be
turned on us? Is our hubris so high that we think no one else can replicate
what we built?

~~~
ngcc_hk
Our eye and hand was developed mainly to focus against other humans.

Our military has to study this ...

But officially one has to study this as dual use as one has to prepare the
natural evolution of say SARS to another strain. Can’t be sitting duck, let
evolution run its course (2% death rate is not high but times 1.4 billion it
is 28m people). Hence there is a case to study it, even change it. But then
...

Just like we should fight hiv. But then someone in china use human to
experiment on it.

It is not there is no case. There are. Just stupidity of human ...

------
remarkEon
to someone who doesn’t know anything about the relevant science (me) the use
of the word “insertions” seems to imply this was engineered. Can someone who
actually understands this explain what this document is saying?

~~~
317070
Well, the conclusion of this paper is that the odds of this virus coming to be
naturally are very small. Which is a very scientific way of saying "we think
this was man-made".

But, that is what the paper is saying. Extraordinary claims, extraordinary
evidence is what I think. I feel the evidence here is quite small, but I'm not
a bio-data-scientist.

~~~
ericb
Is it an _extraordinary_ claim? The sequence matching should be easy to verify
as the genome has been published. If the sequences are short or common enough
maybe it would be a more likely coincidence.

That said: What are the priors on a "natural" virus erupting in _the only city
in China with a level 4 biohazard facility?_

Source:
[http://english.www.gov.cn/state_council/ministries/2018/01/0...](http://english.www.gov.cn/state_council/ministries/2018/01/04/content_281476001535134.htm)

~~~
SketchySeaBeast
So if it's not extraordinary it's still going to require evidence, which
without peer review we still pretty much have none.

~~~
gamegod
This is _evidence_ , but it requires _corroboration_ from other evidence. Peer
review doesn't provide additional evidence - it's just a sober second opinion
that lends credence (or not) to the proposed evidence and interpretation.

Just wanted to clarify the language here.

~~~
SketchySeaBeast
Totally right - and thank you for the clarification in language.

------
tkems
[https://web.archive.org/web/20200131195339/https://www.biorx...](https://web.archive.org/web/20200131195339/https://www.biorxiv.org/content/10.1101/2020.01.30.927871v1.full.pdf)

------
sam36
The amazing thing is last week someone on 4chan posted this:
[https://i.imgur.com/Jkq8tYK.png](https://i.imgur.com/Jkq8tYK.png) Which shows
that the virus had been modified. 4chan wins once again at sleuthing.

~~~
codingslave
This lab theory has been systematically censored across the internet for the
last week or so. For me it has been fascinating to watch content on it pop up
and then disappear.

~~~
LargoLasskhyfv
_Psyberwar_ in action...

------
buboard
The study is probably bunk and sensational. check the comments by this
redditor :
[https://www.reddit.com/r/China_Flu/comments/ewt9ep/scientifi...](https://www.reddit.com/r/China_Flu/comments/ewt9ep/scientific_paper_uncanny_similarity_of_unique/fg4ewbn/)

[https://www.reddit.com/r/China_Flu/comments/ewuotw/discussio...](https://www.reddit.com/r/China_Flu/comments/ewuotw/discussion_biorxiv_preprint_on_2019ncov_spike/fg4jjrq/)

The real question is: how far are we from this becoming real ?

~~~
zozbot234
Interesting, that user claims to be especially familiar with the 'gag' protein
where the paper claims to find a match. User explicitly says that the
"matching" portions claimed in the paper are so tiny as to be negligible, and
_not_ unique to HIV. They claim that this is easily verifiable with a simple
'blast' search. Could someone comment on these claims?

~~~
TimonKnigge
see
[https://twitter.com/trvrb/status/1223337991168380928](https://twitter.com/trvrb/status/1223337991168380928)

------
dcolkitt
Ignoring the political implications, how would HIV insertions change the
virulence and epidemiology of the infection?

~~~
droithomme
In the paper they hypothesize:

> Due to the presence of gp120 motifs in 2019-nCoV spike glycoprotein at its
> binding domain, we propose that these motif insertions could have provided
> an enhanced affinity towards host cell receptors. Further, this structural
> change might have also increased the range of host cells that 2019-nCoV can
> infect.

------
JulianMorrison
I wonder if this could happen because someone with a retrovirus got both
infections at once?

~~~
zozbot234
It's not even necessarily someone with HIV - HIV is just _one_ virus that is
especially well-studied. If horizontal gene transfer in viruses _is_ more
common than we expect it to be, this genetic material could've been picked up
from just about anywhere and we wouldn't necessarily know about that source.

------
codingslave
This would be a really scary outcome. As has been commented elsewhere, there's
confirmed events of at least four virus leaks from labs in Beijing.

Evidence/article on it here:

[https://thebulletin.org/2014/03/threatened-pandemics-and-
lab...](https://thebulletin.org/2014/03/threatened-pandemics-and-laboratory-
escapes-self-fulfilling-prophecies/)

Not only that, but just last year there was a case of a Chinese scientist who
was banished from a Canadian bio lab level 4 for stealing virus samples, as
well as a Harvard Academic found to be taking money from the Chinese gov to
help develop the lab in Wuhan.

None of this proves the lab theory, but I do believe that with enough genetic
analysis the truth will come out.

~~~
uwuhn
I don't like how people are saying that theories regarding it being
accidentally leaked are conspiratorial in nature.

Intentional leaking? Sure, I think it's fair to consider that a conspiracy
theory. But not accidental.

~~~
AndrewBissell
It would be conspiratorial in nature because it questions the Chinese
government's official narrative that the virus emerged from a seafood market,
and implies they're covering up the truth.

Of course, people usually use the term "conspiratorial" to be synonymous with
"untrue" or even "patently absurd."

~~~
busterarm
We already know for sure that the initial cases did not originate in the
seafood market and that the market was just an infection vector for subsequent
cases.

Recently available data shows that the first few cases happened in November.

------
jonplackett
How long would it take for any other scientists to confirm or deny this?

------
greesil
Maybe we should wait for peer review before we jump to any conclusions.

------
drtillberg
I generally agree with the folks who flagged this posting on HN (I didn't
though) because the thought of ... airborne, highly contagious HIV in an early
phase pandemic ... is a really very un-HN-like thought ... the mere
theoretical possibility it _could_ be true is the sort of thing I'd hope might
inspire a generation to make our leaders globally take a time out on heated
rhetoric and the ongoing technological arms race.

------
hprotagonist
This work was subsequently retracted:
[https://www.statnews.com/2020/02/03/retraction-faulty-
corona...](https://www.statnews.com/2020/02/03/retraction-faulty-coronavirus-
paper-good-moment-for-science/)

------
lisk1
My dose of speculation. So far we have strong evidence that this is a biolab
virus, probably they were experimenting with this virus on animals the lab
personal didn't realize on time how easy this virus could be transmitted by
air, probably they were using the public transport from home to work during
the incubation period thats how it boomed all of a sudden.

------
perseusprime11
It does seem like something escaped a lab or a human trial gone wrong. Here's
a better explanation: [https://jameslyonsweiler.com/2020/01/30/on-the-origins-
of-th...](https://jameslyonsweiler.com/2020/01/30/on-the-origins-of-
the-2019-ncov-virus-wuhan-china/)

------
heinrichhartman
2019-nCov is "The novel coronavirus (2019-nCoV), informally known as the Wuhan
coronavirus."

source:
[https://en.wikipedia.org/wiki/Novel_coronavirus_(2019-nCoV)](https://en.wikipedia.org/wiki/Novel_coronavirus_\(2019-nCoV\))

------
shanebkk
This is all just guys stirring up trouble, conspiracy theories abound.

~~~
ngcc_hk
The virus is real. How it spread and where it comes from is an important
analysis needed. SARS seems from eating wild cat and they are not sold there
(there after decade there are selling in that market still but not those
type).

You learn. But so far due to the source is far away from more reliable
scientific base (hk in 2003), no one knows. Hence one have to reconstruct.

These might be wrong but investigation is needed. “ For his contemporaries,
the ideas presented by Copernicus were not markedly easier to use than the
geocentric theory and did not produce more accurate predictions of planetary
positions. ”

Let the river flow. Dead water you can step in twice is not good water.

------
seaghost
Have in mind that this paper is not peer reviewed.

------
cwkoss
"The finding of 4 unique inserts in the 2019-nCoV, all of which have identity
/similarity to amino acid residues in key structural proteins of HIV-1 is
unlikely to be fortuitous in nature."

Does this lend support to the theory that the coronavirus was engineered in
Wuhan's bioweapons laboratory?

~~~
mc32
If that is ever proven and a cover up ensues I’d like to think the people
would at last slough off their gov.

~~~
croissants
I'm not sure that realizing your totalitarian government is more dangerous and
less principled than you thought is going to encourage rebellion.

------
narrator
If someone with deep pockets may be liable, there will be a well funded effort
to debunk this.

~~~
busterarm
You mean like the government of China?

~~~
narrator
...or a well funded PR campaign to assign blame to somebody else.

------
herogreen
Twitter thread by Dr. Eric Feigl-Ding on this yet-unreviewd publication:
[https://threadreaderapp.com/thread/1221990534643929089.html](https://threadreaderapp.com/thread/1221990534643929089.html)

------
brutt
As predicted in Contagion (2011).

[https://en.wikipedia.org/wiki/Contagion_(2011_film)#Scientif...](https://en.wikipedia.org/wiki/Contagion_\(2011_film\)#Scientific_response)

~~~
brutt
Seriously, this particular mutation of unknown bat virus + HIV is predicted in
film. I recommend to watch it: it's very scientific, and has almost no action.

