No, the 2019-nCoV [coronavirus] genome doesn’t really seem engineered from HIV

The Prepared ^ | 1/31/2020 | Ari Allyn-Feuer

[catnipman]

They found that all four of these spike protein inserts appear as matches to at least one sequence in at least one variant of the HIV virus. The sequences come from the gp120 and Gag proteins in HIV, the former of which is also a viral envelope recognition protein. This has led many to credulously assume that this is evidence, or even a strong indication, that 2019-nCoV was engineered from its bat ancestor by humans inserting HIV sequences.

But they’re wrong; it’s still not engineered. An analysis of the paper clearly reveals that:

1. There is nothing remarkable about the fact that 2019-nCoV’s sequence diverges from its nearest known relative, or that its unique sequences are conserved among cases of 2019-nCoV.

2. The sequence matches with HIV are very short and appear in hypervariable regions of both virus, and similar overlaps are seen between 2019-nCoV sequences and many other organisms.

3. The unique biological properties that HIV sequences could theoretically impart to another virus are completely missing from 2019-nCoV, and 2019-nCoV has no unique clinical properties that are outside what is known to be possible for a coronavirus.

In other words, the sequence overlap is not actually uncanny, and there is no big scoop here. The group in India fell prey to some of the pitfalls of bioinformatics research.

The 2019-nCoV genome does not contain remarkable genomic properties which need explaining, and for which we’d look to some kind of bioengineering as a cause.

2019-nCoV continues to give every appearance of being a wild coronavirus that jumped from bats to humans by way of an animal intermediary in the Huanan seafood market in Wuhan in late 2019.

[KobraKai]

I freaking HATE article titles like this! “No, such and such does not mean such and such”

Whenever I read that I know I’m in for Spin City on whatever the topic is.

[Lopeover]

This assumption is being passed, but I will believe the micro-biologist who said there was. This is not caused by bat eating. The origins of this virus is purposeful.

[Lopeover]

Yes. This is a weaponized virus.

[Lopeover]

Were they going to use it on their Hong Kong citizens or us?

[MD Expat in PA]

Biorxiv is a preprint server for uploading finished manuscripts, before (or during) the process of submitting them to a journal for publication. It is not peer reviewed and there seems to be but only very basic screening and a check against plagiarism (in other words, does it follow the basic outline of a scientific paper and ensuring it is not a word for word copy of another paper). Thta doesn’t mean everything posted there is garbage, but also doens’t mean everthing posted there is valid.

https://www.researchgate.net/post/What_is_biorxiv_And_what_do_people_use_it_for

7th Jul, 2018
Bernhard Hommel
Leiden University

But the problem is that such servers blur the line between peer-reviewed articles and fake news. Many authors and readers treat pre-publications just like peer-reviewed papers accepted by a journal, and so we read twitter messages about „evidence for xyz“ with a link to unreviewed papers with sometimes questionable methodology and conclusions, and laypeople (and I‘m afraid some researchers as well) take that as scientific evidence already. That has the potential to undermine the credibility of our science.

Criticisms in the comment section of the Biorxiv paper – “Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1 gp120 and Gag”:

Brian Hanley • 7 hours ago • edited

I agree with Jason Weir, Song Yang, and others.
Regarding these purported HIV sequences. I studied gp120 structure in an transmission electron microscopy lab in grad school. gp120 has long non-conserved regions that effectively hypermutate. This is a major mechanism of HIV immune system evasion, because it changes the gp120 presented region so fast the immune system can’t keep up with it.

This happens because HIV is an RNA virus. It has a couple of mutations per replication on average. In late stagesof infection there can be 500K to 1 million copies per milliliter. do the math on that. Because of this, we call HIV a quasi-species. It’s got a very bushy tree within one person that is infected.

Within the quasi species of HIV, in the gp120 non-conserved high mutationregions you are going to find just about any short sequence there sooner or later. These inserts are short, up to 15 or so nucleotides, but mostly 5 to 8. And this is the spike protein, which is an area that mutates and finds new receptors.

If you want to look at anengineered virus, look up SHIV (simian HIV). That was designed and produced in a laboratory. It has huge regions transferred from other viruses. It makes monkeys sick with human-like HIV.
I think that this paper is ignorant and amateurish pseudoscience. No. Absolutely not. This is not some escaped bioweapon.

Jason Weir • 14 hours ago

I blasted each of the four 2019 - nCoV inserts shown in Table 1 and received 100% identity with a number of other hits other than HIV-1. For example, BLAST-P results for insert RSYLTPGDSSSG received 100% identity with Spike glycoprotein from a bat coronovirus with Genbank accession number GenBank: QHR63300.1. It is thus much closer to a known bat coronovirus than it is to HIV-1. Likewise each of the other three inserts have 100% amino acid identity to other non-HIV sources. The paper is thus highly misleading in that it does not discuss the other blast hits to non HIV-1 related sources, some of which have high identity than those from HIV-1. The implications of the paper that 2019 - nCoV coronovirus has elements of HIV-1 virus inserted into it should be treated with scepticism.

-Jason Weir (Department of Ecology and Evolutionary Biology, University of Toronto)

Read others here:

https://www.biorxiv.org/content/10.1101/2020.01.30.927871v1.article-info

And something that jumped to me as well:

Kenrod • 12 hours ago

It strikes me that the phrase “uncanny similarity” and continued use of the word uncanny in the manuscript is not scientific. Unless there is a way to measure or gauge a comparison via some sort of statistics this reads more like astrology and is irresponsible.

[Swordmaker]

“Author’s note: I have a Ph.D. in bioinformatics, and am a principal data scientist at a major pharmaceutical company. This paper isn’t directly in my wheelhouse, but it’s pretty close.”

Translation: he’s a computer nerd with a special emphasis in biology data, not anything having to do with virology. He’s blowing smoke screens about his expertise and his alphabet soup behind his name.

[Swordmaker]

Yes. This is a weaponized virus.

If so, it’s a poor one. 2.2% fatality rate and a very poor virulence. It’s been in the wild since December in a densely populated area of 15 million and under 15,000 reported infections and fewer than 300 deaths. That’s not a weapon.

[Diogenesis]

this does seem engineered/designed/weaponized

the rising prevalance and rising
death rate is higher than SARS

there are very few recoveries so far.

the four HIV inserts are unlikely to be natural.

“Once is happenstance.
Twice is coincidence.
Three times is enemy action.”
Ian Fleming

[null and void]

In other words, the coronavirus was not "engineered" to contain HIV virus portions ...

In other words, HE SAYS the coronavirus was not "engineered" to contain HIV virus portions ...

Color me skeptical.

Bring Out Your Dead

Post to me or FReep mail to be on/off the Bring Out Your Dead ping list.

The purpose of the “Bring Out Your Dead” ping list (formerly the “Ebola” ping list) is very early warning of emerging pandemics, as such it has a high false positive rate.

So far the false positive rate is 100%.

At some point we may well have a high mortality pandemic, and likely as not the “Bring Out Your Dead” threads will miss the beginning entirely.

*sigh* Such is life, and death...

If a quarantine saves just one child's life, it's worth it.

[SoConPubbie]

If so, it’s a poor one. 2.2% fatality rate and a very poor virulence. It’s been in the wild since December in a densely populated area of 15 million and under 15,000 reported infections and fewer than 300 deaths. That’s not a weapon.

All of those "data-points" you just posted were brought to you courtesy of a Communist Regime who wouldn't know the truth if it bit them in the ass!

Communists lie! That's what they do.

[RaceBannon]

Possibility that HIV virus is in Corona virus, intentional, man made
https://www.biorxiv.org/content/10.1101/2020.01.30.927871v1.full.pdf

[RaceBannon]

Abstract:
We are currently witnessing a major epidemic caused by the 2019 novel coronavirus (2019-
nCoV). The evolution of 2019-nCoV remains elusive. We found 4 insertions in the spike
glycoprotein (S) which are unique to the 2019-nCoV and are not present in other coronaviruses.
Importantly, amino acid residues in all the 4 inserts have identity or similarity to those in the HIV1 gp120 or HIV-1 Gag. Interestingly, despite the inserts being discontinuous on the primary
amino acid sequence, 3D-modelling of the 2019-nCoV suggests that they converge to constitute
the receptor binding site. 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. This work provides yet unknown insights on 2019-nCoV and sheds light on
the evolution and pathogenicity of this virus with important implications for diagnosis of this virus.

Possibility that HIV virus is in Corona virus, intentional, man made
https://www.biorxiv.org/content/10.1101/2020.01.30.927871v1.full.pdf

[null and void]

I don’t think all these nations have optimal medical facilities, or the latest medicines.

No they don't. But perhaps they haven't had fatalities simply because the 153 patients simply haven't been sick long enough for the disease to run its course.

[null and void]

So the author doesn't really know if it is or isn't. I cannot take his opinion as gospel, yet at any rate. We shall wait and see what transpires on this issue.

I'll be fascinated if he suddenly buys a beach mansion on Bora Bora...

...and pays for in in Yuan!

[PghBaldy]

They were treating other corona viral infections with HIV drugs years ago. Nothing odd about this.

(June 2015) https://www.in-pharmatechnologist.com/Article/2015/06/22/South-Korea-mulls-combining-HIV-drugs-with-antivirals-to-combat-MERS?utm_source=copyright&utm_medium=OnSite&utm_campaign=copyright

[Caipirabob]

Who the hell would engineer such a virus anyway?!?

Oh, @#$% chicoms.

"Underwear Gnone" warfare.

Phase 1: Create lethal virus

Phase 2: Oops...

Phase 3: Profit!

[DrewsMum]

Bkmark

[null and void]

but from this sentence it seems like the HIV parts that could cause trouble aren’t here? This is just like a late abortion...

If you define "trouble" as causing AIDS, yes.

If you mean causing a fatal strain of flu that bypasses all the normal flu vaccination targets and latch on to other sites, those are there.

<Tinfoil>

5hit's gonna get real when someone decides that this was deliberately done by a gay researcher in Canada's lab who was upset about the slow progress on AIDS vaccinations, figuring that the genes in a highly contagious flu would force more research in this area. Even if true, he couldn't foresee it being stolen by his dear friend the nice Chinese co-worker, nor that China would use a more virulent version of flu, and certainly that China would be so negligent (or stupid, or just plain evil enough to lose control of it) Still, a lot of people with that lifestyle will become mob targets.

Would China use this to reduce their population? They used the one child policy and forced abortions and sterilizations to enforce it, didn't they?

And there is the issue of African Swine flu. Most of China's main protein source has been wiped out. Face a billion hungry rioters blaming you, or a quarter billion survivors afraid to gather in groups and grateful to you for saving them?

</Tinfoil>.

[LuigiBonnafini]

I asked my son, who has a PHD in Microbiology (focus on genetic engineering) about the idea that this is a man-made virus. this is his response:

Dad,

Long story short: This is outside my wheelhouse, but what I see doesn’t convince me of much.

The relevant publication (at-least one of them) might be: https://www.biorxiv.org/content/10.1101/2020.01.30.927871v1.full.pdf

The paper claims that there are a few dozen genomic sequences from the current virus on NCBI: https://www.ncbi.nlm.nih.gov/

Indeed, such files are available: https://www.ncbi.nlm.nih.gov/genome/genomes/86693?

I pulled all of the spike glycoprotein sequences:
https://www.ncbi.nlm.nih.gov/protein/QHN73795.1
https://www.ncbi.nlm.nih.gov/protein/QHN73810.1
https://www.ncbi.nlm.nih.gov/protein/QHO60594.1
https://www.ncbi.nlm.nih.gov/protein/QHO62877.1
They all appeared to be identical.

I used a portion of the protein sequence in a ProteinBlast (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins), which indicated that it was closely related to other known coronaviruses (e.g. SARS, and a bat coronavirus).

I then retrieved one version of the HIV GAG sequence (https://www.ncbi.nlm.nih.gov/protein/AAD39400.1), and attempted to align it with each of the spike glycoprotein sequences with SIM Align (https://web.expasy.org/sim/). This allignement didn’t show an impressive degree of similarity.

I tried the same thing with GP120 (https://www.ncbi.nlm.nih.gov/protein/NP_579894.2), which was similarly unimpressive.

I’m not sure how much similarity we’re expecting, but there are only a few residues in a row that are ever identical. The degree of similarity may be a fluke, or it may be statistically significant, but it’s far from the case that 2019-nCoV has been convincingly spliced together from HIV.

It might be more-impressive if there was overlap in the DNA sequences of 2019-nCoV and HIV. So, I pulled the actual genomic sequence for both an ran another allignment, this time with Clustal Omega. The results may be available here: https://www.ebi.ac.uk/Tools/services/web/toolresult.ebi?jobId=clustalo-I20200131-215248-0865-94258030-p2m

That actually shows some more -interesting stuff... HIV is a lot smaller than 2019-nCoV, so most of the genomes don’t overlap. The program is able to generate some weak overlap for virtually all of the HIV genome, but there’s a 1-in-4 that any given base pair can be matched, so that’s not a surprise. The odd thing is that there are some portions of the HIV genome that fail to allign at all to 2019-nCoV. It’s probably just a statistical anomaly.

If someone wanted to make some sort of hybrid HIV/Coronavirus, they went to great pains to make it subtle in 2019-nCoV.

[DrewsMum]

So you saying the Chinese scientist expelled from a level 4 lab where they work with deadly viruses in canada ..... and she had made several trips back and forth from wuhan.... you saying there’s NO reason whatsoever to ask any questions at all? Huh?