Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1 gp120 and Gag

Biorxiv ^ | 01/31/20 | Staff

[winoneforthegipper]

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 HIV-1 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

[winoneforthegipper]

Thanks was hoping for that knowledge.

Interesting though that a few questions they raised appear to have some merit.

[DEPcom]

That is explain why I heard some HIV drug is know to work against this virus.. It was floating around twitter about three days ago. I think they were using the HIV drug for treatment in China.. I will have to go search for the news source for it.

[edwinland]

Thanks for that info. Can you elaborate a bit more?

[DEPcom]

Here is the article. Follow the money. Very Very interesting AbbVie's HIV Drug Aluvia Seen as Potential Treatment for Coronavirus

[ProtectOurFreedom]

From the pdf full paper. "Weaponized" is certainly a very good question. The "unconventional evolution of 2019-nCoV" and "novel evolutionary aspects" certainly raises questions, doesn't it?

Section: Insertions in Spike protein region of 2019-nCoV
We found four new insertions in the protein of 2019-nCoV- “GTNGTKR” (IS1), “HKNNKS” (IS2), “GDSSSG” (IS3) and “QTNSPRRA” (IS4) (Figure 2). To our surprise, these sequence insertions were not only absent in S protein of SARS but were also not observed in any other member of the Coronaviridae family (Supplementary figure). This is startling as it is quite unlikely for a virus to have acquired such unique insertions naturally in a short duration of time.

...there has been a clear change in the preference of host from previous coronaviruses to this virus

Section: Discussion
Our results highlight an astonishing relation between the gp120 and Gag protein of HIV, with 2019-nCoV spike glycoprotein. These proteins are critical for the viruses to identify and latch on to their host cells and for viral assembly. Since surface proteins are responsible for host tropism, changes in these proteins imply a change in host specificity of the virus. According to reports from China, there has been a gain of host specificity in case 2019-nCoV as the virus was originally known to infect animals and not humans but after the mutations, it has gained tropism to humans as well.

NOTE: "Tropism" in viruses and other pathogens refers to the way in which different viruses/pathogens have evolved to preferentially target specific host species, or specific cell types within those species.

Section: Conclusions
...Taken together, our findings suggest unconventional evolution of 2019-nCoV that warrants further investigation. Our work highlights novel evolutionary aspects of the 2019-nCoV and has implications on the pathogenesis and diagnosis of this virus.

[samtheman]

As preprints, papers hosted on bioRxiv are not peer-reviewed, but undergo basic screening and checked against plagiarism. Readers may offer comments on the preprint. It was inspired by and intends to complement the arXiv repository, which mostly focuses on physics and connected disciplines

from Wikipedia entry for bioRxiv

[ProtectOurFreedom]

I forgot that they were testing an HIV drug for this new virus. Good job linking the two! This paper is by Indian authors at IIT and University of Delhi, not the typical Chinese authors we’ve seen in the Lancet papers. That is certainly suspicious.

Good job!

[rdcbn]

The chinese spies who were stealing corona virus and shipping it to china were experts in HIV and Ebola

[Tolerance Sucks Rocks]

So is this HIV-1 like structure indicative of its being manmade, or do viruses exchange RNA the way bacteria can exchange DNA?

[Tolerance Sucks Rocks]

It sounds more like the Chicomms might have plucked four small pieces out of an HIV virus and inserted them into a coronavirus, thus creating this Novel Coronavirus.

[Ancesthntr]

“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.”

---

“...unlikely to be fortuitous in nature.”

Fortuitous:

adj. Happening by accident or chance. synonym: accidental.

adj. Resulting in good fortune; lucky.
Accidental; casual; happening by chance; coming or occurring without any cause, or without any general cause; random.

---

IOW, this is not a naturally-evolved virus. Well, that’s a BIG problem - not just from the standpoint of treating the disease (though apparently HIV drugs help - which are in limited supply), but from the standpoint of “WTF kind of regime are we dealing with here in China?”

Now, I don’t think that most on FR, or anyone with a bit of common sense and knowledge of History, was under much of an illusion about the kindheartedness of the Chinese leadership. But the fact that they APPEAR to have weaponized a very communicable disease (twice or so as easy to spread as the common flu) by attaching elements of a disease that is very hard to cure, says that these guys are close to making the Nazis look like a bunch of softies.

***If*** this actually happened, I would absolutely expect that EVERYONE is going to sweep this under the rug because it could easily mean WW3 if the general public found out and believed it - and if tens of millions get sick around the world, they will believe it.

[ProtectOurFreedom]

Speed is clearly taking precedence over peer review. I'm not a microbiologist, but they did document their methods, logic, reasoning and sources well. They didn't look at "all sorts of organisms" -- they restricted their research to coronaviruses. I don't see any reason to slander this as "ludicrous and non-rigorous." Please elaborate if you have information to discredit this work. Can you explain why should this analysis be expanded beyond coronaviruses to "all sorts of organisms"?

We retrieved all the available coronavirus sequences (n=55) from NCBI viral genome database and we used the GISAID (Elbe & Buckland-Merrett, 2017) to retrieve all available full-length sequences (n=28) of 2019- nCoV as on 27 Jan 2020. Multiple sequence alignment of all coronavirus genomes was performed by using MUSCLE software (Edgar, 2004) based on neighbour joining method. Out of 55 coronavirus genome 32 representative genomes of all category were used for phylogenetic tree development using MEGAX software (Kumar et al., 2018).

On careful examination of the sequence alignment we found that the 2019- nCoV spike glycoprotein contains 4 insertions. We found that these 4 insertions are unique to 2019-nCoV and are not present in other coronaviruses analyzed. Another group from China had documented three insertions comparing fewer spike glycoprotein sequences of coronaviruses . Another group from China had documented three insertions comparing fewer spike glycoprotein sequences of coronaviruses.

So two other research groups in China documented three novel insertions.

[Tolerance Sucks Rocks]

If these fools deliberately released a man-made virus into Wuhan, they should swing from ropes.

[DEPcom]

Look up the stock AbbVie. I wonder if the Dr. Evil will try to make some money while killing people. Dr. Evil would have not release it, if they did not have a treatment in place.

[winoneforthegipper]

That and their location would be very extraordinary to occur naturally, I believe to be their position.

[Diogenesis]

it is time to put their heads on pikes.

[LilFarmer]

IF this is the case, could that be why people keep relapsing? Like the paper I posted today On the coronavirus live thread about many patients not building up am immunity after recovering from the virus.

[ProtectOurFreedom]

RNA in viruses evolves, but the authors point out "our findings suggest unconventional evolution of 2019-nCoV" and "novel evolutionary aspects" without postulating why that may have happened.

The authors show a diagram of the "Maximum likelihood genealogy show the evolution of 2019- nCoV". Take a look at all the animals that are in the ancestry of this virus. It is astonishing. You probably can't read it -- it is a bit more legible in the original pdf -- but it includes birds (Thrush, Magpie, Robin, Sparrow, Moorhen, Night Heron, Wigeon, Turkey) and mammals (Mink, Beluga Whale, Pigs, Ferret, Feline, Camel, Bats, Rats, Cows, Rabbits, and Humans).

[winoneforthegipper]

Thanks, I did not know of that issue.

[LilFarmer]

Recovered coronavirus patients still need to strengthen protection: doctor
Xinhua
20:56 UTC+8, 2020-01-31
New Coronavirus Outbreak

Cured patients are still at risk of reinfection with the novel coronavirus (2019-nCoV) and should strengthen protection, a Chinese respiratory doctor said Friday.

“Usually, certain antibodies will be produced after a virus infection, which will have a protective effect on the human body. However, some antibodies may not last that long,” said Zhan Qingyuan, a doctor with the China-Japan Friendship Hospital, at the daily press conference held by the National Health Commission (NHC)”

https://www.shine.cn/news/nation/2001310991/