More Re The Origin Of The Coronavirus

What you'll find below is basically a twitter thread that appears at Zerohedge under this title:

"What Are The Odds?" - A Timeline Of Facts Linking Covid-19, HIV, & Wuhan's Secret Bio-Lab

What I've done is to strip out the embeds to make it read smoothly and edit it out some of the more technical details. Then I pasted in the abstract and conclusion from a paper by Indian scientists who suggest that the virus behind Covid-19 was engineered based on the model of HIV1 (the technical details are beyond me). I have also added a limited number of comments of my own, in the hope of pointing to the significance of certain points.

The author of the original twitter thread and the link to that thread:

Scott Burke,  CEO of crypto-related firm Groundhog, ...

Again, the question is: If this virus was engineered and then escaped "into the wild," what was the purpose of the engineering? Legitimate scientific inquiry? Use as a bioweapon when perfected? Both? Do the seemingly extreme reactions of governments around the world--compared to flu outbreaks--indicate that they may know things that aren't being shared?

Here is Scott Burke:



A disclaimer: I am not a virologist. This is me synthesizing what we have learned since the outbreak began and reviewing public scientific papers. I believe each of the following statements is a solid fact, backed up by a citation.

...

So there’s original SARS, which is a type of coronavirus. SARS infects cells through the ACE2 receptor in hosts. 

The S spike protein plays a key role in how the virus infects cells. Each of the little spikes that surround the coronavirus is a spike protein (or S protein). That’s what gives the coronavirus it’s name - it’s “crown” of these spikes.

The S protein binds to the targeted cell through the ACE2 receptor, and boom, your cell is infected and becomes a virus replication factory.

After the first SARS outbreak, there was a “land rush” to find other coronaviruses. A collection of SARS-*like* coronaviruses was isolated in several horseshoe bat species over 10 years ago, called SARS-like CoVs, or SL-CoVs. Not SARS exactly, but coronaviruses similar to SARS.

[Elsewhere I've read that the similarity of Covid-19 to SARS is in the 81-87% range. Thus the description of the virus as "SARS-like".]

In 2007, a team of researchers based in Wuhan, in conjunction with an Australian laboratory, conducted a study with SARS, a SARS-like coronavirus, and HIV-1.

The researchers noted that if small changes were made to the S protein, it broke how SARS-CoV worked - it could no longer go in via ACE2. So they inferred the S protein was critical to the SARS attack vector. 

They also predicted based on the S-ACE2 binding structure, that SARS-like CoVs were not able to use this same attack method (ACE2 mediation).

They decided to create a pseudovirus where they essentially put a SARS-like CoV in a HIV envelope.

It worked.

Using an HIV envelope, they replaced the RBD (receptor binding domain) of SL-CoV with that of SARS-CoV, and used it to successfully infect bats through ACE2 mediation.

[I'm speculating here, but it appears that the purpose of the HIV envelope would be to make it more difficult for an organism to resist infection, whether through natural resistance, through mutation of the SARS virus, or through vaccination. Read the abstract/conclusion of the Indian paper in light of this comment.]

12 years goes by ...


A SARS-like CoV begins sweeping the globe that is far more infectious than previous outbreaks. 

Ground Zero for this outbreak (not first human patient, but first spreading event) is considered to be Wuhan Seafood Market. 

Wuhan Seafood Market is 20 miles from the National Biosafety Laboratory at Wuhan Institute of Virology.

Amidst the outbreak, a team of Indian bioinformatics specialists at Delhi University released a paper pre-print...

COVID-19 has a unique sequence about 1,378 nucleotide base pairs long that is not found in related coronaviruses. [The Indian researchers] claimed to identify genetic similarities in this unique material between COVID-19 and HIV-1.

Specifically, they isolated 4 short genetic sequences in key protein structures (the receptor binding domain, or RBD).

Two of the sequences were perfect matches (albeit, short), and two of the sequences were matched but each with an additional string of non-matching material appearing in the middle of the sequence.

[Here are the paper's abstract and conclusion:]

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. 

Conclusions

Our analysis of the spike glycoprotein of 2019-nCoV revealed several interesting findings: First, we identified 4 unique inserts in the 2019-nCoV spike glycoprotein that are not present in any other coronavirus reported till date. To our surprise, all the 4 inserts in the 2019-nCoV mapped to short segments of amino acids in the HIV-1 gp120 and Gag among all annotated virus proteins in the NCBI database. This uncanny similarity of novel inserts in the 2019- nCoV spike protein to HIV-1 gp120 and Gag is unlikely to be fortuitous. Further, 3D modelling suggests that at least 3 of the unique inserts which are non-contiguous in the primary protein sequence of the 2019-nCoV spike glycoprotein converge to constitute the key components of the receptor binding site. Of note, all the 4 inserts have pI values of around 10 that may facilitate virus-host interactions. 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. 

[In other words, the authors of this paper believe that the novel features of Covid-19 were engineered on the model of HIV1 rather than being the result of random mutation of a SARS-like virus.]

The paper was criticized and numerous attempts have been made to debunk it. After the criticism, the authors voluntarily withdrew it, intending to revise it based on comments made about their technical approach and conclusions.

One key debunking attempt claims this:

The same sequences are found in a variant called BetaCoV/bat/Yunnan/RaTG13/2013, which had been found “in the wild” in bats.

This is an attempt to prove that it was not engineered, but mutated naturally in the wild.

But there’s a problem...

This strain was only known by and studied at the Wuhan Virology Institute, and although they claim it was discovered in 2013, it wasn’t published or shared with the scientific community until immediately after the Indian paper, on January 27, 2020.

The RatG13 strain publication and the HIV research paper from 2008 share an author.

I discovered this on my own by comparing the two papers and then quickly realized this scientist’s contact information was the information that ZeroHedge was suspended from Twitter for sharing.

Their article identifies this author in question including some contact information from the Wuhan Virology Institute web site.

You can read the public comments and discussion of the original paper here:

There is a line of inquiry about how the sequences are remarkably stable in between the “bat” CoV and the nCoV, where in nature they would likely have mutated in between their shared evolution. Also a call for greater scientific evidence that the strain was collected in the wild.

Here is the only point in this thread where I will offer my opinion rather than a list of facts: In light of all the previous facts, the efforts to debunk the paper are not yet convincing in my view. 

The RaTG13 paper makes the claim that, oh, that HIV-related material you identified that happens to protein fold to become a perfect attack vector for nCoV to attack ACE2?

It’s a relative of this other secret virus which came from the wild which we forgot to tell the scientific community about until now for no reason.

Here’s the secret virus - it came from bats - and here’s the new virus, see, they have the same HIV-related sequences... so... bats!

Totally not secret pathogen research which escaped the lab.

What are the odds that a SARS-like coronavirus with overlapping genetics from HIV mutated and crossed over into humans, next door to a laboratory which had been enhancing coronavirus with HIV for over a decade? And conversely, what are the odds it leaked out of the laboratory?