In Feb of 2020, a preprint showing that the SARS2 spike protein has 4 regions of homology with HIV-1 (bit.ly/3rmBtYD) was forced to retract.
So where are these regions in the 3D protein structure?
😲All 4 regions are missing!
Surgically ...
Missing residues usually indicate flexible loops.
So where are these loops? What are they doing?
The first 3 are from the HIV-1 gp120 gene which allows it to bind to host cells containing the CD4 receptor: mostly immune cells like T-cells and macrophages.
O no, what if ...
Someone alerted Fauci to the same problem: bit.ly/3qtU06e
What if the spike protein can interact with the CD4 receptor? Bad news.
Here are the regions in the structure. Spike forms a homo-trimer. The regions (red, yellow, and blue) come together at a peripheral point.
Below is a zoomed-in version for subunit A, with the 3 missing loops drawn in by hand. Note how close their connectors (shown as solid spheres) are in 3D.
So 3 regions with homology to the CD4 binding domain of HIV-1:
- are missing in the structure
- come together in 3D
Should we conclude that the SARS2 spike protein can interact with CD4?
Of course not
If the powers-that-be hadn't forced the retraction of the preprint, we would have had an answer by now
A Moderna patent (US 9587003) filed in 2017 contains a DNA sequence that ended up being the unexpected insertion of the notorious Furin Cleavage Site (FCS) in SARS-CoV-2.
Its devastating effect on infectivity and transmission in the pandemic are well-documented.
Interestingly, Ralph Baric in the University of North Carolina (UNC) has tested vaccines for Moderna, and is also the world's expert in engineering hybrid versions of corona viruses.
No that couldn't possibly be connected ...
There are 2 baffling aspects op the FCS insert: the presence of a Proline (P) which is suboptimal, and the CGG-CGG codon pair encoding two Arginine residues, which extraordinary rare (1 in 2 million).