SARS-CoV-2 Spike Protein and its amyloid properties

Fragments once again

One of the recurring themes in many of my articles this year has been the same. The deep, layered complexity of SARS-CoV-2 and how it impacts the body, with a large focus on the brain, for multiple reasons, both personal and societal alike.

I have a couple of dozen articles focusing on neurodegeneration alone, covering multiple ways the virus and its Spike Protein affect the brain, memory, cognition (the capacity to think), cognitive processing (the velocity you think), and complex task solving (how you deal with modern tasks, work). Adding variables to this are latent viruses and their role in long-term neuropathology, retroviruses, and the intricate role “misfolded proteins” play in this.

The papers we will cover are not super complex on their own, but our work will add complexity to them. First and foremost.

SARS-CoV-2 induces Alzheimer’s disease–related amyloid-β pathology in ex vivo human retinal explants and retinal organoids

Here, the authors used human retinas from rapid autopsies (less than 4 hours) to model their research. The famous phrase “The eyes are the window to the soul” has an equivalent in medicine and biology, as the eyes are one of the pathways to the nervous system and the brain; in this case, the eyes are the road to the brain. The eyes and the brain shares cell types such as neurons and glial cells, structures, and even its blood-brain barrier (blood-retina barrier).

In previous studies, Amyloid Beta (Aβ) plaques found in the brains of Alzheimer’s patients were also present in their retinas. Thus, the argument is that the retina is a viable model for studying the Central Nervous System aspect of the disease. Their first step is to validate their models, such as testing the neurons electric pulses, making sure they function as expected.

Next, they tested the retinas, vitreous (gel-like substance in your eyes), optic nerves and cornea from human Alzheimer’s patients, and controls (people without it), and as one would expect, they found a significant concentration of Amyloid beta in human retinas from post-mortem patients. The next step of the paper is why we are here, although the validating data is nice to have.

They generate human retinal organoids, which means using human stem cells to create a layered, biologically complex mimic of the entire human eye structure, following it at different time points throughout two months to ensure it had the appropriate structure. Then they performed single-cell RNA sequencing (enabling you to “see” what is happening at a single cell level) of these retinal organoids following treatment with SARS-CoV-2 Spike S1.

There are some receptors (the small Lego block that needs another Lego block to start cell processes) that are more abundant in certain cells or parts of the body, and by using the scRNA approach the authors predicted that Retinal Ganglion Cells (your eyes neurons) and Macroglia (the main supproter cells in the retine, like astrocytes in the brain) expressed really high levels of NRP1, a receptor that has been shown to be targeted by the virus.

They observe this visually (Figure D) by adding Spike S1 to the cells, meaning they see that Spike S1 protein binds to neurons. With the binding confirmed, next they treat (meaning mix together) the human retinal organoids with a curcumin-derived staining, after they expose the organoids to Spike S1, and observed that retinal organoids expose to Spike S1 start accumulating amyloid Beta.

The organoid is a model for their research, so they analyze postmortem human retinal tissue from patients with Covid without dementia or mild cognitive impairment, patients with Alzheimer’s disease, and cognitively normal controls, both postmortem Covid and Alzheimer’s disease samples had Amyloid plaques. Using Multiplex Immunofluorescence (you use an antibody targeting a specific protein to visualize multiple proteins) they observed increased levels of Amyloid Beta in the Covid samples.

If you read the title, you know what to expect in this precise part. They cultured human retinal explants from rapid autopsies with Spike S1, with a staining substance to visualize how much amyloid accumulated, and that is precisely what was observed, Spike S1 induces amyloid in ex vivo human retinas. So in “healthy” retinas, S1 alone leads to the accumulation of amyloid beta. Inhibiting the expression of NRP1 stopped this process. I will leave the authors own remarks here.

We speculate that SARS-CoV-2 in the CNS induces a rapid innate immune response. We believe that SARS-CoV-2 works through NRP1 and several other receptors, and once amyloid-β is produced and secreted, it binds to Spike 1 protein with high molecular affinity, which leads to amyloid-β aggregation and encapsulation as a defensive mechanism (13, 16, 19, 54). The improper clearance and repeated infections over time may exacerbate the amyloidopathy in Alzheimer’s disease and high-risk groups.

I have argued for years, and have been proven accurate multiple times, there is an incredible complexity in regards to the amyloid aspect of SARS-CoV-2, and as expected, there is a higher chance of this being a defense mechanism, last resort rather than a catastrophic scenario.

The real concern is that the Spike S1 can often be found floating around the body, and the fragment alone is able to engage with this and other receptors, causing an assortment of pathologies. The S1 also harbors the small grooves that Endotoxin and HMGB1 bind, enhancing its inflammatory effects and accelerating amyloid creation and accumulation. Endotoxin is one of the most powerful instigators for this process.

Little is talked about everywhere on how your eyes, as well as your mouth and nose are direct entry points for the virus. That is why this paper is significant, because unless you are using glasses (normal, protective ones are even better), you are being infected via that route, certain Covid strains are well known to cause a lot of eye symptoms, conjunctivitis, irritation, and the like.

The virus will use the nerves in your head to travel to the brain, causing neurological inflammation, increasing the oxidative burden, and over time, creating a burden that is rather difficult to reverse, a long-term aspect that not many pay attention. And yes, if Spike S1 from the virus does this, the mRNA vaccine will also do it. Over 2 years ago, I covered how a significant number of vaccinated individuals experienced increased clotting in their eyes vasculature, which leads to both visual and cognitive impairment over time (or outright losing vision itself). As a closing comment on all of this, read the title of the second article referenced below.

SARS-CoV-2 invades the brain using the nerves

Spike protein S2 enhances amyloid-β production

If so many parts of the Spike Protein can cause accumulation of amyloid beta, which is neurotoxin, and also instigate accumulation by indirect means, knowing which specific section of the Spike does it is of extreme importance, from both a clinical standpoint, but also to understand the dynamics, as if you understand something, you can address it.

In this paper, the authors focused precisely on this, focusing on trying to elucidate which part of the Spike Protein induces the formation of amyloid clots, given their role in Long Covid, and overall in the damage to the vasculature over time, micro and macro.

SARS-CoV-2 spike protein amyloid fibrils impair fibrin formation and fibrinolysis

They used the original Wuhan Spike protein, arguably the “nastiest” version of the Spike with the highest potential for sequelae, acute, or long-term, and selected 7 fragments. The focus on the Wuhan Spike is simple, first it has been one of the most tested viral proteins in history, it has an absurd amount of literature on it, and second, it was used in all novel vaccines.

So the readers understand aspects of research, I will explain how they choose these fragments. Researchers will often use tools, and algorithms that read an entire protein, and following precise instructions (in the algorithm) using large data sets, it can predict which segments of a large protein, in this case, to form amyloid proteins. Amino acids like Valine (V), Isoleucine (I), Phenylalanine (F), and Tyrosine (Y) are highly "amyloidogenic." WALTZ has a scoring system for each amino acid's tendency to form a beta-sheet, and also scores based on where the amino acids are located.

They synthesize the 7 fragments and use Thioflavin T, a fluorescent paint that binds to the characteristic structure of amyloid fibrils and glows, and all seven peptides showed increased fluorescence, meaning they form amyloids, they follow up by using electron microscopy to visualize the amyloid fibril structures.

Each Spike fragment behaved differently in their tests in a sense, Spike 601 delay clot formation by literally sequestrating fibrinogen, which is crucial for forming the structures that stop bleeding and form clots. Spike 365 and 684 both were able to interweave themselves with amyloid fibrils, forming amyloid structures/clots. Spike 685 resulted in the strongest amyloid clot structure, resulting in a clot that could not be dissolved by normal cellular response (clot lysis). This was also the case for Spike 365 and 532 but not as drastic as 685.

Mixing the 7 fragments with amyloid created a mixture that delayed fibrin clot lysis, meaning it delayed the body's capacity to dissolve the structures. Delayed, not impaired, and this will be extremely important later. In fact, while all findings in this paper are important, this is the most significant one by far.

Given that in their model, Spike 601 and 685 had the most significant effects, their next step was visualizing and understanding how they occur, especially 685 which forms amyloid clots that are incredibly resistant to being dissolved. They do it by using two different fluorescent colors that bind to different molecules, fibrinogen in green, Spike amyloid in red. Co-localization, seeing yellow or orange as a mixture of red and green colors, indicates physical interaction.

On A you can see their previous findings, Spike 601 amyloid fibrils have a high affinity to soluble fibrinogen, they “glue” themselves directly, forming large clumps, this shows how 601 slows down clot formation, by quite literally stealing fibrinogen before thrombin can act on it (it cuts fibrinogen and forms fibrin that forms clots). On B, you see the opposite, 685, the Spike fragment that creates undissolvable clots doesn’t bind to fibrinogen.

On C, in the Fibrin image, that tree branch looking thing is a normal fibrin structure. Dotted on its surface are small red points, and in the superimposed image (Spike 601+Fibrin), you can observe minor yellow, thus Spike 601 amyloids remain outside the fibrous structure of the clot, and thus the clot can be dissolved by plasmin.

On D, in the superimposed image, you can observe the opposite, and expected for Spike 685, Spike 685 amyloid is bound, misfolded, and the spike-amyloid is embedded into its structure. This makes the fibrin clot amyloid-based, it is like adding steel bars to a structure, making it extremely hard to “hammer it down”.

This is visual confirmation with cutting-edge microscopy work. In A-i and ii you can see the Spike Amyloid fibrils, they look like classic fibrils, and yes, that is what some forms of amyloid look like. Not as horrific as one would expect. On B i and ii, especially compared to A-i, you can see Spike 601 fibrils coated in fibrinogen nodules (the pink arrows), the opposite is observed in B-iii and iv, the yellow circles and arrow show fibrinogen nodules being pushed away.

C-i is the normal byproduct of a clot being dissolved. C-ii and iii show the remnants of a clot formed from Spike 601, the clot is dissolved, but some amorphous material is left. And slightly larger aggregates, too, although the clot is dissolved. On C-iv and v you can see large, highly aggregated granular structures, these are not normal clots, these are the infamous, resistant to being dissolved, misfolded amyloid-based clots.

The Spike-amyloid mix is the most important part of the paper because of how hard it is to get the very specific fragment floating in your body, to interact with and go through a precise series of molecular cascades to induce the pathological effects, the mix is the one that is most accurate on demonstrating how you body will respond to the viral Spike Protein. The pathological effects will occur, and within the theme of long-term consequences, it will likely contribute to long-term disease, rather than acute, easily observable effects, especially in regards to damage to the microvascular system.

Not solely purified fragments, pathological effects exist, and I have mentioned endotoxin for a reason. The amyloidogenic fragment 192 is located directly within the NTD, the fragments 365 and 532 are found in the RBD (532 at the very end basically), 601 and 685, the highly pathological ones are at the S1/S2 boundary, with 685 being precisely after the infamous Furin Cleavage Site, exposing the S2 part.

Fragment 192, fragment 365, and 1166 are direct key endotoxin binding sites. Fragment 532 is adjacent to an endotoxin binding site, which starts at 553, and 601 and 685 are located close to endotoxin binding sites. The most problematic fragment is 685 because it is one of the few fragments that has a higher likelihood of floating around and creating amyloid-based clots that resist being dissolved.

So the Spike protein can create Amyloid-beta, the bad amyloid from Alzheimer’s by simply binding to neurons, it also has the NTD and, worse yet, the RBD, which both contain amylodogenic parts and endotoxin binding sites, and endotoxin itself is one of the most potent inducers of amyloid fibril accumulation. Under current physiological circumstances, this is a more likely scenario, especially given the brunt damage the immune system takes from even a mild infection.

I do personally asked myself, how much of this is precise, extremely detailed molecular engineering work, and how much is just stumbling upon things and an accident.


The most important aspect of a infection to recover from is maintaing a healthy, functional circulatory system, as the virus and its chimeric Spike Protein cause a severe burden to it, affecting both your blood vessels, how your body transport liquids, and lastly and most important, the glymphatic system, the very thing you need to remove waste and clear misfolded protein before they accumulate enough to induce pathological change. (You can find a lot more context for the last paragraphs by searching for any article with Long-Term in its title)

And in case you forgot. The reason I try to understand everything from a Complexity perspective is precisely because if you understand something, you can address or fix it.

Ketones help the body dissolve misfolded proteins

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