Oops: There goes the N-Terminal Domain

You have to write about what you know. There are a lot of different topics that interest me, I found an interesting book I could recommend to anyone, but I want to discuss the topic again today where I have something of value to point out: SARS-COV-2.

For previous posts on the topic, to understand what we’re talking about, I recommend looking here and here.

To summarize again, essentially what we’re dealing with is that most of the world’s population is protected from SARS-COV-2 today by antibodies against the N-Terminal Domain of the Spike protein. Individual amino acids can change to overcome certain antibodies, but when something changes the overall folding of the N-terminal domain, almost all the remaining functional antibodies become useless overnight.

The big example I’ve documented before are changes to the cysteine amino acids. Those amino acids bind to each other and thereby decide how the protein is folded. Introduce a new cysteine or remove an existing cysteine and the whole N-Terminal Domain is folded differently, making the antibodies useless.

But there are other ways to achieve the same result, as I found out today.

When you remove 156 and 157 from Spike, you change how the N-Terminal Domain is folded. Delta removed 156 and 157, but in Omicron amino acids 156 and 157 were back.

This was apparently enough to make most of the vaccine derived antibodies against the N-Terminal Domain useless:

This was Delta though, so antibodies against the RBD still worked. So we would want to know, if these mutations were to return, right?

Well have a look at this.

We’re only going to look at lineages that have the S:31 deletion, that puts a glycan on S30, to avoid antibodies there.

You can see here why I’m only interested in those lineages:

It’s emerging convergently on basically all the JN.1 descendants and is at 7.3% of sequenced viruses today. It’s now very fit, due to the 4 amino acid insertion of BA.2.86*.

So now we’re going to look among sequences with S:31-, to see whether any have any interesting Spike deletions:

Seven sequences suddenly emerged with the deletion that gave Delta its refolded N-Terminal Domain. Oops.

Now let’s look at all the available sequences, to see the percentage that removed S:157:

So we see that big Delta era, when this deletion was widespread. We see a small bump about a year after its demise, that never managed to take off. But now we see it jumping up again in recent days. This fits the broader pattern we can see, of Omicron steadily evolving to become more Delta-like again.

The added glycan on S:30 thanks to the deletion of S:31 would be expected to make a bunch of NTD antibodies useless. But other NTD antibodies would still be neutralizing the virus. But that results in a situation, where the benefit to be had from avoiding those antibodies will have increased dramatically for variants that already deleted S:31. Within those lineages, S:157- presumably has a fitness benefit again.

And in case you’re wondering: S:157- added to S:31- is not a fluke. There are three separate lineages that added S:157-, in two different countries (Ireland and Thailand). So it’s real.

I don’t know what the “right” way is to rearrange the N-Terminal Domain. S:31- seems a very basic ingredient, enabled by the insertion unique to the BA.2.86* family.

But what are the next ingredients for the recipe?

-More glycans (look for amino acids changing to Asparagine, Serine or Threonine)?

-More deletions, that trigger folding differences? Well, turns out that’s an important method.

-Addition or removal of Cysteine? That seems an important method as well.

-More insertions? That could take a long time.

I think you probably have different viable paths, resulting in the same outcome: An NTD that changed the way it’s folded enough to make the antibodies useless.

Keep in mind, that all these deletions in the NTD have the effect of improving the ability of the virus to fuse cells together.

This damages the body, but allows the virus to escape people’s antibody response.

Whether you like it or not, we’re not dealing with a virus that is growing milder.

Rather, we’re dealing with a virus that’s now starting to resemble the Delta variant again. It has Delta’s furin cleavage site and it is reacquiring Delta’s deletion that changes how the NTD is folded. And as I previously showed, fusogenicity is steadily rising.

The really big problem we’re dealing with

But here’s the real problem. The scary thing about the vaccines, is that they actually work. They don’t save everyone’s lives. They certainly don’t prevent people from catching the virus. But they appear to have provided some general protection.

You observe in rodents for example, that you can completely(!) prevent brain infection, by vaccinating them against Spike.

Sounds great, right? Well yes, until you realize that this vaccine induced protection can fail dramatically effectively overnight. I have shown you how: Simply change how the NTD is folded, that’s all it takes.

If you are unvaccinated, your brain has had four years to gradually adjust to the brave new world of an evolving SARS virus.

I have sought to help people deal with that reality.

I recommended you all some of the following options:

-Physical exercise, especially jogging and weight lifting above your shoulders.

-Natto and serrapeptase, to destroy molecular clutter, like amyloid and fibrin, as well as break down Spike proteins.

-Cannabinoids, to encourage neurons to expel the amyloid.

-Psilocybe mushrooms, to massage your brain’s blood vessels.

-Nicotine, has been found to work well to reduce the viral load in the brain.

-Salvia divinorum, has been found to help repair blood vessels in the brain.

Some of you will have listened and some of you will have ignored me.

But you can all go look for yourself, to observe the reality that this virus has the ability to damage the brain, it happened to quite a few children, I’ve seen comments from people who had it happen to their own children.

But given time and help, the brain can repair mild insults, especially when we’re young. Stem cells from the blood are even able to spontaneously move into the brain to repair it, even in adults. I did not know this, I had always thought the brain depends on its own existing stem cell population.

But now contrast this, to a situation where people’s immune system is stuck on an antibody response that’s just going to end up completely powerless against this virus. Up until now, they have presumably never noticed anything wrong. Their brain is healthy, they don’t feel tired, anxious or depressed.

But the virus has been growing steadily more neurovirulent over time. People’s immune systems have had time to adjust to that situation, assuming their innate immune system got to do the job it is supposed to do.

But now imagine people whose antibody response against this virus that has steadily grown more neurovirulent and fusogenic fails overnight. The brain would be expected to be very vulnerable.

You can all look up what the bird flu is doing to the foxes and the cats that drink raw milk, or eat infected birds. Their brain swells up and they die. That virus infects endothelial cells in the brain, just like SARS-COV-2.

That’s the problem we’re dealing with and I really don’t know what you’re supposed to do right now, to protect vaccinated people who currently depend on high levels of antibodies against the N-Terminal Domain to stop their brain from being infected.

I would imagine that you want to reduce the acute inflammation people suffer.

Cannabinoids would presumably help with that. In addition, Psilocybe mushrooms reduce inflammation and bind to M-protease.

But it’s not looking good at all.

Four years have passed. You would expect unvaccinated people’s brains to have adapted, with defective interfering viral particles and RNA in mature neurons and endothelial cells from previous infections, vascular and lymphatic adaptations, NK cells and dendritic cells that have taken up residence in the brain, functional compensation within the brain itself, with functions shifting to different parts of the brain, trained innate immunity of endothelial cells and adaptation to co-occuring bacterial infections.

How are you going to compensate for that to protect people, whose brains were until now completely protected from infection?

That’s what I would like to know.

It’s like sending off two people to a triathlon, only one of whom has been training for it.

26 Comments

  1. Hi, I´m rather new to your blog. Interesting reads for sure.

    What do you believe is the main reason for this not being more widely discussed?

    All best,
    Erik

    • >What do you believe is the main reason for this not being more widely discussed?

      Almost everyone who understands what’s going on, is complicit in peddling the vaccines.

      And all the “antivaxxers” settled on the idea of this virus being a nothingburger. Problem with that idea being, that viruses exposed to constant antibody pressure grow more virulent over time. But that’s just a level of complexity that’s not going to draw people to your substack.

      • What do we know about the background of this class of viruses prior to tracking changes with this one?

        I find it surprising that despite having this technology available for a long time to track small differences we do not necessarily hear about with the flu or other widespread communicable illness.

        The reason I ask, and I am ignorant to this so it may be a dumb question, but what are these changes and evolutions in relation to? Does this happen all the time with all viruses?

        Also I really cant seem to get a sense of how we know how the folding of viruses impacts their function. I am aware of crystallography for proteins but does that apply to viruses.

        As this goes on I get more confused on what I thought I previously knew in relation to my anecdotal experience. Now I question everyones cold, and they say they have covid but I wasnt doing that before 2020 so I am starting to feel like it is silly to pathologize everything as what seems to be called a form of AIDS in some circles.

      • Why would a majority of them be complicit even though they understand that virulence would potentially increase (if I understand you correctly)? Shouldn’t we at least hear from a sizeable minority?

        Not arguing against your case, but I can’t seem to get my head around that.

        • You can find some of them who think something’s going to happen in the N-Terminal Domain that will cause virulence to jump up. Ryan Hisner is an example. But again, he’s self-taught too.

          But most of them just seem to think the vaccine worked pretty well and if the virus changes substantially, they’re just going to update it.

          That’s not going to work, because it’s going to be covered by glycans and interfering IgG4 antibodies, but that requires really studying all of it.

    • > What do you believe is the main reason for this not being more widely discussed?

      Because we are dealing with political factors on top of biological ones. Imagine a world in which jabbies are well-known to be very vulnerable to a virus that purebloods can survive — and transmit. The State would try to lock up purebloods, starve them, and inject them with some garbage to lower their immune systems to the same level that the State’s servants downgraded theirs. “Level the playing field”, even if this can mean extinction of the human species.

      Being considered an enemy of the State has had a lethality close to 100% in the 20th century. Now with computers and tracking, it would be awfully close to 100%. On the other hand, going through something like the Plague of Justinian or the Black Death only had a lethality between 30% and 60%. I’d prefer the plague any day.

  2. You
    >The scary thing about the vaccines, is that they actually work. They don’t save everyone’s lives. They certainly don’t prevent people from catching the virus. But they appear to have provided some general protection.<

    Yeah, otherwise how would NEGATIVE EFFICACY show up in the data?

    I notice that you and Bossche are more worried about the evolution of the SARS virus than side effects of the mRNA injections.

    • Yeah, you could say they are more worried about the collective (herd) side-effects. GVB has said that he follows reports on the individual side-effects, but it’s not his field.
      Occassionaly, he mentions the effects of a dysfunctional immune system.

      • I agree with RR that this weird, synthetic virus that was unleashed on the world in 2019, accidentally or intentionally, is far from a nothingburger.

        It’s nasty, it’s thriving, it can incorporate into our DNA, and it’s been mutating/evolving far faster than a coronavirus should.

        It’s been really interesting to follow this incredible drama, watching how interested parties divide into different camps. One of those camps is neuroscientist JJ Couey, who has become convinced that it’s not possible for a respiratory virus to do what they’re claiming. He thinks covid has been biowarfare, and “cloned RNA” was intentionally seeded in Seattle, Italy, NY to create the appearance of a pandemic.

        https://youtu.be/E8cJ1Wa6U3o?si=w1z06egLic3juzOx

    • You can choose whether to get yourself injected.

      You can’t choose whether to get infected.

      If people take the experiential genetic technology, that’s on them and the data is there. Uptake rates are now nil anyway and what can you do? You can’t uninject yourself. That topic is simply no longer interesting or relevant.

    • I agree, early in 2020/2021 I believe there was a conflation of symptoms associated with the virus that actually were relevant to the injections people recieved.

      If I recall correctly symptoms did not start skyrocketing until after 2021. At which point omicron was ‘spreading’ but again what the heck is the control for all this stuff. How are mRNAs supposed to travel without constantly mutating. Virology is extrmely suspect in my mind. It always gives a means to trot out somethjng horrific.

      GVB was calling for major death “soon” for years and I feel misdirection is happening at this stage.

  3. Note by the way, what I pointed out back in February:

    >https://www.rintrah.nl/sars2-vaccination-is-encouraging-steadily-more-virulent-new-omicron-variants-to-evolve/

    >As I have said before, you can now expect deletions to emerge, around these regions:

    >14-26 (N1), 141-156 (N3) and 246-260 (N5).

    And here we are, halfway through May and we have S:31 removed, followed by some changes to amino substititions to N1… now followed by the deletion of S:157.

    It’s not hard to predict this stuff. It just requires understanding that:

    -BA.2.86 gave more room for NTD deletions through the 4 amino acid insertion at 16.

    -There is now concentrated antibody pressure on an immunogenic region of the NTD, corresponding to these three loops.

  4. Another informative update.

    I seem to recall reading one of your older COVID/SARS2/vaccine articles where you wrote in the comments section that you personally hated studying biology in high school because you were being forced to rote-learn the Latin names for all the bones in the mammalian skeleton which didn’t interest you at all.

    So considering that, it’s remarkable that you have been interested enough to devote huge numbers of hours studying and acquiring such a large amount of knowledge on the subjects of virology and immunology in the last ~3 years.

    I can relate to that in a similar way, I was bored a lot in high school biology and got relatively poor grades, but will happily read Dawkins’ books on evolution and all of the archived articles on this website that discuss the evolutionary trajectory of the pandemic.

  5. I am already doing the following. Homeschooling my child. Trying to change my job to a remote job. Plant an organic garden. Minimize being among folks or limit it to outdoors. I’m taking OLE, spirulina, chaga, milk thistle and other herbs daily or alternating. After being in the public I take fermented garlic once I return home. A week before we went to post office and it was packed. I heard a few people coughing. A day later I felt something was in my eye when we were in the park. We could not find anything. Then my next eye started feeling somewhat irritated and had a little mucus overnight. I figured I must have caught something via my eyes. Did a hot compress over my eyes and put some castor oil in my eyes. Now before if I’m going to be in the public I put castor oil on my eye lashes before and after I come back hoping some of it goes in my eyes and protects from viruses.

      • Thanks, Mehen. Both spirulina and chlorella can have them, but only taking small amounts, 1 gram each. I’m more into herbs. Have been fascinated by wild medicinal plants since I was a kid. Maybe I was a herbalist in my previous life.

  6. The human body is like alien technology. And whoever says he understands this alien technology is a fool in my eyes.

    “N-Terminal Domain” is like Miasma. You think this science is settled, Rintrah, and then you build castles in the air on it …

    I don’t believe one word from this “science”, it’s all fairy tales.

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The patients in the mental ward have had their daily dose of xanax and calmed down it seems, so most of your comments should be automatically posted again. Try not to annoy me with your low IQ low status white male theories about the Nazi gas chambers being fake or CO2 being harmless plant food and we can all get along. Have fun!

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