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SciTech Chronicles. . . . . . . . .December 24th, 2025
Vol IV Issue 53 Who Said this? To be led by a coward is to be controlled by all that the coward fears Today, 371 links Curated Today's Five
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SciTech Chronicles. . . . . . . . .December 24th, 2025
Vol IV Issue 53 Who Said this? To be led by a coward is to be controlled by all that the coward fears Today, 371 links Curated Today's Five
Rhesus Macaque Killer Cell Ig-like Receptor Domain 0 Glycans Impact Surface Expression and Ligand Specificity
Abstract Defining the MHC class I ligands of rhesus macaque killer cell Ig-like receptors (KIRs) is fundamental to NK cell biology in this species as a model for infectious diseases and comparative immunogenetics. Several rhesus macaque KIRs belong to a phylogenetically distinct group with a three-amino acid deletion in domain 0 (D0). This deletion results in polymorphic differences in potential…
How the innate immune system manages to cope with antibody resistant SARS2 varieties
December 17, 2024 Radagast
"So, as I have been documenting over the past few years now, we’ve seen a situation in which the new coronavirus, SARS-COV-2, become forced to evolve first into increasingly infectious variants (Alpha, Delta) with higher ACE2 affinity and then into highly antibody evasive variants (the Omicron variants). This then results in a population that has a relatively wide range of antibodies, to a wide range of Spike epitopes.
That results in a situation, where SARS-COV-2 becomes increasingly forced to increase its inherent antibody resistance. That involves the accumulation of sugar molecules (glycans) on the N-Terminal Domain, that prohibit the antibodies from binding that are now necessary for neutralization. This interplay between the vaccine, the immune system and the virus, is a process that takes many years to unfold.
What critical thinkers would ask themselves, is why we don’t just see every virus that regularly reinfects humans develop a bunch of glycans on its surface, if that allows viruses to render an antibody response useless. Logic would suggest there has to be some sort of cost involved for a virus, in covering a viral protein in these glycans that prohibit antibodies from binding to the protein.
This is a correct assessment. The innate immune system evolved various mechanisms to recognize basic patterns that pathogens and misbehaving cells in our bodies tend to display. As one example, our cells are forced to display small bits of proteins they’re producing in their MHC molecule on their surface. This allows your T cells to inspect whether they’re producing the right proteins, or whether their protein factory was hijacked by a virus.
Many viruses thus evolved mechanisms to interfere in this phenomenon, by stopping cells from displaying the MHC molecule on their surface altogether, so that the T cells can’t inspect what’s going on. The human immune system of course has to have ways to deal with that behavior of viruses. So what you see is that our Natural Killer cells, a population part of the innate immune system, treat it as suspicious when a cell fails to produce the MHC molecule, and weigh it as a factor part of their complex calculation on whether a cell should be killed or not.
The innate immune system has various other such clever mechanisms. There are specific molecules it produces, that allow it to recognize proteins that are unusually densely covered in these antibody-blocking glycans. These molecules are called Lectins. Lectins are what we call carbohydrate binding proteins that seek out sugar groups part of bigger molecules.
When it comes to the immune system, C-type Lectins appear to be the most relevant in our defense. These are proteins expressed by most cells part of the innate immune system. There are many different types of C-type Lectins and they tend to look specifically for proteins that have a high density of glycans.
That is, the recognition is density dependent. A normal protein part of our body may have some glycans, but a very high density of glycans on a protein reveals to the innate immune system that something weird may be going on that requires intervention.
As I have explained a few times before, natural immunity results in the expansion of the population of plasmacytoid dendritic cells, which recognize viral RNA and/or DNA. This is only possible when the first exposure occurs in the absence of an adaptive immune response induced by previous vaccination, as otherwise the B cells will just deal with an infection, before the plasmacytoid dendritic cells ever get to see the virus and proliferate in response.
When the plasmacytoid dendritic cells detect viral RNA/DNA, through their toll like receptors, they start to produce large amounts of Interferon alpha, which is a molecule that evolved to interfere in just about every step of the viral reproductive cycle. However, how much Interferon alpha they produce, is also dependent on secondary factors.
One of these factors, is whether their own specialized C-type lectin receptors like CLEC4C, recognized some protein that’s densely covered in glycans. If that is the case, they boost their interferon alpha production. For the plasmacytoid dendritic cells it becomes easier to realize it’s time to do their job, when the glycan density on the Spike protein starts to increase.
Another place where you see the innate immune system respond differently in breakthrough infections versus natural immunity, is in the brain. What you see here is that a population of monocytes gets to enter the brain upon infection, that does not get to enter the brain if someone was vaccinated before being infected. You also see an increase in Natural Killer cells and Dendritic cells in the brain.
The natural killer cells recognize whether a cell is infected by the virus and then decide whether the infected cells should be killed or not. But the monocytes and the dendritic cells also have an important job: Their job is to “eat” viral particles.
The dendritic cells try to capture viral particles, so that they can then degrade the viral particles with their lysosomes. But how do the denritic cells capture viral particles? They use their C-type lectin receptors for that!
In other words, what you would expect to see, is that as the dendritic cells now become faced with variants of SARS-COV-2 with more glycans on the Spike protein, they start to be able to do their job more effectively.
In essence, what’s currently happening is that SARS-COV-2 is being forced by the mass vaccination experiment, to evolve in a direction that makes it easier for the innate immune system to recognize the virus.
This is good for young people, as their innate immune system tends to be strong and capable. After all, it has to be able to protect them against all sorts of pathogens, as they normally don’t have any adaptive immunity yet against most of the pathogens that circulate (except for the passive adaptive immunity from breastfeeding).
You would expect this to cause problems however, for people whose adaptive immune system is mainly responsible for suppressing this virus. After vaccination, antibody concentration are about fifty times higher than normally seen after infection.
Constant breakthrough infections have not stimulated innate immunity. Rather, they just recall and broaden the adaptive immune response developed as a consequence of vaccination with non-live vaccines.
Once antibodies against the Receptor Binding Domain became unable to solve the problem, the immune system developed a type of antibody that targets part of the Receptor Binding Domain and part of the N-Terminal Domain (the N1 loop), to which the virus then responded with BA.2.86, which has a unique insertion mutation exactly in the part where these antibodies bind.
This BA.2.86 lineage wiped out all other lineages, revealing that most of the world’s population depends very strongly on the antibody response to keep the virus under control. The body then developed antibodies to this new version of the N1 loop, to which the virus then began to respond by putting the glycans on the N1 loop.
This is why you’re dealing with a situation where everyone keeps catching SARS-COV-2 and getting sick as a result.
All these elegant receptors our innate immune cells have to recognize glycoproteins like the Spike protein, like the C type lectin receptors, tend to depend on the Spike protein not being covered by antibodies. If there are antibodies on the Spike protein, those receptors bump into the antibodies, rather than managing to bind the Spike protein.
This is important to understand: If the antibodies are already on the job, they have to solve the job. And so when the virus has mutated to make the antibodies that bind to it of poor quality and to mainly keep around enhancing antibodies, that bind in places where they won’t stop the Spike protein from correctly binding to the ACE2 receptor, the immune system is forced to start targeting more and more regions of the Spike protein (immune refocusing).
Worst of all perhaps, some of these antibodies directed against SARS-COV-2, seem to cross-react with other respiratory viruses, like Influenza, where they bind to the glycans, but don’t neutralize the protein. So, these antibodies against SARS-COV-2, seem to be making it more difficult for the immune system to deal with other respiratory viruses too, because it’s just much harder for the C-type lectin receptors of the innate immune cells to bind to a protein when it already has these antibodies on it, particularly on its glycans.
You see an epidemic of various respiratory viruses around the world right now, sickening people at abnormally high levels. You need to be asking yourself, what the cause of that is. Some of it may be damage to the immune system, some of it may be due to antibodies against SARS-COV-2 interfering in the innate immune system’s ability to deal with those viruses. I already warned about this long ago.
The point I wish to make clear however with this post, is that it’s inappropriate to expect that the evolution of SARS-COV-2 towards a glycan-covered antibody resistant virus would increase its inherent virulence for everyone.
Instead, what you would expect to see, is that as these glycans accumulate on the Spike protein, the virus will increasingly begin to sicken people who depend on an adaptive immune response against it, whereas when the innate immune system handles the response to this virus, the impact on people’s health will start to decline.
Who cares about any of these details? Well, I’m explaining this for a reason. Immunologists are currently in the process of developing new types of SARS-COV-2 vaccines, that manage to evade recalling the original antigenic sin antibodies and encourage the development of new antibodies instead.
BUT THIS IS THE WRONG APPROACH!
You are very clearly dealing with a virus, that is increasing its glycan density!
And when a virus is rapidly increasing its glycan density, the immune system becomes increasingly dependent on the innate immune response to deal with it, as it just becomes easier to recognize it through the C-type lectins, while the most important parts of the virus for antibody mediated neutralization become inaccessible due to the glycans!
You have to figure out how to suppress the adaptive immune response, allowing the innate immune system to take over and do its job. I have seen just one approach that looks viable to me: Cannabinoids like CBD can suppress adaptive immunity, while encouraging NK cell activity.
It’s not coincidence, that you see better immunological functioning in HIV infected people with strong cannabis use. You see a DECREASED VIRAL RESERVOIR, in cannabis using HIV infected people. Because HIV rapidly mutates and establishes persistent infections, an antibody response is the wrong tool for the job. HIV already covers itself in a dense glycan shield.
Heavy cannabis use has the effect in HIV infected people of shifting their immune response to HIV more towards dependence on the innate immune system. For a respiratory virus like SARS-COV-2, which is still mostly targeting the lungs of vaccinated people, vaporized cannabis would seem like a proper candidate to me, to reduce the immunological abnormalities that were induced by vaccination. The terpenes are also known to have beneficial stimulating effects on the innate immune system.
Look, I understand this is just a weird blog, but look around you. People are coughing everywhere. They’re collapsing on stage. The hospitals are overwhelmed, there’s an epidemic of “walking pneumonia”, at record levels that have never been seen before since we started measuring in the 90’s. People don’t have to believe me, you can just connect the dots yourself.
This is not just some inherent trait of SARS-COV-2, it is mostly a consequence of provoking an inappropriate immune response towards SARS-COV-2. It really doesn’t have to be like this."
I have previously expressed my amazement at the remarkable resilience of complex biological systems, such as the mammalian immune system, in
"I have previously expressed my amazement at the remarkable resilience of complex biological systems, such as the mammalian immune system, in mitigating and/or postponing the severe consequences of C-19 vaccine-induced viral immune escape on human health (https://www.voiceforscienceandsolidarity.org/scientific-blog/to-whom-it-may-concern). This resilience seems particularly applicable to viral immune escape mechanisms that threaten the survival of the host species. I have proposed that mutations in the glycosylation pattern of SARS-CoV-2 could eventually drive viral evolution toward enhanced virulence, potentially resulting in rapid death (https://www.voiceforscienceandsolidarity.org/scientific-blog/predictions-gvb-on-evolution-c-19-pandemic). It is, therefore, reasonable to investigate whether evolutionary changes in the virus’s glycosylation profile could also contribute to attenuating viral virulence and/or delaying an explosion in mortality rates in highly C-19 vaccinated populations.
Based on the literature on viral glycosylation, as cited in one of my previous contributions on this topic (https://www.voiceforscienceandsolidarity.org/scientific-blog/predictions-gvb-on-evolution-c-19-pandemic), it seems highly likely that changes in viral glycosylation can lead to increased viral virulence. In the following discussion, and as an addition to a previous contribution, I explain why such changes could take longer to be selected under immune pressure compared to amino acid changes that directly enhance viral infectivity.
Glycosylation refers to the attachment of sugar molecules (glycans) to proteins or lipids. Glycans can either be N-linked or O-linked[1]. In viruses, glycosylation often occurs on surface proteins, such as the spike protein of coronaviruses or the hemagglutinin of influenza viruses. Glycans can shield critical viral epitopes and thereby mask these epitopes from antibody recognition, allowing the virus to evade immune detection and neutralization. This evasion can lead to higher virulence when glycosylation promotes viral infection or replication in an immunologically naïve population, or when it facilitates the transinfection of the virus to target tissues in immunologically experienced populations that remain susceptible to breakthrough infections. This is plausible, as glycosylation is known to modulate receptor binding affinity and specificity, potentially modifying the binding of antibodies to cell surface-expressed binding sites and altering the susceptibility of certain tissue cells.
While amino acid mutations in surface proteins responsible for viral infectivity can readily increase viral infectiousness and transmissibility (e.g., by preventing neutralizing antibodies from binding to the receptor-binding site on the ‘infectious’ viral protein) and confer an immediate fitness benefit, the selection of glycosylation changes may occur more slowly. This is because glycosylation involves both the protein sequence and the host's glycosylation machinery, adding complexity to the selection dynamics and how changes manifest. Since glycosylation changes can compromise viral fitness by reducing the efficiency of host cell entry or decreasing viral replication rates (e.g., due to alteration of protein folding, structural stability, or function), the natural selection of ‘beneficial’ immune escape mutations in the virus’s glycosylation pattern of surface proteins might require a distinct and sustained immune selection pressure, targeted at different viral epitopes that are not involved in mediating intrinsic viral infectiousness. This is because viral glycosylation patterns are often a balance between immune evasion and maintaining efficient host cell entry and replication.
In summary, it is reasonable to state that, compared to direct amino acid changes, the evolutionary dynamics of viral glycosylation reflect a more intricate and context-dependent process that shapes viral adaptation under immune pressure, affecting their ability to persist and spread in host populations. Variants of SARS-CoV-2 are just one example of viruses that have exhibited mutations affecting their glycosylation (specifically, of the spike protein) when placed under sustained immune pressure[2]. The emergence of new immune escape variants endowed with beneficial glycosylation changes therefore likely requires selection over longer evolutionary periods.
Unfortunately, despite numerous precedents (e.g., Influenza virus, HIV-1, Human Rhinovirus, and Hepatitis C virus) and extensive documentation in virology textbooks, the significance of glycosylation mutations in SARS-CoV-2 and their potential impact on the outcome of the pandemic when selected under strong and sustained immune pressure is poorly understood and certainly underestimated."
[1] N-linked Glycosylation: The glycan/ sugar is attached to the nitrogen atom (N) of the side chain of the amino acid asparagine (Asn). O-linked Glycosylation: The glycan/ sugar is attached to the oxygen atom (O) of the hydroxyl group of the side chains of the amino acids serine (Ser) or threonine (Thr).
[2] For example, the emergence of variants like Delta and Omicron involved changes in the glycosylation pattern of the spike protein, contributing to altered immune responses and vaccine effectiveness.
Arenaviruses such as Lassa virus (LASV) can cause severe hemorrhagic fever in humans. As a major impediment to vaccine development, delayed
Binding studies with monoclonal antibodies indicated that envelope glycans reduced nAb on-rate, occupancy and thereby counteracted virus neutralization. In infected mice, the envelope glycan shield promoted protracted viral infection by preventing its timely elimination by the ensuing antibody response. Thus, arenavirus envelope glycosylation impairs the protective efficacy rather than the induction of nAbs, and thereby prevents efficient antibody-mediated virus control. This immune evasion mechanism imposes limitations on antibody-based vaccination and convalescent serum therapy.
Description Sub-lineage of: KP.2.3 Earliest sequence: 2024-5-7, Italy — EPI_ISL_19198507 Most recent sequence: 2024-6-28, USA, California —
I was digging a bit spike mutations in recent KP.3.1.1 samples, when i met this S:P139S lineage. It didnt appear super fast but then @ryhisn