Clearing up misinformation about the spike protein and COVID vaccines

What is the spike protein?

The spike protein is a type of protein on the surface of the SARS-CoV-2 virus that helps the virus infect cells. The COVID vaccines available in the U.S. work by getting the body to produce this protein (with some modifications) so that the body will generate neutralizing antibodies to it. 

There is evidence that the spike protein by itself, even without the rest of the virus present, can cause harm to the body. 

In Part I of this article I’ll summarize some of the evidence for this. This is not really controversial at this point.

However, what is controversial is that some people have asked: if spike is dangerous, might we be endangering people by giving them vaccines that make the body produce spike?

Fact-checking articles that try to shoo away this concern usually refer to the fact that the spike encoded by the vaccines are different from “wild-type” spike (spike from the virus), and for this reason, they are safe. They also state that there is no evidence that the vaccine spike is harmful. 

In Part II, I’ll look into the evidence that shows that vaccine-encoded spike is not harmless.

In Part III, I’ll discuss how most responses to concerns about vaccine-encoded spike usually misconstrue the concern, or don’t actually back up their statements with any data. 

In Part IV, I’ll argue that we should consider the possibility that vaccine-encoded spike protein can cause lasting harm even in people that don’t have obvious or serious “adverse events” from the vaccine.

In Part V, I’ll link to statements from other scientists or doctors who have concerns about the vaccines.

Before we go any further:

I am not anti-vax. I am double-vaxed with Moderna. I used to be a biologist. I believe vaccines have saved many lives. However, not all vaccines are the same. And not all vaccines are equally safe, and we need to be able to have an open and honest discussion about this.

Part I- The spike protein of SARS-CoV-2 is cytotoxic

I’ll briefly summarize some studies on spike protein toxicity.

SARS-CoV-2 Spike Protein Impairs Endothelial Function via Downregulation of ACE 2:

In this study, researchers created a “pseudovirus” that was surrounded by SARS-CoV-2 spike proteins, but did not contain any actual virus. When this pseudovirus was administered to hamsters intratracheally (the hamsters inhaled it), it resulted in damaged vascular endothelial cells (the inner lining of arteries, veins, or capillaries).

The S1 protein of SARS-CoV-2 crosses the blood-brain barrier in mice:

The S1 subunit of the spike protein was able to cross the blood-brain barrier in mice, at least when injected intravenously. Spike also ended up in other organs.

The SARS-CoV-2 spike protein alters barrier function in 2D static and 3D microfluidic in-vitro models of the human blood-brain barrier:

This study used an advanced in vitro model of the human blood-brain barrier to show that the spike protein promoted loss of barrier integrity, i.e., poked holes in the blood brain barrier.

The SARS-COV-2 Spike protein disrupt human cardiac pericytes function through CD147-receptor-mediated signaling: a potential non-infective mechanism of COVID-19 microvascular disease:

The spike protein binds to cells in the heart called pericytes, which line the small vessels of the heart. This triggers a cascade of changes which disrupt cell function, and leads to inflammation. 

There are other studies about spike toxicity, but you get the point. The spike is bad news.

Part II- The spike protein from COVID vaccines is not harmless

As I mentioned earlier, the spike encoded by the COVID-vaccines is slightly modified from the virus (wild-type) spike. Specifically, two proline mutations were introduced in order to lock or stabilize the spike protein into its prefusion conformation, and make it more immunogenic, i.e., make it provoke more of an immune response, or produce more neutralizing antibodies, compared to wild-type spike protein. You can read more about this tweak here or here.

The Moderna, BioNTech-Pfizer, and J&J vaccines all utilized this tweak.

Here’s a section from the Nature article on the design of the Moderna (mRNA-1273) vaccine, where the authors mention the changes made to spike:

Notice how there is no mention of whether the changes to the spike protein will lead to it being more safe?

That’s because the dangers of the spike protein were not known at the time of vaccine design. The studies about spike toxicity didn’t start coming out till late 2020. Moderna had already begun its phase 1 trial by March 2020 , Pfizer had begun its trial in early May of 2020, and the J&J trial had started in July 2020. The idea to use prefusion-stabilized proteins in coronaviruses, meanwhile, dates back to 2018, according to the patent.

I think this means that even if the changes made to the vaccine-encoded spike did make them safe, it would have been by accident.

I have seen many fact-checkers claim that this “stabilization into the prefusion conformation” renders the vaccine-encoded spike safe. However, (1) can we admit that this was not the original purpose of the stabilization? Yes, this change may lead to more neutralizing antibodies, and yes, this change means the spike can’t bind to ACE2, and these are good things, but this is not the same as rendering the spike safe. (2) To my knowledge no studies were actually conducted to show that these changes rendered the spike safe. 

Unfortunately for us, there seems to be plenty of evidence that spike from the vaccine is not safe.

I won’t go into the studies that look into the “officially recognized” adverse side effects from the vaccines; these include Guillain-Barré Syndrome, myocarditis, pericarditis, and thrombotic thrombocytopenia. These have been discussed elsewhere, in peer reviewed journals. I also won’t go into the statistics of adverse events from the vaccines, but you should be aware of Matthew Crawford, a statistician who has made the argument that we are likely grossly underestimating vaccine-induced mortality. To my knowledge, his arguments have not been refuted, despite there being a $1 million bounty on proving his arguments wrong.

I will instead focus on the adverse events that are not “officially recognized” by health authorities, and mostly unknown by the general public. And more specifically, I will focus on the bits of evidence that convinced me that spike encoded by the vaccines are not safe.

For that we need to look at the stories of doctors and patients.

1. Vax recipients with long-hauler like symptoms

COVID long haulers are those who experience ongoing symptoms for many months after recovering from infection with SARS-COV-2. Dr. Ram Yogendra is part of a group of doctors that studies and treats these patients.

This group recently discovered something fascinating. They found that these long haulers had bits of spike protein (S1 subunit) in their non-classical monocytes, which are immune cells that you can think of as “garbage collector” cells.

Now, these immune cells are supposed to gobble up “garbage” so perhaps it’s not outrageous that they would find bits of spike in them, post infection. But what they found was that in long haulers, these bits of spike had managed to persist amongst the monocytes for months after infection. For whatever reason, spike wasn’t getting cleared from the monocytes. This is a problem, because these monocytes are essentially sick, and sick monocytes release all kinds of chemicals that cause inflammation.

Here's where this relates to the COVID vaccines: they discovered that there were some vaccine recipients who had never had COVID, who were also experiencing long-haul like symptoms that were persisting for months after vaccination. They found that these patients also had bits of spike in their non-classical monocytes.

The results in the COVID long hauler patients are in a preprint here. The results from the post-vax patients will be published soon, and I will link to it as soon as a preprint is out. In the meantime, you can hear Dr. Yogendra go over the results in an interview he gave on the Dr Been show:

This is a long video, but the relevant discussion about the monocytes (in both long haulers and post-vax long haulers) occurs within the first 20 minutes.

At about 59:21 min in Dr. Yogendra elaborates on their findings:

“In terms of the clinical presentation, the patients with the post vaccine group, they’re tending to have more neurological symptoms than the long covid patients… seems to be more vascular in nature. Now there seems to be some overlap in terms of symptomatology. But I’ve had some patients that are having… tremors on the telemedicine. So, you know as a clinician you can tell, we just have these instincts that we develop in clinical practice, we know when someone is sick. You and I, Dr. Been, we know it’s the color of their skin, their eyes, their mucus membranes. Just that overall appearance, and some of these post-vax patients are definitely in rough shape and I think it’s probably more neurological in nature and we’re still trying to investigate the pathogenesis behind it”

At about 1:15:00:

“I also think it’s a little disingenuous, for any healthcare professional, to tell these patients: take it, it’s safe and the evidence suggests it is. No, we should be honest with the people. We should say, look, so far it’s suggestive that it’s safe but there’s a lot we don’t know. There’s the whole issue of informed consent. We have to be open with people… Transparency with the general public is important… People are not stupid. We’re not a bunch of sheep Dr. Been. So if you tell people, look this is what it is, these are the risks, these are the benefits. I feel like it would be much more impactful for the vaccine hesitancy…

I will say one thing about the vaccine… the S1 subunit that we found. What I wanted to do now for the paper was to look at people who got vaccinated and had no symptoms, and here’s the interesting thing we just found out last Friday.”

Here’s a key part to pay attention to:

“Some of them have S1 spike proteins in them, 5 months after the vaccine, no symptoms.

It’s a very small number, so we can’t make any conclusions, people can’t be up in arms about this. It does warrant further investigation.”

I want to make it clear that Dr. Yogendra is not an anti-vaxxer, and has mentioned that he has been vaccinated with one of the COVID vaccines. Nowhere does he say that no one should be getting vaccinated.

But I just want to get personal here for a moment. I had a WTF moment when I listened to this video. We were told the spike from the vaccine is “safe.” We were told that it stays near the site of injection. We were told that there was no way that spike could persist in the body.

I felt I had been completely duped by the official narrative. In fact they had no way of knowing the things they were claiming, because the issue of vaccine spike safety was never studied.

Let’s summarize the findings:

Vaccine encoded spike can 1) persist for much longer than we want, sometimes months, within non-classical monocytes, and 2) can end up all over the place, including the brain, because these monocytes can cross the blood brain barrier, and 3) can cause prolonged symptoms and/or damage for months after vaccination. It also appears, but still needs to be confirmed that 4) bits of spike were found in monocytes even in some vaccine recipients that had no symptoms.

Of course, the results of the post-vax patients are not published yet. However, I assume whatever methods they used to determine these results were the same as the methods used in the preprint studying the COVID long haulers. So I will bucket this as “very likely true” for now. You could convince me otherwise, if you showed me that the methods used by this research group were flawed, or that Dr. Yogendra, and his collaborators like Dr. Bruce Patterson, were lying.

2. Curious cases of neurological symptoms shortly after vaccination

Next, let’s look at this study that looked at two cases of neurological symptoms that developed shortly after COVID-vaccination.

New-Onset Neurologic Symptoms and Related Neuro-Oncologic Lesions Discovered After COVID-19 Vaccination: Two Neurosurgical Cases and Review of Post-Vaccine Inflammatory Responses (Jun 2021)

Case 1:

This was the case of a 58 year old woman who had had a melanoma (skin cancer) removed eight years ago.

Two weeks following her second dose of a COVID-19 vaccine, she developed slurred speech, drooling and Bell’s palsy left facial droop. 

After a biopsy they determined that “Final pathology was consistent with a metastatic malignant melanoma”

It turned out that the melanoma she’d had previously had spread to her brain and remained undiagnosed till now. Note: to be clear no one is saying that the vaccine caused the melanoma or its spreading to the brain. What the authors are saying is that the vaccine seemed to lead to neurological symptoms that made her underlying brain condition suddenly obvious.

Case 2:

A 52 year old woman had severe headache, fever, and neck stiffness four days after her first dose of a COVID-19 vaccine. A biopsy eventually revealed that she had a grade IV glioblastoma- a highly malignant brain tumor that arises from astrocytes.

The authors make it clear that these cases do not demonstrate that the brain tumors were caused by the vaccines.

“However, these two independent processes both came to the clinical forefront following vaccination. We hypothesize that the inflammatory response to the COVID vaccine may have played a role in increasing clinical symptoms in these patients, potentially in relation to the COVID-19 spike protein.”

To restate it: these patients had underlying brain issues that had been undiagnosed. After vaccination, some kind of inflammatory response, possibly from the spike protein, seemed to increase symptoms to the point where the underlying brain issues became known.

Here were the thoughts that went through my head after reading this study:

  • Did spike protein, or monocytes with spike, get into their brains? Remember the study in mice that showed spike crossing the blood brain barrier? 

  • These women had underlying issues (tumors) in their brains and that might be why they experienced such obvious neurological symptoms after vaccination. 

  • What would it look like if spike got into the brains of people without underlying issues? 

  • Would it look like headache or brain fog? 

  • And could that cause permanent brain damage?

3.  Women reporting changes in menstruation shortly after vaccination

For months, some women have been reporting changes in menstruation since getting jabbed. I’ve even heard of some cases of post-menopausal women who suddenly started bleeding again. I have no idea what percentage of women are affected, but for months, they were gaslit or labelled “anti-vax” for even talking about their symptoms.

I believe these women. Read one woman’s account here:

The Covid vaccines may affect periods. Are we allowed to talk about this?

By the way, changes to menstruation were not tracked in vaccine safety trials. And there’s limited data when it comes to effects on fertility. So don’t believe people who say that the vaccines don’t affect fertility; they have no way of knowing this.

Luckily the NIH is finally starting to look into this after many months of women speaking out.

Note however, that this is still not an “officially recognized” side effect, so it is not listed on the CDC site. So if you were thinking about getting vaccinated and went to the CDC site for information, you wouldn’t see anything about it there.

4. Stories like Maddie de Garay’s.

Maddie de Garay is a twelve year old girl who was part of a Pfizer COVID vaccine trial from Dec 2020 to Jan 2021. Shortly after her second shot she developed extreme chest pain, nerve pain, GI issues, memory loss, erratic blood pressure and heart rate. She is now in a wheelchair and has to eat through a feeding tube.

Media outlets like CNN and the NYTimes won’t touch stories like these, so you’ll generally only find them on alternative or right wing sites like Fox.

In a horrible Catch-22: because these stories only appear on alternative or right wing sites, liberals will automatically discount them, and so our polarization continues.

There are others out there who have testified before congress about their debilitating vaccine adverse events. You can watch videos of these individuals and decide for yourself whether you believe them or not.

I’m not saying these cases are common; they seem to be rare events. But how can we explain such wide-ranging side effects, without invoking the spike protein?

Loose spike protein, either in the bloodstream or within monocytes or through some other mechanism, seems to be the best working theory we have right now that would explain these wide-ranging effects.

Lastly, let’s get back to informed consent. Can we have informed consent, in such a media climate?

Part III- Fact-checking the fact-checkers

For this part I will respond to fact-checking websites that claim that vaccine-encoded spike is not dangerous.

If you google “spike protein cytotoxic” you’ll find headlines like:

“No sign that the COVID-19 vaccines’ spike protein is toxic or ‘cytotoxic’” (Politifact)


“Fact Check- COVID-19 vaccines are not ‘cytotoxic’” (Reuters Fact Check)


“FALSE: Conspiracy theory that COVID-19 vaccines’ spike are ‘cytotoxic’ debunked by experts”

These fact checking articles are beyond shoddy.

The Politifact article says:

“Experts say there is no evidence that the spike proteins produced by the Moderna and Pfizer vaccines, or the spike protein created by genetic material in the Johnson & Johnson vaccine, are toxic.”

It then proceeds to explain some basic facts about vaccines that do not address any of the concerns about vaccine-encoded spike, like “Our immune systems recognize that the protein doesn’t belong there and begin building an immune response and making antibodies, like what happens in natural infection against COVID-19. At the end of the process, our bodies have learned how to protect against future infection.”

It further reiterates how there is no evidence that the spike protein from vaccines is toxic:

“An FDA spokesperson told PolitiFact: ‘There is no scientific data to indicate that the spike protein in mRNA vaccines is toxic or that it lingers at any toxic level in the body after vaccination.’”

It keeps quoting from different people who basically say the same thing. Here’s what vaccine expert Dr. Paul Offit of the Children’s Hospital of Philadelphia, had to say: he is “not aware of any major dangers from the spike protein.”

You see what this article did here? It didn’t assume that the burden of proof was on the vaccine manufacturers to show that the vaccine spike was safe. It just said that “there was no evidence” that it was not safe. 

Let’s also look at the Reuters article. The article says:

“Research shows that spike proteins (here) remain stuck to the cell surface around the injection site and do not travel to other parts of the body via the bloodstream, they added. The 1% of the vaccine that does reach the bloodstream is destroyed by liver enzymes.”

First of all this paragraph is confusing. The first sentence is talking about the spike protein supposedly remaining stuck to the cell surface around the injection site. The second sentence is talking about the percentage of vaccine that reaches the bloodstream. This reads like it was written by someone who doesn’t have a clear understanding of what they are writing about. Intern?

But I digress. When you go to the “here” link that is supposed to show that the “spike proteins remain stuck to the cell surface” it takes you to the “Vaccine Knowledge Project” website, which doesn’t say anything about the spike remaining “stuck” or not traveling to other parts of the body. I read through everything on that webpage, and even searched for “spike” on the whole website, just in case the wrong page had been linked to. There is nothing saying that spike remains stuck or does not travel to other parts of the body. Maybe I missed it, so if you see something about that please reach out to me.

I should also say that even if this website had said anything about spike remaining stuck, it’s not a study, or a published paper, or a preprint of a study, or information coming from the mouths of researchers. It’s a website that someone made for general audiences to gain some understanding about some basic facts about the vaccines. Note to fact checkers: you’re a crappy fact checker if you are not linking to original studies, whenever possible.

Of course, in this case there is no study that exists showing that vaccine-encoded spike stays where it’s supposed to, or that the spike is safe. We don’t even know how much spike gets produced, and how much that varies across individuals. Again, if someone is aware of such studies, please share them with me.

The article continues:

“Pharmacologist Sabina Vohra-Miller ( produced a Twitter infographic explaining how spike proteins from the vaccine are harmless (here).”

Here’s the infographic:

This infographic will age badly.

“No organ involvement”


“Spike protein from vaccines is harmless”


“MRNA vaccines do not impact fertility”


Oh by the way, fun fact. Look at this guy who is a Pfizer board member and also Chairman of Reuters: James C. Smith

Nothing to see here folks, move along.

Lastly, let’s look at an article that’s a bit better, by Derek Lowe: Spike Protein Behavior

From the article:

“The Spike protein produced by vaccination is not released in a way that it gets to encounter the ACE2 proteins on the surface of other human cells at all: it's sitting on the surface of muscle and lymphatic cells up in your shoulder, not wandering through your lungs causing trouble.”

So questions: when one of the cells presenting spike dies, which will eventually happen, what happens to the spike? Could the dying cell release debris all over the place? Debris that includes spike, or spike protein fragments?

Anyway, I don’t actually need for him to answer. I already know that sometimes spike ends up where it’s not supposed to, and sometimes it leads to lasting symptoms, and sometimes, it even ends up persisting among non-classical monocytes for months. Whoops.

Part IV- Adverse events are not binary

We act like someone either has an adverse event, or not; it’s 0 or 1. But things in biology are often not binary.

In reality we should think of “adverse events” as on a continuum. Some people, for whatever unlucky reason, have very obvious symptoms, perhaps because they express a lot more spike than the average person, or more spike gets loose, or more spike ends up persisting in their monocytes. 

But for every person who expresses a lot of spike, there are probably more people who express medium or small amounts of spike. That spike could be causing subclinical damage; small amounts of damage to the heart, the brain, the blood vessels, etc., that are barely perceptible, at least in the short term.

How can we discount that even a small amount of spike can’t lead to permanent damage? Especially if it is possibly persisting for months?

We can’t. We don’t know.

As far as I know, the heart cannot regenerate itself; it just scars. And although the latest research in neuroscience indicates that brain cells can sometimes regenerate, I’d rather not let any of my brain get damaged in the first place, thank you very much.

But WAIT you might say: all these side effects from the vaccine are also potential side effects from COVID itself! It’s worse to get infected! That’s why it’s better to get the spike from the vaccine rather than the spike from the virus!

Maybe. But this could very well depend on your underlying risk of bad outcomes from COVID, which would depend a lot on age and health (also last I heard, the vaccines haven’t been doing so well in preventing infection and transmission against the new variants… and there’s been talk of giving boosters… because their efficacy is waning… and it appears the vaccinated shed the same amount of virus as the unvaccinated from their nasal passages… though maybe they do clear it quicker… but the situation keeps changing every few weeks… so let’s not get into that now). 

At the very least, we should have an open discussion on the risks vs benefits of the vaccines, compared to infection. Any fair comparison needs to consider the fact that these vaccines lose efficacy over time, whereas natural infection leads to more lasting, and broader, immunity. It also needs to consider the fact that SARS-COV-2 infection outcomes are vastly improved when patients get effective early treatment and have done simple things to boost immunity, like maintain good vitamin D, C, and zinc status.

The bigger point though, is this:

Are you telling me that we can’t have a vaccine, mRNA or otherwise, where the antigen is not toxic?  

Of course not. These vaccines are the beta versions. I hope there will be better ones in the future. 

I haven’t even gone into any of the concerns about the long term health implications of the novel technologies used in some of these vaccines. Of course we don’t know the long term impacts of the lipid nanoparticles used to encapsulate the mRNA vaccines, or the codon optimization used, which would not alter the amino acid sequence of the protein expressed but could affect protein conformation, or the fact that N1-Methylpseudouridine was used to replace uridine in the mRNA. No one knows what the long term impacts of these will be.

In the meantime, even while ignoring these concerns, can we admit that the current vaccines are highly flawed for using the spike as the antigen? And that health officials are not being transparent with the public?

Part V- Who else is concerned?

Let’s look at statements from scientists and doctors who have been voicing concerns about the vaccines.

Here is a letter from over one hundred scientists and physicians from all over the world:

Urgent Open Letter from Doctors and Scientists to the European Medicines Agency regarding COVID-19 Vaccine Safety Concerns

And another from a UK group of doctors:

Open Letter from UK doctors: Safety and Ethical Concerns Surrounding COVID-19 Vaccination in Children to Dr June Raine, Chief Executive, MHRA

And here is a letter in BMJ Opinion, from several clinicians and scientists:

Why we petitioned the FDA to refrain from fully approving any covid-19 vaccine this year

From the BMJ letter:

“We also call on FDA to require a more thorough assessment of spike proteins produced in-situ by the body following vaccination—including studies on their full biodistribution, pharmacokinetics, and tissue-specific toxicities. We ask the FDA to demand manufacturers complete proper biodistribution studies that would be expected of any new drug and request additional studies to better understand the implications of mRNA translation in distant tissues.

We call on data demonstrating a thorough investigation of all serious adverse events reported to pharmacovigilance systems, carried out by independent, impartial individuals, and for safety data from individuals receiving more than two vaccine doses, in consideration of plans for future booster shots.”

There are numerous scientists and physicians voicing concerns, but shockingly, they do not get attention from most large media outlets. When they do, it’s usually from right wing sources, which usually means that most liberals will automatically discount them.

Even worse, some of these doctors and scientists have been vilified, threatened, or subjected to media hit jobs.

The political climate surrounding the COVID vaccines is dangerous

I leave you with this incredible piece of information:

Spreading False Vax Info Might Cost You Your Medical License

From the second paragraph:

“Due to a dramatic increase in the dissemination of COVID-19 vaccine misinformation and disinformation by physicians and other health care professionals on social media platforms, online and in the media… physicians who willfully generate and spread COVID-19 vaccine misinformation or disinformation are risking disciplinary action by state medical boards, including the suspension or revocation of their medical license.”

Really pause on that for a moment. They refer to a “dramatic increase” in something. They’re calling it misinformation and disinformation. Others would call it “concerns.” 

Physicians and other health care professionals are raising concerns, but the current media and regulatory climate prefers to shut them up, rather than consider whether there might be something to their concerns.

What could go wrong?

Acknowledgements to @alexandrosm, @Wezuwezu, @ibeckermayer, @satrapo86, @GanineVanalst, @Volishun, @SinCara, @evatallaksen, @jonatanpallesen, @EduEngineer for their contributions in collating sources.