Return of the revenge of the COVID vaccine “spike” in your DNA

As repetitive as I have been with respect to this, there is nothing new under the sun when it comes to antivaccine myths, misinformation, and disinformation, and that applies to COVID-19 vaccines. If public health officials and messengers had paid more attention to the tactics and tropes of the antivaccine movement, including its central conspiracy theory, maybe they would have been more prepared for the onslaught of antivaccine misinformation that was unleashed as the mRNA COVID-19 vaccines were undergoing clinical trials and when they were finally initially approved under an emergency use authorization (EUA) near the end of 2020. They didn’t, and here we are, which is why, having seen it before multiple times last year, In addition to various claims of how “toxic” the SARS-CoV-2 spike protein that vaccines induce cells to make as an antigen are, I’m faced with the return of the revenge of the antivaccine lie that mRNA-based COVID-19 vaccines “permanently alter your DNA” (they don’t, nor do they “hack the software of life“, nor are they really “gene therapy“) this time from Jessica Rose, who is affiliated with James Lyons-Weiler‘s antivaccine “institute” with the humble name of Institute for Pure and Applied Knowledge (IPAK).

Unfortunately, a week ago I saw this zombie lie resurrected yet again in the form of an article on Substack (where the cranks who’ve been banned from Twitter, Facebook, YouTube, etc. all go) by Rose titled It does incorporate into human DNA. And it’s probably messing up embryogenesis, subtitled, These injectable convid-1984 products are perfect bioweapons—either by design or accident. Who cares which. The outcome is the same. Of course, although these sorts of lies have long been known as “zombie lies” because they always rise from the dead after seemingly having been killed, I tend to like to call them “slasher” lies, in a nod to old 1980s horror movie slashers like Jason Voorhees, Michael Myers, and Freddie Krueger, all of whom have seemingly died many times at the end of one movie installment, only to show up to kill more college kids again in a new installment.

Once more unto the breach, I guess! I suppose that while I’m here I should link to the two studies published last week and cited by Rose in her Substack to support her nonsensical claims that (1) the finding of a short nucleotide sequence in the spike protein mRNA sequence used in the Moderna vaccine is slam dunk evidence that SARS-CoV-2 was “engineered” and that the “lab leak” hypothesis for SARS-CoV-2 is true and (2) that SARS-CoV-2 “permanently alters your DNA” by being reverse transcribed and integrated into the DNA in its recipient’s chromosomes. Let’s just say that neither Rose’s cited study from Lund University in Sweden about the supposed reverse transcription of the Pfizer/BioNTech mRNA-based vaccine into the DNA of human cells nor the study by Ambati et al about MSH3 homology support these hysterical claims.

Before I proceed, let’s just reiterate that the idea that vaccines can “permanently alter your DNA” is not new to mRNA-based COVID-19 vaccines, although the nature of these vaccines makes that claim easier for antivaxxers to sell as plausible to those not familiar with molecular biology. Indeed, if you really look carefully at it, the claim that vaccines somehow changes your DNA actually dates back to before scientists even understood DNA as the basis of heredity, as illustrated, for example, by this famous “Cow-Pock” cartoon from 1802 by satirist James Gillray about smallpox vaccine:

Savvy readers will notice how much a meme that was going around a year or so ago about the mRNA vaccines is very much of a piece with this 220-year-old cartoon:

Truly the more times change, the less antivaxxers seem to. There is no real difference between the cartoon from 1802 and this meme from 2021. Only scientific knowledge has changed, so that antivaxxers can claim that mRNA vaccines somehow “change your DNA.

The “central dogma” of molecular biology, or: Why mRNA vaccines do not “alter” your DNA

Before I discuss the two studies and the claims being made about them not just by Jessica Rose but by a number of antivaxxers, let’s take a look at some basic biology and molecular biology, so that you understand why her claims are so beyond the ken. I realize that I’ve done this before, but it’s been a while; so instead of just including links to my previous discussions, I’ll include a brief explanation of something out of Biology 101, so that we’re all on the same page. If you know all of this, you can probably skip to the next section. If not, let’s proceed.

mRNA vaccines rely on the “central dogma” of molecular biology. As I’ve said many times before, I’ve always hated the use of the word “dogma” associated with science, but no less a luminary than Francis Crick first stated it in 1958, and it has been restated over the years in various ways. Perhaps my favorite version of the central dogma was succinctly stated by Marshall Nirenberg in 1958 and has since been commonly paraphrased to say, “DNA makes RNA makes protein”, which about summed up all of molecular biology in five words. (Why I used the past tense in a moment.) In any event, for purposes of understanding the very basics of RNA vaccines, this is the main sequence that you need to understand.

It’s true, of course, that DNA replicates from a DNA template and results in a double-stranded molecule that is very stable, as it has complementary sequences that tightly bind to each other in a sequence-specific fashion. This DNA template is unwound by enzymes that use the template to make RNA, which is single-stranded. That RNA—when used to code for a protein called a “messenger RNA” or “mRNA”—is then used by a ribosome to make protein out of amino acids. Again, to put it simply, each nucleotide equals one letter of the code; each three-nucleotide sequence (codon) equals one “word” that translates to an amino acid. Given that there are four nucleotides, there are 64 possible codons. Since there are only 20 amino acids, that means that most amino acids are encoded by more than one combination of nucleotides or more than one codon; i.e., the genetic code is redundant. Of course, as is the case with nearly everything in biology, it’s more complicated than that, as these diagrams show:

There are complexities that go beyond this seemingly simple scheme, of course. mRNA doesn’t always start out fully formed. Often it’s made as a longer precursor molecule, parts of which are spliced out by enzymes, to produce the final mRNA sequence before the mRNA molecule is used as a template to make protein. There are also other complexities that go beyond the central dogma, such as retroviruses, which make DNA using RNA templates, and microRNA, which can regulate gene expression by binding to specific sequences on mRNAs and blocking transcription and/or inducing the breakdown of the mRNA molecule, for instance. You don’t really need to know the gory details of these processes or others, though, except retroviruses, whose ability to “reverse the flow of information”, so to speak, by transcribing DNA off of an RNA template using an enzyme known as reverse transcriptase will be very relevant to the discussion of the Swedish paper. HIV is the retrovirus that is the most well-known because of its ability to cause AIDS.

Complexities and exceptions aside, RNA vaccines consist mainly of, well, RNA. One problem with RNA vaccines is that RNA is an inherently unstable molecule. It is, after all, a messenger. It doesn’t need to persist any longer than the message needs to be made. In aqueous solution, RNA molecules rapidly degrade. Indeed, the instability of RNA is why public health experts have been concerned about distributing RNA vaccines. Both Pfizer/BioNTech and Moderna adopted a similar strategy in designing their mRNA to encode the SARS-CoV-2 spike protein with stabilizing mutations added to lock this surface protein into a form easily recognizable to the immune system and therefore make it a better antigen. Pfizer and Moderna also used modified nucleosides (the RNA equivalent to DNA nucleotides) that are more stable to make their RNAs, and placed their RNA within a lipid nanoparticle (LNP) delivery system in which LNPs fuse with the cell membrane to deliver the RNA to the cytoplasm.

Naked mRNA of kind used in the Pfizer/BioNTech and Moderna vaccines rely on a very simple mechanism in which the LNPs deliver the mRNA for the SARS-CoV-2 spike protein to muscle cells, which then use the mRNA as a template to make spike, which is then displayed on the surface of the cell to be recognized by the immune system. Some of the vaccine does manage to get to the regional lymph nodes, where they incite an immune reaction as well. This is part of the reason why COVID-19 vaccines have been found to produce false positives in mammography done too soon after vaccination by causing temporary enlargement of the lymph nodes under the arm, which is why mammography recommendations have changed to incorporate waiting at least six weeks after receiving an intramuscular COVID-19 vaccine in the deltoid muscle before undergoing screening mammography.

Before I go on, let me emphasize that, even though SARS-CoV-2 is an RNA virus, it is not the same thing as a retrovirus and the mRNA in LNPs is not the same thing as RNA in retroviruses. Whereas SARS-CoV-2, like most RNA-based viruses, uses an enzyme called an RNA-dependent RNA polymerase (RdRp) to make copies of its RNA genome from an RNA template, retroviruses use an enzyme called reverse transcriptase to produce a DNA copy of their genetic information, which can then integrate into the human genome. That’s why, in order to produce a suitably fear-mongering narrative, antivaxxers usually have to look very hard for highly unusual, artificial, or special case experiments. Guess what? Rose found them.

The dreaded “Cow-Pock” all over again

So let’s see what Jessica Rose wrote about these studies. Her message is, unsurprisingly, very much like that of antivaxxers 220 years ago:

I started to write this article yesterday but not one, but two papers of great interest to me have been published recently and require dissection and dissemination. They are entitled: “MSH3 Homology and Potential Recombination Link to SARS-CoV-2 Furin Cleavage Site” and “Intracellular Reverse Transcription of Pfizer BioNTech COVID-19 mRNA Vaccine BNT162b2 In Vitro in Human Liver Cell Line“, respectively.

Let me be clear here: These COVID-19 injectable products are perfect bioweapons – either by design or accident. Who cares which. The outcome is the same.

Regarding the first paper, Rose writes:

Background for future: MSH3 (MutS Homolog 3) is gene that encodes a protein that is responsible for maintaining the stability of our genomes and suppressing tumor formation. This protein is DNA mismatch repair (MMR) protein which means that it recognizes and repairs bad base (nucleotide) insertions, deletions and mis-incorporations that come about inherently as part of DNA recombination and replication as well as DNA repair. You might have heard me talk about this in some of my presentations in reference to the recently-published paper describing 2 enzymes characterized to be inhibited by the spike protein.

…we found that the spike protein localizes in the nucleus and inhibits DNA damage repair by impeding key DNA repair protein BRCA1 and 53BP1 recruitment to the damage site.

This more recent paper shows the presence of a 19 nucleotide-long sequence (19mer) that in fact, contains the sequence that encodes the furin-cleavage site of the SARS-nCoV-2 spike protein. In other fact, this 19mer has 100% sequence identity (100% query cover and matched identity anti-parallel complementarity 5′-3′) with patented sequences from as early as 2015. (I am checking on the link to MSH3.)1

Aha! There’s the conspiracy theory! First, though, I’ll just note that this is far from the first time that I’ve seen the claim that COVID-19 vaccines somehow interfere with DNA repair. Last time around, it was the claim that the vaccine somehow interferes with a process known as non-homologous end joining (NHEJ) and thereby make those receiving it much more susceptible to cancer. That claim was deceptive. Indeed, the study was very poor quality and had no biological relevance to human cancer risk, although it did contribute to the fascist antivax claim that vaccines somehow “pollute” the blood, making the unvaccinated “purebloods“. Unsurprisingly, it’s exactly the paper Rose cited. The first paper, it turns out, is incredibly thin gruel, just a bunch of BLAST DNA searches carried out using a very small segment of DNA sequence that produced what are almost spurious results.

I might revisit that study in a future post, but it’s the second study that interests me more because it’s more than just in silico messing around and JAQing off. There were actual experiments involved (poorly designed and executed experiments, but experiments nonetheless):

Perhaps even more disturbing from a biological point of view, is something that many of us have hypothesized to be possible, has now been proven to be the case. Another new paper (link above) confirms that the Pfizer mRNA incorporates into human DNA. IN AS LITTLE AS 6 HOURS.

We detected high levels of BNT162b2 in Huh7 cells and changes in gene expression of long interspersed nuclear element-1 (LINE-1), which is an endogenous reverse transcriptase.

Huh is right. Huh cells are ‘immortal’ liver tumor cells and grow ad-infinitum if you give them love. They are good for using in assays that involve viral propagation. LINE-1 is a reverse transcriptase that we carry and comprises ~17% of our genome! LINE-1 retrotransposons are necessarily active during embryogenesis are aberrantly active in tumorigenesis.

BNT162b2, in case you don’t remember, is the generic name for the Pfizer/BioNTech mRNA-based COVID-19 vaccine whose trade name is now Comirnaty. Rose’s claim, as has often been the case, rests on a kind of experiment that’s been done before to try to “prove” that the RNA virus SARS-CoV-2 can somehow mimic a retrovirus and insert its genetic sequence into the DNA of the human genome, just like HIV. (In this case, as you will see, it’s supposedly part of the sequence coding for the SARS-CoV-2 spike protein that finds its way into your DNA, because of course it is.) That’s why I’ll discuss this study first.

Artificial, thy name is this study

Before I discuss this study, let’s just reiterate that, for all the caveats to the central dogma of molecular biology, for the vast majority of cases in normal mammalian cellular biology, information does not “flow backwards” from RNA to DNA. One of those wrinkles, HIV and other retroviruses, requires two different enzymes to accomplish this “backwards” flow of genetic information. The first is the aforementioned reverse transcriptase, which “reverse transcribes” RNA sequences into DNA, destroying the RNA template in the process. However, that is not enough, as reverse transcriptase does not integrate the DNA strands thus produced into the human genome. A second enzyme is needed, a retroviral integrase. Integrases insert the double-stranded DNA produced by reverse transcriptase into the host’s chromosomal DNA; you can view this as a “point of no return,” after which the viral DNA becomes part of the host DNA, a form in which it is called a provirus, and a property of retroviruses that allow them to persist for so long in their hosts.

Retroviruses are not the only source of reverse transcriptase, as noted by Jessica Rose. Mammalian cells have very low levels of reverse transcriptase activity, so low that they’re usually not detectable under normal circumstances. One source is telomerase, which adds sequences known as telomere repeat sequences to the ends of chromosomes using an RNA template, to forestall the obligate chromosome shortening that occurs with each round of cellular replication. (Excessive telomerase activity is associated with the unlimited replicative potential of cancer.) Then there is LINE-1, mentioned by Rose and the focus of the paper.

LINE stands for long interspersed nuclear elements (LINEs). They are what are known as retrotransposons, also known as class 1 transposable elements or transposons via RNA intermediaries. Basically, retrotranposons can copy and paste themselves into different locations in the genome by making RNA and converting that RNA back into DNA through reverse transcription. Because it’s simple, I’ll “borrow” an illustration of how they work from Wikipedia:

You might reasonably be wondering at this point what LINE-1 could have to do with genetic sequences from the vaccine somehow getting into the human genome, thereby “permanently altering your DNA”. You’d be correct to wonder and likely would wonder even more if I told you that most LINEs in our genome are inactive and don’t make any functional enzyme and that they greatly prefer their own RNA and don’t randomly reverse transcribe just any old RNA. After all, retrotransposition (the process) requires that retrotransposons be able to replicate themselves and then paste the new copies elsewhere in the genome. It doesn’t matter that, as Rose points out, LINE-1 does make up approximately 17% of the human genome. Very little of it is active in normal physiology, although increased LINE-1 is associated with cancer, neuropsychiatric disorders, and retinal diseases. (I almost hated to say that because it gives antivaxxers ideas.)

So what does the study cited by Rose claim? What did the investigators do? First, let’s look at the investigators’ rationale:

A recent study showed that SARS-CoV-2 RNAs can be reverse-transcribed and integrated into the genome of human cells [25]. This gives rise to the question of if this may also occur with BNT162b2, which encodes partial SARS-CoV-2 RNA. In pharmacokinetics data provided by Pfizer to European Medicines Agency (EMA), BNT162b2 biodistribution was studied in mice and rats by intra-muscular injection with radiolabeled LNP and luciferase modRNA. Radioactivity was detected in most tissues from the first time point (0.25 h), and results showed that the injection site and the liver were the major sites of distribution, with maximum concentrations observed at 8–48 h post-dose [26]. Furthermore, in animals that received the BNT162b2 injection, reversible hepatic effects were observed, including enlarged liver, vacuolation, increased gamma glutamyl transferase (γGT) levels, and increased levels of aspartate transaminase (AST) and alkaline phosphatase (ALP) [26]. Transient hepatic effects induced by LNP delivery systems have been reported previously [27,28,29,30], nevertheless, it has also been shown that the empty LNP without modRNA alone does not introduce any significant liver injury [27]. Therefore, in this study, we aim to examine the effect of BNT162b2 on a human liver cell line in vitro and investigate if BNT162b2 can be reverse transcribed into DNA through endogenous mechanisms.

This is thin gruel as a rationale. I note that I’ve discussed the cited study before, which involved the intravenous injection of a large amount of LNPs with a different mRNA than the vaccine’s spike protein mRNA, again an artificial design intended to make determination of the biodistribution of the LNPs possible given that in an intramuscular injection the vast majority of the mRNA remained at the injection site and in nearby lymph nodes.

I also note that it is not a new claim that SARS-CoV-2 itself is reverse transcribed in the infected cell to integrate with the host genome. This is a study from last summer that antivaxxers previously used to claim that, based on the supposed ability of SARS-CoV-2 to reverse transcribe, the vaccine could do the same. Let’s just say that this study was justifiably harshly criticized as not reproducible, very rare, and almost certainly artifacts of the experimental conditions used, given that appropriate controls weren’t used. To cite Ed Nirenberg again, no, SARS-CoV-2 is not reverse-transcribed to any significant extent, the publication of the study in PNAS notwithstanding.

I get the same vibes from this new study. So what did the authors do? They did indeed take Huh7 liver cells and expose them to the Pfizer/BioNTech vaccine (BNT162b2), at 200,000 cells/well in 24-well plates. Then they did this:

BNT162b2 suspension was then added in cell culture media to reach final concentrations of 0.5, 1.0, or 2.0 μg/mL. Huh7 cells were incubated with or without BNT162b2 for 6, 24, and 48 h. Cells were washed thoroughly with PBS and harvested by trypsinization and stored in −80 °C until further use.

After 48 hours, the cells were harvested. RNA was extracted for PCR, and in other experiments genomic DNA was extracted from the cells. Of particular importance however, is that the segment of the nucleic acid for the spike protein that was amplified by PCR was this:

Why did they pick primers that amplified only this segment of the gene for spike protein? PCR efficiency drops off the longer the segment that is amplified, and a 444 base segment is actually rather long for quantitative real time PCR. In any event, this choice means that the only thing that can be said is that perhaps this segment of spike was reverse transcribed. Another thing to note is that a very high concentration of vaccine was used, microgram quantities for only 200,000 cells. That in and of itself is very artificial, but that’s not all that’s artificial. As Ed Nirenberg points out, Huh7 was derived from a liver cancer. Unsurprisingly, the Huh7 genome is, as is the case with many cancer-derived cell lines, really messed up.

He also notes that L-1 expression is substantially overexpressed in cancer (i.e., cancer cells have a lot more of it than normal cells).

In fact, cancer cell genomes substantially overexpress L1:https://t.co/uDDgSrly46

L1 expression is directly related to the cell's DNA damage response:https://t.co/LV9NCaQVX7

L1 levels are even being proposed as a biomarker to cancer screening:https://t.co/3Of4JFnqYV

— Edward Nirenberg 🇺🇦 (@ENirenberg) February 26, 2022

In other words, the investigators stacked the deck by using a cell line that has a high level of LINE-1. If I were a peer reviewer for this study, I would have demanded that the investigators use a more genomically “normal” cell line. No cell line that is immortal—can propagate indefinitely—has a “normal” genome, but some have genomes that are less messed up than others. There are a number of respiratory cell lines, for instance, that could work, or what about simple primary cultures of vascular endothelial cells, such as HUVECs (human umbilical vein endothelial cells)? Why did they use only one cell line? In general, if you see a paper that uses only one cell line, be very, very skeptical, not just for COVID-19 but for any basic science studies.

So back to the paper. What did the authors find? Yes, they found that the vaccine, as expected, drove spike mRNA expression, leading to high levels in the cells, while not having much effect on LINE-1 expression, concluding that increased LINE-1 expression compared to control was observed at 6 h by 2.0 µg/mL BNT162b2, while lower BNT162b2 concentrations decreased LINE-1 expression at all time points. If you look at the figure, I call noise, because it doesn’t make a lot of physiologic sense that the lower vaccine concentrations would depress LINE-1 expression but lead to increased expression only at the 6 hour time point.

Hilariously, this chart is the very same one included in Rose’s article, but she fails to see its shortcoming. Amusingly, the authors used two-tailed Student’s t-tests to compare these differences, which is not the correct statistical test for multiple time-dependent comparisons, and the finding of this result is most consistent with noise. Had I been a peer reviewer, I would definitely have called out the statistics used.

But what about reverse-transcribed DNA for spike? Yes, the authors did detect that in the genomic DNA isolated from the cells. They even sequenced the amplified segment and found that it was the same spike sequence targeted by the PCR primers. Checkmate, scientists! Not quite, and the authors even add some weasel words:

In this study we present evidence that COVID-19 mRNA vaccine BNT162b2 is able to enter the human liver cell line Huh7 in vitro. BNT162b2 mRNA is reverse transcribed intracellularly into DNA as fast as 6 h after BNT162b2 exposure. A possible mechanism for reverse transcription is through endogenous reverse transcriptase LINE-1, and the nucleus protein distribution of LINE-1 is elevated by BNT162b2.

Note that this study most definitely did not show that this reverse transcription had anything to do with LINE-1, leaving the authors to speculate. They could have presented evidence that LINE-1 was responsible, perhaps by knocking it out to produce cells that don’t make it or using siRNA that targets the LINE-1 mRNA to decrease its level, and showing that that it blocked the reverse transcription of spike. They didn’t do that. So they speculate, and antivaxxers ignore that this is speculation to present it as a fact that SARS-CoV-2 is reverse transcribed through the reverse transcriptase activity of LINE-1.

Next:

Our study shows that BNT162b2 can be reverse transcribed to DNA in liver cell line Huh7, and this may give rise to the concern if BNT162b2-derived DNA may be integrated into the host genome and affect the integrity of genomic DNA, which may potentially mediate genotoxic side effects. At this stage, we do not know if DNA reverse transcribed from BNT162b2 is integrated into the cell genome. Further studies are needed to demonstrate the effect of BNT162b2 on genomic integrity, including whole genome sequencing of cells exposed to BNT162b2, as well as tissues from human subjects who received BNT162b2 vaccination.

This led to some epic handwaving:

The cell model that we used in this study is a carcinoma cell line, with active DNA replication which differs from non-dividing somatic cells. It has also been shown that Huh7 cells display significant different gene and protein expression including upregulated proteins involved in RNA metabolism [56]. However, cell proliferation is also active in several human tissues such as the bone marrow or basal layers of epithelia as well as during embryogenesis, and it is therefore necessary to examine the effect of BNT162b2 on genomic integrity under such conditions. Furthermore, effective retrotransposition of LINE-1 has also been reported in non-dividing and terminally differentiated cells, such as human neurons [57,58].

Sure thing, guys, but no. This is, as I said, just handwaving.

As Ed Nirenberg asks, why didn’t they bother to do the necessary follow-up experiments to determine if this DNA sequence is actually integrated into the genome? Come to think of it, why didn’t they do PCR of the entire spike sequence to show that the full length sequence had been reverse-transcribed? Or even just do PCR of different fragments from the spike sequence? It boggles the mind.

None of this stops Rose from going straight off the end of the plank of science to this conclusion:

LINE-1 retrotransposons are also involved during early embryonic development. Since LINE-1 expression levels are significantly increased then what effect is this over-expression having on embryogenesis?

We found that too much or too little LINE-1 expression caused development to come to a halt. This means that the precise timing and level of retrotransposon expression is critical for the development of the embryo.”

I need a walk. This article will be updated.

I can hardly wait for Rose’s “updates”, given how far she had to reach to find some rationale to take a highly artificial experiment that almost certainly doesn’t show that the mRNA for the SARS-CoV-2 spike used in COVID-19 vaccines is reverse transcribed under normal conditions, much less “integrated” into the genome of the cells in which it finds itself. I’m guessing that her “updates” will be as hilariously off base as her original post.

The “slasher” lie about COVID-19 vaccines “permanently altering” your DNA always comes back

As I like to say, in antivaxland, everything old is new again in the age of COVID-19. However, as the pandemic grinds on, entering its third year, even everything old that was new again when COVID-19 struck is becoming old. The idea that COVID-19 vaccines “permanently alter your DNA” has now spawned a number of—if you’ll excuse my use of the term—variants. What Jessica Rose is promoting, aided and abetted by these awful studies published in bottom feeding journals, is simply helping to spread variants of this particular conspiracy theories, her recent amusing whining about supposed “hit pieces” notwithstanding.