Vials of Pfizer and Moderna are Contaminated with Large RNA Fragments and Antibiotic Resistant Genes for Kanamycin and Neomycin

Sequencing of the content of several Moderna and Pfizer vials has been published in this excellent post. It contains detailed technical description of methods used. I am not an expert in these techniques, but the person who did this analysis is an expert with access to the necessary equipment and tools:

• Deep sequencing of the Moderna and Pfizer bivalent vaccines identifies contamination of expression vectors designed for plasmid amplification in bacteria

mRNA genetic impurities remain an unresolved problem:

I and several other authors have discussed that it appears to be impossible to manufacture these products to the current Good Manufacturing Practice (cGMP) standards. Specifically, the issue of mRNA instability has never been resolved. mRNA, especially large sequences, is fragile and unstable and breaks during manufacture and administration resulting in random fragmentation, which is deemed a genetic impurity – a contaminant that can pose significant risk of production of unknown aberrant proteins or other cellular or genetic machinery damage. Of note, production of a specific precisely defined protein in a reproducible manner has NEVER been demonstrated with these injections. When I reported on this I was using information from leaked EMA documents from the end of 2020.

A critic could say, but surely Pfizer and Moderna have improved their “prototype warp speed” hastily scaled up manufacturing process and are now making a much better, more pure concoction. That’s now proven not to be the case.

The post by Anandamide confirms that this issue has not been addressed at all in the span of 2.5 years and the product is just as non-compliant as before, and the bivalent version is worse than the original as they now contain long RNA fragments which are more likely to cause even more damage.

Results

Fragment analysis of each vial is depicted in Figure 1. RNA fragmentation is evident in both brands and all lots but is particularly notable in Pfizer vials. Surprisingly, mRNA products longer than the anticipated length of the mRNA were also observed in the bivalent vaccines.

Figure 1. Agilent Tape Station Electrophoresis of the Bivalent vaccines. Moderna mRNA-1273.214 (Top) and the Pfizer bivalent vaccine (Bottom).

 

These longer fragments are not seen in Patel et al. with the monovalent vaccines.

Antibiotic resistant bacteria brought to your microbiome by Pfizer and Moderna:

The second very important issue I would like to comment on has to do with the antibiotic resistance.

Bacteria acquire resistance to antibiotics through two principal routes: chromosomal mutation and the acquisition of mobile genetic elements such as plasmids by horizontal gene transfer. Every year more people die from antibiotic resistant infections, and recent predictions estimate that by 2050 antibiotic-resistant bacteria will kill more people than cancer. Bacterial infections are dangerous to people with compromised immune systems, specifically in intensive care units the antibiotic resistance affects up to 50% of critical patients, doubling their mortality risk.

A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria. In nature, plasmids often carry genes that benefit the survival of the organism and confer selective advantage such as antibiotic resistance. While chromosomes are large and contain all the essential genetic information for living under normal conditions, plasmids are usually very small and contain only additional genes that may be useful in certain situations or conditions. Artificial plasmids are widely used as vectors in molecular cloning, serving to drive the replication of recombinant DNA sequences within host organisms. In the laboratory, plasmids may be introduced into a cell via transformation. Synthetic plasmids are available for procurement and can be ordered from a variety of suppliers.

Resistance to antibiotics is also a widely used tool in molecular biology. Plasmid transformation into E. coli is a fairly inefficient process– just 1 out of 10,000 cells on average! Without some means of quickly determining which cells successfully received the correct plasmid, scientists would spend hours to days trying find their correct clones. Additionally, the presence of a plasmid is disadvantageous from the bacterium’s perspective – a plasmid-containing cell must replicate the plasmid in addition to its own chromosomal DNA, costing additional resources to maintain the plasmid. Adding an antibiotic resistance gene to the plasmid solves both problems at once – it allows a scientist to easily detect plasmid-containing bacteria when the cells are grown on selective media, and provides those bacteria with a pressure to keep your plasmid.

Molecular biologists engineering antibiotic resistance – what can possibly go wrong? Until recently, this problem was relatively small scale.

Enter the “mRNA Revolution”:

Below is the chart from Pfizer’s EMA submission describing the process of making drug substance (mRNA itself which is subsequently encapsulated into LNPs – ER: lipid nanoparticles). Note in Step 1 “Linear DNA Template” as a process input, this is the template (akin to a photo negative) from which RNA will be transcribed. That template is made by the commercial plasmid DNA process.

This is the section of the Pfizer EMA Chemistry Manufacturing and Control documents describing the plasmid template (starting material for making mRNA):

Control of Materials – Source, History and Generation of Plasmids

Plasmid Used for Production of the Linear DNA Template

Manufacture of the BNT162b2 drug substance is achieved using in vitro transcription that includes a linear DNA template as a starting material.  The linear DNA template is produced via plasmid DNA from transformed DH10B Escherichia coli cells.  The plasmid, pST4-1525, is a 7,824 base pair plasmid designed for the production of BNT162b2.  In addition to the sequence coding for the transcribed regions, the plasmid DNA contains a promoter for the T7 RNA polymerase, the recognition sequence for the endonuclease used for linearization, the kanamycin resistance gene, and an origin of replication.

Figure S.2.3-1. pST4-1525 Plasmid Map

Table S.2.3-4. Functional Elements of pST4-1525

Note the second line in this table “This gene (aph(3’)-II) encodes kanamycin resistance to bacterial host cells used for plasmid production”. Kanamycin is an antibiotic, the resistance gene for the plasmid is used as a “marker” and to increase the biomanufacturing yields.

With the introduction of mass scale, billion-dose mRNA manufacturing, it has been estimated that the DNA template inputs must be now manufactured in KILOGRAMS.

About a year ago I received a report from a German scientist who separated RNA, DNA and protein from Pfizer and Moderna vials. The DNA content was shockingly high, exceeding the thresholds of acceptance by ~100-200 times.

In that experiment, neither DNA nor RNA were sequenced, but we suspected the DNA came from untranslated DNA matrix and from manufacturing process impurities that were not properly removed.

Here is the discussion from the sequencing results of Pfizer and Moderna vial contents. We can now confirm that the antibiotic resistance genes and other contaminants are plentiful in these shots:

The EMA set limits for dsDNA contamination at less than 330ng/mg RNA. This is roughly 1 part per 3,030 mRNA molecules. It is not clear how they set these standards.

Note: EMA did not set these standards. Pfizer simply told them these should be the standards and there was no discussion on justification of it.

For instance, a shot containing 34 trillion mRNAs with a 1 part per 3,000 plasmid contamination rate would equate to over 10 billion dual antibiotic resistant plasmids being transfected per patient. The sequencing evidence we now have on hand confirms that most of this DNA is in-fact the expression plasmid DNA, complete with spike protein, SV40 mammalian expression promoters, dual antibiotic resistance and high copy origins of replication that are compatible with both mammalian and bacterial amplification.

Contamination of double stranded DNA (dsDNA) in these vaccines is a significant concern. The EMA specified dsDNA limits in this vaccines below 0.33% (330pg/mg). This is roughly 1 DNA molecule for 3,000 mRNA molecules. While the Moderna vaccines are meeting this specification, the Pfizer vaccines are 10 fold higher in contamination with 1 DNA molecule per 350 mRNAs. This is 1 replication competent plasmid per 350 mRNA molecules and equates to billions of antibiotic resistant plasmids injected per person per shot.

The EMA had good reason to monitor the dsDNA levels in the vaccines. DsDNA injections can induce type I interferon responses via STING in mammals. If these dsDNAs are packaged into LNPs, they can transfect and transform both mammalian and bacterial cells in the patient’s microbiome. Its not clear how the EMA settled on their acceptable dsDNA contamination and if they had considered contaminating DNA that was capable of amplifying inside the host.

The vectors contain mammalian promoters, bacterial origins of replication in addition to the neomycin and kanamycin resistance genes. Circular plasmids like this are used for stable transfection and continued expression of genes in mammalian cells with the strong SV40 promoter. This could lead to prolonged spike expression in patients injected with these constructs. Bacteria transformed with these plasmids would replicate 50-300 copies of the plasmid per cell. It is not know if the bacteria would also express the spike protein in these plasmids but the presence of T7 promoters in some of the vectors implies this is likely.

Patient use of neomycin or kanamycin after vaccination with these plasmids could enable the the selection of neomycin and kanamycin resistant bacteria in the gut microbiome. It is unclear if the spike protein in these expression vectors is expressed in bacteria. Nevertheless, inoculating billions of people with dual antibiotic resistance, high-copy number plasmids could be a step backwards in our fight against antibiotic resistance.

For additional analysis and discussion, I also recommend Jessica Rose’s post on this topic.