Digesting the plasmid DNA
More Pfizer shenanigans and regulatory failure plus WHAT HAPPENED IN SEPT 2022?
When the EMA granted marketing authorization to Pfizer/BioNTech to its modRNA vaccine, they subjected them to a number of Specific Obligations and Recommendations as part of their Terms and Conditions.
I think the EMA regulated these drugs slightly differently than the FDA or HC because they used an established pathway, Conditional Marketing Authorization (CMA) normally used for drugs used for cancer and the like. So they were able to impose Specific Obligations and Recommendations with regards to manufacturing.
Specific Obligations: Obligations imposed on the manufacturer under exceptional circumstances (EMA 2022) that include pre-specified data or endpoints and time frames for completion. These Specific Obligations (SO) are binding conditions to the marketing authorization and are lifted once the required obligations are fulfilled. Specific Obligations are submitted within the annual reassessment/renewal or as a variation application.
Then there are Recommendations
Recommendations: Requirements for further development of the product such as quality or purity, those that optimize the risk/benefit ratio of the product, or are of concern to prescribers or patients. Although recommendations are not binding, they are “important considerations in view of the potential future use of the medicinal product” by the manufacturer
There were a total of 4 Specific Obligations with regards to manufacturing, each with 3-5 subparts and a total of 12 Recommendations for the mRNA manufacturing. There were also a bunch more Recommendations on the LNPs and formulation as well. That is a hefty number given they were to do with manufacturing. There were only 2 Specific Obligations regarding the clinical trials IIRC. This gives you an idea of how serious the manufacturing problems were.
Steps in Purification of the modRNA
As we know, after the in vitro transcription of mRNA from the linearized plasmid DNA we need to clean up stuff, so we only get nice clean mRNA. Here you can see the second step is when they add the enzyme DNase 1 to chew up all the linear DNA template as a starting material. What do you NOT see as part of the clean up process?
PFIZER/BIONTECH DO NOT USE ANY CHROMATOGRAPHIC TECHNIQUES TO REMOVE CONTAMINANTS.
THIS IS CONSIDERED STANDARD.
Did they think their filtration was going to do the job? Seriously? I thought I had missed up but no, there are no chromatorgraphic techniques used. Together with the quality of the DNase1 and lack of robustness and repeatability, this is looking less and less a “mistake.”
Residual DNA Amounts in the First Few Process 2 Lots
As part of the assessment and comparability to Process 1 lots, residual DNA was measured using qPCR. Here are the results of the first few lots. PPQ=Process Performance Quality lots; the FDA had asked for 3 of these to be performed before they got the EUA. These lots would be used as standards for the modRNA drug substance for ALL FUTURE lots. So they should be of the highest purity and quality possible.
What do you see here? Those first few lots had VERY LOW amounts of residual DNA measured by qPCR. But that last lot? 20Y513C501? What is going on with that??? Well the EMA had the same question. And that is when they imposed a Recommendation 7
EMA Recommendation 7
Provide results of studies performed to enhance robustness of DNase digestion step.
I dont know about you, but how can the process go from 23ng DNA/mg RNA to 211ng DNA/mg RNA basically from one day to the next? And why include this lot as part of the PPQ lots which are going to be used as the standard lots for the future? This means that a large leeway in residual DNA will likely be allowed.
German FOIA on Recommendation 7
Thanks to @a_concerned_amyloidosis on X (modarnlife on substack), and a FOIA request to the EMA by some enterprising Germans, we have what is known as a Type 1B variation report on whether BioNTech and Pfizer addressed this recommendation.
Here is the timeline.
Submission was made MAR 2021
rDNA in PPQ lot #3 (20Y513C501) was increased compared to PPQ1 and PPQ2
EMA preliminary assessment APR 2021
Partially fulfilled MAY 2021
Pfizer identified the likely root cause, and testing of enzymes by end of second quarter 2021 will prevent further issues
Further Submission JAN 2022
Pfizer states new DNase I small scale studies were initiated to increase robustness but data was inconclusive so adjustment to DNase step not required
UV 260nm
1 U of DNase1 degrades 1 ug of plasmid DNA in 10min at 37C
Request for Supplementary Information FEB 2022
Pfizer states minor adjustments to both IVT and DNase1 digestion have been implemented and consistent rDNA levels shown
EMA Concludes Partially fulfilled MAR 2022
What happened after MAR 2022? Well the EMA was waiting for a resolution
EMA Assessment of Meeting Requirements for Recommendation 7 (DNA Digestion)
RECOMMENDATION CONSIDERED INCOMPLETE
Correlation of DNase 1 activity and levels of residual DNA measured by in-house methods needs to be evaluated
Data provided by Pfizer was NOT FOUND ACCEPTABLE, and data should be required to support no change in DNase digestion step is required.
Requested data from 2 additional European sites (not just the Pfizer US Andover site)
But THEN THEY DID THIS
ISSUE NOT FURTHER PURSUED
Final Step
On SEP 16 2022, the EMA recommended standard marketing authorisations for both SPIKEVAX and COMIRNATY
Both vaccines were granted conditional marketing authorization subject to imposed conditions on data from ongoing clinical trials and to provide additional data on the pharmaceutical quality of the vaccine, given the planned scale-up.
Companies have provided ALL requested additional data on the pharmaceutical quality of the vaccines
If you all remember, it was SEP 2022 when the clinical comparison trial of those 252 patients of Process 2 lots were close because of Real World Evidence? Those patients who were to be compared in the clinical trial as an amendment to Polack et al? Remember?
WHAT HAPPENED IN SEPT 2022 THAT ALL ONGOING SPECIFIC OBLIGATIONS AND RECOMMENDATIONS ON MANUFACTURING WERE JUST GRANDFATHERED IN DUE TO RWE OR SOME OTHER UNKNOWN FACTOR?
Was it the death of the Queen? Biden calling the end of the “pandemic?” What?
Implications
It appears that Pfizer had no intention to improve the residual DNA levels despite having had low levels in the very first Process 2 lots.
Why did Pfizer/BioNTech not provide data and evidence of small scale studies of the DNA digestion step so that a YEAR after the EMA, there are still outstanding issues regarding this step?
Why did Pfizer obfuscate and basically tell the EMA all’s good? You don’t need this information? And why did the EMA acquiese?
Were these high levels of residual DNA left in on purpose? Along with the SV40 enhancer/promoter?
What happened in SEP 2022 that prompted the EMA to state all requested data on quality has been provided? Where is that data? The DNA digestion step did not meet the requirements of Recommendation 7 in MAR 22. Was it closed off later? If so, why did the Type 1B variation not include this important fact?
The more you dig, the weirder it gets. I am beginning to think the Pfizer/BioNTech vaccine was really a DNA “vaccine” with just enough RNA to make antibodies schmantibodies.
Thoughts?
In an earlier mRNA batch RNA-RF200321-06, Pfizer admitted "Incorrect DNase I stock solution used, leading to higher values of residual DNA template".
Perhaps they made the same mistake again?
perhaps they had worn down, demoted, fired or otherwise reduced the remaining few honest people at EMA standing in the way? check out the stock prices around that time, too - perhaps the corporate overlords were anxious for a little pick-me-up to year's end? pfizer-biontech actually fulfilling it's obligations is the only thing i'm absolutely certain was not the case