Correction to today's earlier post
SARS-COV2's protein contains many secondary initiation sites relative to both Pfizer/BioNTech and Moderna's vaccine, although Pfizer/BioNTech's still do contain these possibly concerning sites.
In today’s post there were a few issues with the interpretations of the sequences, so I find it necessary to issue a formal correction. This correction is for the following article:
Did Pfizer/BioNTech insert additional translational regions into their COVID vaccines? (Correction)
Modern Discontent is a reader-supported publication. To receive new posts and support my work, consider becoming a free or paid subscriber. ’ *Additional sentence inserted below for more context, as we…
In writing the article I made the fallacy of interpreting amino acid sequences as determining codons, which is not the proper approach, as it would provide no way of checking for the second mechanism outlined in the article (i.e. adjacent codons may lead to the sequence of AUG which may lead to out-of-frame reads).
So although there were 13 methionine residues found in the original spike protein sequence, which are close to Moderna’s sequence, Moderna’s sequence can’t tell us of any “hidden” AUG sequences in the spike protein.
I did additional digging to try to find the spike’s DNA sequence, with one available sequence being found.
This sequence is hard to interpret due to the line breaks and spacing, so I decided to move the sequence in a word-like document and look at it from there.
In rebutting statements from my prior article, it’s apparent that the spike protein, based on the sequence examined, has many of these secondary initiation sites, noted in red below (aside from two blue regions which I highlighted in the prior article):
That’s a lot of red and blue- 78 to be exact (77 without the start codon). Given that the actual sequence has about 13 methionine residues, this tells us that around 64 secondary initiation sites made by adjacent codons exist within SARS-COV2’s original sequence, which is a HUGE difference than just 13 residues.
This is an egregious oversight which I didn’t consider until I posted my article. I’m keeping the original up for posterity’s sake, with this being the additional context provided to highlight the error.
In looking at this sequence it’s quite apparent that both Pfizer/BioNTech’s sequences contain far fewer of these secondary initiation sites, with Moderna appearing to not have any- maybe Promosome has something when it comes to their lawsuit, and maybe this may mean that Pfizer/BioNTech may be seeing a lawsuit in the future if it’s found that they utilized this same methodology.
Overall, when comparing AUG/ATG regions in both the spike, Pfizer/BioNTech, and Moderna, the breakdown (excluding the authentic start codon) is the following:
Native spike- 77
Pfizer/BioNTech- 29
Moderna- 13
I suppose I missed one ATG sequence when looking at the GitHub document, and this makes more sense that Moderna’s number of methionine matches the native spike. Again, maybe Promosome has something to their lawsuit, so it will be interesting to see what comes in the future.
As a comparison, the below sequence is for Moderna’s vaccine (the first ATG is for the start codon and was not included in the overall number of sequences):
And the one below is for Pfizer/BioNTech (note the last 6 are from the stop codon and 3’-UTR region and were not included in the above 29 value):
Apologies for the eyesores, but again it doesn’t seem as if Pfizer intentionally inserted these sequences by way of optimizing their codon. However, what likely may have occurred is that a mix of codon optimization along with some of the removal of secondary initiation sites may have occurred. The latter would be hard to argue, and it’s likely the former can explain how the regions of secondary initiation sites in Pfizer/BioNTech’s vaccine appear more scrambled relative to the native spike sequence (that is, they don’t appear to be in the same places, as can be seen by the adjacent ATG-ATG near the end of the sequence).
It does seem apparent that Moderna seems to have removed all instances of these secondary initiation sites that did not encode for methionine. It’s a bit hard to look at the sequence and not infer that the secondary initiation sites were cleaned up.
Now, the question remains whether these secondary initiation sites may be problematic. This raises an interesting concern over how many cryptic peptides may be produced by the native spike during an actual infection, and may be worth considering given the wide array of symptoms seen by people infected.
Pfizer/BioNTech do still have nearly double the number of secondary initiation sites relative to Moderna, and thus can be more prone to the production of cryptic peptides. So there may still be something worth investigating with respect to Pfizer/BioNTech’s vaccine.
Overall, this doesn’t appear to be a damning critique of Pfizer/BioNTech that I made it out to be in the prior post, but does still raise some interesting issues with respect to cryptic peptide formation. It'd be interesting to consider whether the body has ways of dealing with these off-proteins, and if the sites are different in the Pfizer/BioNTech vaccine relative to the native spike then one should also infer that different cryptic peptides would be produced.
Again, apologies for completely overlooking the actual genetic sequence for the spike.
Who really knows just how intrusive and dangerous this thing is.... the deeper you go the more questions it raises. What does the spike area look like in sars1 as compared to sars2? Do you know what type of vaccines were tried on sars1?
Ancestral sequence is text-converted in the upload at my resource hub... though the linebreak-free segment is at the bottom of the document and harder to find / understand https://unglossed.substack.com/p/unglossed-resource-hub
Initiation is more a question of physical RNA structure and whether this promotes ribosomal entry and synthesis at a particular "atg" (aug). For the virus, this in turn is a question of a given atg's proximity and relationship with the nearest upstream body regulatory sequence, which is like a notch in the sequence between every coding protein that allows fixing on a copy of Orf1's template leader sequence, which is the ribosomal entry promoter. So generally only atg's that are 5'-proximate in a given coding protein are eligible for consideration as alternate initiation sites. These can result in functional internal ORFs if the leader sequence gets fixed to the atg in question, or if cellular ribosomes tend to slip past the canonical atg and land on the atg in question more than rarely. A third way to get unexpected proteins is fusion via deletion, so say a subgenomic spike RNA molecule is being printed out but it suddenly skips some monomers, maybe that's going to make an unexpected hybrid protein of some type.
For N protein, for example, with my w's for c's substitution, the ancestral sequence looks like:
taaawgaawaaawtaaaatgtwtgataatggawww
where taa is the STOP for Orf8, awgaaw is the TRS-B that promotes attaching a copy of the TRS-L, first atg starts N protein, second atg starts Orf9b protein - the second atg is only +10 monomers of the first.
For spike it's different, the first downstream atg is not until +180 monomers, but it's +204 atg that is suspected as an iORF, see S iORF1 on Fig 4 https://www.nature.com/articles/s41586-020-2739-1. This coincidentally is over one of the commonly used primers and featured in the Single Gene Target Failure that marks Alpha, BA.1, and some of the BA.2/4/5 mutants in PCR. So maybe the virus keeps trying to kick out this iORF because it parasitizes spike expression.