Can codon usage shed light on Spidroin?
I reached out to a well published scientist in the Over lapping Open Reading Frame literature (OvORF) for their take on this mysterious overlapping ORF in the vaccine. I sent them the NCBI reference and a few SnapGene images and asked, what do you think of this? Most people would ignore such a cold call but this is indeed quite a feat. One of the longer overlapping ORFs on record happens to be in the vaccine injected into billions of people.
Their response was enlightening in describing the mechanism of what happened but left me more perplexed as to how it happened. If the author wants me to cite them for this keen insight you deserve it and I will edit this thread instantly. Forgive me for not doing it outright but I have a policy of not enlisting others with out permission given the radioactive nature of this topic. This cancel culture I would not enlist on anyone without their advance permission.
To understand this insight you have to understand that the Codon table is degenerate. There are more than one code for each Amino acid. Just like Eskimos have 100s of words for snow, genomes have multiple words for each amino acid and their preferential usage of certain words can pin down their origin story. Leucine, Arginine and Serine have 6 different codons and methionine only has one codon.
Codon optimization tries to use the codons that best match the genetic dialect of the organism the nucleic acid is targeting for expression.
Human genomes tend to use ‘Color’, while viruses may instead use ‘Colour’ to say the same thing. For example, you might find viruses always use UUU when coding for Phe but human use UUC (a made up example for illustrative purposes). These biases can inform on the origin of a sequence. This played a roll in the origin of the Furin cleavage site.
So lets look at the codon usage in Pfizer Spike vs Pfizer Spidroin, the C19 virus and what human genomes tend to use.
Pfizer Spike codon frequencies as percentages.
Thats a lot to digest. So narrow it down to just the amino acids that are the reverse complements of Stop codons. If these are used on the Spike strand they will induce stops on their reverse complement or antisense strand.
UAA Stop →UUA or Leucine
UAG Stop → CUA or Leucine
UGA Stop → UCA or Serine
Shown in purple below
So if you want to avoid making stop codons in one frame on the reverse strand you will avoid using these codons in the Spike strand. You cant avoid the amino acid but instead of using color you can use colour and get the same message across without incurring the risk of the word making a misspelling when read backwords.
What do we see in Pfizer Spike? An exclusive usage (97%) of one codon for Leucine (CTG) but the absolute avoidance of TTA (UUA) and CTA (CUA) at 0%.
Thats really odd. What about Serine UCA? Again, the avoidance of UCA (0.01%).
Serine UCA Also avoided?
But I thought Pfizer codon optimized this for humans?
Doesn’t look like it.
OK- so maybe they made exclusive codon use for the other amino acids in spike?
Thats not the case either. There are many amino acids that have 50/50 splits in codon usage (Proline and Arg), 64/36 splits with Threonine, 78/22 splits with Asn, 72/28 splits with Glu and Asp.
So why did they only skew Leucine and Serine to avoid the use of the anti-Stop codons?
Both Moderna and Pfizer claimed to have codon optimized the spike sequence for its human host but both companies came up with wildly different sequences (~90% identical)?
If I were running codon optimization, I would want to ensure lots of stop codons on the reverse strand and would do the exact opposite of what was done here. I’d exclusively use the codons that produce stops on the reverse strand, not exclusively avoid them, particularly in light of the human codon bias calling for it.
This seems like a deliberate intention to produce more ORF capacity on the opposite strand while simultaneously failing to disclose them.
In other news, Alan found this gem made of rock solid Irony.
You might need to pour some bleach or horse dewormer on your eyes and read that again. Moderna’s own patent justifies the use of mRNA to avoid plasmid based insertional mutagenesis.
While this is happening, Wikipedia is mutating the SV40 history to the new woke version of the story.
You might want to also visit ChatGPT before its recoded to woke mode. Look at this long discussion with ChatGPT on what should occur if SV40 was found in another vaccine. It suggests a crisis level response is warranted.
Or just watch this riveting testimony byto understand the scope of the problem.
A more accurate depiction of the history of SV40 can be heard in this discussion on this podcast with RFKJr.