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.
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?
This information at least suggests that more comparisons need to be done between the native spike and the vaccines aside from the spike formation. It's sort of a reminder that the production of spike should be taken into consideration. A comparison could probably be done to SARS-COV as well, although the biggest problem is determining if this is a genuine concern or just a lot of smoke. I just find it interesting that Promosome raised this concern about these secondary initiation sites. It's also something that would have to be examined with respect to the adenoviral vaccines and see if they contain some of these secondary initiation sites as well.
With SARS-COV I believe it was an attenuated or antigen vaccine. It certainly wasn't any carrying genetic material as far as I am aware, but I haven't dug deeply into these things.
Jun 9, 2023·edited Jun 9, 2023Liked by Modern Discontent
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.
I'm not sure why this comment didn't show up in my notifications, but Substack seems to be acting wonky in that regard. I generally can't tell when someone comments now.
That's really interesting. I looked at all of this more as food for thought, although I wasn't sure the degree to which it would translate into anything actually meaningful. I saw an article where they mentioned the RNA conformation for Moderna's mRNA appeared different than that of Pfizer's. I'm curious if that may be due to codon optimization on Pfizer's part, or due to the removal of the ATG sequences.
That part about spike actually makes sense. When I did PCR testing for COVID I always considered that the S drop during Alpha was likely due to loss of primer binding through the 69-70 deletion.
I'll try looking deeper into the Nature article. It does seem very pertinent. On just assumption alone, do you think that the codon optimization in Pfizer would be an issue? It does seem as if several of the ATG sequences are out of place relative to the native sequence.
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?
not easy to figure out.
This information at least suggests that more comparisons need to be done between the native spike and the vaccines aside from the spike formation. It's sort of a reminder that the production of spike should be taken into consideration. A comparison could probably be done to SARS-COV as well, although the biggest problem is determining if this is a genuine concern or just a lot of smoke. I just find it interesting that Promosome raised this concern about these secondary initiation sites. It's also something that would have to be examined with respect to the adenoviral vaccines and see if they contain some of these secondary initiation sites as well.
With SARS-COV I believe it was an attenuated or antigen vaccine. It certainly wasn't any carrying genetic material as far as I am aware, but I haven't dug deeply into these things.
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.
I'm not sure why this comment didn't show up in my notifications, but Substack seems to be acting wonky in that regard. I generally can't tell when someone comments now.
That's really interesting. I looked at all of this more as food for thought, although I wasn't sure the degree to which it would translate into anything actually meaningful. I saw an article where they mentioned the RNA conformation for Moderna's mRNA appeared different than that of Pfizer's. I'm curious if that may be due to codon optimization on Pfizer's part, or due to the removal of the ATG sequences.
That part about spike actually makes sense. When I did PCR testing for COVID I always considered that the S drop during Alpha was likely due to loss of primer binding through the 69-70 deletion.
I'll try looking deeper into the Nature article. It does seem very pertinent. On just assumption alone, do you think that the codon optimization in Pfizer would be an issue? It does seem as if several of the ATG sequences are out of place relative to the native sequence.