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Bert Hubert Profile picture
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24 Mar, 4 tweets, 2 min read
BREAKING! Stanford scientists have analysed the Moderna and BioNTech vaccines to determine the mRNA code in there. This is the first time we are seeing the Moderna sequence. Get it here while it is still online: github.com/NAalytics/Asse…
To see what this means, do head over to this page: berthub.eu/articles/posts…
So how different is the mRNA in the Moderna, BioNTech/Pfizer & CureVac vaccines? There are 1274 codon positions. 808 are identical across all 3 vaccines. 103 are unique to Moderna, 249 unique to BioNTech, 230 to CureVac:
And a slightly different comparison, "wild type" SARS-CoV-2 versus the two approved mRNA vaccines. 213 out of 1274 codon positions are identical across all three. 244 unique to Moderna, 155 to BioNTech. The vaccines share 767 modifications:

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More from @PowerDNS_Bert

Bert Hubert Profile picture
30 Jan
Recently I learned something about DNA that blew my mind, and in this thread, I'll attempt to blow your mind as well. Behold: Chargaff's 2nd Parity Rule for DNA N-Grams.
If you are into cryptography or reverse engineering, you should love this.
Thread: Image
DNA consists of four different 'bases', A, C, G and T. These bases have specific meaning within our biology. Specifically, within the 'coding part' of a gene, a triplet of bases encodes for an amino acid Image
Most DNA is stored redundantly, in two connected strands. Wherever there is an A on one strand, you'll find a T on the other one. And similarly for C and G:

T G T C A G T
A C A G T C A

(note how the other strand is upside down - this matters!) Image
Read 12 tweets
Bert Hubert Profile picture
31 Dec 20
New leader in the BioNTech vaccine RNA optimization challenge: @pkuhar! With some pretty Python code that can server as a great starting point for other entries: github.com/unrelatedlabs/…. Context: berthub.eu/articles/posts…
New leader @naomicodes, 76% , using DNA Chisel from edinburgh-genome-foundry.github.io/DnaChisel/ - well done!
New leader @sanxiyn! 78.3% using codon frequency optimization.
Read 6 tweets
Bert Hubert Profile picture
31 Dec 20
Reverse engineers! Cryptographers! I have a fun challenge & contest for you. The BioNTech SARS-CoV-2 vaccine contains copy-pasted RNA from the actual virus. The vaccine RNA encodes for (almost) the unmodified virus S protein. But, the RNA has been optimized somehow. But how? 1/
You can change RNA quite a lot without changing the protein that comes out. It is known that replacing RNA letters to G and C to the RNA enhances vaccine efficiency. And lo, the designers of the vaccine have done just that - GC content went from ~36% to ~57%: 2/
In the graph above, the red dots are vaccine changes that _lower_ the number of G and C though. And we don't know why they did that. In other places, it appears simpler rules have been used to optimize the RNA. The goal is now: can we reverse engineer the algorithm they used? 3/
Read 6 tweets
Bert Hubert Profile picture
24 Dec 20
Preparing a blog post on the BioNTech/Pfizer vaccine & compared the live SARS-CoV-2 spike protein to the one in the mRNA vaccine. And indeed as described, it only differs by two amino-acids. The two Proline substitutions that make the vaccine work (KV -> PP, with the !!): 1/3
If the vaccine would have contained the unmodified Spike protein, this would have "looked" different from the real one. The real one is mounted in the virus body, which gives it a certain shape. With these two changes, the vaccine protein "looks normal" to our immune system. 2/3
This proline substitution trick was discovered in *2017* based on studies on SARS-CoV-1 and MERS, two related viruses. These studies noted that this tiny change made the protein *50 times* more recognizable. Iow we'd be toast without this invention ncbi.nlm.nih.gov/pmc/articles/P… 3/3
Read 4 tweets
Bert Hubert Profile picture
24 Dec 20
"S glycoprotein signal peptide (extended leader sequence), which guides translocation of the nascent polypeptide chain into the endoplasmic reticulum" - part of the BioNTech/Pfizer vaccine. I don't ever want to hear anyone question fundamental science again. 1/2
The level of control and understanding we now have over our biology came from literally millions of person-years spent working on things that at the time were obscure and "useless". And now? We can leverage all this into a 95% efficient vaccine _at the first try_. 2/2
Coda:
Read 4 tweets
Bert Hubert Profile picture
23 Dec 20
Shout out to @BioNTech_Group who found time to answer this small time blogger's question! @hildabast I have it in writing now, a 30 microgram dose of BNR162b2 actually contains 30 micrograms of mRNA. And in addition, there are the lipids, salts, sucrose and water.
This means that by my calculations, every shot of this vaccine contains around 2000 billion mRNA strands that encode the stabilised spike protein. At 0,53*10^-21 grams per RNA nucleotide, this represents ~25 petabyte of mRNA per injection. #cantwait
If this doesn't give you the shivers I don't know what will:
Read 7 tweets

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