I like mice…
So does some lab that derived Omicron.
Very good read.
You’ll see how Molnupiravir could not have done this alone.
Random C->U mutations are not elevated in omicron but GC-AT are different in early omicron Vs post outbreak.
Mice host!
GC-AT mutations are a signature of ROS damage that makes 8-OxoG.
ROS is elevated in febrile viral infections.
These authors looked at early omicron Vs post outbreak omicron and see a difference here suggesting omicron had a different host at some point.
Mice fit the bill.
Another kind cat sent me this paper.
Another important point is the Ka/Ks analysis they do (dN/dS).
This shows 6.6X higher selective pressure on spike but not on the rest of the SARs genome.
Mice + selection against spike (vax of MAbs) could do this.
Lab derived.
Just to clarify.
C-> U is the most common mutation in C19.
It’s also the mutation Molnupiravir makes.
So for Molnupiravir to be responsible for this, you would need more C->U than background C->U mutation rates….
And you need them focused on Spike.
And you need mis-sense SNPs.
This isn’t an endorsement or Molnupiravir which is a trainwreck.
You do not approve a viral and human mutagen mid pandemic unless you want to fuel a leaky vaccine company with a perpetual booster gravy train.
2)pseudouridine and N1-methyl should be better spelled out. Xia et al conflates the two and we will spell this out more.
PseudoU wobbles more the methylpseudoU but both significantly alter Tm and thus are ‘stickier’ bases than disrupt translation.
Very thorough.
Not only applied a live-dead like PCR looking at sgRNA, they also cultured the virus and looked for immune histochemistry confirmation of proteins.
Great chat with @jjcouey
I have some errors to confess to as I spoke to fast.
1)I was enrolled in a PhD program at UW but dropped out to focus on my job when the HGP starting racing with Craig Venter. So No PhD.
3)The vaccines have N1-Methyl Pseudouridine and I shouldn't shorthand this to Pseudouridine as the former has less wobble than the latter. N1-Methyl does alter the Tm and increase base stacking in RNA but its methyl group steals one potential H-bond.
Let’s have a look at the methods section of the paper.
2 rounds of 45 cycles of PCR?
This is what you do if you want to make polymerase slippage errors near GC rich triplet repeats.
People this library illiterate shouldn’t have the keys to $20K NovaSeq runs.
Having engineered very accurate sequencers, to address PCR polymerase error, you must utilize DNA barcodes that get attached to your PCR products in the first cycle of PCR. Any barcode that over amplifies through the PCR process is discounted.