Omicron. It not what you think it is.
Omicron is a name given by the WHO not from a scientific reason but mostly for journalist not calling it “The south African variant #2”.
But BA.2 is not (!!!!) BA.1 as I explained in the thread attached.
Can it evade our immune response? Well, look at it’s RBD, 16 NS SNP's, 12 are shared with BA.1.
No one will be surprised if it’ll be somewhere in the BA.1 level.
Is it more severe? Well, I hope not.
But I also hope the Israeli national soccer team reach the finals at the world cup. In scientific work we should relate to hope as a bias factor.
We cannot know how different it's symptoms are until more data gathered. Just as was with BA.1
So, I think the responsible thing to do is (*) to relate to BA.2 as a completely different variant, outcompeting BA.1. With all what it means.
(*) until more reliable clinical data gathered.
Oh and if someone in the WHO is here – The letter Pi is still waiting. Just saying.
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Is BA.2 different?
BA.2 share 32 mutations with BA.1, but it also has 28 (!) unique mutations.
28, That's a lot. it’s more than the defining in α,β,δ, and most of Δ main clades.
I took the defining mutations of BA.1 & BA.2 (NS only), and compared the resemblance between the 2 variants in main parts of the genome. Some difference in S1. E is the same, N & M are different in 1 mutation between the two variants.
And...quite a difference when we go to ORF1ab
SARS-COV-2 translate non structural proteins and negatively select stop codons and frame shits within those for a reason.
RNA replication, proof reading, inhibition of innate immunity and more. Mediated by nonstructural proteins. affecting transmissibility and severity.
Omicron is a weird variant.
Together with @SternLab i took a dive into it's strangeness from the genomic point of view by analyzing the defining mutations of the 3 Omi’s (BA.1/2/3) and 65 other variants having a long branch in the tree and high % of NS mutations.
The strangest thing of course is the RBD mutations. There are a lot. As seen, they are not in line with the trend of many other variants.
But when looking at S1 (non RBD), Omi’s seems more in line with the general trend.
I see a lot of Omi samples with Delta mutations recently. Maybe contamination maybe convergence.
I went to look at it.
I took all non UK Omi samples from 26.12 (~17.5K) and looked for ones with Delta mutations (21j or 21i) using a code by @DrorBendet. I found 890 samples.
Here we can see that most of the samples are with 1-3 delta mutations. As we go to higher #delta mutations the probability for this to be a lab contamination is going up.
Here are the # of samples with each mutation. What pops up immediately is that the most prevalent ones are the more converged with other variants.