How different is Omicron (o) ?
(more points for thought)
I took the %🧬 in different countries at the 3 genomic take overs:
α Vs. basal lineages
Δ Vs. α
o Vs. Δ
1/7
In each country I took the %🧬 from when there is at least 1% after which there is a steady increase (to prevent bias from low coverage /borders🧬 ) and until it reached ~80 % (or the local peak). Just to mark the main local rise.
2/7
The separation between the rise in the country of origin and the other countries does not demonstrate that the variant broke the borders only after it took over nationally as the data are lacking the initial lag growth phase which theoretically prolonged the graphs.
3/7
Aside the slope, o’s global takeover characterized by a shorter period. Further evidence for its Rt.
So what effected most of o's Rt - R0 or immune evasion? α faced no vaccine and low recovery %, not much immunity to evade. Didn't came close to o's dynamics. Is it a hint?
4/7
Regarding the focus here on 3 VOC’s, it’s purely as they are the 3 global takeover events.
In terms of VOCs the R Indeed correlates to the time of their rise : β <α <γ <Δ <ο.
But, the 5 VOCs were defined as such only because of their high R… at the time they rise.
5/7
But (!) : There were dozens upon dozens of variants that came up on the global radar. Many faced Δ more successfully than α,β and even γ, but since they arrived after the diminish of basal lineages, their R didn’t appear to be special.
They are VOCs no less than α, β &γ.
6/7
here some variants which origin is estimated which succeeded for a local taking over (in a way) and their local rise.
These are just a sample, There was a variety of variants. But than Δ took over and raised the bar of R to get spotted In the global🧬 radar. until... o.
7/7
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UK reports Delta Omicron recombination, this time it's the real thing.
I will try to answer 3 questions here:
1.Was this expected? 2.Is this the report from Cyprus?
3.Should we be concerned?
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1.Was this expected? Yes.
Recombination occurs when a cell is infected with 2 variants.
when 2 variants are in high # & % recombination is more likely to be visible. it is likely to occurred during the Δ times, but if AY.4 recombined with AY.3, that's gonna be hard to spot
2/8
For example:
When α rose and mostly replaced B.1.177 in the UK, XA (recombinant of those 2) detected. github.com/cov-lineages/p…
Wanna know how different BA.2 can be? look BA.3
(Yes, there is a 3rd one).
ill show here that if we apply the logic some use to explain BA.2, BA.3 should also be successful, and it’s not.
(TL;DR Genetics are more complexed than what we would like to think.)
1/8
In terms of GISAID # seq’s :
BA.1/2/3 has 528,773, 10,873 & 86 (respectively).
BA.3 did manage to transmit in the population. It was found in 9 countries in 3 continents. In Poland and SA it seems to transmit over time.
But in comparison to the other two BA’s… it sucks.
2/8
Those are the positions in which BA.3 mutated ,only NS and del’s(S gene marked in the middle).
Blue – shared with BA.2
Red – shared with BA.1
Grey – unique.
(Recombination shout’s out of course.) 3/8
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 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.