What about non-BA.1-variants of Omicron? #3
Comments
corneliusroemer
added
enhancement
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You're right, could add the other Omicrons. But then they're so rare, most B.1.1.529 are actually BA.1 just bad sequences. Current situation mostly down to laziness on my side, 1% is hardly noticeable ;) |
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FYI, I have updated the code in my fork to count BA.1, BA.2 and BA.3. Instead of adding them together, I plot them individually like this:
The code is easily adjustable, for example to monitor BA.1.1 as well once it appears in the Entwicklungslinien file. I'm still not sure what to do with the B.1.1.529 calls. I could plot them, but I'm not sure if it adds any meaningful information.
(first image is served live and will update daily, the second one is a static upload) |
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Oh that's amazing, I had thought about doing something like that but time...
If you want to submit a PR happy to merge.
Some thoughts:
I would drop BA.3 since it's not relevant for now. BA.1 vs. BA.2 is very
very interesting on its own.
Maybe also get rid of the dot size legend as it's not that important to
know the scale. Relative dot size is informative enough.
Leave B.1.1.529 out, these are bad quality samples so screw them ;)
…On Thu, Jan 13, 2022, 02:00 Lena Schimmel ***@***.***> wrote:
FYI, I have updated the code in my fork
<https://github.com/lenaschimmel/desh-data> to count BA.1, BA.2 and BA.3.
Instead of adding them together, I plot them individually like this:
[image: Live embedding from my repo]
<https://github.com/lenaschimmel/desh-data/raw/main/plots/omicron_N_logit.png>
The code is easily adjustable, for example to monitor BA.1.1
<cov-lineages/pango-designation#360> as well
once it appears in the *Entwicklungslinien* file.
I'm still not sure what to do with the B.1.1.529 calls. I could plot them,
but I'm not sure if it adds any meaningful information.
[image: omicron_N_logit]
<https://user-images.githubusercontent.com/1325019/149246528-2d2cb348-c27a-4755-8ab6-990a2987596b.png>
*(first image is served live and will update daily, the second one is a
static upload)*
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Thanks for the feedback! I agree to all of that. What's your take on BA.1.1? Is it worth to track it even before it is properly marked in Entwicklungslinien.csv? Overall prevalence of S:R346K within German BA.1 sequences seems to be around 34%, based on a simple |
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Wouldn't include BA.1.1 separately
It'd be a mess because it's not independent but a descendant of BA.1.
BA.1 and BA.2 for themselves and compared is what's most interesting I think
…On Thu, Jan 13, 2022, 11:38 Lena Schimmel ***@***.***> wrote:
Thanks for the feedback! I agree to all of that.
What's your take on BA.1.1? Is it worth to track it even before it is
properly marked in Entwicklungslinien.csv?
Overall prevalence of S:R346K within German BA.1 sequences seems to be
around 34%, based on a simple grep -i CGCCACCAaATTTGCA on the fasta file.
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Currently only cases with
lineage == 'BA.1'are counted as Omicron (see source).There are some cases with lineage
BA.2,BA.3or justB.1.1.529. Shouldn't they be counted as well? Otherwise, I think the wording on the graph should be updated from "Omikron" to "BA.1".To date, these are all 32 of them (sorted by
DATA_DRAW), making up 1,37% of total Omicron cases including those:The text was updated successfully, but these errors were encountered: