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corneliusroemer
What about non-BA.1-variants of Omicron?
Currently only cases with lineage == 'BA.1' are counted as Omicron (see source).
There are some cases with lineage BA.2, BA.3 or just B.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:
IMS_ID DATE_DRAW SEQ_REASON PROCESSING_DATE SENDING_LAB_PC SEQUENCING_LAB_PC lineage scorpio_call
IMS-10183-CVDP-81E05ED2-68B2-45C9-AE92-FE0747BD7C1A 2021-11-30 Y 2021-12-10 22081 22081 B.1.1.529 Probable Omicron (B.1.1.529-like)
IMS-10261-CVDP-0EC19B38-8711-4617-8D20-B19F3C75E2F8 2021-12-01 A[B.1.1.529] 2021-12-13 32105 32105 B.1.1.529 Probable Omicron (B.1.1.529-like)
IMS-10004-CVDP-E64B5426-4FB5-4D41-AFEC-77D84720E886 2021-12-02 A[B.1.1.529] 2021-12-20 21502 21502 BA.3 Omicron (BA.3-like)
IMS-10338-CVDP-DEB4E3F4-4E65-4E95-9E9B-77EB04A50226 2021-12-03 X 2021-12-17 64283 B.1.1.529 Omicron (B.1.1.529-like)
IMS-10641-CVDP-677D2DB5-8A78-4238-BF38-CC4BC8247275 2021-12-03 N 2021-12-27 06120 06120 B.1.1.529 Probable Omicron (B.1.1.529-like)
IMS-10013-CVDP-2857098B-37D6-49EA-B92A-748F97328D42 2021-12-06 N 2021-12-18 01665 04779 B.1.1.529 Probable Omicron (B.1.1.529-like)
IMS-10004-CVDP-17A54357-705F-43BD-81F4-1A87C79F9FA4 2021-12-06 N 2021-12-20 21502 21502 B.1.1.529 Probable Omicron (B.1.1.529-like)
IMS-10209-CVDP-93C23280-BFE2-4DD7-A9DE-460B5420EE08 2021-12-06 X 2021-12-28 78467 78467 BA.2 Omicron (BA.2-like)
IMS-10036-CVDP-B81B32E6-AD2D-4E05-9109-7B35544A6407 2021-12-07 A 2021-12-21 12247 16321 B.1.1.529 Probable Omicron (B.1.1.529-like)
IMS-10001-CVDP-FD7B08A6-39E9-462A-BB81-34D2D72DE174 2021-12-07 A[Y] 2021-12-25 87435 87435 B.1.1.529 Omicron (B.1.1.529-like)
IMS-10183-CVDP-DB2FDBCC-5F6A-445D-9F75-20D87840C180 2021-12-09 N 2021-12-17 22081 22081 B.1.1.529 Probable Omicron (B.1.1.529-like)
IMS-10183-CVDP-75514806-B96C-4825-B5FD-EF389CC8D1EA 2021-12-10 Y 2021-12-17 22081 22081 B.1.1.529 Probable Omicron (B.1.1.529-like)
IMS-10183-CVDP-DCCF53C4-C30E-4D1C-A2B7-ECD99B7551EE 2021-12-10 N 2021-12-17 22081 22081 B.1.1.529 Probable Omicron (B.1.1.529-like)
IMS-10261-CVDP-BB754EC4-4185-4B28-A872-DA062436D447 2021-12-13 A[B.1.1.529] 2021-12-22 32105 32105 B.1.1.529 Probable Omicron (B.1.1.529-like)
IMS-10004-CVDP-40148A1B-A7BC-4302-B4EB-9993F89C48F8 2021-12-13 A[B.1.1.529] 2021-12-28 21502 21502 BA.2 Omicron (BA.2-like)
IMS-10001-CVDP-0EA49D87-CBD9-48B0-8536-7F5AFFAC321F 2021-12-14 A[Y] 2021-12-25 87435 87435 B.1.1.529 Probable Omicron (B.1.1.529-like)
IMS-10001-CVDP-36C59D9E-72E8-4B2C-A635-0D69C4B9C9FB 2021-12-14 A[Y] 2021-12-25 87435 87435 B.1.1.529 Probable Omicron (B.1.1.529-like)
IMS-10150-CVDP-1D7B1F19-0AA1-486C-BFE2-2DE49596B981 2021-12-16 X 2021-12-22 51375 92637 BA.2 Omicron (BA.2-like)
IMS-10183-CVDP-FF1E061C-F0E6-41BE-9DA0-35154066D3C0 2021-12-17 N 2021-12-24 22081 22081 B.1.1.529 Probable Omicron (B.1.1.529-like)
IMS-10261-CVDP-DFACA834-5290-4855-BC54-AC7AB9B0B49B 2021-12-17 A[B.1.1.529] 2021-12-27 32105 32105 B.1.1.529 Probable Omicron (B.1.1.529-like)
IMS-10001-CVDP-F576FBA5-8F15-4E9E-8E70-F3287A33FDDB 2021-12-19 A[Y] 2021-12-25 87435 87435 B.1.1.529 Probable Omicron (B.1.1.529-like)
IMS-10001-CVDP-909F8C1F-9DF7-47B0-AA3C-C981406B56C0 2021-12-19 A[Y] 2021-12-25 87435 87435 B.1.1.529 Probable Omicron (B.1.1.529-like)
IMS-10001-CVDP-4BBE02BC-9479-4E6F-8B28-9F575E60A615 2021-12-19 A[Y] 2021-12-25 87435 87435 B.1.1.529 Omicron (B.1.1.529-like)
IMS-10001-CVDP-295624E6-E260-4456-9B36-E67512ACEA20 2021-12-20 A[Y] 2021-12-25 87435 87435 B.1.1.529 Probable Omicron (B.1.1.529-like)
IMS-10001-CVDP-047F5A00-3CE6-4038-8308-6F85FA8E40E5 2021-12-20 A[Y] 2021-12-25 87435 87435 B.1.1.529 Probable Omicron (B.1.1.529-like)
IMS-10001-CVDP-FEEEA8B2-0F57-40BE-A50D-4D7A6B0031E6 2021-12-20 A[Y] 2021-12-25 87435 87435 B.1.1.529 Probable Omicron (B.1.1.529-like)
IMS-10001-CVDP-AB0193AA-F6E3-4569-8C70-4E507F1037D0 2021-12-20 A[Y] 2021-12-25 87435 87435 B.1.1.529 Probable Omicron (B.1.1.529-like)
IMS-10001-CVDP-76508575-1AC0-4E0F-94C6-8FCDE164BE02 2021-12-20 A[Y] 2021-12-25 87435 87435 B.1.1.529 Omicron (B.1.1.529-like)
IMS-10001-CVDP-1E673F95-62A2-4576-A94F-8A46797FEF14 2021-12-20 A[Y] 2021-12-25 87435 87435 B.1.1.529 Probable Omicron (B.1.1.529-like)
IMS-10337-CVDP-6549EC0D-4E8F-427A-96ED-6E2F47E00941 2021-12-20 X 2021-12-28 23538 23538 BA.2 Omicron (BA.2-like)
IMS-10001-CVDP-3F43636E-F55C-4C1C-BD9A-EF792ED6E550 2021-12-21 A[B.1.617.2] 2021-12-25 87435 87435 B.1.1.529 Probable Omicron (B.1.1.529-like)
IMS-10004-CVDP-E9819B99-144D-4AE6-A47C-46042F231AEF 2021-12-22 N 2021-12-28 21502 21502 B.1.1.529 Probable Omicron (B.1.1.529-like)
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 ;)
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)
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 https://github.com/cov-lineages/pango-designation/issues/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)
— Reply to this email directly, view it on GitHub https://github.com/corneliusroemer/desh-data/issues/3#issuecomment-1011608441, or unsubscribe https://github.com/notifications/unsubscribe-auth/AF77AQP5XMN6RHABRC2BWQDUVYP4DANCNFSM5K6IFWVQ . You are receiving this because you commented.Message ID: @.***>
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.
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.
— Reply to this email directly, view it on GitHub https://github.com/corneliusroemer/desh-data/issues/3#issuecomment-1012008857, or unsubscribe https://github.com/notifications/unsubscribe-auth/AF77AQOJQ4EVN62IZ3GBBTDUV2TRJANCNFSM5K6IFWVQ . You are receiving this because you commented.Message ID: @.***>