What about non-BA.1-variants of Omicron?

[lenaschimmel]

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)

[corneliusroemer]

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 ;)

[lenaschimmel]

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)

[corneliusroemer]

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)* — Reply to this email directly, view it on GitHub <#3 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AF77AQP5XMN6RHABRC2BWQDUVYP4DANCNFSM5K6IFWVQ> . You are receiving this because you commented.Message ID: ***@***.***>

[lenaschimmel]

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.

[corneliusroemer]

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 <#3 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AF77AQOJQ4EVN62IZ3GBBTDUV2TRJANCNFSM5K6IFWVQ> . You are receiving this because you commented.Message ID: ***@***.***>