KP.3.1.1+S:D111N(202 seqs,>10 places)

[xz-keg]

From sars-cov-2-variants/lineage-proposals#2108
KP.3.1.1+G21893A(S:D111N)

S:D111N is one of the newly-emerged beneficial mutations on KP.3.1.1 backbone. 16% global advantage on cov-spectrum.

https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=KP.3.1.1*&aaMutations1=S%3AD111N&nextcladePangoLineage1=KP.3.1.1*&analysisMode=CompareToBaseline&
S:D111N is very convergent on KP.3.1.1, here I exclude lineages that clearly do not belong to the main branch, and keep those seqs placed under artifact, flip-flop, or other convergent mutations in the count.

GISAID query:G21893A, C12616T,A13121T, -24095, -1354,-29716,-13297,-16332,-25595,-9699,-6066,-4851,-11094,-6391,-27692,-27128,-21855,-25998,-6536,-6286 (may include more -s)
No. of seqs: 53(Australia 5 Brazil 2 Canada 3 Denmark 3 UK 7(England, Scotland, Wales) France 1 Germany 1 Ireland 2 Israel 1 Italy 2 South Korea 1 Spain 1 Sweden 1 USA 23(MD,MI,MN,NY,PA,SD,GBW from Greenland))

First: EPI_ISL_19462720, Spain, 2024-7-14
Latest: EPI_ISL_19465014, England, 2024-9-26

usher

[Mydtlwn]

@corneliusroemer

[FedeGueli]

Query unchanged in comparison to the last update right? @xz-keg

[FedeGueli]

@corneliusroemer

When you will start designating i suggest if you have time to check S:D111N all over the tree it seems a new hotspot for convergence.

[xz-keg]

Query unchanged in comparison to the last update right? @xz-keg

yeah but it will certainly add a lot of new -s in the future.

When number of seqs* number of -s>number of mutation spots, it will be unsafe to assume every - belongs to a separate branch.

[FedeGueli]

Thx @xz-keg

[xz-keg]

73 now, also in Slovakia.

[FedeGueli]

10/73 in October , it is fast

[Mydtlwn]

@corneliusroemer

[FedeGueli]

There is now a branch under this defined by Orf1b:T267A and S:V3A 21 samples in Ontario, so likely a cluster
Query for it: A14266G,G21893A

[xz-keg]

massive upload from Canada, making it 138.

[FedeGueli]

11 in October without counting the two clusters in NY and Ontario. Likely good but in my view not super good

[FedeGueli]

Anyway there is the top branch that is accumulating spike mutations (S:V3A,S:D264H) while spreading in the cluster:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_3a28d_a1a290.json?c=userOrOld&label=id:node_7257266

[FedeGueli]

Anyway there is the top branch that is accumulating spike mutations (S:V3A,S:D264H) while spreading in the cluster:
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_3a28d_a1a290.json?c=userOrOld&label=id:node_7257266

39 for this sub branch now

[DailyCovidCases]

178 seqs now
@corneliusroemer designation needed:

[xz-keg]

designated MC.27

[Over-There-Is]

16205e7

[FedeGueli]

MC.27 via 16205e7#diff-ead4244ff49c81bc758e9f068f5ef42156bd985b9c86de8fa4d6fcd7f2829090R1303