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cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme
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KP.3.1.1+S:D111N(165 seqs,>10 places) #2804

Open xz-keg opened 1 month ago

xz-keg commented 1 month ago

From https://github.com/sars-cov-2-variants/lineage-proposals/issues/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. image

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 image

Mydtlwn commented 1 month ago

@corneliusroemer

FedeGueli commented 1 month ago

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

FedeGueli commented 1 month ago

@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 commented 1 month ago

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 commented 1 month ago

Thx @xz-keg

xz-keg commented 1 month ago

73 now, also in Slovakia.

FedeGueli commented 1 month ago

10/73 in October , it is fast

Mydtlwn commented 3 weeks ago

@corneliusroemer

FedeGueli commented 2 weeks ago

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 commented 2 weeks ago

massive upload from Canada, making it 138.

FedeGueli commented 2 weeks ago

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

FedeGueli commented 2 weeks ago
Screenshot 2024-11-05 alle 14 17 27

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 commented 3 days ago

Screenshot 2024-11-05 alle 14 17 27 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 commented 3 days ago

178 seqs now @corneliusroemer designation needed: Screenshot (91)