Recent KP.3.3 + Orf1a:I1367L branch got S:S31del expanding fast (12 seqs, 6 countries )

[FedeGueli]

Edited: This new "DeFLuQE" lineage popped up in the KP.3.3 branch defined by Orf1a:I1367L that has been tracked by @ryhisner and independently proposed in #2707 I strongly recommend to read his analysis in depth in the dedicated issue. The s:s31del branch was first tracked during the past weeks in https://github.com/sars-cov-2-variants/lineage-proposals/issues/1700 by @josetteschoenma and me.

Defining mutations: #2707 =[ KP.3.3 > Orf1a:I1367L (A4364C) ]> T8263C > Orf1a:V1236I (G3971A), S:S31del (del21653-55), C25416T Query: G3971A,C25416T,T8263C,T3565C Samples:7 First sampled on 6/28 in Canary Islands Countries: 5, Canary, Spain(GBW), US (NY,Florida) , Denmark, England IDs: EPI_ISL_19258203, EPI_ISL_19289755, EPI_ISL_19289951, EPI_ISL_19296640, EPI_ISL_19298060, EPI_ISL_19298340, EPI_ISL_19299722 Tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_17d76_a3bee0.json?c=userOrOld&label=id:node_7022526

[FedeGueli]

cc @ryhisner @corneliusroemer

[FedeGueli]

While i was proposing this @ryhisner independently proposed the parental branch starting with Orf1a:I1367L , a mutation he was tracking in chronics since long time and was specifically under his spotlight on this KP.3.3 branch. I strongly recommend to read his precious analysis at #2707
while i will mention it in the main proposal.

[FedeGueli]

9 new country Iceland

[FedeGueli]

ping @corneliusroemer the KP.3.3 twin of KP.3.1.1 with a known chronic infected patient mutation described by Ryan. It seems fast.

[FedeGueli]

+1 Wales

[FedeGueli]

+2 denmark Ping @corneliusroemer this seems as fast as KP.3.1.1 lets see how fast it reaches 25 and 50

[FedeGueli]

designated MR.1 via https://github.com/cov-lineages/pango-designation/commit/cd468f9ca4056e59046e7f9aed74ab9a01627aeb