Description
From sars-cov-2-variants/lineage-proposals#1509
Other than KP.1.1.1(S:K182N), other seqs on the Orf1b:L2213F branch of KP.1.1 have another NTD mutation set that usher doesn't display.
KP.1.1+C20104T(Orf1b:L2213F)+del22115_22117,T22118A(S:N185-, F186I)
GISAID query: T22926C,C7113,T22118A,A24819G
GISAID query for S:S31F sub-branch: T22926C,C7113,T22118A,C21654T,A24819G
GISAID query for S:K478T rev further branch:C7113,T22118A,C21654T,-22995,A24819G
GISAID query for S:F32S further branch:C7113,T22118A,C21654T,-22995,T21657C
GISAID query for recombinant with additional S:T22N but losing S:K1086R:C25587T, C26195T,A26927G (#2791)
K478T branch--KP.2
Breakpoint between 22119 and 24818
Additional mutations: C21627A,C25587T, C26195T,A26927G
S:T22N
Orf3a:T268M
one of C25587T,C26195T,A26927G from a JN.1.11.1* branch(multiple potential choices)
C21627A and the other 2 of C25587T,C26195T,A26927G are private
No. of seqs: 117(Australia 1 Canada 10 Denmark 2 UK 35 France 14 Germany 1 India 2 Ireland 1 Japan 12 Nepal 2 South Korea 1 Singapore 7 Spain 5 Thailand 1 USA 20(2 from Qatar, 2 from France, 1 from India, 1 from South Africa, 2 from UK))
Usher doesn't display this deletion+mutation and simply put it next to KP.1.1.1. Most seqs on KP.1.1+Orf1b:L2213F branch that is not KP.1.1.1 are in this branch.
Further stepwise S:S31F-S:K478T-recombinant losing S:K1086R but getting S:T22N branch found by @FedeGueli :
https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice3_genome_test_50bcb_9e8d40.json?label=id:node_5730247
