JN.1.4.5 subbranch with S:S31F, R346T, F456L on C28948T branch being misplaced (47 seqs, 12 regions) and further S:T22N(35, 11) then S:K478Trev(14, 6) then S:R190S, S255F, A522P(TH 3), mainly in Yunnan and Thailand

[Over-There-Is]

Transferred from sars-cov-2-variants/lineage-proposals#1851
JN.1.4.5> C28948T(Orf9c:T72I)> G22599C(S:R346T), T22928C(S:F456L)> C21654T(S:S31F)> C21627A(S:T22N)> A4872G(Orf1a:Y1536C)> A22995Crev(S:K478Trev)> A2133G(Orf1a:K623R), T4608C(Orf1a:M1448T), G22132T(S:R190S), C22326T(S:S255F), G23126C(S:A522P)
It's placed on a JN.1.4> C5284T> T22928C> G22599C> T5284Crev branch with XED now.
S:T22N and S:K478Trev branch is found by @xz-keg.
S:R190S, S255F, A522P branch is found by @ryhisner.

Query: C774T, G22599C, T22928C, C28948T (39)
Query for dropout sequences: C21627A, C28948T, -C22995A, -T22928C (2)
Query for S:T22N branch: C774T, C21627A, C28948T, -A2069T(30)
Query for S:K478Trev branch: A4872G, C21627A, -C22995 (8)
Query for S:R190S, S255F, A522P branch: A2133G,C8293T,G22132T(3)

Earliest sequence: 05-06 Krabi, Thailand EPI_ISL_19175337
Latest sequence: 11-27 Mae Sot, Tak, Thailand EPI_ISL_19642997
Regions Detected:
China 19(Mainland 18; Taiwan 1, imported from unknown), Thailand 10, Myanmar 3, Singapore 2, Japan 1(from Thailand), Korea 1;
France 2, Denmark 1, Ireland 1, Netherlands 1.

A Singaporean sequence has no S:S31F. But S:24-26 deletion is not detected in this sequence, so it's believable that there is a dropped-out S:S31F.

Tree for S:R190S, S255F, A522P branch:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_3e53f_6e4020.json?f_userOrOld=uploaded%20sample&label=id:node_11810000

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_5441a_ab3380.json?c=country&label=id:node_7102588

Sequences:

EPI_ISL_19175337, EPI_ISL_19175346, EPI_ISL_19175349,
EPI_ISL_19180980, EPI_ISL_19220434, EPI_ISL_19242375,
EPI_ISL_19242475, EPI_ISL_19242480, EPI_ISL_19285716,
EPI_ISL_19291460, EPI_ISL_19340768, EPI_ISL_19372385,
EPI_ISL_19388703, EPI_ISL_19444197, EPI_ISL_19444207,
EPI_ISL_19462030, EPI_ISL_19501913, EPI_ISL_19563652,
EPI_ISL_19573049, EPI_ISL_19573051, EPI_ISL_19573081,
EPI_ISL_19594493, EPI_ISL_19594553, EPI_ISL_19594570,
EPI_ISL_19594621, EPI_ISL_19594681, EPI_ISL_19594722,
EPI_ISL_19594756, EPI_ISL_19594779, EPI_ISL_19594862,
EPI_ISL_19594866, EPI_ISL_19594872, EPI_ISL_19594876,
EPI_ISL_19594985, EPI_ISL_19595420, EPI_ISL_19595460,
EPI_ISL_19641549, EPI_ISL_19641558, EPI_ISL_19641563,
EPI_ISL_19642996-19642997

[Over-There-Is]

Thailand/NIC_BKK_1964/2024|EPI_ISL_19573049|2024-11-05 has S:K478Trev too, but it belongs to C23191T branch.

[Over-There-Is]

Myanmar 3, old sequences

[FedeGueli]

+2 Thailand spotted and analyzed by @ryhisner:
they have three additioanl spike mutations: S:R190S, S:S255F,S:A522P
cc @Over-There-Is please add to the proposal and the title , crediting Ryan for this branch
Defining
#2843>>ORF1a:K623R (A2133G), ORF1a:M1448T (T4608C),S:R190S (G22132T),S255F (C22326T),S:A522P (G23126C)
Query: A2133G,T4608C,G22132T
Samples: 2
Places 1 Thailand
tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/hgPhyloPlace/subtreeAuspice1_genome_test_3e53f_6e4020.json?f_userOrOld=uploaded%20sample&label=id:node_11810000

[xz-keg]

@corneliusroemer this deserves designation.

[FedeGueli]

43/32/10/3
due to 2 samples from Ohio in the 22N/478T branch

[xz-keg]

+1 Singapore

[FedeGueli]

45/31/9 recent Ohio

[Over-There-Is]

K478Trev:Ireland