sars-cov-2-variants / lineage-proposals

Repository to propose and discuss lineages
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2 JN.1.4.5 FLiRT subbranches being misplaced (16 seqs, 8 regions / 5 seqs, LU 4, FR 1) #1851

Closed Over-There-Is closed 1 month ago

Over-There-Is commented 2 months ago

Branch 1: JN.1.4.5+S:S31F, R346T, F456L on C28948T branch

JN.1.4.5> C28948T> C21654T(S:S31F), G22599C(S:R346T), T22928C(S:F456L) It's placed on a JN.1.4> C5284T> T22928C> G22599C> T5284Crev branch now.

Query: C774T, G22599C, T22928C, C28948T

Earliest sequence: 05-06 Krabi, Thailand EPI_ISL_19175337 Latest sequence: 08-30 Singapore Regions Detected: Thailand 5, China 4(Mainland 3; Taiwan 1, imported from unknown), France 2, Singapore 2, Denmark 1, Japan 1(from Thailand), Korea 1.

A Singaporean sequence has no S:S31F. But S:24-26 deletion is not detected in this sequence, so I believe there is a dropped-out S:S31F.

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_4e302_4618f0.json?c=country&label=id:node_7154810 image

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

Branch 2: JN.1.4.5+S:F59S, R346T, F456L

JN.1.4.5> C10519T, G11389A, A13901G(Orf1b:D145G), T18125C(Orf1b:V1553A), A21231T, T21738C(S:F59S), G22599C(S:R346T), T22928C(S:F456L), C29358T It's placed on JN.1.18.6 now.

Query: G11389A, A13901G

Earliest sequence: 05-22 Metz, Grand Est, France EPI_ISL_19189761 Latest sequence: 06-26 Luxembourg EPI_ISL_19306808 Regions detected: Luxembourg 4, France 1

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice2_genome_test_4e302_4618f0.json?c=country&f_userOrOld=GISAID%20and/or%20public&label=id:node_7247062 image

Sequences: EPI_ISL_19189761, EPI_ISL_19306808, EPI_ISL_19306824, EPI_ISL_19306916, EPI_ISL_19306926

FedeGueli commented 2 months ago

Br.2 could not be a recombinant with one of the JN.1.18 +59S branches?

FedeGueli commented 2 months ago

Br.1 now 11 Br,2 dead

FedeGueli commented 1 month ago

Both dead or Dying

xz-keg commented 3 weeks ago

Branch 1 now 16, it seems to get S:T22N and S:K478T rev, Japan EIS from Thailand @FedeGueli

image

xz-keg commented 3 weeks ago

Suggest to change the proposal (or make a new one) specified on B1-S31F+T22N branch.

FedeGueli commented 3 weeks ago

Suggest to change the proposal (or make a new one) specified on B1-S31F+T22N branch.

@Over-There-Is propose Branch 1 in the main page with the specific sublineage found by @xz-keg please

Query: A4872G ,C21627A Tree: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_1bdbd_4eb600.json?f_userOrOld=uploaded%20sample&label=id:node_7086363

FedeGueli commented 6 days ago

Suggest to change the proposal (or make a new one) specified on B1-S31F+T22N branch.

@Over-There-Is propose Branch 1 in the main page with the specific sublineage found by @xz-keg please

Query: A4872G ,C21627A Tree: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_1bdbd_4eb600.json?f_userOrOld=uploaded%20sample&label=id:node_7086363

this 22N 31F branch went up to 7 with a recent Irish sample