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Repository for suggesting new lineages that should be added to the current scheme
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FL.21 (or XBB.1.9.1) sublineage with Orf7a:T14I, Orf8:C90S(42 seq, 3 countries) then S:F456L(31 seq, 8 states in USA) #2282

Closed Over-There-Is closed 11 months ago

Over-There-Is commented 11 months ago

Query: C9166T, A10564T(Edited) Query for F456L sequences: C9166T, A10564T, T22928C

Transferred from sars-cov-2-variants/lineage-proposals#617

FL.21> T2845C, C4543T, C9166T, A16431G, C27434T(Orf7a:T14I), T28161A(~Orf8:C90S~) Or XBB.1.9.1> C27434T(Orf7a:T14I)> T2845C, C4543T, C9166T, A10564T, A16431G, T28161A(~Orf8:C90S~) Then> C5144T> T22928C(S:F456L)

Earliest sequence: 04-22 Virginia, USA EPI_ISL_17593231 Earliest sequence with F456L: 06-23 Louisiana, USA EPI_ISL_18053704 Latest sequences: 08-31 Houston, Texas, USA EPI_ISL_18264671 *A sequence from Tennesse was assigned as collected on 01-24, but according to phylogenic tree, its collecting date is probably mislabeled.

Regions detected: US 8+31(Texas 5+23, California 1+2, Tennesse 1+1, Louisiana 1, New Jersey 1, New York 1, North Carolina 1, Virginia 1, Wisconsin 1), Spain 2(Castilla y Leon 1, Murcia 1), UK 1(England) The number of sequences with F456L is bolded.

https://nextstrain.org/fetch/github.com/Over-There-Is/subtreeAuspice/raw/main/subtreeAuspice_genome_1644e_1aac30.json?label=id:node_6918650 2023-09-14 (3)

Sequences: EPI_ISL_17593231, EPI_ISL_17806562, EPI_ISL_17808967, EPI_ISL_17855155, EPI_ISL_17955566, EPI_ISL_17955640, EPI_ISL_18053704, EPI_ISL_18057201, EPI_ISL_18057212, EPI_ISL_18069723, EPI_ISL_18072239, EPI_ISL_18076295, EPI_ISL_18080870, EPI_ISL_18090095, EPI_ISL_18104390, EPI_ISL_18107733, EPI_ISL_18118197, EPI_ISL_18163828, EPI_ISL_18163946, EPI_ISL_18163973, EPI_ISL_18164002, EPI_ISL_18164401, EPI_ISL_18164596, EPI_ISL_18210849, EPI_ISL_18212504, EPI_ISL_18222756, EPI_ISL_18233897, EPI_ISL_18241729, EPI_ISL_18256236, EPI_ISL_18256260, EPI_ISL_18256388, EPI_ISL_18264671, EPI_ISL_18266867, EPI_ISL_18267510, EPI_ISL_18275701, EPI_ISL_18275792
corneliusroemer commented 11 months ago

Almost all US-Texas, US produces 40% of global samples so 40 isn't much.

The RBD genotype is boring, just another XBB.1.9.1 + 456L

Over-There-Is commented 11 months ago

F456L> G15380A(Orf1b:S638N)> A22995G(S:K478R), C24989T(S:P1143S) 3seq

FedeGueli commented 11 months ago

F456L> G15380A(Orf1b:S638N)> A22995G(S:K478R), C24989T(S:P1143S) 3seq

worth tracking it separately could you reopen the original issue and add this one please? (G15380A, C24989T,C9166T, A10564T)