cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme
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New XBB.1.5 sublineage with Orf1b:L1681F(NSP14_L157F) and S:F456L(T22928C) 71 seqs 14 countries #2069

Closed FedeGueli closed 1 year ago

FedeGueli commented 1 year ago

Transferred from https://github.com/sars-cov-2-variants/lineage-proposals/issues/224 Defining mutations: XBB.1.5 > C24130T > Orf1b:L1681F ( C18508T = NSP14_L157F ) , S:F456L (T22928C)

Tree: https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_1bc72_b239e0.json?f_userOrOld=uploaded%20sample&label=id:node_6800911 Schermata 2023-06-27 alle 20 01 53

Schermata 2023-06-27 alle 20 01 25

Gisaid query: C24130T ,C18508T,T22928C,T23019C,C24130T ,C18508T,T22928C,T23018C

Samples: EPI_ISL_17501116, EPI_ISL_17501127, EPI_ISL_17516924, EPI_ISL_17654258, EPI_ISL_17658202, EPI_ISL_17660153, EPI_ISL_17662414, EPI_ISL_17671275, EPI_ISL_17737756, EPI_ISL_17776739, EPI_ISL_17785440, EPI_ISL_17786197, EPI_ISL_17799142, EPI_ISL_17809979, EPI_ISL_17837344-17837345, EPI_ISL_17852519, EPI_ISL_17853832, EPI_ISL_17853966,

FedeGueli commented 1 year ago

To be noted that, out of 6 sequences from June, 2 are from Argentina (25 uploaded from there)

FedeGueli commented 1 year ago

Multiple samples Uploaded from Uruguay and one from Bolivia

it represents 3 out of 7 of recent sequences from uruguay

cc @corneliusroemer

FedeGueli commented 1 year ago

last samples coming from California, Texas Puertorico

FedeGueli commented 1 year ago

+2 Utah

FedeGueli commented 1 year ago

+3 US +1 Brazil

FedeGueli commented 1 year ago

This is widespreaad and keeps on growing.

FedeGueli commented 1 year ago

But it cant compete: https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=Orf1b%3AD54N&nucMutations1=C24130T%2CC18508T%2CT22928C%2CT23019C%2CC24130T%2CC18508T%2CT22928C%2CT23018C&analysisMode=CompareToBaseline&

FedeGueli commented 11 months ago

Designated JZ.1 via https://github.com/cov-lineages/pango-designation/commit/856edb1d6ddfd8de6931fff829d9d7614b85a885