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cov-lineages / pango-designation

Repository for suggesting new lineages that should be added to the current scheme
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XBB.1.5 without T17124C branch with Orf1b:K82R and S:G181R - 10 sequences #1975

Closed FedeGueli closed 1 year ago

FedeGueli commented 1 year ago

In the XBB.1.5 branch without T17124C there is a little cluster defined by S:G181R with a significant international spread hinting to an higher than sampled circulation. I spotted it looking at chinese samples collected after 1st April.

Defining mutations: XBB.1* >>>G27915T > T23018C > ORF1b:K82R (A13712G) > C29686T >S:G181R (G22103C)

Tree: Schermata 2023-04-30 alle 09 14 20 https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_14234_e0c7a0.json?c=gt-ORF1ab_4483&label=id:node_5911779

Gisaid query: A13712G, C29686T , G22103C

Sequences:8 (3 from Shanghai) EPI_ISL_17182954, EPI_ISL_17221841, EPI_ISL_17262339, EPI_ISL_17307261, EPI_ISL_17481560, EPI_ISL_17536885-17536887,

Over-There-Is commented 1 year ago

according to genbase, all these 3 sequences are imported from Malaysia.

FedeGueli commented 1 year ago

according to genbase, all these 3 sequences are imported from Malaysia.

thx! headline modified

corneliusroemer commented 1 year ago

according to genbase, all these 3 sequences are imported from Malaysia.

Thanks for the info @Over-There-Is! GISAID seems to have dropped that metadatum :(

FedeGueli commented 1 year ago

10 sequences as today. one from Nepal.

FedeGueli commented 1 year ago

Transferred to pre proposal Repo : https://github.com/sars-cov-2-variants/lineage-proposals/issues/9