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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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KP.2.3/XEC Recombinant(26 seqs, 10 countries) #2774

Open Fearuncle opened 5 days ago

Fearuncle commented 5 days ago

Big thanks to @Over-There-Is From: https://github.com/sars-cov-2-variants/lineage-proposals/issues/2023 image tree: https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_ed35_40f680.json?f_userOrOld=uploaded%20sample KP.2.3 / XEC recombinant Query: C3505T, T5701C, C9286T

Break point: 9286/~15402 Mutations based on JN.1: C593T(Orf1a:H110Y), C3505T, T5701C(private), C7113T(Orf1a:T2283I), C9286T / C18657T, C19716T, C21627A(S:T22N), T21738C(S:F59S), T22928C(S:F456L), C23039G(S:Q493E), G24872T(S:V1104L), C25006T, C28291A(Orf9b:P3H), G28884C(N:R204P)

5' donor: KP.2.3> C9286T> C593T> C3505T, A15402G(=JN.1+C593T, C3505T, C7113T, C9286T / A15402G, G17334T, C22000A, G22599C, T22928C, G24872T, G25593T, C28714T, 3 seqs, DE 2, NL 1) 3' donor: XEC(=JN.1+C18657T, C19716T, C21627A, T21738C, T22928C, C23039G, G24872T, C25006T, C28291A, G28884C)

Earliest sequence: 07-19 Denmark EPI_ISL_19332668 Latest sequence: 09-02 England, United Kingdom EPI_ISL_19406440 Regions detected: UK 5, Austria 3, Germany 3, Sweden 2, Denmark 1, Netherlands 1, Ukraine 1

Sequences: EPI_ISL_19332668, EPI_ISL_19364165, EPI_ISL_19368841, EPI_ISL_19368849, EPI_ISL_19372478, EPI_ISL_19373085, EPI_ISL_19381036, EPI_ISL_19381934, EPI_ISL_19385623, EPI_ISL_19389047, EPI_ISL_19389054, EPI_ISL_19390181, EPI_ISL_19406420, EPI_ISL_19406440, EPI_ISL_19410161, EPI_ISL_19410789

And 1 sequence seem also related to this branch: EPI_ISL_19378121(potential contaminated)

aviczhl2 commented 5 days ago

7 countries including Ukraine.

aviczhl2 commented 4 days ago

+2 netherlands +2 Slovenia, 20 now.

Fearuncle commented 4 days ago

now in 8 countries

Over-There-Is commented 3 days ago

Also in United States now.

Over-There-Is commented 3 days ago

Break point: 9286/~15402

The left slash here should be a right slash to avoid the tilde forming delete line , like this: ~without slash~ /~left slash/~ \~right slash\~. My typo. Sorry.

Fearuncle commented 1 day ago

9 countries

Fearuncle commented 8 hours ago

In Croatia EPI_ISL_19416657