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Repository for suggesting new lineages that should be added to the current scheme
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XEC subbranch with Orf9b:R32L on Orf1a:A599T branch(63 seqs, 11 countries) and its recombinant with KP.3.1.1(4 sequences, DE 3, US 1) #2813

Open Over-There-Is opened 20 hours ago

Over-There-Is commented 20 hours ago

Transferred from sars-cov-2-variants/lineage-proposals#2173.

XEC> G2060A(Orf1a:A599T)> G28378T(Orf9b:R32L)

Query: -C1684A, T3565C, C19716T, G28378T, -C6701T, -C18687T, -A21766T, -G25234T ("-"s are added to remove convergent sequences)

Earliest sequence: 08-07 Schleswig-Holstein, Germany EPI_ISL_19364163 Latest sequence: 10-11 Asturias, Spain EPI_ISL_19497008 Regions detected: Denmark 9, UK 9, Germany 8, Italy 8, Netherlands 7, Sweden 7, France 5, Spain 4, US 3(1 from Denmark, 1 pooled, 1 not on GISAID), Luxembourg 2, Belgium 1

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_7f5f_7a0d10.json?c=country&label=id:node_7267532 image

Sequences: EPI_ISL_19364163, EPI_ISL_19378139, EPI_ISL_19383090, EPI_ISL_19410252, EPI_ISL_19415557, EPI_ISL_19417577, EPI_ISL_19417585, EPI_ISL_19421034, EPI_ISL_19426850, EPI_ISL_19431751, EPI_ISL_19433943, EPI_ISL_19435638-19435640, EPI_ISL_19436766, EPI_ISL_19436780, EPI_ISL_19443858, EPI_ISL_19444527, EPI_ISL_19447700, EPI_ISL_19447703, EPI_ISL_19448892, EPI_ISL_19448913, EPI_ISL_19450798, EPI_ISL_19451326, EPI_ISL_19451444, EPI_ISL_19451506, EPI_ISL_19451675, EPI_ISL_19456847, EPI_ISL_19456850, EPI_ISL_19456875, EPI_ISL_19458753, EPI_ISL_19463326, EPI_ISL_19464961, EPI_ISL_19467664, EPI_ISL_19468204, EPI_ISL_19468795, EPI_ISL_19472522, EPI_ISL_19477073, EPI_ISL_19477087, EPI_ISL_19477236, EPI_ISL_19477238, EPI_ISL_19477492, EPI_ISL_19477776, EPI_ISL_19478671, EPI_ISL_19478700, EPI_ISL_19481383, EPI_ISL_19481474, EPI_ISL_19481484, EPI_ISL_19481515, EPI_ISL_19481533, EPI_ISL_19484080, EPI_ISL_19485103, EPI_ISL_19485195, EPI_ISL_19485671, EPI_ISL_19486463, EPI_ISL_19488255, EPI_ISL_19488579, EPI_ISL_19493850, EPI_ISL_19493952, EPI_ISL_19494033, EPI_ISL_19497008, EPI_ISL_19497087, PQ409725.1

KP.3.1.1 / XEC

Query for recombinant: C1684A, C19716T, G28378T

Mutations based on KP.3: C1684A(private?), C12616T / T17334Grev, C18657T, C19716T, C21627A, T21738C, C25006T, C28291A, G28378T(Orf9b:R32L), G28884C Breakpoint: 12616\~13121 C1684A is in 2 sequences from different branches, or it could be private.

09-02~10-01, Bayern, Germany 3 Date unavailable, Ohio, US 1 Sequences: EPI_ISL_19424919, EPI_ISL_19477344, EPI_ISL_19488853, EPI_ISL_19497066

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_29260_7a80e0.json?c=country&label=id:node_7268393 image

FedeGueli commented 15 hours ago

I suggest to use this query: T3565C, G28378T, G2060A,-C18687T,-C27944T, -G25234T,-A11983T it finds 66