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sars-cov-2-variants / lineage-proposals

Repository to propose and discuss lineages
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JN.1.29.1(S:F456L) subbranch with S:R346T(28 seqs, 4 countries) and further S:L56V(15 seqs, 3 countries) #1813

Open Over-There-Is opened 1 month ago

Over-There-Is commented 1 month ago

Found with @aviczhl2 's phylogenic tree analysis tool.

JN.1.29.1> C8917T> G22599C(S:R346T)> G18318T, C20930T(Orf1b:T2488M)> A259G, A28984G> T21728G(S:L56V) Query: C8917T, A9935G, G22599C, -A405G

Earliest sequence: 03-26 Eusebio, Ceara, Brazil EPI_ISL_19282419 Latest sequences: 06-30 California, USA(imported from Spain) EPI_ISL_19273788 Regions detected: Brazil 18, US 4(including 1 in Puerto Rico, 2 from Spain, 1 from unknown), UK 1

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_3adbf_bc87e0.json?f_userOrOld=uploaded%20sample image

Sequences: EPI_ISL_18952414, EPI_ISL_18961998, EPI_ISL_18998958-18998959, EPI_ISL_19043828, EPI_ISL_19064049, EPI_ISL_19133577, EPI_ISL_19230423, EPI_ISL_19254506, EPI_ISL_19269974, EPI_ISL_19271357, EPI_ISL_19273788, EPI_ISL_19282403-19282404, EPI_ISL_19282406-19282409, EPI_ISL_19282420, EPI_ISL_19282423-19282424, EPI_ISL_19287115, EPI_ISL_19288494
FedeGueli commented 1 month ago

Sorry i ve missed this one

FedeGueli commented 3 weeks ago

I see three of this one uplaoded today from brazil all with 56V but Gisaid shows one only when querying, i think the trick of white metadata and mutation by Gisaid is back. For examples there were at least 25 JN.1.55.2 flirt uploaded todaybut the best query i ve found catches only 4 or 5 . cc @aviczhl2