JN.1.16 (456L) got S:R346T (35 Samples , 15 countries)

[FedeGueli]

Another combo 456L-346T on Jn.1 Backbone is growing it was tracked as Branch 41 in sars-cov-2-variants/lineage-proposals#1089

Defining: JN.1.16(S:F456L) > S:R346T (G22599C)
Query: ,T22928C, T3565C, G22599C, T27810C,-C835T,-T26066C,-C13620T,-A405G,-C1938T,-G25290T,-C26894T,-G24872T ,-C1762A,-C774T, -A18093G ,-T1871G,-C11747T,-G1156T,-G21255T,-T16342C
Samples: 22 ( the above query manage to find 24 but two are from unrelated dead lineages: one Netherlands and one Ukraine-Env that i failed to exclude)
EPI_ISL_18860864, EPI_ISL_18882963, EPI_ISL_18888321,
EPI_ISL_18909091, EPI_ISL_18916650, EPI_ISL_18916652,
EPI_ISL_18916659, EPI_ISL_18931021, EPI_ISL_18931348,
EPI_ISL_18931393, EPI_ISL_18931429, EPI_ISL_18932646,
EPI_ISL_18937081, EPI_ISL_18937393, EPI_ISL_18937515,
EPI_ISL_18938829, EPI_ISL_18938846, EPI_ISL_18941397,
EPI_ISL_18945718, EPI_ISL_18945932, EPI_ISL_18949269,
EPI_ISL_18949473

Tree:

https://nextstrain.org/fetch/genome-test.gi.ucsc.edu/trash/ct/subtreeAuspice1_genome_test_5c93a_6e19c0.json?c=gt-S_346&label=id:node_6982680

Countries:

[xz-keg]

Or JN.1.18+S:F456L.

[FedeGueli]

Or JN.1.18+S:F456L.

oh damn would you mean i m tracking that two times? checked not. yeas could be JN.1.18 too.

[FedeGueli]

https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?nextcladePangoLineage=JN.1*&nucMutations1=T22928C%2CT3565C%2CG22599C%2CT27810C%2CC13620C%2CA405A%2CC1938C%2CG25290G%2CC26894C%2CG24872G%2CC1762C%2CC774C%2CA18093A&analysisMode=CompareToBaseline& anyway it seems fast

[xz-keg]

Or JN.1.18+S:F456L.

oh damn would you mean i m tracking that two times? checked not. yeas could be JN.1.18 too.

I mean the order may change and this branch may one day becomes JN.1.18+F456L. Actually they are just two ways to view the path and are not distinguishable.

[corneliusroemer]

Yeah that's why I'm hesitant with designation - both names are equally appropriate. Have to make a choice at some point.

[FedeGueli]

QUERY UPDATED STILL NOT PERFECT

[FedeGueli]

Query updated now 34 samples from 15 countries (many found in GBW)

[xz-keg]

Is there a way to extract GBW lineage prevalence and growth rate by countries?

[FedeGueli]

Is there a way to extract GBW lineage prevalence and growth rate by countries?

Only manually you can try proposing this in covspectrum github as ENHancing issue

[xz-keg]

Only manually you can try proposing this in covspectrum github as ENHancing issue

Yeah the origin countries are also not on usher tree.

[FedeGueli]

35 query updated

[xz-keg]

Designated JN.1.16.1

[FedeGueli]

Designated Jn.1.16.1 via b316ca1